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Building on these key discoveries, a team of scientists at Vertex, led byNegulescu, initiated research in 1998 into compounds that modulate the function of the CFTR protein. The research led to the development in 2012 of the first compound that corrects the underlying protein defect responsible for disease symptoms. The drug restored cells ability to transport chloride and ushered in a new era of CF treatment, sparking the development of combination-drug therapies.

The combined contributions of Welsh andNegulescu represent the complete biomedical arc from basic discovery to application to the saving of lives, said theShaw Prize in Life Science and Medicine selection committee in announcing the shared award.

Welsh was quick to share the credit for this work.

I am honored to receive this award, which would not have been possible without so many other people who contributed:terrific mentors, talented and creative students and trainees, my tireless and innovative assistants, my cherished colleagues, he says. The support and environment of the University of Iowa made this possible. The Cystic Fibrosis Foundation, National Institutes of Health, Howard Hughes Medical Institute, Carver Trust, and Pappajohn Biomedical Institute provided crucial support along the way. I am deeply grateful.

TheShaw Prizeconsists of three annual awards: the Prize in Astronomy, the Prize in Life Science and Medicine, and the Prize in Mathematical Sciences.The award is managed and administered by The Shaw Prize Foundation, based in Hong Kong.

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Welsh wins 2022 Shaw Prize in Life Sciences and Medicine | Carver College of Medicine - The University of Iowa

This transcript has been edited for clarity.

Peter Higgins, MD, PhD: Hello. I'm Dr Peter Higgins, and welcome to Medscape's InDiscussion series on Crohn's disease. Today we'll be discussing gene therapy trials. Given the recent successes with sickle cell anemia, how far away are we from intestinal gene therapy in Crohn's disease? First, let me introduce my guest, Dr Judy Cho. Dr Cho is professor of pathology, molecular, and cell-based medicine at Mount Sinai in New York, where she is the dean of translational genetics and director of the Charles Bronfman Institute for Personalized Medicine. Dr Cho's many important discoveries include early work on identifying NOD2 and the IL-23 receptor as risk alleles for Crohn's disease. Welcome to InDiscussion, Judy. Just to get us started, what is it about researching and treating inflammatory bowel disease (IBD) that first drew you to this field?

Judy Cho, MD: It was during my GI fellowship at the University of Chicago. What's great about IBD is you're treating a very specialized disorder. You're making a positive impact in patients. And because it affects teenagers and young adults, you're really functioning as a primary care physician. That was back in the days that I was actively seeing patients. In addition, the GI tract is very accessible, so you can actually study the tissues involved. And then I really started getting into genetics when a lot of the colon cancer genes were being discovered.

Higgins: Great. Certainly a lot of understanding of the mechanisms of IBD has come out of this genetic research through the consortium that you lead. I got interested in this very recently after seeing some really amazing results of several forms of gene therapy for sickle cell anemia in a couple of recent publications that have been remarkable. And as someone who trained in a sickle cell center during residency at Duke, I for many years held out hope that gene therapy could make a difference for sickle cell patients. That variance, of CRISPR-Cas techniques, really seems to be making serious headway in recent publications. Very recently some of my more science-savvy patients ask me when some version of gene therapy will be available for Crohn's disease, which is an interesting and complicated question because it's not quite the same or as simple as sickle cell. There could be a number of barriers to overcome before this could become a viable approach. I think it might only be available for some patients, if ever. So I wanted to sit down with an expert in IBD genetics and talk through what the road to gene therapy for Crohn's disease might look like in the near future. Judy, let's start with the very recent data on gene therapy in sickle cell anemia. Can you explain for us how this gene therapy was done, how there were two different approaches, and how successful these initial clinical trials have been for sickle cell patients in preventing hospitalizations in sickling crisis?

