Cell and Gene Therapy: Rewriting the Future of Medicine – Technology Networks

Cell and gene therapies seek to correct the root cause of an illness at the molecular level. These game-changing medicines are reshaping how we address previously untreatable illnesses transforming peoples lives.

Cell and gene therapy represent overlapping fields of research with similar therapeutic goals developing a treatment that can correct the underlying cause of a disease, often a rare inherited condition that can be life-threatening or debilitating and has limited treatment options.

While these technologies were initially developed in the context of treating rare diseases caused by a single faulty gene, they have since evolved towards tackling more common diseases, says Professor Rafael J. Yez-Muoz, director of the Centre of Gene and Cell Therapy (CGCT) at Royal Holloway University of London.

A powerful example is the chimeric antigen receptor (CAR) T-cell therapies, which have been approved for treating certain blood cancers. The approach involves genetically modifying a patients T cells in the laboratory before reintroducing them into the body to fight their disease.

For the first time, we had an example of gene therapy to treat a more common disease demonstrating that the technology has wide applicability, enthuses Yez-Muoz.

To date, 24 cellular and gene therapy products have received approval from the US Food and Drug Administration (FDA) including life-changing treatments for patients with rare diseases, such as inherited forms of blindness and neuromuscular conditions. A variety of gene and cell-based therapies for both rare and common diseases are also currently in development across many therapeutic areas, offering hope for many more families in coming years.

This webinar will provide an introduction to the regulatory framework for cell and gene therapies and highlight the importance of chemistry, manufacturing and controls. Watch to learn about regulatory concerns, safety and quality testing throughout the product lifecycle and key acronyms and terminology.

Gene therapies seek to introduce specific DNA sequences into a patients body to treat, prevent or potentially cure a disease. This may involve the delivery of a functional gene into cells to replace a gene that is missing or causing a problem or other strategies using nucleic acid sequences (such as antisense oligonucleotides or short interfering RNAs [siRNAs]) to reduce, restore or modify gene expression. More recently, scientists are also developing genome-editing technologies that aim to change the cells DNA at precise locations to treat a specific disease.

The key step in successful gene therapy relies on the safe and efficient delivery of genetic material into the target cells, which is carried out by packaging it into a suitable delivery vehicle (or vector). Many current gene therapies employ modified viruses based on adenoviruses, adeno-associated viruses (AAV), and lentiviruses as vectors due to their intrinsic ability to enter cells. But non-viral delivery systems such as lipid nanoparticles (LNPs) have also been successfully employed to deliver RNA-based therapeutics into cells.

A big advantage of using viral vectors for gene delivery is they are longer lasting than non-viral systems, states Dr. Rajvinder Karda, lecturer in gene therapy at University College London. Many of the rare diseases were aiming to tackle are severe and we need to achieve long-term gene expression for these treatments to be effective.

While improved technological prowess empowers the development of CRISPR-edited therapies, supply-chain and manufacturing hurdles still pose significant barriers to clinical and commercialization timelines. Watch this webinar to learn more about the state of CRISPR cell and gene therapies, challenges in CRISPR therapy manufacturing and a next-generation manufacturing facility.

Viral-vector gene therapies are either administered directly into the patients body (in vivo), or cells harvested from a patient are instead modified in the laboratory (ex vivo) and then reintroduced back into the body. Major challenges for in vivo gene delivery approaches are with the safe and efficient targeting of the therapeutic to the target cells and overcoming any potential immune responses to the vectors.

As well as getting the genetic material into the affected cells, we also need to try and limit it reaching other cells as expressing a gene in a cell where its not normally active could cause problems, explains Dr. Gerry McLachlan, group leader at the Roslin Institute in Edinburgh.

For example, the liver was identified as a major site of toxicity for an AAV-based gene therapy approved for treating spinal muscular atrophy (SMA), a type of motor neuron disease that affects people from a very young age.

Unfortunately, these viruses are leaky as theyre also going to organs that dont need therapy meaning you can get these off-target effects, says Karda. Theres still work to be done to develop and refine these technologies to make them more cell- and organ-specific.

It is also important to ensure the gene is expressed at the right level in the affected cells too high and it may cause side effects and too little may render the treatment ineffective. In a recent major advancement in the field, scientists developed a dimmer switch system Xon that enables gene expression to be precisely controlled through exposure to an orally delivered small molecule drug. This novel system offers an unprecedented opportunity to refine and tailor the application of gene therapies in humans.

Download this whitepaper to discover an electroporation system that resulted in CAR transfection efficiencies as high as 70% in primary human T cells, can avoid the potential risks associated with viral transduction and is able to produce CAR T cells at a sufficient scale for clinical and therapeutic applications.

In 1989, a team of researchers identified the gene that causes the chronic, life-limiting inherited disease cystic fibrosis (CF) the cystic fibrosis transmembrane conductance regulator (CFTR). This was the first ever disease-causing gene to be discovered marking a major milestone in the field of human genetics. In people with CF, mutations in the CFTR gene can result in no CTFR protein, or the protein being made incorrectly or at insufficient levels all of which lead to a cascade of problems that affect the lungs and other organs.

Our team focuses on developing gene therapies to treat respiratory diseases in particular, were aiming to deliver the CTFR gene into lung cells to treat CF patients, says McLachlan.

The results of the UK Respiratory Gene Therapy Consortiums most recent clinical trial showed that an inhaled non-viral CTFR gene therapy formulation led to improvements in patient lung function.

While this was encouraging, the effects were modest and we need to develop a more potent delivery vehicle, explains McLachlan. Weve also been working on a viral-based gene therapy using a lentiviral vector to introduce a healthy copy of the CTFR gene into cells of the lung.

Kardas team focuses on developing novel gene therapy and gene-editing treatments for incurable genetic diseases affecting the central and peripheral nervous system and Yez-Muoz is aiming to develop new treatments for rare neurodegenerative diseases that affect children, including SMA and ataxia telangiectasia (AT).

But a significant barrier for academic researchers around the world is accessing the dedicated resources, facilities and expertise required to scale up and work towards the clinical development and eventually the commercial production of gene and cell therapies. These challenges will need to be addressed and overcome if these important advancements are to successfully deliver their potentially life-changing benefits to patients.

Download this app note to discover how electron activated dissociation can obtain in-depth structural characterization of singly charged, ionizable lipids and related impurities, decrease risk of missing critical low abundance impurities and increase confidence in product quality assessment.

After many decades of effort, the future of gene and cell therapies is incredibly promising. A flurry of recent successes has led to the approval of several life-changing treatments for patients and many more products are in development.

Its no longer just about hope, but now its a reality with a growing number of rare diseases that can be effectively treated with these therapies, describes Yez-Muoz. We now need to think about how we can scale up these technologies to address the thousands of rare diseases that exist and even within these diseases, people will have different mutations, which will complicate matters even further.

But as more of these gene and cell-based therapies are approved, there is a growing urgency to address the challenge of equitable access to these innovative treatments around the world.

Gene therapies have the dubious honor of being the most expensive treatments ever and this isnt sustainable in the longer term, says Yez-Muoz. Just imagine being a parent and knowing there is an effective therapy but your child cant access it that would be absolutely devastating.

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Cell and Gene Therapy: Rewriting the Future of Medicine - Technology Networks

Excision BioTherapeutics Awarded California Institute for Regenerative Medicine (CIRM) Grant to Support Ongoing Phase 1/2 Trial Evaluating EBT-101 as…

SAN FRANCISCO, Sept. 29, 2022 (GLOBE NEWSWIRE) -- Excision BioTherapeutics, Inc., a clinical-stage biotechnology company developing CRISPR-based therapies intended to cure viral infectious diseases, todayannounced that the California Institute for Regenerative Medicine (CIRM) has awarded Excision a $6.85 million grant to support the clinical development of the EBT-101 program for human immunodeficiency virus type 1 (HIV-1).

Daniel Dornbusch, Chief Executive Officer of Excision, commented, We are honored that CIRM has recognized the potential value of the EBT-101 program and our dual-guide RNA CRISPR approach to developing curative therapies for HIV-1 as well as other serious viral diseases with significant unmet needs. The CIRM grant provides further validation for the EBT-101 clinical trial, which is the first ever to evaluate an in vivo CRISPR-based therapy in an infectious disease. The grant will provide Excision with important funding to advance the trial and potentially demonstrate the safety and efficacy of removing viral DNA from people affected by the HIV pandemic.

Excision recently reported the first participant in the EBT-101 Phase 1/2 clinical trial was dosed in July 2022, with initial findings indicating the therapeutic has been well tolerated to-date. The participant continues to be monitored for safety and is expected to qualify for analytical treatment interruption (ATI) of their background anti-retroviral therapy (ART) in an evaluation of a potential cure.

To date only a handful of people have been cured of HIV/AIDS, so this proposal of using gene editing to eliminate the virus could be transformative, says Maria T. Millan, MD, President and CEO of CIRM. In California alone there are almost 140,000 people living with HIV. HIV infection continues to disproportionately impact marginalized populations, many of whom are unable to access the medications that keep the virus under control. A functional cure for HIV would have an enormous impact on these communities, and others around the world.

About EBT-101EBT-101 is a unique, in vivo CRISPR-based therapeutic designed to cure HIV infections after a single intravenous infusion. EBT-101 employs an adeno-associated virus (AAV) to deliver CRISPR-Cas9 and dual guide RNAs, enabling a multiplex editing approach that simultaneously targets three distinct sites within the HIV genome. This allows for the excision of large portions of the HIV genome, thereby minimizing potential viral escape.

About the EBT-101 Clinical ProgramThe EBT-101 Phase 1/2 trial is an open-label, multi-center single ascending dose study designed to evaluate the safety, tolerability and preliminary efficacy of EBT-101 in approximately nine participants with HIV-1 who are suppressed on antiretroviral therapy. The clinical program is supported by preclinical studies that included positive long-term non-human primate safety data and efficacy data in humanized mice showing the potential to cure HIV when treated with EBT-101. The primary objective of the trial is to assess the safety and tolerability of a single dose of EBT-101 in study participants with undetectable viral load on antiretroviral therapy (ART). Biodistribution, pharmacodynamic, and efficacy assessments will also be conducted. All participants will be assessed for eligibility for an analytical treatment interruption (ATI) of their background ART at Week 12 post EBT-101 administration. Following the initial 48-week follow up period, all participants will be enrolled into a long-term follow up protocol. For more information, see ClinicalTrials.gov identifiers NCT05144386 (Phase 1/2 trial) and NCT05143307 (long-term follow up protocol).

About CIRMAt CIRM, we never forget that we were created by the people of California to accelerate stem cell treatments to patients with unmet medical needs, and act with a sense of urgency to succeed in that mission.To meet this challenge, our team of highly trained and experienced professionals actively partners with both academia and industry in a hands-on, entrepreneurial environment to fast track the development of todays most promising stem cell technologies.With $5.5 billion in funding and more than 150 active stem cell programs in our portfolio, CIRM is one of the worlds largest institutions dedicated to helping people by bringing the future of cellular medicine closer to reality. For more information go towww.cirm.ca.gov.

About Excision BioTherapeutics, Inc.Excision BioTherapeutics, Inc. is a clinical-stage biotechnology company developing CRISPR-based therapiesas potentialcures for viral infectious diseases. EBT-101, the Companys lead program, is anin vivoCRISPR-based therapeutic designed to cure HIV infections after a single intravenous infusion. Excisions pipeline unites next-generation CRISPR nucleases with a novel gene editing approach to develop curative therapies for Herpes Virus, JC Virus,which causes PML, and Hepatitis Bvirus. Excisions foundational technologies were developedin the laboratories of Dr. KamelKhaliliat Temple University andDr. JenniferDoudnaatthe University of California, Berkeley.For more information, please visitwww.excision.bio.

Contact:InvestorsJohn Fraunces - LifeSci Advisors917-355-2395jfraunces@lifesciadvisors.com

MediaRobert Flamm, Ph.D.Burns McClellan, Inc.212-213-0006 ext. 364rflamm@burnsmc.com

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Excision BioTherapeutics Awarded California Institute for Regenerative Medicine (CIRM) Grant to Support Ongoing Phase 1/2 Trial Evaluating EBT-101 as...

Fighting Breast and Ovarian Cancer With a Lupus Antibody – Yale School of Medicine

Of the 1.5 million people living with lupus in the United States, 90% are women. This disease turns the bodys immune system against itself, potentially causing extreme pain, fatigue, difficulty thinking clearly, and cardiovascular disease.

Officially known as systemic lupus erythematosus, lupus is distinct among autoimmune diseases in the way circulating antibodies proteins that when functioning properly help to protect against disease react against DNA, the bodys instructions for building cells and passing traits from parents to children.

Drs. Peter M. Glazer and James Hansen discovered that one specific lupus antibody, known as 3E10, can penetrate cancer cells and make them sensitive to and killed by standard radiation and chemotherapy methods. Notably, this technique has shown significant effectiveness in killing cancer cells with DNA repair deficiencies, such as those with mutations in the tumor-suppressing BRCA2 gene that lead to higher rates of breast and ovarian cancer.

Now, nearly a decade since this discovery and with he help of a grant from Womens Health Research at Yale, researchers are close to advancing a treatment toward clinical trials while learning more about how this lupus antibody penetrates and kills cancer cells.

This discovery has unlocked promising new pathways for treatment of BRCA-related cancers that affect so many women around the world, said Glazer, the Robert E. Hunter Professor of Therapeutic Radiology, professor of genetics, and chair of the Department of Therapeutic Radiology. We have learned a great deal about how 3E10 interacts with DNA, and we continue to explore how this knowledge could be used to create therapies for other types of difficult-to-treat cancers.

Dr. Glazer and his colleague Dr. James E. Hansen, associate professor of therapeutic radiology, licensed the rights for their antibody discovery to a company, Patrys, Ltd., that has validated the work and developed 3E10 as a cancer therapy for human use. An earlier human study in Switzerland attempting to use 3E10 as a vaccine for lupus had already demonstrated that it is nontoxic. Phase 1 clinical trials could begin as early as next year, Dr. Glazer said, likely for patients with cancers related to mutations of BRCA1/2 genes or of another tumor suppressing gene known as PTEN.

This is very promising, Glazer said. I think it will be important to identify the right subgroup of patients for which this is most effective.