Cho: Thanks for bringing up these examples, because these are very exciting new approaches for gene therapy to treat. What is the single gene disorder with sickle cell? It's a single base pair substitution in the hemoglobin B gene, and one of the things about sickle cell is it obviously has tremendous morbidity and mortality. It really does have a major effect. And so targeting and trying to treat the specific molecular defect for sickle cell anemia is very logical but not easy. Two back-to-back New England Journal articles (Frangoul et al, Kanter et al) used two different molecular approaches for treating sickle cell. And it's based upon a very interesting clinical observation, which is that the hemoglobin that's present in adults involves genes that are coded by two different gene areas: hemoglobin A and hemoglobin B in adults. But that's different in the prenatal and fetal time, where you have hemoglobin A and hemoglobin F. And so the observation is, well, you always have the genetics that you have. But yet sickle cell tends not to present right away because you have remaining hemoglobin F. So the observation that hemoglobin F can be protective against these sickle cell anemia patients who carry the hemoglobin B mutation was the important clinical observation, and that actually formed the basis for some of the treatments to induce hemoglobin F in patients who then subsequently go on and present with sickle cell anemia.

There's a particular transcription factor called BCL11, which normally serves to repress the expression of hemoglobin F. And so with both of these approaches, one using CRISPR, the other one using lentiviral transduction, both increased the expression of hemoglobin F, thereby reducing the complications of sickle cell that you typically see. So when you carry the hemoglobin B mutation, what that does is it has the tendency to sickle the red blood cells, and you can see a lot of the complications that you typically see with sickle cell anemia, including a lot of clotting complications or thromboembolic complications. By enhancing hemoglobin F, you actually can reduce side effects. And as you pointed out that in addition in one of the papers, they actually replaced it with a normal copy of hemoglobin B. So both of these studies are involved. They're promising. They're incredibly transformative. And most importantly, the side effects: These were chronic effects. They were able to reduce the complications of those thromboembolic diseases.

Higgins: It's pretty amazing that a single treatment has produced results out to 2 or 3 years and essentially taken people who are having sickle cell crisis about once a month and basically eliminated those with a single treatment. And I think that's what's gotten some of my science-savvy patients excited about: Wow, could I get one treatment and essentially eliminate my Crohn's flares? You mentioned specifically that sickle cell is a single gene. What makes Crohn's disease less attractive as at least a first case for gene therapy?

Cho: Crohn's disease is a polygenic disease. For most cases where you have disease onset in the teenage years or young adulthood, we believe it's caused by many, many genetic variants acting together. Now, in some cases of very-early-onset IBD, you can have a single gene disorder that we think largely drives these diseases. These single gene diseases usually present very early, either in the neonatal period or in early childhood, and probably two of the most important pathways that are involved in these single gene forms of Crohn's are the loss-of-function mutations interleukin 10 as well as a loss-of-function mutation in a gene called Xiap, or XIAP X-linked inhibitor of apoptosis, which is downstream of NOD2 signaling. But for most polygenic forms of IBD, the biggest effect mutation is in the gene that we discovered, together with Gabriel Nuez at the University of Michigan as well as investigators from France, that these loss-of-function mutations in the bacterial sensing gene NOD2 confer the highest risk in European ancestry Crohn's disease.

Higgins: And how common is NOD2 in European ancestry Crohn's disease? Is that a large percentage of patients or not that many?

Cho: It's probably a little bit over a third. So probably somewhere between 35% and 40% of those with European ancestry Crohn's disease carry at least one copy of a disease-associated NOD2 risk allele. And if you carry one copy of these loss-of-function NOD2 variants, it increases your risk of developing disease by about 1.5-fold to twofold. If you carry two copies or are a compound heterozygote of the NOD2 risk alleles, it increases your risk anywhere from eightfold to 12-fold.

Higgins: That's a fair number of people. It certainly wouldn't be the majority who might, in theory, be eligible for some NOD2 direct gene therapy. Now, this is pretty different because in addition to the immune cells, which obviously come from the bone marrow, the gut is affected. Would it be appropriate to have a lentivirus focused on the bone marrow or the gut? Or would you need both?

Cho: That's a great question. One of our colleagues here at Mount Sinai, Louis Cohen, is actively studying this, together with support from the Helmsley foundation. And for years, Louis and Jean-Frederic Colombel had started a bone marrow transplant effort in the most severe Crohn's patients who had basically failed every form of existing biologics. It was kind of out of desperation. The bone marrow studies have actually shown beneficial effects, which is great. The bad news is that the disease comes back. And so if you take those two things together, what you might then consider is that if we believe that it's the NOD2 deficiency from the hematopoietic stem cells from the bone marrow. If you think that's what's really driving disease, then by using these types of approaches CRISPR, lentiviral you may actually have a long-lasting effect. The challenge is that you want to start this in some of the sickest patients with Crohn's disease. It's too early to say whether it's going to make the difference, but the fact that you actually have transient benefit in bone marrow transplantation in some sets of these very sick Crohn's patients indicates that this might be a positive approach.

Higgins: I've seen a few IBD patients in the Midwest who've had bone marrow transplants and have done well for a while. The data for Northwestern were very interesting. They reported that most of the patients were able to be drug free in remission for 3-5 years, but it was interesting that the ones who recurred early tend to be smokers. So there's an environmental factor, and as much as anything, it's felt like they were resetting the immune system, not necessarily changing the immune system. Whereas doing this CAS CRISPR on NOD2 might actually change their immune system so they wouldn't recur. Does that seem reasonable?

Cho: Exactly. We published a paper last year. We describe some of the mechanisms of blood monocytes, which ultimately are coming from the bone marrow in terms of how these blood monocytes may have abnormal cellular differentiation, resulting in an increased risk for Crohn's disease. And so if we think the defect really is blood monocytes and with trafficking to the intestine being altered, it does make sense to try to do gene therapy of these hematopoietic stem cells. It should be stated, however, that there's a substantial literature that NOD2 is expressed in Paneth cells as well, and Paneth cells are important cells in the intestinal epithelial crypt bases that secrete a variety of antimicrobial peptides. So certainly, a bone marrow transplant would not correct those types of defects.

Higgins: So if we figured out that we needed to correct the Paneth cells and we wanted that to be lasting, would we actually have a gut-focused lentivirus or an orally ingested lentivirus that would try to change the stem cells in the crypts?

Cho: It's an interesting idea. Each one of the crypts has its own stem cell history. It's an interesting question because one of the features of Crohn's disease is it tends to be very focal. And so you could even envision kind of local therapy. But in my opinion, the first step to try would really be those hematopoietic stem cells similar to the sickle cell stores.

Higgins: Yeah. I was impressed. And I don't know if it was beginner's luck, but the folks doing sickle cell were able to change hemoglobin expression in the neighborhood of 99% of cells for a really long time with a single treatment. Do you think, though, with the way NOD2 works or at least as well as we understand it today, even if we got 50% correction or 80% correction, would that potentially be enough to change the phenotype?

Cho: I think so. Absolutely. And again, the genetics give us some insight into this. If you have one defective allele vs two defective alleles. I think the 50%-80% correction of the hematopoietic stem cells I would guess again; we're just guessing right now would have a substantive positive impact.

Higgins: And I would imagine the NOD2 homozygotes, the folks who tend to get very early disease often in their pre-teen years and tend to have stricturing and really complicated disease are probably the ones that would benefit the most. I would imagine that a single CRISPR-Cas would probably modify the 3' end of NOD2 and just cover multiple versions of NOD2 defects.

Cho: Yes, most of the mutations in NOD2 are in the 3' part of the gene. It's a part of the gene that actually senses a bacterial product. So it's that failure to sense correctly. I do actually think molecularly that approach makes sense when you try to get all three of the major NOD2 mutations because they're all in that same area of the gene.

Higgins: So theoretically, you might have one cassette that you would swap out for the 3' end of NOD2.

Cho: That's exactly right.

Higgins: We talk about Crohn's as a polygenic disease, and obviously sickle cell is a lot easier. They made one change that was spectacularly successful, but occasionally you can run into somebody who's got a NOD2 mutation. IL23R mutation, ATG16L, IL10 you name it. Does it seem reasonable that if we see success with NOD2, it might help that portion? But if they have multiple hits, we may not take care of the whole story. How many hits, as far as we know, does the average Crohn's patient have?