After publishing the results, Dr. Glazer and his colleagues leveraged the data to obtain a pair of large multiyear grants from the National Institutes of Health. With this funding and the help of Yale graduate student Audrey Turchick, the team has discovered that inside a cancer cell, 3E10 sticks to a DNA repair protein called RAD51. This causes the lethality for cancer cells that are deficient in BRCA1 and BRCA2 genes by preventing the cells from conducting the routine DNA repair necessary to sustain themselves.

With ongoing funding from the NIH, Dr. Glazers team, including structural biologist Dr. Franziska Bleichert, is building on these findings to enhance the anti-cancer potency of 3E10 and develop therapeutic strategies by identifying ways for the antibody to stick more strongly to RAD51.

In addition, an MD/PhD student in the lab, Elias Quijano, helped identify the capacity of 3E10 to bind with RNA a type of molecule used to carry out DNA instructions and carry RNA into a cancer cell, potentially with instructions that can kill the cell. Quijano and Drs. Glazer, Stephen Squinto, and Bruce Turner co-founded Gennao Bio, a company seeking to develop this method of cancer-fighting therapy.

This was an unexpected discovery that turns out may be very useful, Glazer said. We have some data showing the efficacy of this method against tumors in a laboratory model. It is a versatile platform, because it can deliver different types of RNA in a similar way to how the COVID-19 mRNA vaccines work.

The research continues, thanks in large part to the investment WHRY made so many years ago.

I think that type of funding is extremely valuable, Glazer said of his WHRY grant. It allowed us to do the sets of exploratory experiments we needed to do to demonstrate our approach was viable and get the larger grants. We showed this is feasible, this is promising.

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Fighting Breast and Ovarian Cancer With a Lupus Antibody - Yale School of Medicine

Cellular & Gene Therapy Guidances | FDA

Should you find a link that does not work within any Guidance document, Rule or other document posted on the FDA Web site, please try searching for the document using the document title. If you need further assistance, please go to Contact FDA.

Considerations for the Development of Chimeric Antigen Receptor (CAR) T Cell Products; Draft Guidance for Industry3/2022

Human Gene Therapy Products Incorporating Human Genome Editing; Draft Guidance for Industry3/2022

Policy for Certain REMS Requirements During the Tocilizumab Shortage Related to the COVID-19 Public Health Emergency; Guidance for Industry and Health Care Professionals12/2021

Interpreting Sameness of Gene Therapy Products Under the Orphan Drug Regulations; Guidance for Industry9/2021

Studying Multiple Versions of a Cellular or Gene Therapy Product in an Early-Phase Clinical Trial; Draft Guidance for Industry9/2021

Manufacturing Considerations for Licensed and Investigational Cellular and Gene Therapy Products During COVID-19 Public Health Emergency; Guidance for Industry1/2021

Human Gene Therapy for Neurodegenerative Diseases; Draft Guidance for Industry1/2021

Chemistry, Manufacturing, and Control (CMC) Information for Human Gene Therapy Investigational New Drug Applications (INDs); Guidance for Industry1/2020

Long Term Follow-up After Administration of Human Gene Therapy Products; Guidance for Industry1/2020

Testing of Retroviral Vector-Based Human Gene Therapy Products for Replication Competent Retrovirus During Product Manufacture and Patient Follow-up; Guidance for Industry1/2020

Human Gene Therapy for Hemophilia; Guidance for Industry1/2020

Human Gene Therapy for Rare Diseases; Guidance for Industry1/2020

Human Gene Therapy for Retinal Disorders; Guidance for Industry1/2020

Evaluation of Devices Used with Regenerative Medicine Advanced Therapies;Guidance for Industry2/2019

Expedited Programs for Regenerative Medicine Therapies for Serious Conditions;Guidance for Industry2/2019

Regulatory Considerations for Human Cells, Tissues, and Cellular and Tissue-Based Products: Minimal Manipulation and Homologous Use; Guidance for Industry and Food and Drug Administration StaffUpdated: 12/2017

Same Surgical Procedure Exception under 21 CFR 1271.15(b): Questions and Answers Regarding the Scope of the Exception; Guidance for Industry11/2017

Deviation Reporting for Human Cells, Tissues, and Cellular and Tissue-Based Products Regulated Solely Under Section 361 of the Public Health Service Act and 21 CFR Part 1271; Guidance for Industry9/2017

Recommendations for Microbial Vectors Used for Gene Therapy; Guidance for Industry9/2016

Design and Analysis of Shedding Studies for Virus or Bacteria-Based Gene Therapy and Oncolytic Products; Guidance for Industry8/2015

Considerations for the Design of Early-Phase Clinical Trials of Cellular and Gene Therapy Products; Guidance for Industry6/2015

Determining the Need for and Content of Environmental Assessments for Gene Therapies, Vectored Vaccines, and Related Recombinant Viral or Microbial Products; Guidance for Industry3/2015

Guidance for Industry: BLA for Minimally Manipulated, Unrelated Allogeneic Placental/Umbilical Cord Blood Intended for Hematopoietic and Immunologic Reconstitution in Patients with Disorders Affecting the Hematopoietic System3/2014. (This guidance finalizes the draft guidance of the same title dated June 2013.)

IND Applications for Minimally Manipulated, Unrelated Allogeneic Placental/Umbilical Cord Blood Intended for Hematopoietic and Immunologic Reconstitution in Patients with Disorders Affecting the Hematopoietic System - Guidance for Industry and FDA Staff3/2014. (This guidance finalizes the draft guidance of the same title dated June 2013.)

Guidance for Industry: Preclinical Assessment of Investigational Cellular and Gene Therapy Products(This guidance finalizes the draft guidance entitled Guidance for Industry: Preclinical Assessment of Investigational Cellular and Gene Therapy Products dated November 2012) 11/2013

Guidance for Industry: Preparation of IDEs and INDs for Products Intended to Repair or Replace Knee Cartilage12/2011. (This guidance finalizes the draft guidance of the same title dated July 2007.)

Guidance for Industry: Clinical Considerations for Therapeutic Cancer Vaccines10/2011. (This guidance finalizes the draft guidance of the same title dated September 2009.)

Guidance for Industry: Potency Tests for Cellular and Gene Therapy Products1/2011. (This guidance finalizes the draft document of the same name, dated October 2008.)

Guidance for Industry: Cellular Therapy for Cardiac Disease(This guidance finalizes the draft guidance entitled Guidance for Industry: Somatic Cell Therapy for Cardiac Disease dated March 2009 (April 2, 2009, 74 FR 14992). 10/2010.

Guidance for Industry: Considerations for Allogeneic Pancreatic Islet Cell Products9/2009

Guidance for FDA Reviewers and Sponsors: Content and Review of Chemistry, Manufacturing, and Control (CMC) Information for Human Somatic Cell Therapy Investigational New Drug Applications (INDs)4/2008

Eligibility Determination for Donors of Human Cells, Tissues, and Cellular and Tissue-Based Products; Guidance for Industry8/2007

Guidance for Industry: Guidance for Human Somatic Cell Therapy and Gene Therapy3/1998

12/10/2021

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Cellular & Gene Therapy Guidances | FDA

Pfizer and Sangamo Therapeutics reopen recruitment for haemophilia A gene therapy trial – PMLiVE

Pfizer and Sangamo Therapeutics have reopened the recruitment of their phase 3 study evaluating giroctocogene fitelparvovec, an investigational gene therapy for patients with moderately severe to severe haemophilia A, the companies announced.

The reopening comes after the two partners voluntarily paused the trial in November 2021 after patients treated with the therapy experienced blood clotting protein Factor VIII activity greater than 150%, raising concerns that they may be at increased risk of harmful clotting events.

The US Food and Drug Administration (FDA) subsequently placed a clinical hold on the trial, before lifting it in March this year. However, the partners kept the voluntary pause in place while working to meet all necessary conditions, including approval of updated trial protocols by regulatory authorities.

People living with haemophilia A lack sufficient functioning Factor VIII protein to help their blood clot. The condition occurs in around one in 5,000 male births annually, and more rarely in females. People with haemophilia can experience bleeding episodes that can cause pain, irreversible joint damage and life-threatening haemorrhages.

The phase 3 AFFINE study is an open-label, multicentre, single arm study to evaluate the efficacy and safety of a single infusion of giroctocogene fitelparvovec in more than 60 adult male participants, aged 18-64 years, with moderately severe to severe haemophilia A.

Eligible study participants will have completed at least six months of routine FVIII prophylaxis therapy during the lead-in phase 3 study in order to collect pretreatment data for efficacy and selected safety parameters, the companies stated.

The primary endpoint in AFFINE is the impact of giroctocogene fitelparvovec on annualised bleeding rate (ABR) after 15 months of follow-up. This will be compared to ABR on prior FVIII prophylaxis replacement therapy.

The secondary endpoints include FVIII activity level after the onset of steady state and after 15 months following infusion of giroctocogene fitelparvovec.

Trial sites will begin to resume enrolment this month, with dosing expected to resume in October and all trial sites anticipated to be active by the end of 2022, the companies outlined.

Giroctocogene fitelparvovec has been granted Orphan Drug, Fast Track and regenerative medicine advanced therapy designations by the FDA, as well as Orphan Medicinal Product designation by the European Medicines Agency.

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Pfizer and Sangamo Therapeutics reopen recruitment for haemophilia A gene therapy trial - PMLiVE

The surprising link between circadian disruption and cancer may have to do with temperature – EurekAlert

image:For mice placed in chronic jet lag (CJL) conditions, they showed a 68% increase in tumor burden when compared to mice placed in 12 hours of light, 12 hours of darkness (12:12 LD). view more

Credit: Scripps Research

LA JOLLA, CADisruptions in circadian rhythmthe ways that our bodies change in response to the 24-hour light and dark cyclehave been linked to many different diseases, including cancer. The connection between the two has been poorly understood, even though shift workers and others with irregular schedules experience these disruptions regularly. But a new discovery from Scripps Research is helping answer what may be behind this correlation.

Published in Science Advances on September 28, 2022, the findings highlight that chronic circadian disruption significantly increased lung cancer growth in animal models. By identifying the genes implicated, the researchers are illuminating the mysterious link between our sleeping patterns and disease, which could help inform everything from developing more targeted cancer treatments to better monitoring high-risk groups.

There has always been a lot of evidence that shift workers and others with disrupted sleep schedules have higher rates of cancer, and our mission for this study was to figure out why, says senior author Katja Lamia, PhD, associate professor in the Department of Molecular Medicine.

To answer this question, the scientists used a mouse model with expressed KRAS the most commonly mutated gene in lung cancer. Half of the mice were housed in a normal light cycle, meaning 12 hours of light and 12 hours of darkness. The other half were housed in a light cycle meant to resemble that of shift workers, where the light hours were moved earlier by eight hours every two or three days.

The findings aligned with what the researchers initially thought: mice that were exposed to the irregular, shifting light patterns had an increased tumor burden of 68%.

But when they used RNA sequencing to determine the different genes involved in the cancer growth, they were surprised that a collection in the heat shock factor 1 (HSF1) family of proteins was the main culprit.

This is not the mechanism we were expecting to find here. HSF1 has been shown to increase rates of tumor formation in several different models of cancer, but it has never been linked to circadian disruption before, Lamia says.

HSF1 genes are responsible for making sure proteins are still made correctly even when a cell is under extreme stressin this case, when it experiences changes in temperature. The team suspects that HSF1 activity is increased in response to circadian disruption because changes in our sleep cycles disturb the daily rhythms of our bodies temperature.

Normally, our body temperature changes by one or two degrees while were sleeping. If shift workers dont experience that normal drop, it could interfere with how the HSF1 pathway normally operatesand ultimately lead to more dysregulation in the body, Lamia adds. She believes cancer cells may exploit the HSF1 pathway to their own benefit and create mutant, misfolded proteins, but says more research is needed in this area.

These findings help shape not only our understanding of how circadian rhythms impact cancer, but also potentially a preventative way of protecting more vulnerable groups who are at risk. By non-invasive monitoring of body temperature, it may be possible to optimize shift workers schedules and even halt this type of dysregulation that can lead to cancer.

With these discoveries in hand, the scientists are now evaluating if HSF1 signaling is required to increase tumor burden and isnt solely just a correlation.

Now that we know theres a molecular link between HSF1, circadian disruption and tumor growth, its our job to determine how theyre all connected, Lamia says.

In addition to Lamia, authors of the study, Circadian disruption enhances HSF1 signaling and tumorigenesis in Kras-driven lung cancer, include Marie Pariollaud, Lara H. Ibrahim, Emanuel Irizarry, Rebecca M. Mello, Alanna B. Chan, Michael J. Bollong and R. Luke Wiseman of Scripps Research; Brian J. Altman of University of Rochester Medical Center; and Reuben J. Shaw of Salk Institute.

Funding for this research was provided by the National Institutes of Health grant CA211187 (KAL), Brown Foundation for Cancer Research (KAL), National Institutes of Health grant DK107604 (RLW), National Institutes of Health grant R00CA204593 (BJA) and National Science Foundation/DBI-1759544 (EI).

About Scripps Research

Scripps Research is an independent, nonprofit biomedical institute ranked the most influential in the world for its impact on innovation by Nature Index. We are advancing human health through profound discoveries that address pressing medical concerns around the globe. Our drug discovery and development division, Calibr, works hand-in-hand with scientists across disciplines to bring new medicines to patients as quickly and efficiently as possible, while teams at Scripps Research Translational Institute harness genomics, digital medicine and cutting-edge informatics to understand individual health and render more effective healthcare. Scripps Research also trains the next generation of leading scientists at our Skaggs Graduate School, consistently named among the top 10 US programs for chemistry and biological sciences. Learn more atwww.scripps.edu.

Circadian disruption enhances HSF1 signaling and tumorigenesis in Kras-driven lung cancer

28-Sep-2022

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The surprising link between circadian disruption and cancer may have to do with temperature - EurekAlert

NIH Funds Miller School Researchers Novel Work to Develop Gene Therapy for Hearing Loss-related Usher… – InventUM | University of Miami Miller…

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The National Institute on Deafness and Other Communication Disorders (NIDCD) has awarded Xue Zhong Liu, M.D., Ph.D., Marian and Walter Hotchkiss Endowed Chair in Otolaryngology at the University of Miami Miller School of Medicine, a five-year, $3.5 million R01 research grant to develop a precision medicine approach to treat hearing loss (HL) in Usher syndrome (USH).