Cho: We can't answer that precisely. The other thing is that there's such a thing as winner's luck. NOD2 was kind of the first gene we associated outside of the MHC (major histocompatibility complex) associated with IBD. So winner's luck means that you're going to find the biggest effect genes first. And as we find more and more loci that are associated, there have smaller effects. So the hope would be that if you kind of hit a few of the biggest ones which you've listed NOD2, IL23R, the autophagy pathway that actually might be enough because you're just kind of tipping over and you're passing some type of threshold. And the final point we'll make about IL23R is that most of us, probably myself and yourself included, are walking around with what is the risk allele. And that is actually why the association with IL23R is particularly interesting; about 1 out of every 7 European ancestry individuals are heterozygous carriers for a protective allele. So you might think, well, yeah, that's why not just make everyone a protective allele. And obviously that's being targeted now by therapies that are presently approved for IBD to block the IL-23 pathway.

Higgins: So I'm thinking about whether the big genes are probably the top three or four. What percentage of Crohn's patients who are on biologics and have pretty bad disease have one of those big four?

Cho: Probably the majority. It's actually a very exciting vision you have there, Peter. Why not correct all the big three or four and be done with it?

Higgins: I don't know technically how easy it is with a bone marrow transplant to do multiple edits where we'd be editing NOD2 with one construct, IL23R with a different one, ATG16L with a third. But if that were technically possible, you might have kind of a general approach to the majority of Crohn's patients.

Cho: I think it's an exciting vision. I think if we can get the first one done, why not do the top three to five? That opens up the question of how much of the risk is conferred by stromal cells, the epithelial cells, as opposed to the hematopoietic stem cells? But it is an exciting vision that I hadn't really thought of seriously. But why not do it? If you're going to do it

Higgins: Yeah, it's really interesting. And I've found the bone marrow literature really interesting because it's a very blunt instrument and they're still doing trials in the UK, continuing with bone marrow transplant for severe Crohn's. But if we could do it in a much targeted way with a lot fewer side effects, it would be pretty amazing.

Cho: Yes, the autologous bone marrow transplants are pretty safe, but I mean, these are the sickest of the sick patients. And so that's really where you have to do these types of experiments to start with. But that's often in the cancer field how things started as well. So yes, I agree that's an exciting approach.

Higgins: So imagining a future 5 years from now, we've got effective vectors, we've got rodent trials, possibly even cotton-top tamarin trials that seem to work. Who would be the first patients, if you were hypothetically designing a trial, to approach about this kind of therapy?

Cho: Well, again, Louis Cohen is actually doing this at Mount Sinai right now for these really treatment-refractory patients. And it's exactly the same fraction we've already genotyped them. It's kind of like 30%-40% are NOD2 carriers. So it's probably a confluence of multiple risk alleles plus some environmental things as well. So there's no reason to think that the genetics are going to be any different in these refractory patients, and that's probably the group to go after.

Higgins: Makes sense. While we have many more choices with biologics, there just seems to be a group of patients who are often diagnosed before age 10 and have just dreadful refractory disease. And it does seem that identifying those folks and having this approach would be pretty effective. Do you think in terms of the monogenic IBD, XIAP and IL-10, is this going to happen, possibly even earlier?

Cho: It's a great question. It actually does make sense that that would be another cohort. I do think that it's completely logical. XIAP is definitely expressed in stromal cells as well. But that would not put me off that because they're often severe, they often have severe perianal disease IL-10 as well. It's a great point. And to a substantial effect they're already cured by standard bone marrow transplant. But your point, that maybe a more targeted therapy may be the way to go, is interesting. And certainly for those centers that see a lot of these patients that are doing bone marrow transplants, it makes perfect sense that that should be the approach for the very small subset of IBD patients.

Higgins: Where do you think this is in terms of timeline? Obviously when you're doing science and you're trying to translate this to medicine, unexpected things will happen. But if you're trying to imagine specific trials and genes or possibly multiple genes, how far away do you think it might be?

Cho: I like that Bill Gates quote where we overestimate the change that can happen in the next 3 years and underestimate the amount that can happen in the next 10 years. I think what's going to work, we're going to know in the next 10 years.