There is no cure for USH, and current treatments inadequately address this inherited condition that can cause not only HL but also vision loss.

Todays treatment for Usher syndrome is limited to cochlear implants or hearing aids, which help to address the hearing loss, but there is no biological treatment for HL and the blindness. There is an unmet need to develop alternative treatment options, Dr. Liu said.

The NIH grant will fund Miller School research aimed at developing and testing novel therapy approaches with gene editing. Gene editing is a group of technologies that allow scientists to change an organism's DNA. CRISPR-Cas9 is a popular gene editing technology developed to treat genetic disorders.

The Miller School is one of a select few sites in the world conducting research to apply CRISPR/Cas9 gene editing for HL including Usher syndrome, said Dr. Liu, who also is vicechair of the Department of Otolaryngology and professor of otolaryngology, human genetics, biochemistry, and pediatrics at the Miller School.

Gene- and cell-based therapies using genome editing offer the promise of treatment for a variety of inherited disorders but have not been used successfully for human hereditary HL, including Usher syndrome.

Dr. Liu, along with his collaborator Dr. Zheng-Yi Chen from the Massachusetts Eye and Ear Infirmary, Department of Otolaryngology, Harvard Medical School, aim to pave the way for the development of gene therapy approaches that would address HL Usher syndrome patients hearing.

We will use CRISPR/Cas9 to correct mutations in three different Usher genes shown in our preliminary data to cause most inherited hearing loss in USH, he said. This will involve strategies to rescue hearing in transgenic USH mouse models and developing CRISPR/Cas9 editing strategies to disrupt USH mutations, using human inner ear organoids derived from patient-induced pluripotent stem cells.

The NIH-funded study could lead to patient-specific treatment, based on a patients USH genetic mutations. In the meantime, Dr. Liu has developed a collaborating program with the University of Miami Ear Institute and Bascom Palmer Eye Institute to provide better care for people with Usher syndrome.

Recent breakthroughs in genetic screening, gene- or cell-based therapeutics, and gene editing for the inner ear can lead to novel therapies for multiple classes of hereditary hearing loss. We are excited as this is the first gene therapy NIH grant using CRISPR/Cas9 at UM for common sensory disorders, said Fred Telischi, M.D., M.E.E., chair of otolaryngology, professor of neurological surgery and biomedical engineering, and the James R. Chandler Chair in Otolaryngology.

This grant was awarded by the NIDCD as part of its high-impact program to help meet an unmet patient need, Dr. Liu said. Our aim is to lay the foundation for moving genome editing approaches closer to clinical trials on humans with Usher syndrome, which accounts for about 50% of all hereditary deaf-blindness cases, including in children.

The Genetic Hearing Loss Clinic at University of Miami Ear Institute is a multi-disciplinary program that provides diagnostic, molecular testing, genetic counseling, and intervention options for patients and families who are dealing with various types of HL.

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A Study of Rucaparib in Patients With Metastatic Castration-resistant …

University of Alabama at Birmingham Birmingham, Alabama, United States, 35294 Mayo Clinc Phoenix, Arizona, United States, 85259 Arizona Oncology Associates Tucson, Arizona, United States, 85704 Alliance Research Centers Laguna Hills, California, United States, 92653 VA Greater Los Angeles Healthcare System Los Angeles, California, United States, 90073 University of Southern California Los Angeles, California, United States, 90211 Stanford University Palo Alto, California, United States, 94305 Sharp Memorial Hospital San Diego, California, United States, 92123 Pacific Hematology Oncology Associates San Francisco, California, United States, 94115 San Francisco VA Health Care System San Francisco, California, United States, 94143 UCSF Helen Diller Family Comprehensive Cancer Center San Francisco, California, United States, 94158 Redwood Regional Medical Group Santa Rosa, California, United States, 95406 Kaiser Permanente Medical Center (Vallejo) Vallejo, California, United States, 94589 Rocky Mountain Cancer Centers Aurora, Colorado, United States, 80012 Yale School of Medicine New Haven, Connecticut, United States, 06510 4701 Ogletown Stanton Rd. Newark, Delaware, United States, 19713 Georgetown University Medical Center Washington, District of Columbia, United States, 20007 Boca Raton Community Hospital, Inc. Boca Raton, Florida, United States, 33486 Florida Cancer Specialists Fort Myers, Florida, United States, 33980 University of Florida Health Cancer Center Orlando, Florida, United States, 32806 Moffitt Cancer Center Tampa, Florida, United States, 33612 Atlanta Urological Group Atlanta, Georgia, United States, 30312 University of Chicago Comprehensive Cancer Center Chicago, Illinois, United States, 60637 Ochsner Medical Center New Orleans, Louisiana, United States, 70121 University of Maryland Greenebaum Cancer Center Baltimore, Maryland, United States, 21201 Walter Reed Hospital Bethesda, Maryland, United States, 48202 Massachusetts General Hospital Boston, Massachusetts, United States, 02114 VA Ann Arbor Healthcare System Ann Arbor, Michigan, United States, 48105 Henry Ford Hospital Detroit, Michigan, United States, 48202 Fairview Hospital Edina, Minnesota, United States, 55435 Minnesota Oncology Hematology, P.A. Minneapolis, Minnesota, United States, 55404 Minnesota Veterans Research Institute Minneapolis, Minnesota, United States, 55417 HCA Midwest Division - Kansas City Kansas City, Missouri, United States, 64132 Alegent Health Bergan Mercy Hospital , GU Research Network Omaha, Nebraska, United States, 68130 Nebraska Cancer Specialists Omaha, Nebraska, United States, 68130 Comprehensive Cancer Centers of Nevada Las Vegas, Nevada, United States, 89119 Premier Urology Associates dba/AdvanceMed Research Lawrenceville, New Jersey, United States, 08648 Rutgers Cancer Institute of New Jersey New Brunswick, New Jersey, United States, 08901 Roswell Park Buffalo, New York, United States, 14263 NYU Perlmutter Cancer Center New York, New York, United States, 10016 Memorial Sloan Kettering CC New York, New York, United States, 10065 Weill Cornell Medical College/NewYork-Presbyterian Hospital New York, New York, United States, 10065 Premier Medical Group of the Hudson Valley PC Poughkeepsie, New York, United States, 12301 University of Rochester Rochester, New York, United States, 14642 SUNY Upstate Medical University Syracuse, New York, United States, 13210 Carolina Urology Partners Concord, North Carolina, United States, 28025 The Urology Group Cincinnati, Ohio, United States, 45212 Kettering Cancer Center Kettering, Ohio, United States, 45429 Clinical Research Solutions Middleburg Heights, Ohio, United States, 44130 VA Portland Health Care System Portland, Oregon, United States, 97219 Consultants in Medical Oncology Hematology Horsham, Pennsylvania, United States, 19044 SCRI - Tennessee Oncology Nashville, Tennessee, United States, 37203 Texas Oncology Medical City Dallas Dallas, Texas, United States, 75320 UT Southwestern Medical Center Dallas, Texas, United States, 75390 UT Health Science Center Houston, Texas, United States, 77030 Texas Oncology - Tyler Tyler, Texas, United States, 75702 Virginia Oncology Associates Norfolk, Virginia, United States, 23502 VA Puget Sound Seattle, Washington, United States, 98108 Northern Cancer Insitute, St. Leonards Saint Leonards, New South Wales, Australia, 2065 Royal Hobart Hospital Hobart, Tasmania, Australia, 7000 Peninsula & Southeast Oncology Frankston, Victoria, Australia, 3199 Barwon Health, University Hospital Geelong Geelong, Victoria, Australia, 3220 Cabrini Hospital Malvern, Victoria, Australia, 3144 Southside Cancer Care Centre Miranda, Australia, 2228 Orange Health Services Orange, Australia, 2800 St John of God Hospital, Subiaco Subiaco, Australia, 6008 Riverina Cancer Care Centre Wagga Wagga, Australia, 2650 ZNA Middelheim Antwerp, Belgium, 2020 Universitair Ziekenhuis Gent Gent, Belgium, B-9000 AZ Groeninge Kortrijk, Belgium, 8500 CHU Sart-Tilman Lige, Belgium, 4000 Equipe de Recherche Clinique, Dpartement d'Oncologie/Hmatologie Lige, Belgium, 4000 AZ DELTA Roeselare, Belgium, B-8800 Juravinski Cancer Centre Hamilton Health Services Hamilton, Ontario, Canada, L8V5C2 London Health Science Center - Victoria Hospital London, Ontario, Canada, N6A 4L6 The Ottawa Hospital Ottawa, Ontario, Canada, K1H8L6 Princess Margaret Hospital Toronto, Canada, M5G 2M9 Copenhagen University Hospital Copenhagen, Denmark, 2100 Herlev Hospital Herlev, Denmark, 2730 Vejle Sygehus Vejle, Denmark, 7100 Centre Franois Baclesse Caen, France, 14000 Centre Georges Franois Leclerc Dijon, France, 21079 Clinique Victor Hugo Centre Jean Bernard Le Mans, France, 72000 Hpital Priv La Louvire Lille, France, 59800 Polyclinique de Gentilly (Centre D'Oncologie De Gentilly) Nancy, France, 54100 Institut Curie Paris, France, 75248 Hpital Priv des Ctes d'Armor Plrin, France, 22190 CRLCC Eugene Marquis Rennes, France, 35042 Gemeinschaftspraxis fur Hamatologie & Onkologie Augsburg, Germany, 86150 Charite Universitatsmedizin Berlin Berlin, Germany, 12200 Universitatsklinikum Carl Gustav Carus Dresden, Germany, 01307 Universitatsklinikum Dusseldorf Dusseldorf, Germany, 40225 Urologische Gemeinschaftspraxis Emmendingen, Germany, 79312 Universitaetsklinikum Hamburg-Eppendorf (UKE) Hamburg, Germany, 20246 Universitaetsklinikum Heidelberg Heidelberg, Germany, 69120 Universitatsklinikum Jena Jena, Germany, 07747 Universittsklinik Kln Kln, Germany, 50937 Universittsklinikum Schleswig-Holstein Lbeck, Germany, 23538 Medizinischen Fakultt Mannheim der Universitt Heidelberg Mannheim, Germany, 68167 Studienpraxis Urologie Nrtingen, Germany, 72622 University of Tuebingen Tuebingen, Germany, 72076 Die Gesundhehitsunion DGU Wuppertal, Germany, 42103 Cork University Hospital Cork, Ireland, T12 DFK4 St. Vincent's University Hospital Dublin, Ireland, D04T6F4 St James's Hospital Dublin, Ireland, D08 NHY1 Adelaide & Meath Hospital, Incorporating the National Children's Hospital Dublin, Ireland, Dublin 24 Mater Misericordiae University Hospital Dublin, Ireland, Dublin 7 Rambam Health Care Campus (RHCC), Rambam Medical Center Haifa, Israel, 3109601 Hadassah University Hospital Jerusalem, Israel, 71120 Meir Medical Center Kfar Saba, Israel, 4428164 Rabin Medical Center-Beilinson Campus Petach Tikva, Israel, 4941492 Chaim Sheba Medical Center Ramat Gan, Israel, 52621 The Tel Aviv Sourasky Medical Center (Ichilov Hospital) Tel Aviv, Israel, 64231 Ospedale San Donato, Azienda USLSUDEST Arezzo, Italy, 52100 Ospedale Santa Maria delle Croci Faenza, Italy, 48018 IRCCS Istituto Nazionale dei Tumori (INT) Milano, Italy, 20133 IEO Instituto Europeo di Oncologia Milano, Italy, 20141 University of Modena and Reggio Emilia Medical Oncology Modena, Italy, 41124 Azienda Ospedaliera San Camillo-Forlanini Rome, Italy, 00152 Azienda Opsedaliera S. Maria di Terni Terni, Italy, 05100 Santa Chiara Hospital, Dept Medical Oncology Trento, Italy, 38122 Hospital Universitari Germans Trias i Pujol Badalona, Spain, 08916 Hospital del Mar, Servicio de Oncologa Barcelona, Spain, 08003 Hospital Clnic i Provincial de Barcelona-Oncology Barcelona, Spain, 08036 Instituto Catalan de Oncologia Barcelona, Spain, 08908 Hospital Universitari Germans Trias i Pujol Barcelona, Spain, 08916 Hospital General Universitario de Guadalajara Guadalajara, Spain, 19002 Hospital Universitario Lucus Augusti. Lugo, Spain, 27003 MD Anderson Cancer Center - Madrid Madrid, Spain, 28033 Hospital Universitario Ramn y Cajal Madrid, Spain, 28034 Hospital 12 de Octubre Madrid, Spain, 28041 Hospital Universitario La Paz Madrid, Spain, 28046 Hospital Puerta de Hierro-Majadahonda Madrid, Spain, 28222 Hospital Universitario Central de Asturias Oviedo, Spain, 33011 Corporacio Sanitaria Parc Tauli Sabadell, Spain, 8208 Marques de Valdecilla University Hospital (HUMV) Santander, Spain, 39008 Hospital Universitario Virgen del Roco Sevilla, Spain, 41013 Instituto Valenciano de Oncologia IVO Valencia, Spain, 46009 Wexham Park Hospital Slough, Berkshire, United Kingdom, SL2 4HL Mount Vernon Cancer Centre Northwood, England, United Kingdom, HA6 2RN Royal Marsden Hospital Sutton, Surrey, United Kingdom, SM2 5PT Oxford University Hospitals Headington, United Kingdom, OC3 7LJ Royal Liverpool Hospital Liverpool, United Kingdom, L7 8XP London Health Science Center - Victoria Hospital London, United Kingdom, N6A 4L6 Guy's Hospital London, United Kingdom, SE1 9RT Sarah Cannon Research Institutute - UK London, United Kingdom, W1G 6AD Southampton General Hospital Southampton, United Kingdom, SO16 6YD Musgrove Park Hospital Taunton, United Kingdom, TA1 5DA The Clatterbridge Cancer Centre NHS Foundation Trust Wirral, United Kingdom, CH63 4JY

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A Study of Rucaparib in Patients With Metastatic Castration-resistant ...