Higgins: I certainly think of a lot of clinic patients who our current approaches are just not quite good enough for and for whom we would love to have a whole other tool in the arsenal. It's pretty amazing to think about seeing the successes in sickle cell and thinking that this could actually happen for our Crohn's patients. In the big picture, big takeaways, I think it's reasonable that NOD2 would probably be first, that doing hematopoietic cells and doing bone marrow transplants is at least the starting point. We may not need to treat the gut directly at all, and this is actually starting to happen at Mount Sinai at least. Hopefully, if we see successes, this may not be more than a decade away with success. Yeah, fingers crossed on this one, for sure.

I want to thank you for having this conversation. I think it's a really exciting new field, and thank you for bringing your expertise in IBD genetics to share with us.

Cho: Thanks so much, Peter. It's been fun.

Sickle Cell Anemia

Crohn's Disease

Inflammatory Bowel Disease

CRISPR-Cas systems: Overview, Innovations and Applications in Human Disease Research and Gene Therapy

CRISPR-Cas9 Gene Editing for Sickle Cell Disease and -Thalassemia

Biologic and Clinical Efficacy of LentiGlobin for Sickle Cell Disease

Causes of Crohn's disease

IL-10R Polymorphisms Are Associated With Very-Early-Onset Ulcerative Colitis

Characterization of Crohn Disease In X-Linked Inhibitor of Apoptosis-Deficient Male Patients and Female Symptomatic Carriers

A Frameshift Mutation in NOD2 Associated With Susceptibility to Crohn's Disease

Extended Haplotype Association Study in Crohn's Disease Identifies a Novel, Ashkenazi Jewish-Specific Missense Mutation in the NF-B Pathway Gene, HEATR3

Autologous Stem Cell Transplant for Crohn's Disease

Stem-Cell Transplantation for Crohn's Disease: Same Authors, Different Conclusions?

A Myeloid-Stromal Niche and gp130 Rescue in NOD2-Driven Crohn's Disease

Expression of NOD2 in Paneth Cells: A Possible Link to Crohn's Ileitis

Role of ATG16L, NOD2 and IL23R in Crohn's Disease Pathogenesis

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Episode 2: Are We Any Closer to Intestinal Gene Therapy in Crohn's Disease? - Medscape

NEW YORK Based on findings from a small case series, a team of researchers based in the United Arab Emirates (UAE) is pursuing more widespread use of rapid whole-genome sequencing (rWGS) for infants being treated for complex, difficult-to-diagnose medical conditions, including pediatric cases from locations and populations that are underrepresented in genetic studies.

"[P]roviding a genetic diagnosis as early as possible will not only be life-saving, but will also significantly reduce healthcare costs in this setting by reducing unnecessary diagnostic workup and inappropriate treatments and interventions plans, both of which are very costly," senior and corresponding author Ahmad Abou Tayoun, a clinical molecular geneticist affiliated with the Al Jalila Children's Specialty Hospital and Center for Genomic Discovery at Mohammed Bin Rashid University of Medicine and Health Sciences, explained in an email.

As they reported in Genome Medicine on Tuesday, he and his colleagues performed rWGS on one male and four female infants being treated for complex conditions affecting multiple organ systems in the pediatric intensive care unit (ICU), along with their parents. The children were between the ages of 1 day and 90 days old, they noted, and came from the UAE, Kenya, Jordan, the Philippines, and Pakistan.

With genome sequence data on the infants and their parents, the team was able to make molecular diagnoses for three of the children, returning the results within 37 hours, on average.

"This study demonstrates the feasibility and clinical utility of performing rWGS locally for critically ill children from this genetically underrepresented population and highlights the need for investments in pediatric genomics within local healthcare institutions, in the Middle East and globally, to deliver timely diagnoses and management," the authors wrote.

The results contrast with standard-of-care testing which ranges from targeted single-gene testing or chromosomal microarrays to exome sequencing that is typically more time-consuming and currently limited to specific centers in the UAE and other parts of the Middle East, Abou Tayoun explained.

Such tests are often not available at local testing centers in the Middle East or Africa, necessitating testing outside of a patient's home country, he noted. That can cause wait times to stretch out several weeks, delaying diagnoses and treatment, while potentially contributing to poor communication of results, particularly if patients and providers do not have genetic counselors at centers nearby.

In contrast, Abou Tayoun explained, "rWGS has recently been shown to provide timely diagnoses (within a few hours) and management plans for critically ill patients in intensive care settings."