CRISPR-Based HIV Gene Therapy Administered To First Human Patient – IFLScience

In a clinical trial, the first patient has received a single dose of a new human immunodeficiency virus (HIV) gene editing therapy, researchers at the Lewis Katz School of Medicine at Temple University and Excision BioTherapeutics, Inc have reported.

In a collaborative effort, the researchers are currently running aphase 1/2 clinical trial to evaluate the safety and efficacy of their therapy, calledEBT-101, which is based on gene editing technology known as CRISPR.

Nearly 40 million people worldwide suffer from the effects of HIV, and more than 40 years after the discovery of HIV/AIDS, there still are no curative treatments, said Professor Kamel Khalili, who helped lead the trial, in a statement.

EBT-101 can potentially address long-standing unmet needs of individuals living with HIV/AIDS by removing viral DNA from their cells, thereby eradicating infection.

When HIV infects, it takes long-term hold and hides from the immune system in cells, compromising the patient's immunity over time and eventually leading to the development of AIDS the progressive failure of a patient's immune system. There is currently no cure for HIV, but various treatments and medications can help manage the infection and slow or prevent the progression of the disease.

The therapy currently being trialed, which uses CRISPR gene editing to removeHIV viral DNA from infected cells, is a major step towardfinding a therapeutic cure.

We are well-positioned to collect key data that will enable our efforts to translate the success this approach has shown in animal models to human clinical trial participants, Khalili added. We look forward to investigating this hypothesis through the EBT-101 clinical program and are pleased that the EBT-101 Phase 1/2 trial is proceeding as planned.

The first patient to receive a single dose of EBT-101 in the current trial is currently under medical supervision and will soon be assessed to see if there is any viral rebound and whether the single curative treatment worked as planned. This will be a deciding factor in whether or not the patient is able to stop their current antiretroviral therapy in the future.

The official start of the Phase 1/2 clinical trials for EBT-101 brings us one extremely significant step closer to creating a potential cure for HIV/AIDS, said Dr Amy J. Goldberg, Interim Dean of the Katz School of Medicine. This amazing milestone speaks to the exceptional research acumen and scientific knowledge of Drs. Khalili and Burdo and their teams outstanding members of the Temple family.

For further details, you can view the clinical trial information at ClinicalTrials and follow its progress.

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CRISPR-Based HIV Gene Therapy Administered To First Human Patient - IFLScience

Adverum Biotechnologies to Participate in the Jefferies Cell and Genetic Medicine Summit – Adverum Biotec – Benzinga

REDWOOD CITY, Calif., Sept. 23, 2022 (GLOBE NEWSWIRE) -- Adverum Biotechnologies, Inc. ADVM, a clinical-stage company that aims to establish gene therapy as a new standard of care for highly prevalent ocular diseases, today announced that Peter Soparkar, chief operating officer of Adverum Biotechnologies, will present at the Jefferies Cell and Genetic Medicine Summit on September 29, 2022, at 9:30 a.m. ET.

The on-demand webcast corporate presentation may be accessed underEvents and Presentationsin the Investors section of Adverum's website. A replay of the webcast will be available on the website for 90 days following the presentation.

About Adverum Biotechnologies

Adverum Biotechnologies ADVM is a clinical-stage company that aims to establish gene therapy as a new standard of care for highly prevalent ocular diseases with the aspiration of developing functional cures to restore vision and prevent blindness. Leveraging the research capabilities of its proprietary, intravitreal (IVT) platform, Adverum is developing durable, single-administration therapies, designed to be delivered in physicians' offices, to eliminate the need for frequent ocular injections to treat these diseases. Adverum is evaluating its novel gene therapy candidate, ixoberogene soroparvovec (Ixo-vec, formerly referred to as ADVM-022), as a one-time, IVT injection for patients with neovascular or wet age-related macular degeneration. By overcoming the challenges associated with current treatment paradigms for these debilitating ocular diseases, Adverum aspires to transform the standard of care, preserve vision, and create a profound societal impact around the globe. For more information, please visitwww.adverum.com.

Corporate & Investor Inquiries

Anand ReddiVice President, Head of Corporate Strategy, External Affairs and EngagementAdverum Biotechnologies, Inc.T: 650-649-1358E:areddi@adverum.com

Media

Megan TalonAssociate Director, Corporate CommunicationsAdverum Biotechnologies, Inc.T: 650-649-1006E:mtalon@adverum.com

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Adverum Biotechnologies to Participate in the Jefferies Cell and Genetic Medicine Summit - Adverum Biotec - Benzinga

The New England Journal of Medicine Publishes Pivotal Tofersen Data that Show Benefits in Rare, Genetic Form of ALS – GlobeNewswire

CAMBRIDGE, Mass., Sept. 21, 2022 (GLOBE NEWSWIRE) -- Biogen Inc. (Nasdaq: BIIB) today announced that The New England Journal of Medicine(NEJM) has published detailed results from the Phase 3 VALOR study and the combined analysis of VALOR and its open label extension (OLE) study evaluating tofersen for the treatment of superoxide dismutase 1 (SOD1) amyotrophic lateral sclerosis (ALS). There is currently no treatment targeted for SOD1-ALS.

I see three key take home points from these data.First, tofersen clearly leads to lowering of SOD1 protein, as would be expected.Second there is substantial lowering of neurofilament levels, which I interpret as potentially slowing the underlying disease process. And third, there is a meaningful clinical benefit when looking at the later time points in the open label extension, said Timothy Miller, M.D., Ph.D., principal investigator of VALOR and ALS Center co-Director at Washington University School of Medicine, St. Louis. We are grateful to the dedication from participants, their families, and the sites for taking part in this important study.

Data from the combined analysis were previously presented at the European Network to Cure ALS (ENCALS) annual meeting and included within Biogens New Drug Application for tofersen that was recently accepted for priority review by the U.S. Food and Drug Administration. The application was given a Prescription Drug User Fee Act action date of January 25, 2023.

The ALS community has been actively pursuing new medicines for decades. To have data like these published in NEJM gives us energy and hope. We are now seeing in the data what we suspected about tofersen for a long time that it has the potential to make a clinical difference for people living with SOD1-ALS, said Merit Cudkowicz, M.D., co-principal investigator of the VALOR trial and co-founder of the Northeast ALS Consortium, Director of the Healey & AMG Center for ALS and Chair of Neurology at Massachusetts General Hospital and the Julieanne Dorn Professor of Neurology at Harvard Medical School. The lowering of neurofilament, a marker of axonal injury and neurodegeneration along with the clinical data, highlights the potential of tofersen.

About VALOR and the OLEVALOR was a six-month Phase 3, randomized, double-blind, placebo-controlled study to evaluate the effects of tofersen 100 mg in adults with ALS associated with a SOD1 mutation. In total, 108 participants were randomized in VALOR (n=72 to tofersen 100 mg and n=36 to placebo). Of these participants, 95 enrolled in the ongoing OLE. At the time of the analysis all participants had an opportunity for at least 12 months of follow-up, with a median exposure to tofersen of approximately 20 months (range: 1 34 months).

The primary endpoint of VALOR was change from baseline to week 28 in ALS Functional Rating Scale-Revised (ALSFRS-R) total score. Secondary endpoints included changes in total cerebrospinal fluid SOD1 protein concentration, plasma neurofilament light chain (NfL), slow vital capacity and handheld dynamometry in 16 muscles.

As previously reported in October 2021, VALOR did not meet the primary endpoint. However, trends of reduced disease progression across multiple secondary and exploratory endpoints were observed. The combined VALOR and OLE 12-month data, in which the clinical analyses adjusted for neurofilament levels as a marker of the disease progression rate at baseline, showed sustained reductions in SOD1 protein (a marker of target engagement) and neurofilament (a marker of neurodegeneration) and slowed decline in clinical function, respiratory function, strength, and quality of life with earlier initiation of tofersen.

In the 12-month data, the most common adverse events (AEs) in participants receiving tofersen in VALOR and the OLE study were procedural pain, headache, pain in the arms or legs, falls, and back pain. Most AEs in both VALOR and the OLE were mild to moderate in severity. Serious neurologic events including myelitis, chemical or aseptic meningitis, radiculitis, increased intracranial pressure and papilledema, were reported in 6.7 percent of participants receiving tofersen in VALOR and its OLE.

About TofersenTofersen is an antisense drug being evaluated for the potential treatment of SOD1-ALS. Tofersen binds and degrades SOD1 mRNA to reduce synthesis of SOD1 protein production. In addition to the ongoing open label extension of VALOR, tofersen is being studied in the Phase 3 ATLAS study designed to evaluate whether tofersen can delay clinical onset when initiated in presymptomatic individuals with a SOD1 genetic mutation and biomarker evidence of disease activity. Biogen licensed tofersen from Ionis Pharmaceuticals, Inc. under a collaborative development and license agreement.

About Amyotrophic Lateral Sclerosis and SOD1-ALSAmyotrophic lateral sclerosis (ALS) is a rare, progressive and fatal neurodegenerative disease that results in the loss of motor neurons in the brain and the spinal cord that are responsible for controlling voluntary muscle movement. People with ALS experience muscle weakness and atrophy, causing them to lose independence as they steadily lose the ability to move, speak, eat, and eventually breathe. Average life expectancy for people with ALS is three to five years from time of symptom onset.1

Multiple genes have been implicated in ALS. Genetic testing helps determine if a persons ALS is associated with a genetic mutation, even in individuals without a family history of the disease. Currently, there are no genetically targeted treatment options for ALS. Mutations in the SOD1 gene are responsible for approximately 2 percent of the estimated 168,000 people who have ALS globally (SOD1-ALS).2Life expectancy in SOD1-ALS varies widely with some patients surviving less than a year.3

Biogens Continuous Commitment to ALSFor over a decade, Biogen has been committed to advancing ALS research to provide a deeper understanding of all forms of the disease. The company has continued to invest in and pioneer research despite making the difficult decision to discontinue a late-stage ALS asset in 2013. Biogen has applied important learnings to its portfolio of assets for genetic and other forms of ALS, with the goal of increasing the probability of bringing a potential therapy to patients in need. These applied learnings include evaluating genetically validated targets in defined patient populations, pursuing the most appropriate modality for each target and employing sensitive clinical endpoints. Today, the company has a pipeline of investigational drugs being evaluated in ALS, including tofersen and BIIB105.

About BiogenAs pioneers in neuroscience, Biogen discovers, develops, and delivers worldwide innovative therapies for people living with serious neurological diseases as well as related therapeutic adjacencies. One of the worlds first global biotechnology companies, Biogen was founded in 1978 by Charles Weissmann, Heinz Schaller, Sir Kenneth Murray, and Nobel Prize winners Walter Gilbert and Phillip Sharp. Today, Biogen has a leading portfolio of medicines to treat multiple sclerosis, has introduced the first approved treatment for spinal muscular atrophy, and developed the first and only approved treatment to address a defining pathology of Alzheimers disease. Biogen is also commercializing biosimilars and focusing on advancing one of the industrys most diversified pipelines in neuroscience that will transform the standard of care for patients in several areas of high unmet need.

In 2020, Biogen launched a bold 20-year, $250 million initiative to address the deeply interrelated issues of climate, health, and equity. Healthy Climate, Healthy Lives aims to eliminate fossil fuels across the companys operations, build collaborations with renowned institutions to advance the science to improve human health outcomes, and support underserved communities.

We routinely post information that may be important to investors on our website atwww.biogen.com.Follow us on social media-Twitter,LinkedIn,Facebook,YouTube.

Biogen Safe HarborThis news release contains forward-looking statements, including statements made pursuant to the safe harbor provisions of the Private Securities Litigation Reform Act of 1995, including statements about results from the Phase 3 VALOR study of tofersen or its OLE; the potential clinical effects of tofersen; the potential benefits, safety and efficacy of tofersen; the clinical development program for tofersen; the potential approval of tofersen; the identification and treatment of ALS; our research and development program for the treatment of ALS; the potential of our commercial business and pipeline programs, including tofersen; and risks and uncertainties associated with drug development and commercialization. These forward-looking statements may be accompanied by words such as aim, anticipate, believe, could, estimate, expect, forecast, intend, may, plan, potential, possible, will, would and other words and terms of similar meaning. Drug development and commercialization involve a high degree of risk and only a small number of research and development programs result in commercialization of a product. Results in early stage clinical trials may not be indicative of full results or results from later stage or larger scale clinical trials and do not ensure regulatory approval. You should not place undue reliance on these statements or the scientific data presented.

These statements involve risks and uncertainties that could cause actual results to differ materially from those reflected in such statements, including without limitation, uncertainty of success in the development and potential commercialization of tofersen; the risk that we may not fully enroll our clinical trials or enrollment will take longer than expected; unexpected concerns may arise from additional data, analysis or results obtained during our clinical trials; regulatory authorities may require additional information or further studies, or may fail or refuse to approve or may delay approval of our drug candidates, including tofersen; the occurrence of adverse safety events; the risks of unexpected hurdles, costs or delays; failure to protect and enforce our data, intellectual property and other proprietary rights and uncertainties relating to intellectual property claims and challenges; product liability claims; and the direct and indirect impacts of the ongoing COVID-19 pandemic on our business, results of operations and financial condition. The foregoing sets forth many, but not all, of the factors that could cause actual results to differ from our expectations in any forward-looking statement. Investors should consider this cautionary statement, as well as the risk factors identified in our most recent annual or quarterly report and in other reports we have filed with the U.S. Securities and Exchange Commission. These statements are based on our current beliefs and expectations and speak only as of the date of this news release.

We do not undertake any obligation to publicly update any forward-looking statements, whether as a result of new information, future developments or otherwise.

References:

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The New England Journal of Medicine Publishes Pivotal Tofersen Data that Show Benefits in Rare, Genetic Form of ALS - GlobeNewswire

Alzheimer’s disease risk linked to newly discovered protein mutation – Medical News Today

Mitochondria are structures within the cell that convert energy from food into energy the cell can use. Each cell contains hundreds to thousands of mitochondria. Although most DNA is found inside the cells nucleus, mitochondria also contain a small amount of DNA, known as mitochondrial DNA.

In the early 2000s, researchers realized that short sections of mitochondrial DNA encode small (less than 100 amino acids long), biologically active proteins, now referred to as mitochondrial microproteins. The first mitochondrial microprotein to be discovered was called humanin.

There is growing evidence that humanin and other similar mitochondrial microproteins play a role in several age-related conditions, including Alzheimers disease.

Alzheimers disease is the most common type of dementia, characterized by progressive mental deterioration. According to the CDC, as many as 5.8 million Americans were living with Alzheimers disease in 2020.

The Cohen Laboratory at the University of Southern California (USC), one of the three laboratories that independently discovered humanin in 2003, has discovered a new microprotein connected to the risk of Alzheimers disease.

Their latest research, published in the journal of Molecular Psychiatry, revealed that a mutation in the newly discovered SHMOOSE microprotein is associated with a higher risk for Alzheimers disease across four cohorts. According to the researchers, nearly 1 in 4 individuals with European ancestry have the mutated version of the protein.

Dr. Pinchas Cohen, professor of gerontology, medicine, and biological sciences and senior author of the study, told Medical News Today:

The implications are not immediate, but we believe that [relatively soon], the SHMOOSE SNP [single nucleotide polymorphism] genetic variant that is found in over 20% of Europeans may guide both the classification of individuals that are at risk for Alzheimers that may benefit from certain preventive measures and also could inform the selection of medical interventions that will become available in the near future. A bit further ahead, SHMOOSE [protein] analogues may become available as therapeutics for individuals who carry the SNP and develop dementia, in a precision medicine approach.

Brendan Miller, Ph.D., first author of the study, studied mitochondrial DNA sequences from the Alzheimers Disease Neuroimaging Initiative (ADNI) database, searching for small variations in the genes called single nucleotide polymorphisms or SNPs. He found that a mutation in one particular mitochondrial SNP (rs2853499) was associated with a greater risk of Alzheimers disease and brain atrophy.

Dr. Miller and his colleagues then discovered that the mutated SNP causes a change in a mitochondrial microprotein, which they called SHMOOSE. The researchers used a technique called immunoprecipitation to isolate the SHMOOSE microprotein from the mitochondria of nerve cells.

When they analyzed this sample using mass spectrometry, they detected and identified two unique protein fragments from the SHMOOSE microprotein. The researchers reported that this is the first unique mass spectrometry-based detection of a mitochondrial-encoded microprotein to date.

Having identified a microprotein associated with a higher risk of Alzheimers disease, the researchers followed up on their discovery by carrying out studies in rats and cell culture experiments.

They found that the SHMOOSE microprotein accumulates in the mitochondria of neurons (nerve cells), where it binds to the inner mitochondrial membrane protein mitofilin. The SHMOOSE microprotein appears to act on the brain by influencing mitochondrial gene expression and boosting mitochondrial oxygen consumption. The researchers noted that mutated SHMOOSE microprotein was less effective at boosting oxygen consumption and impacted gene expression differently.

Dysregulated mitochondrial associated brain energetics is one of the multiple pathways thought to be important for Alzheimers disease, Andrew Saykin, PsyD, ABCN, Professor and Director of the Center for Neuroimaging and Indiana Alzheimers Disease Research Center, told MNT.

George Perry, Ph.D., Professor and Semmes Foundation Distinguished University Chair in Neurobiology at the University of Texas at San Antonio, told MNT that this study is very important as it links risk of [Alzheimers disease] to cellular metabolism. There are numerous cell biology and biochemical studies that highlight this [] and finding genetic data further support[s] this view.

Dr. Saykin observed that with further development and validation there could be implications of this and other microproteins for early detection, longitudinal monitoring, and potentially for therapeutic targeting.

MNT also discussed the studys findings with Tal Nuriel, Ph.D., Assistant Professor of Pathology and Cell Biology at Columbia University Irving Medical Center. Dr. Nuriel told MNT that most Alzheimers disease-related gene mutations discovered in the past are either very rare variants or common variants that confer a very small risk.

He said the mutation, or variant, in the SHMOOSE microprotein appears to confer a moderate risk for Alzheimers disease and is relatively common in the population and [this] alone makes it interesting.

Dr. Nuriel added that the fact that this is a microprotein that can theoretically be administered as a therapeutic agent is valuable. He cautioned that there will be a very long road ahead before any therapy derived from this microprotein could become a reality. Importantly, its unclear whether this SHMOOSE microprotein would enter the brain if given subcutaneously or intravenously. And if it doesnt enter the brain, this would greatly limit its ability to be used therapeutically.

When asked about the next step in the research following this discovery, Dr. Cohen told MNT, Our immediate plan is to treat mice that have been engineered to develop Alzheimers disease with SHMOOSE over several months and assess the improvement in their symptoms and performance. We will also work on developing longer acting analogues of the pep[t]ide.

The researchers noted in the study that SHMOOSE is yet another microprotein of a growing number that modify mitochondrial biology. According to a recent review, thousands of DNA sequences with microprotein-coding potential are currently unverified or functionally uncharacterized.

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Alzheimer's disease risk linked to newly discovered protein mutation - Medical News Today

Epigenetic and transcriptomic alterations in offspring born to women with type 1 diabetes (the EPICOM study) – BMC Medicine – BMC Medicine

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Epigenetic and transcriptomic alterations in offspring born to women with type 1 diabetes (the EPICOM study) - BMC Medicine - BMC Medicine

Editas Rumored to be in Advanced Discussions around Potential Sale of Oncology Assets – BioSpace

From left: Editas CMO Baisong Mei and CEO Gilmore O'Neill/courtesy of Editas Medicine

CRISPR gene editing leader Editas Medicineoften makes biotech headlines for its therapies for sickle cell and retinal diseases. Less often does it make the news for its preclinical cancer pipeline which could be why the company is reportedly considering a sale of these assets.

Editas is in "advanced discussions" regarding the sale of its preclinical oncology lineup, according to reporting from Endpoints News. When asked to confirm the rumors, Cristi Barnett, VP & head of corporate communications at Editas told BioSpace,We have long shared our plans to pursue development and commercialization opportunities through partnerships, specifically with oncology and our iNK program.

Barnett added that with a new leadership team onboard, Editas undertook a strategic review to inform opportunities.

Investors seemed to agree with the notion as Editas stock rose4.2% following the report.

Editas has given its C-Suite a makeover this year. In April, the company appointed genetic medicine veteran Gilmore ONeill as president and CEO.

ONeill wasted no time in bringing on board Sanofi veteran Baisong Mei to serve as the companys new chief medical officer. Mei has deep experience in the hemophilia space at both Sanofi and Bayer. He replaced Lisa Michaels, who was terminated by the company in February.

Editas presented data on one of its oncology assets, EDIT-202, last week at the European Society of Gene and Cell Therapy 29th Annual Meeting in Edinburgh, Scotland. EDIT-202 is a gene-edited iPSC-derived NK cell therapy that maintains prolonged persistence, high cytotoxicity and enhanced in vivo control of solid tumors, according to Editas.

Currently, there is no change to our program or plans. EDIT-202is advancing toward IND-enabling studies, Barnett said. She added that Editas will share additional updates on this program later this year including additional preclinical data at an upcoming medical meeting.

Also at ESGCT, Editas presented preclinical data from another program, EDIT-103, which is being developed to treat rhodopsin-associated autosomal dominant retinitis pigmentosa (RHO-adRP), a progressive type of retinal degeneration.

In a non-human primate model, the therapy demonstrated nearly 100% knockout of the endogenous RHO gene. Additionally, the replacement RHO gene produced over 30% of normal RHO protein levels in the treated area of subretinal injection, the company reported.

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Editas Rumored to be in Advanced Discussions around Potential Sale of Oncology Assets - BioSpace

A Decade of Breast Cancer at the Molecular Level: Pioneering Personalized Medicine – Targeted Oncology

Breast cancer treatment options have significantly expanded in the past decade, welcoming new classes of agents as well as treatments directed at specific patient populations (TIMELINE).

Many believe that these advancements in breast cancer care over the past 10 years owe much to the increased understanding of molecular factors contributing to breast cancer pathogenesis and heterogeneity.1-3

In looking back at the past decade of targeted therapy in breast cancer, Targeted Therapies in Oncology (TTO) spoke with 2 medical oncologists with extensive expertise in breast cancer about how biomarker advancements have transformed the practice of breast cancer management.

I think its fair to say that breast cancer in particular has led the way in molecular therapeutics in oncology, Dennis J. Slamon, MD, director of clinical/translational research at the UCLA Jonsson Comprehensive Cancer Center, told TTO. In part, thats because of all the investment that was made in research [and] because of defi ning this disease not just at a tissue level, but at a molecular level.

Classification of breast cancers into not just hormone receptor and HER2 positivity or negativity, but also into the luminal/basal subtypes has helped to identify treatments that may be more helpful for large groups of patients.1,3 For example, patients with basal-like disease, which is about 15% to 20% of all breast cancers, have triple-negative breast cancer (TNBC) and a poor prognosis. These patients tend to be responsive to chemotherapy treatment.1

The fact that molecular targets did not consistently translate to all breast cancers has become a key underpinning of our understanding of cancer.1 Not all patients benefi t from molecularly targeted treatments. For instance, HER2-positive breast cancer only accounts for about 25% of all breast cancer cases, thus HER2-targeted therapies may only benefi t 25% of all patients with breast cancer.

The same story is coming up again and again, not necessarily the same genes or the same targets or the same pathways, but the fact that there is a diversity of these diseases thats far beyond what we used to use to classify cancers by the tissue in which they arose, Slamon said.

Our understanding of cancer as a potentially more complex disease than previously supposed, began to develop well before 2012, explained Slamon.

That started in breast cancerbefore molecular medicine, as far back as 1899 or 98, when a surgeon recognized the fact that this disease occurred in women and the fact that it may have some hormonal component, said Slamon.4 After we found HER2, the methods of dissecting a tumor molecularly became much more sophisticated and widespread in their use and now, today, there are 14 molecular subtypes of breast cancer. And that is the underpinning of how breast cancer has led the way [in determining that patients with breast cancer] should not be treated with a one-size-fits-all approach. They should be treated with therapeutics that are directed to the appropriate subtype or the class in which they sit.

These molecular subtype characterizations have also shaped the therapeutic strategies within different breast cancer settings. Just thinking about advances in targeted therapies and how we use them to treat breast cancer in the last decade, I separate it into 2 categories1 is how we treat localized breast cancer,when our goal is to cure the cancer, so stages I to III. Most patients are being diagnosed with those earlier stages of breast cancer, Marina Sharifi , MD, PhD, assistant professor and medical oncologist at the University of Wisconsin Carbone Cancer Center, told TTO.

I think one of the major themes over the last 10 years for these nonmetastatic breast cancers is what I refer to as right-sizing therapy. We know that some of the women who have these early breast cancers can have recurrence down the road and we want to try and prevent that. So, 10 to 15 years ago, all of those women got chemotherapy, but even back then we knew that not every woman needs chemotherapy, and we knew that there were some breast cancers that could potentially benefit from more targeted types of therapies. But in the past 10 years, there have been a few developments that have allowed us to determine which women need chemotherapy and which women we can safely avoid exposing to the [adverse] effects of chemotherapy, said Sharifi.

This new prognostic ability has been fueled by advances in genomic testing.5,6 In addition to hormone receptors and molecular subtypes, other prognostic biomarkers that have been incorporated into practice include transcriptomic and proteomic levels and Ki-67 levels. Other biomarkers utilize combinations of genes to determine potential responses to treatment as well as the possibility of recurrence.

And more recently, research has turned to the use of circulating DNA and circulating tumor cells to help identify further prognostic and predictive bbiomarkers for patients with breast cancer.6

Specifically, for estrogen-driven (estrogen receptor [ER] positive) breast cancers, which are the most common type of breast cancer, we have genomic tests that are now used routinely to help us identify women who can safely avoid chemotherapy with that type of breast cancer. Both the MammaPrint and the OncoType DX are genomic tests that we know are effective in identifying which women do need chemotherapy to help maximize their chances of cure and which women have lower-risk breast cancers where the chemotherapy actually wont help them because they dont need it.7,8 That has been a huge development in the fi eld in the last 10 yearsto go from knowing that these tests were out there but not having that confirmation that we know that they predict chemotherapy benefit to having 2 major trials come out in the last 10 years that demonstrate that they can predict chemotherapy benefit, both in women who have those ER-positive breast cancers without lymph node involvement and also women who have ER-positive breast cancer with lymph node involvement. That has been a major advance for the most common type of breast cancer thats diagnosed across the country.9,10

Both the TAILORx (NCT00310180) and RxPONDER (NCT01272037) trials validated the usefulness of the 21-gene Oncotype DX recurrence score assay in patients with hormone receptorpositive, HER2-negative breast cancer. The TAILORx trial showed that among patients with node-negative disease, those with an intermediate Oncotype DX score, or intermediate risk of recurrence, could benefit from treatment with endocrine therapy alone and avoid receiving chemotherapy. Younger patients (.50 years) with a recurrence score of 16 to 25 still showed some benefit from the combination of chemotherapy and endocrine therapy.9 I n R xPONDER, adjuvant chemotherapy use was not considered necessary in most postmenopausal women with node-positive disease and recurrence scores between 0 and 25. Alternatively, premenopausal women were more likely to benefit from adjuvant chemotherapy.10

On the fl ip side, said Sharifi , somehave high-risk TNBC or high-risk HER2-positive breast cancer, those are types of breast cancer where historically we have struggled to cure women. There weve had a number of different advances. In TNBC, weve had the introduction of immunotherapies into our treatment. The KEYNOTE-522 trial [NCT03036488] showed that if wecombine pembrolizumab [Keytruda] with chemotherapy, that has significantly increased the number of women were able to cure of that higher-risk TNBC.11

Approval of neoadjuvant pembrolizumab in combination with chemotherapy for patients with high-risk, early-stage TNBC followed by single-agent adjuvant pembrolizumab by the FDA in 2021 was a signifi cant advancement for the treatment of patients with TNBC.12 Data from the KEYNOTE-522 trial were considered practice changing early on, showing a pathological complete response in 64.8% of patients treated with the regimen.11

Likewise, for HER2-positive breast cancer, we have seen the development of multiple drugs that target HER2, from trastuzumab [Herceptin] and pertuzumab [Perjeta], to ado-trastuzumab emtansine [T-DM1; Kadcyla], that have increased the number of women who were able to cure of their HER2-positive breast cancers, Sharifi said.

Slamon also commented on the proliferation of HER2-targeting therapies in addition to the expansion of other types of targeted agents, benefi tting patients in the TNBC space. [Since] our initial fi nding of HER2 and trastuzumab, now theres a ton of HER2 targeting trastuzumab deruxtecan [Enhertu] and emtansine [Kadcyla], margetuximab [Margenza]the list goes on and on of anti- HER2 therapeutics. Then there are new therapeutics for TNBC; they look at the TROP-2 target on tumor cells, and sacituzumab govitecan [Trodelvy] is the new therapeutic for that.13 As we identify new targets that we can approach with an antibody thatll attach to it, [it could be possible to] make an antibody- drug conjugate [ADC] to allow that antibody to go right to the target protein on the tumor cell and have it released internally and that takes away the systemic effect of the chemotherapy and delivers it right into the cell. Thats a whole new strategy thats coming into its own in a big way now, Slamon told TTO.

The phase 3 ASCENT study (NCT02574455) showed that sacituzumab produced a PFS and overall survival (OS) benefi t over physicians choice of chemotherapy in patients with relapsed or refractory metastatic TNBC. The median PFS with sacituzumab was 5.6 months compared with 1.7 months with chemotherapy. Median OS was 12.1 months with the ADC and 6.7 months with chemotherapy.13

The emergence of these newer targeted therapies has permitted a risk-based tailoring of neoadjuvant and adjuvant therapies in the non-metastatic breast cancer space, observed Sharifi . Another major development over the last 10 years, particularly for the [patients with] TNBC and HER2-positive breast cancers, is a shift towards neoadjuvant chemotherapy, which allows us to identify women with higher risk of recurrence after our standard pre-operative chemotherapy, and then add additional therapy after surgery to reduce their risk. For instance, that is how ado-trastuzumab emtansine is used in HER2-positive breast cancer, and there are other targeted options in this space, including olaparib [Lynparza] for women with germline BRCA mutations, she said.

We have also made great strides in precision oncology in the metastatic breast cancer space, with an expansion of different types of targeted approaches, including mutation-targeted inhibitors, immunotherapy, and ADCs. While all of these developments have helped patients live longer and better with metastatic breast cancer, I think ADCs are the most game-changing new development for treating metastatic breast cancer, Sharifi told TTO. As an example, the ADC trastuzumab deruxtecan, is a HER2-targeting agent [encompassing] trastuzumab linked to a chemotherapy that was initially found to be extremely effective for HER2-positive metastatic breast cancer, even in women who have had multiple prior treatments with different other agents. Even more importantly, however, it has recently been shown to be effective also in women who have low HER2 expression, who would previously have been classifi ed as HER2 negative.14 This has dramatically expanded the group of women with metastatic breast cancer who can benefit from trastuzumab deruxtecan to include what we are now calling HER2-low breast cancers, which are far more common than HER2-positive breast cancers. So thats been an important advance for us in the ADC space just in the last year, said Sharifi.

Data from the phase 3 DESTINY-Breast04 trial (NCT03734029) showed that patients with low HER2 expression can still possibly benefit from HER2-targeted therapy. The trial demonstrated a median progression-free survival (PFS) of 10.1 months with trastuzumab deruxtecan therapy vs 5.4 months with physicians choice of therapy in patients with HER2-low (IHC 1+/IHC 2+, ISH-) metastatic breast cancer who had received 1 to 2 prior lines of chemotherapy. The median OS was 23.9 months with trastuzumab deruxtecan and 17.5 months with physicians choice of chemotherapy.14 These findings led to the FDA approval of trastuzumab deruxtecan in this disease setting just this year.15

The Importance of Individualization

Turning to mutation-targeted therapies, this has also been an active area in metastatic breast cancer treatment in the past 5 years, including the first FDA approval of a drug targeting PIK3CA mutations, [which] are common in many types of cancer and found in almost half of women who have ER-positive metastatic breast cancer, where the drug alpelisib [Piqray] has been approved for women with this type of mutation, Sharifi told TTO.

Approval for alpelisib in breast cancer was supported by fi ndings from the phase 3 SOLAR-1 trial (NCT02437318), which showed that the PI3K inhibitor in combination with fulvestrant led to a median PFS of 11.0 months vs 5.7 months with fulvestrant in patients with PIK3CA-mutant, HR-positive, HER2-negative advanced breast cancer.16

patient with metastatic breast cancer should be getting molecular profi ling to identify possible targeted therapy options, and many patients will now have ADC treatment options that they may be eligible for at some point in their disease trajectory. For patients with localized breast cancer, I think weve also come a long way in being able to individualize therapy and avoid exposing patients to unnecessary [adverse] effects while also being able to augment treatment for patients who are at higher risk of recurrence and cure more women with this diagnosis, Sharifi said.

The basis of this personalized therapy derived from breast cancer-based research, observed Slamon. The gamechanger clearly was [the molecular advancements]. [When] looking at what is big in oncology, its this appreciation that originated in breast cancer and now has spread throughout the field of human oncology about this molecular diversity defining, a) different subtypes, and b) new potential therapeutic targets or pathways, he said.

Sharifi looks to the continued development of ADCs as a cancer treatment modality. Theres a real untapped well of potential targets that were just starting to explore in terms of developing new ADCs and combining them with targeted and immunotherapy approaches, and I think this will move the bar in how were able to combat treatment resistance, said Sharifi.

Slamons view of the future also comprises targeted strategies : As we identify more targets...therell probably be more and newer, perhaps even better, therapeutics than we have currently. Breast cancer has led this field.

REFERENCES:

1. Bettaieb A, Paul C, Plenchette S, Shan J, Chouchane L, Ghiringhelli F. Precision medicine in breast cancer: reality or utopia? J Transl Med. 2017;15(1):139. doi:10.1186/s12967-017-1239-z

2. Cocco S, Piezzo M, Calabrese A, et al. Biomarkers in triple-negative breast cancer: state-of-the-art and future perspectives. Int J Mol Sci. 2020;21(13):4579. doi:10.3390/ijms21134579

3. Low SK, Zembutsu H, Nakamura Y. Breast cancer: The translation of big genomic data to cancer precision medicine. Cancer Sci. 2018;109(3):497-506. doi:10.1111/cas.13463

4. Beatson GT. On the treatment of inoperable cases of carcinoma of the mamma: suggestions for a new method of treatment, with illustrative cases. Trans Med Chir Soc Edinb. 1896;15:153-179.

5. Hou Y, Peng Y, Li Z. Update on prognostic and predictive biomarkers of breast cancer. Semin Diagn Pathol. 2022;39(5):322-332. doi:10.1053/j.semdp.2022.06.015

6. Nicolini A, Ferrari P, Duff y MJ. Prognostic and predictive biomarkers in breast cancer: past, present and future. Semin Cancer Biol. 2018;52(Pt 1):56-73. doi:10.1016/j.semcancer.2017.08.010

7. Cardoso F, vant Veer LJ, Bogaerts J, et al; MINDACT Investigators. 70- gene signature as an aid to treatment decisions in early-stage breast cancer. N Engl J Med. 2016;375(8):717-729. doi:10.1056/NEJMoa1602253

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A Decade of Breast Cancer at the Molecular Level: Pioneering Personalized Medicine - Targeted Oncology

Unspinning the secrets of spider webs – Australian Geographic – Australian Geographic

Home News Unspinning the secrets of spider webs

By Esme MathisOctober 19, 2022

Stronger than steel and more elastic than rubber, spider silk has the potential to transform medicine, engineering, and materials science if only we learn how to produce it.

A new global study, involving University of New South Wales scientists, has analysed the silk properties of spiders across Oceania, Asia, Europe and the USA to better understand how this natural wonder can be emulated in future biomaterials. The research, published in Science Advances, catalogued the silk gene sequences of 1098 species from 76 families.

Up until now, there was a pretty good literature set of how spider silk performs, says Dr Sean Blamires, an evolutionary ecological biologist from UNSW Sydneys School of Biological, Environmental and Earth Sciences. But what has been lacking is a way to generalise across spiders and find out what causes specific properties. Is there a link between genes, protein structures and fibres?

According to Sean, the large data set collected over five years allow scientists to create complex models, using machine learning to understand how and why specific silk properties vary between species, and even between individual spiders.

Just like the Human Genome project has given researchers the ability to identify specific gene sequence mutations that cause specific diseases, this database gives biologists and material scientists the ability to derive direct genetic causes for the properties of spider silk, he says.

There are seven types of spider silk, secreted from different glands within a spider. Out of these, dragline silk is the crowning glory. Known for its strength, durability and flexibility, dragline silk has captured scientists imagination for decades with its tantalising potential.

In a spiderweb, the dragline silk makes up the framework and the radials. Its also the silk that the spider uses when it drops off a web, says Sean. Non-web building spiders might use it to make retreats or use it for signalling with each other, while trapdoor spiders use something very similar.

In Australia, the dragline silk produced by orb-weaving spiders is so tough that it outperforms Kevlar and steels. Its tough, but also flexible.

Most materials are either one or the other, says Sean.

The study measured the mechanical, thermal, structural and hydration properties of dragline silks.

Its hoped this research will provide a blueprint for renewable, biodegradable and sustainable biopolymers. Suggested uses for this lightweight material ranges from bulletproof vests, flexible building materials, biodegradable bottles, and even a non-toxic biomaterial in regenerative medicine, that can be used as a scaffold to grow and repair damaged nerves or tissues.

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Mathematical model could bring us closer to effective stem cell therapies – Michigan Medicine

Until recently, researchers could not see gene expression in an individual cell. Thanks to single cell sequencing techniques, they now can. But the timing of changes is still hard to visualize, as measuring the cell destroys it.

To address this, we developed an approach based on models in basic physics, explained Welch, treating the cells like they are masses moving through space and we are trying to estimate their velocity.

The model, dubbed MultiVelo, predicts the direction and speed of the molecular changes the cells are undergoing.

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Our model can tell us which things are changing firstepigenome or gene expression--and how long it takes for the first to ramp up the second, said Welch.

They were able to verify the method using four types of stem cells from the brain, blood and skin, and identified two ways in which the epigenome and transcriptome can be out of sync. The technique provides an additional, and critical, layer of insight to so called cellular atlases, which are being developed using single cell sequencing to visualize the various cell types and gene expression in different body systems.

By understanding the timing, Welch noted, researchers are closer to steering the development of stem cells for use as therapeutics.

One of the big problems in the field is the artificially differentiated cells created in the lab never quite make it to full replicas of their real-life counterparts, said Welch. I think the biggest potential for this model is better understanding what are the epigenetic barriers to fully converting the cells into whatever target you want them to be.

Additional authors on this paper include Chen Li, Maria C. Virgilio, and Kathleen L. Collins.

Paper cited: Single-cell multi-omic velocity infers dynamic and decoupled gene regulation, Nature Biotechnology. DOI: 10.1038/s41587-022-01476-y

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Mathematical model could bring us closer to effective stem cell therapies - Michigan Medicine

LEXEO Therapeutics to Present New Clinical Data from its Investigational Gene Therapy LX1001 for APOE4-Associated Alzheimers Disease at the 29th…

NEW YORK, Oct. 05, 2022 (GLOBE NEWSWIRE) -- LEXEO Therapeutics, Inc. (LEXEO), a clinical-stage biotech company advancing a pipeline of adeno-associated virus (AAV)-based gene therapy candidates for cardiovascular and central nervous system (CNS) diseases, today announced new clinical data from its ongoing study of LX1001 for APOE4-associated Alzheimers disease will be presented at the 29th European Society of Gene and Cell Therapy Annual Meeting (ESGCT), which is being held live in Edinburgh, Scotland and virtually from October 11-14, 2022.

In an oral presentation, LEXEO will present clinical data from the ongoing study of LX1001 for APOE4-associated Alzheimers disease. LX1001 is an AAV-based investigational gene therapy designed to deliver the apolipoprotein E2 (APOE2) gene into the CNS of APOE4 homozygous Alzheimers disease patients to halt or slow disease progression. This marks the first clinical data from a gene therapy program targeting APOE4-associated Alzheimers disease presented at a scientific meeting.

Details of the oral presentation are:

Title: Gene Therapy in APOE4 Homozygote Alzheimers Disease interim dataPresenter: Michael Kaplitt, M.D., Ph.D., Weill Cornell MedicineDate/Time: Wednesday, October 12th, session start - 9:00 AM ET (15:00 CEST)Session Title: CNS and sensory disease I (Parallel 3a)

To view full event programming, please visit the ESGCT website.

About LEXEO TherapeuticsLEXEO Therapeutics is a New York City-based, clinical-stage gene therapy company focused on addressing some of the most devastating genetically defined cardiovascular and central nervous system diseases affecting both larger-rare and prevalent patient populations. LEXEOs foundational science stems from partnerships and exclusive licenses with leading academic institutions at Weill Cornell Medicine and the University of California, San Diego. LEXEO is advancing a deep and diverse pipeline of AAV-based gene therapy candidates in rare cardiovascular diseases, APOE4-associated Alzheimers disease, and CLN2 Batten disease, and is led by pioneers and experts with decades of collective experience in genetic medicines, rare disease drug development, manufacturing, and commercialization. For more information, please visit http://www.lexeotx.com or LinkedIn.

Media Contact:Evan FeeleyEvoke Canale for LEXEO(619) 849-5392evan.feeley@evokegroup.com

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LEXEO Therapeutics to Present New Clinical Data from its Investigational Gene Therapy LX1001 for APOE4-Associated Alzheimers Disease at the 29th...

A sound approach for effective gene therapy delivery to brain – The Source – Washington University in St. Louis – Washington University in St. Louis

Researchers have been experimenting with different ways to deliver genes to the brain to treat central nervous system diseases and tumors. One of the obstacles, however, is the ability to penetrate the blood-brain barrier while having minimal effect on the other organs in the body.

Hong Chen, associate professor of biomedical engineering at the McKelvey School of Engineering and of radiation oncology at the School of Medicine, both at Washington University in St. Louis, and her team found an effective method to overcome that obstacle using focused ultrasound intranasal delivery (FUSIN). In new research, they found that the intranasally delivered gene therapy had comparable or better outcomes than existing methods while having minimal effect on the bodys other organs.

Results of the research, led by Chen and Dezhuang Ye, a postdoctoral research associate, and collaborators, were published online in the journal eBioMedicineSept. 21. It is the first study to evaluate the potential of FUSIN to deliver adeno-associated viral vectors, small viruses used to deliver gene therapy, in a mouse model.

Read more on the engineering website.

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A sound approach for effective gene therapy delivery to brain - The Source - Washington University in St. Louis - Washington University in St. Louis

Influence of the microbiome, diet and genetics on inter-individual variation in the human plasma metabolome – Nature.com

Untargeted plasma metabolites in Dutch cohorts

In this study, we examined plasma metabolomes in 1,679 fasting plasma samples from 1,368 individuals from two LLD5 sub-cohorts (LLD1 and LLD2) and the GoNL6 cohort (Extended Data Fig. 1 and Supplementary Table 1). The LLD1 cohort was the discovery cohort, with information about genetics, diet and the gut microbiome available for 1,054 participants. Moreover, 311 LLD1 subjects were followed up 4years later (LLD1 follow-up). We also included two independent replication cohorts: 237 LLD2 participants for whom we had genetic and dietary data and 77 GoNL participants for whom only genetic data were available (Extended Data Fig. 1 and Supplementary Table 1). Untargeted metabolomics profiling was done using flow-injection time-of-flight mass spectrometry (FI-MS)10,11, which yielded plasma levels of 1,183 metabolites (Supplementary Table 2). These metabolites covered a wide range of lipids, organic acids, phenylpropanoids, benzenoids and other metabolites (Extended Data Fig. 2a). As we observed weak (absolute rSpearman<0.2) correlations among the 1,183 metabolites (Extended Data Fig. 2b), data reduction was not required and, consequently, all metabolites were subjected to subsequent analyses. We validated the identification and quantification of some metabolites (for example, bile acids, creatinine, lactate, phenylalanine and isoleucine) by comparing their abundance levels from FI-MS with those previously determined by liquid chromatography with tandem mass spectrometry (LC-MS/MS)12 or NMR13 (rSpearman>0.62; Extended Data Fig. 2c,d).

To compare the relative importance of diet, genetics and the gut microbiome in explaining inter-individual plasma metabolome variability, we calculated the proportion of variance explained by these three factors for the whole plasma metabolome profile and for the individual metabolites separately. We have detailed information on 78 dietary habits (Supplementary Table 3), 5.3million human genetic variants and the abundances of 156 species and 343 MetaCyc pathways for each individual of the LLD1 cohort. Diet, genetics and the gut microbiome could explain 9.3, 3.3 and 12.8%, respectively, of inter-individual variations in the whole plasma metabolome, without adjusting for covariates (see the Methods section Distance matrix-based variance estimation; false discovery rate (FDR)<0.05; Fig. 1a and Supplementary Table 4), whereas intrinsic factors (age, sex and body mass index (BMI)) and smoking collectively explained 4.9% of the variance. Together, these factors explain 25.1% of the variance in the plasma metabolome (Fig. 1a).

a, Inter-individual variation in the whole plasma metabolome explained by the indicated factors, estimated using the PERMANOVA method. All, all of the indicated factors combined; smk, smoking status. b, Venn diagram indicating the number of metabolites whose inter-individual variation was significantly explained by diet, genetics or the gut microbiome, as estimated using the linear regression method (FDRF-test<0.05). c, Inter-individual variations in metabolites explained by diet, genetics or the gut microbiome, as estimated using the linear regression method (the lasso regression method was applied for feature selection) with a significant estimated adjusted r2>5% (FDRF-test<0.05). The blue bars represent dietary contributions to metabolite variations, the yellow bars indicate genetic contributions and the orange bars indicate microbial contributions. The other colors indicate the metabolic categories of metabolites (see legend). The yaxis indicates the proportion of variation explained. TMAO, trimethylamine N-oxide.

Next, we tested for pairwise associations between each metabolite and the dietary variables, genetic variants and microbial taxa. We observed 2,854 associations with dietary habits (Supplementary Table 5), 48 associations with 40 unique genetic variants (metabolite quantitative trait loci (mQTLs); Supplementary Table 6), 1,373 associations with gut bacterial species (Supplementary Table 7) and 2,839 associations with bacterial MetaCyc pathways (Supplementary Table 8) (see the Methods sections Associations with dietary habits, QTL mapping and Microbiome-wide associations). In total, 769 metabolites were significantly associated with at least one factor (Fig. 1b and Supplementary Tables 58). We then performed interaction analysis to assess the role of dietmicrobiome, geneticsmicrobiome and dietgenetics interactions in regulating the human metabolome using an interaction term in the linear model (see the Methods section Interaction analysis). Among these, 185 metabolites were associated with multiple factors and seven were affected by either geneticsmicrobiome, geneticsdiet or dietmicrobiome interactions (Supplementary Table 9).

As interactions were limited, we further assessed the proportion of variance of each metabolite that was explained by these factors using an additive model with the least absolute shrinkage and selection operator (lasso) method (see the Methods section Estimating the variance of individual metabolites). In general, the inter-individual variations in 733 metabolites could be explained by at least one of the three factors (FDRF-test<0.05; Supplementary Table 10). In detail, dietary habits contributed 0.435% of the variance in 684 metabolites; microbial abundances contributed 0.725% of the variance in 193 metabolites; and genetic variants contributed 328% of the variance in 44 metabolites (adjusted r2; FDRF-test<0.05; Supplementary Table 10). We also estimated the explained variance of metabolites using Elastic Net14, which is designed for highly correlated features, and found that the estimated explained variances were comparable between linear regression and the Elastic Net regression (Supplementary Fig. 1).

We further compared the variance explained by each type of factor (diet, genetics or the microbiome) and assigned the dominant factor for each metabolite if one factor explained more variance than the other two. Inter-individual variations in 610 metabolites were mostly explained by diet, 85 were explained by the gut microbiome and 38 were explained by genetics (Supplementary Table 10). Hereafter, we refer to these as diet-dominant, microbiome-dominant and genetics-dominant metabolites, respectively. The dominant factors of metabolites highlight their origin. For instance, ten out of the 21 diet-dominant metabolites for which diet explained >20% of the variance (FDRF-test<0.05; Supplementary Table 10) were food components based on their annotation in the Human Metabolome Database (HMDB)15. Similarly, of the 85 microbiome-dominant metabolites, 23 were annotated in the HMDB as microbiome-related metabolites (including 15 uremic toxins). Furthermore, out of the 38 genetics-dominant metabolites, ten were lipid species and eight were amino acids. Taken together, our analysis highlights that one factoreither dietary, genetic or microbialcan have a dominant effect over the other two in explaining the variances of plasma metabolites, with diet or the microbiome being particularly dominant. However, we also found that the variances in 185 metabolites were significantly attributable to more than one factor (Supplementary Table 10), including six metabolites associated with both genetics and the microbiome and 153 metabolites associated with both diet and the microbiome. For example, genetics and the microbiome explained 4 and 5%, respectively, of the variance in plasma 5-carboxy--chromanol (Fig. 1c)a dehydrogenated carboxylate product of 5-hydroxy--tocopherol16 that may reduce cancer and cardiovascular risk17. Another example is hippuric acida uremic toxin that can be produced by bacterial conversion of dietary proteins18, with 13% of its variance explained by diet and 13% explained by the microbiome (Fig. 1c).

Temporal changes in plasma metabolites can reflect changes in an individuals diet, gut microbiome and health status. When assessing the plasma metabolome in the 311 LLD1 follow-up samples, we indeed observed a significant shift in the plasma metabolome, with a significant difference in the second principal component (PPC1 paired Wilcoxon=0.1 and PPC2 paired Wilcoxon=1.3105; Fig. 2a). Baseline genetics, diet and microbiome, together with age, sex and BMI, could explain 59.4% of the variance in the follow-up plasma metabolome (PPERMANOVA=0.004) (Supplementary Fig. 2). We also observed that temporal stability can vary substantially between different metabolites (see the Methods section Temporal consistency of individual metabolites; Supplementary Table 11). Previously, we had assessed the changes in the gut microbiome in the LLD1 follow-up cohort and linked these to changes in the plasma metabolome7. Here, we further checked the temporal variability of the plasma metabolome and assessed the stability of diet-, microbiome- and genetics-dominant metabolites over time. Interestingly, the temporal correlation of the microbiome-dominant metabolites was similar to that of the genetics-dominant metabolites (PWilcoxon=0.51; Fig. 2b), whereas the temporal correlation between diet-dominant metabolites was significantly lower than between microbiome- and genetics-dominant metabolites (PWilcoxon<3.4105; Fig. 2b). However, the dominant dietary, microbial and genetic factors identified at baseline also explained similar variance in metabolic levels in the follow-up samples (Extended Data Fig. 3 and Supplementary Table 10). Our data also revealed a positive correlation between stability and the amount of variance that could be explained: the more variance explained, the more stable a metabolite is over time (Fig. 2c). For a few metabolites, we could not replicate the variance explained at baseline at the second time point, and these metabolites also showed weak or no correlation in their abundances between the two time points. For example, N-acetylgalactosamine showed very weak correlation between the two time points (r=0.13; P=0.02), and its genetic association was not replicated at the second time point.

a, Principal component analysis of metabolite levels at two time points (Euclidean dissimilarity). The green dots indicate baseline samples and the orange dots indicate follow-up samples (n=311 biologically independent samples). The KruskalWallis test (two sided) was used to check differences between baseline and follow-up. b, Temporal stability of metabolites stratified by the dominantly associated factor for each metabolite. The Wilcoxon test (two sided) was used to check the differences between groups. Each dot represents one metabolite. The yaxis indicates the Spearman correlation coefficient of abundances of each metabolite between two time points (n=311 biologically independent samples). In a and b, the box plots show the median and first and third quartiles (25th and 75th percentiles) of the first and second principal components (a) or correlation coefficients (b); the upper and lower whiskers extend to the largest and smallest value no further than 1.5 the interquartile range (IQR), respectively; and outliers are plotted individually. c, Correlation between metabolite stability and the metabolite variance explained by diet (left), genetics (middle) and the microbiome (right). The xaxis indicates the inter-individual variation explained by each factor and the yaxis indicates the Spearman correlation coefficient (two sided) of abundances of each metabolite between the two time points. The dashed white lines show the best fit and the gray shading represents the 95% confidence interval (CI) (n=311 biologically independent samples).

Having established the variances in metabolites explained by diet, genetics and the gut microbiome and the dominant factors that explained most of this variance, we focused on detailing specific associations and on the potential implications of our findings for assessing diet quality and improving our understanding of the genetic risk of complex diseases and the interaction and causality relationships among diet, the microbiome, genetics and metabolism.

We observed 2,854 significant associations (FDRSpearman<0.05) between 74 dietary factors and 726 metabolites (Fig. 3a and Supplementary Table 5; see the Methods section Lifelines diet quality score prediction). Associations with food-specific metabolites can, in theory, be used to verify food questionnaire data. For instance, the strongest association we observed was between quinic acid levels and coffee intake (rSpearman=0.54; P=1.61080; Fig. 3b). Quinic acid is found in a wide variety of different plants but has a particularly high concentration in coffee. Another example is 2,6-dimethoxy-4-propylphenol, which was strongly associated with fish intake (rSpearman=0.53; P=1.51076; Fig. 3c). This association is expected as this compound is particularly present in smoked fish according to HMDB annotation15. In addition, we also detected associations between dietary factors and metabolic biomarkers of some diseases. For example, 1-methylhistidine is a biomarker for cardiometabolic diseases including heart failure19 that is enriched in meat, and we observed significant associations between 1-methylhistidine and meat (rSpearman=0.12; P=7.2105) and fish intake (rSpearman=0.11; P=3.1104) as well as a lower level of 1-methylhistidine in vegetarians (rSpearman=0.15; P=9.7107; Fig. 3d).

a, Summary of the associations between diet and metabolites. The bars represent dietary habits, with the bar order sorted by the number of significant associations. Association directions are colored differently: orange indicates a positive association, whereas blue indicates a negative association. The length of each bar indicates the number of significant associations at FDR<0.05 (Spearman; two sided). b, Association between plasma quinic acid levels and coffee intake. The x and yaxes indicate residuals of coffee intake and the metabolic abundance after correcting for covariates, respectively (n=1,054 biologically independent samples). c, Association between plasma 2,6-dimethoxy-4-propylphenol levels and fish intake frequency (n=1,054 biologically independent samples). The x and yaxes refer to residuals of fish intake and metabolic abundance after correcting for covariates, respectively. d, Differential plasma levels of 1-methylhistidine between vegetarians and non-vegetarians (n=1,054 biologically independent samples). The yaxis indicates normalized residuals of metabolic abundance. The Pvalue from the Wilcoxon test (two sided) is shown. The box plots show the median and first and third quartiles (25th and 75th percentiles) of the metabolite levels. The upper and lower whiskers extend to the largest and smallest value no further than 1.5 the IQR, respectively. Outliers are plotted individually. e, Association between the diet quality score predicted by the plasma metabolome (yaxis) and the diet quality score assessed by the FFQ (xaxis) (n=237 biologically independent samples). In b, c and e, each gray dot represents one sample, the dark gray dashed line shows the linear regression line and the gray shading represents the 95% CI. In b and c, the association strength was assessed using Spearman correlation (two sided; the correlation coefficient and Pvalue are reported) and in e, the prediction performance was assessed with linear regression (F-test; two sided; the adjusted r2 value and Pvalue are reported).

Given the relationship between diet, metabolism and human health, we wondered whether the plasma metabolome could predict diet quality. For each of the Lifelines participants, we constructed a Lifelines Diet Score based on food frequency questionnaire (FFQ) data that reflected the relative diet quality based on dietdisease relationships8. To build a metabolic model to predict an individuals diet quality, we used LLD1 as the training set and LLD2 as the validation set. The resulting metabolic model included 76 metabolites, 51 of which were dominantly associated with diet. The diet score predicted by metabolites showed a significant association with the real diet score assessed by the FFQ in the validation set (r2adjusted=0.27; PF-test=3.5105; Fig. 3e). We also tested four other dietary scores (the Alternate Mediterranean Diet Score20, Healthy Eating Index (HEI)21, Protein Score22 and Modified Mediterranean Diet Score23) and found that the HEI predicted by plasma metabolites was also significantly associated with the FFQ-based HEI (r2adjusted=0.23; PF-test=6.5105; Supplementary Table 12).

Genetic associations of plasma metabolites may provide functional insights into the etiologies of complex diseases. After correcting for the first two genetic principal components, age, sex, BMI, smoking, 78 dietary habits, 40 diseases and 44 medications, QTL mapping in LLD1 identified 48 study-wide, independent genetic associations between 44 metabolites and 40 single-nucleotide polymorphisms (SNPs) (PSpearman<4.21011; clumping r2=0.05; clumping window=500kilobases (kb); Fig. 4a and Supplementary Table 6). All 48 genetic associations were replicated in either LLD1 follow-up or the two independent replication datasets (LLD2 and GoNL; Supplementary Fig. 3 and Supplementary Table 6). We also assessed the impact of physical activity, as assessed by questionnaires24, on the genetics association of metabolism, but found its influence to be negligible (Supplementary Fig. 4). Functional mapping and annotation (FUMA) of genome-wide association studies (GWAS)25 analysis revealed that the identified mQTLs were enriched in genes expressed in the liver and kidney (Extended Data Fig. 4) and related to metabolic phenotypes (Supplementary Table 6).

a, Manhattan plot showing 48 independent mQTLs identified linking 44 metabolites and 40 genetic variants with P<4.21011 (Spearman; two sided). Representative genes for the SNPs with significant mQTLs are labeled. b, Association between a tag SNP (rs1495741) of the NAT2 gene and plasma AFMU levels. c, Association between a SNP (rs13100173) within the HYAL3 gene and plasma levels of N-acetylgalactosamine-4-sulfate. d, Association between a tag SNP (rs17789626) of the SCLT1 gene and plasma mizoribine levels. e, Differences in coffee intake between participants with different genotypes at rs1495741. f, Correlations between coffee intake and AFMU in participants with different genotypes at rs1495741. g, Differences in bacterial fatty acid -oxidation pathway abundance in participants with different genotypes at rs67981690. h, Correlations between bacterial fatty acid -oxidation pathway abundance and 5-carboxy--chromanol in participants with different genotypes at rs67981690. In be and g, the xaxis indicates the genotype of the corresponding SNP and the yaxis indicates normalized residuals of the corresponding metabolic abundance (n=927 biologically independent samples). Each dot represents one sample. The box plots show the median and first and third quartiles (25th and 75th percentiles) of the metabolite levels. The upper and lower whiskers extend to the largest and smallest value no further than 1.5 the IQR, respectively. Outliers are plotted individually. The association strength is shown by the Spearman correlation coefficient and corresponding Pvalue (two sided). In f and h, the xaxis indicates the normalized abundance of coffee intake (f) or the bacterial fatty acid -oxidation pathway (h) and the yaxis indicates the normalized residuals of the corresponding metabolic abundance. Each dot represents one sample (n=927 biologically independent samples). The lines indicate linear regressions for each genotype group separately. Areas with light gray shading indicate the 95% CI of the linear regression lines. The association strength per genotype is shown by the Spearman correlation and the corresponding Pvalue (two sided).

The strongest association we found was between the caffeine metabolite 5-acetylamino-6-formylamino-3-methyluracil (AFMU) and SNP rs1495741 near the N-acetyltransferase 2 (NAT2) gene (rSpearman=0.52; P=1.71066; Fig. 4b), which showed strong linkage disequilibrium (r2=0.98) with a SNP, rs35246381, that was recently reported to be associated with urinary AFMU26. AFMU is a direct product of NAT2 activity and has been associated with bladder cancer risk27. Interestingly, the plasma level of AFMU was associated not only with coffee intake (rSpearman=0.29; P=9.21022; Supplementary Table 5) and the genotype of rs1495741, but also with their interactions (Supplementary Table 9). Individuals with a homologous AA genotype had a similar level of coffee intake, but their correlation between coffee intake and plasma AFMU level was significantly lower compared with individuals with GG and GA genotypes (Fig. 4e,f).

Pleotropic mQTL effects were also observed at several loci, including SLCO1B1, FADS2, KLKB1 and PYROXD2 (Supplementary Table 6). For example, three associations (related to three metabolites, two of them lipids) were observed for two SNPs (rs67981690 and rs4149067; linkage disequilibrium r2=0.72 in Northern Europeans from Utah) in SLCO1B1, which encodes the solute carrier organic anion transporter family member 1B1. Expression of the SLCO1B1 protein is specific to the liver, where this transporter is involved in the transport of various endogenous compounds and drugs, including statins28, from blood into the liver. The SLCO1B1 locus has also been linked to plasma levels of fatty acids and to statin-induced myopathy29. Furthermore, we detected a geneticsmicrobiome interaction between rs67981690 and microbial fatty acid oxidation pathways in regulating plasma levels of 5-carboxy--chromanol (P=1.5103), where the association of the bacterial fatty acid oxidation pathway with plasma levels of 5-carboxy--chromanol was dependent on the genotype of rs67981690 (Fig. 4g,h).

To identify novel mQTLs, we performed a systematic search of all published mQTL studies from 2008 onwards (Supplementary Table 13). This approach identified three novel mQTLs in our datasets (Supplementary Table 13) that were either not located close to previously reported mQTLs (distance>1,000kb) or not in linkage disequilibrium (r2<0.05). The first two novel SNPsrs13100173 at HYAL3 and rs11741352 at ARSBwere associated with N-acetylgalactosamine-4-sulfate (Fig. 4c,d), which is associated with mucopolysaccharidosis30. Interestingly, N-acetylgalactosamine-4-sulfate can bind to HYAL proteins (HYAL1, HYAL2, HYAL3 and HYAL4), suggesting that mQTLs can also pinpoint potential metaboliteprotein interactions. The third novel mQTL was rs17789626 at SCLT1, which was associated with mizoribinea compound used to treat nephrotic syndrome31.

We established 4,212 associations between 208 metabolites and 314 microbial factors (114 species and 200 MetaCyc pathways) (FDRLLD1<0.05; PLLD1 follow-up<0.05; Supplementary Tables 7 and 8). Interestingly, many of the metabolites that were associated with microbial species and MetaCyc pathways are also known to be gut microbiome related based on their HMDB annotations15. For instance, we observed 919 associations with 25 uremic toxins, 142 associations with thiamine (vitamin B1) and 117 associations with five phytoestrogens (FDR<0.05; Supplementary Tables 7 and 8). Uremic toxins and thiamine have been shown to be related to various diseases, including chronic kidney disease and cardiovascular diseases32,33. Phytoestrogens are a class of plant-derived polyphenolic compounds that can be transformed by gut microbiota into metabolites that promote the hosts metabolism and immune system33,34.

To assess whether gut microbiome composition causally contributes to plasma metabolite levels, we carried out bi-directional MR analyses (see the Methods section Bi-directional MR analysis). Here, we focused on the 37 microbial features that were associated with at least three independent genetic variants at P<1105 and with 45 metabolites (Supplementary Table 14). At FDR<0.05 (corresponding to P=2103 obtained from the inverse variance weighted (IVW) test)35, we observed four potential causal relationships at baseline that could also be found in the follow-up in the microbiomes to metabolites direction (Fig. 5ad and Supplementary Tables 15 and 16) but not in the opposite direction (Supplementary Table 17), and these outcomes were maintained following weighted median testing (P<0.03; Supplementary Fig. 5). To ensure that the data followed MR assumptions, we performed several sensitivity analyses, including checking for horizontal pleiotropy (MR-Egger36 intercept P>0.05; Supplementary Table 15) and heterogeneity (Cochrans Q test P>0.05; Supplementary Table 15) and leave-one-out analysis (Extended Data Fig. 5). We did not use causal estimates derived using the MR-Egger method to filter the results, as its power to detect causality is known to be low36. These sensitivity checks further confirmed the reliability of these four MR causal estimates.

a, Analysis of the association between adenosylcobalamin biosynthesis pathway abundance and 5-hydroxytryptophol levels. b, Glycogen biosynthesis pathway abundance versus 5-sulfo-1,3-benzenedicarboxylic acid levels. c, E. rectale abundance versus hydrogen sulfite levels. d, Veillonella parvula abundance versus 2,3-dehydrosilybin levels. In the top panels of ad, the xaxis shows the SNP exposure effect, and the yaxis shows the SNP outcome effect and each dot represents a SNP. Error bars represent the s.e. of each effect size. The bottom panels of ad, show the MR effect size (center dot) and 95% CI for the baseline (blue) and follow-up (green) datasets of the LLD1 cohort, estimated with the IVW MR approach (two sided) (n=927 biologically independent samples at baseline and n=311 biologically independent samples at follow-up).

We further found that increased abundance of microbial adenosylcobalamin biosynthesis (coenzyme B12) was associated with reduced plasma levels of 5-hydroxytryptophol (Fig. 5a)a uremic toxin related to Parkinsons disease37. We also found that plasma hydrogen sulfite levels were related to Eubacterium rectale (Fig. 5c)a core gut commensal species38 that is highly prevalent (presence rate=97%) and abundant (mean abundance=8.5%) in both our cohorts and in other populations39,40,41. As a strict anaerobe, E. rectale promotes the hosts intestinal health by producing butyrate and other short-chain fatty acids from non-digestible fibers42, and a reduced abundance of this species has been observed in subjects with inflammatory bowel disease39,43 and colorectal cancer44 compared with healthy controls. As a toxin, hydrogen sulfite interferes with the nervous system, cardiovascular functions, inflammatory processes and the gastrointestinal and renal system45. Our results thus reveal a potential new beneficial effect of E. rectale.

To further investigate the metabolic potential of individual bacterial species, we applied newly developed pipelines to identify microbial primary metabolic gene clusters (gutSMASH pathways)46 and microbial genomic structural variants (SVs)47. These two tools profile microbial genomic entities that are implicated in metabolic functions. By associating 1,183 metabolites with 3,075 gutSMASH pathways and 6,044 SVs (1,782 variable SVs (vSVs) and 4,262 deletion SVs (dSVs); see Methods), we observed 23,662 associations with gutSMASH pathways and 790 associations with bacterial SVs (FDRLLD1<0.05; PLLD1 follow-up<0.05; Supplementary Tables 1820). These associations connect the genetically encoded functions of microbes with metabolites, thereby providing putative mechanistic information underlying the functional output of the gut microbiome. In one example, we observed that the microbial uremic toxin biosynthesis pathways, including the glycine cleavage pathway (in Olsenella and Clostridium species) and the hydroxybenzoate-to-phenol pathway (in Clostridium species) responsible for hippuric acid and phenol sulfate biosynthesis, were associated with the hippuric acid (Olsenella species: rSpearman=0.15; P=9.3107; Clostridium species: rSpearman=0.18; P=5.9109) and phenol sulfate (rSpearman=0.17; P=4.2108; Extended Data Fig. 6a) levels measured in plasma, respectively (FDRLLD1<0.05 and PLLD1 follow-up<0.05; Extended Data Fig. 6b).

Next, we carried out a mediation analysis to investigate the links between diet, the microbiome and metabolites. For 675 microbial features that were associated with both dietary habits and metabolites (FDR<0.05), we applied bi-directional mediation analysis to evaluate the effects of microbiome and metabolites for diet (see the Methods section Bi-directional mediation analysis). This approach established 146 mediation linkages: 133 for the dietary impact on the microbiome through metabolites and 13 for the dietary impact on metabolites through the microbiome (FDRmediation<0.05 and Pinverse-mediation>0.05; Fig. 6a,b and Supplementary Table 21). Most of these linkages were related to the impact of coffee and alcohol on microbial metabolic functionalities (Fig. 6a).

a, Parallel coordinates chart showing the 133 mediation effects of plasma metabolites that were significant at FDR<0.05. Shown are dietary habits (left), plasma metabolites (middle) and microbial factors (right). The curved lines connecting the panels indicate the mediation effects, with colors corresponding to different metabolites. freq., frequency; PFOR, pyruvate:ferredoxin oxidoreductase; OD, oxidative decarboxylation; HGD, 2-hydroxyglutaryl-CoA dehydratase; TPP, thiamine pyrophosphate. b, Parallel coordinates chart showing the 13 mediation effects of the microbiome that were significant at FDR<0.05. Shown are dietary habits (left), microbial factors (middle) and plasma metabolites (right). For the microbial factors column, number ranges represent the genomic location of microbial structure variations (SVs) in kilobyte unit, and colons represent the detailed annotation of certain gutSMASH pathway. c, Analysis of the effect of coffee intake on the abundance of M. smithii as mediated by hippuric acid. d, Analysis of the effect of beer intake on the C. methylpentosum Rnf complex pathway as mediated by hulupinic acid. e, Analysis of the effect of fruit intake on urolithin B in plasma as mediated by a vSV in Ruminococcus species (300305kb). In ce, the gray lines indicate the associations between the two factors, with corresponding Spearman coefficients and Pvalues (two sided). Direct mediation is shown by a red arrow and reverse mediation is shown by a blue arrow. Corresponding Pvalues from mediation analysis (two sided) are shown. inv., inverse; mdei., mediation.

Coffee contains various phenolic compounds that can be converted to hippuric acid by colonic microflora48. Hippuric acid is an acyl glycine that is associated with phenylketonuria, propionic acidemia and tyrosinemia49. We observed that hippuric acid can mediate the impact of drinking coffee on Methanobrevibacter smithii abundance (Pmediation=2.21016; Fig. 6c). We also observed that hulupinic acid, which is commonly detected in alcoholic drinks, can mediate the impact of beer consumption on the Clostridium methylpentosum ferredoxin:NAD+ oxidoreductase (Rnf) complex (Pmediation=2.21016; Fig. 6d)an important membrane protein in driving the ATP synthesis essential for all bacterial metabolic activities50.

Of the dietary impacts on metabolites through the microbiome (Fig. 6b and Supplementary Table 21), one interesting example is a Ruminococcus species vSV (300305kb) that encodes an ATPase responsible for transmembrane transport of various substrates51. This Ruminococcus species vSV mediated the effect of fruit consumption on plasma levels of urolithin B (Pmediation=2.21016; Fig. 6e). Urolithin B is a gut microbiota metabolite that protects against myocardial ischemia/reperfusion injury via the p62/Keap1/Nrf2 signaling pathway52. Taken together, our data provide potential mechanistic underpinnings for dietmetabolite and dietmicrobiome relationships.

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