Indeed, results in the first five infants assessed suggested that the rWGS approach can provide answers for patients and families from populations that are often overlooked in genetic research, including sites where genomic resources may not be readily available.

In one of the children, a baby born prematurely in Jordan, the team tracked down a pathogenic variant affecting both copies of the chromosome 12 gene POM1, which led to a muscular dystrophy-dystroglycanopathy. While that diagnosis did not alter the care or treatment offered to the infant, the researchers reported, it did bring the infant's diagnostic odyssey to a conclusion and led to additional genetic counseling for family members.

On the other hand, the investigators did get treatment clues for another child diagnosed with the rWGS approach. In a 3-month-old girl from the Philippines, they tracked down pathogenic variants affecting one copy of the LIPA gene. Alterations in that gene have been linked to lower-than-usual levels of a lysosomal acid lipase enzyme, they noted, suggesting the child may benefit from an enzyme replacement therapy that has been approved by the US Food and Drug Administration.

The team also found chromosome 12 tetrasomy molecular features linked to a condition known as Pallister-Killian syndrome in a female infant from Pakistan who was tested when she was just a day old.

"This finding confirmed a clinical diagnosis of Pallister-Killian syndrome and guided management of the patient," the authors explained. "The identification of this tetrasomy using rWGS demonstrates the additional value of this testing where exome sequencing would, most likely, not have detected this arrangement, leading to significant delays in diagnosis until separately ordered clinical chromosomal microarray testing results are obtained."

Even so, Abou Tayoun explained that rWGS requires considerable investments in sequencing, informatics, and data storage technology, staffing, and more factors that have contributed to the unequal distribution of rapid sequencing availability within and between countries.

"[T]he global distribution of rWGS is highly unequal, with implementation in a number of centers within Europe, the USA, and Australia," he wrote, "and lack of such service in other geographical regions such as the Middle East and Africa where the genetic disease burden, specifically recessive disorders, is expectedly high."

While these issues are exacerbated in sites with limited resources or genetics infrastructure, unequal access to rWGS has been documented even in relatively resource-rich settings, as shown through efforts to make rWGS broadly available in California.

"Significant investments in local healthcare infrastructure are needed, globally, for more equitable access of genomic medicine among vulnerable patients," authors of the Genome Medicine study argued.

To that end, Abou Tayoun suggested that some access issues may be overcome by centralizing rWGS at highly specialized tertiary centers in each country, since the price tag for new genomics facilities often reaches into the millions of dollars. Along with infrastructure investments, he explained, larger centers may be better poised to attract those with the expertise and experience needed to generate, analyze, interpret, and communicate clinical findings from the genome sequence-based tests.

In particular, Abou Tayoun highlighted the need for genetic counselors, molecular technologists, genomic analysts, bioinformatic scientists, clinical molecular geneticists, and specialized multidisciplinary pediatric teams to diagnose, treat, and manage pediatric patients with complex or rare genetic conditions.

The team is working to expand from the current study to reach many more pediatric ICU patients. In the process, Abou Tayoun said, the group hopes to "make a convincing case" for more widespread rWGS use in this clinical setting.

"Given its location in Dubai/UAE and the Middle East," he noted, "Al Jalila Childrens Specialty Hospital provides care for a diverse patient population of Middle Eastern, North African, and Asian origins, which is historically not well represented in genetic studies."

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Middle East Team Calls for Local Availability of Rapid WGS to Diagnose Severely Ill Infants - GenomeWeb

Introduction

A chronic daily headache (CDH) comprises a group of headaches occurring at least 15 days per month for three or more consecutive months. We retrospectively investigated the effectiveness of the hybrid treatment strategy for CDH using Kampo medicine combined with Western medication.

We retrospectively investigated 43 consecutive first-visit CDH patients. In addition to Western acute and prophylactic medications, we prescribed three types of Kampo medicines: goreisan, goshuyuto, and kakkontodepending on the patients symptoms. Headache impact test-6 (HIT-6), monthly headache days (MHD), monthly migraine days (MMD), and monthly acute medication intake days (AMD) before, 1- and 3-months after starting the hybrid medications were assessed as outcomes.

Thirty-six women and seven men were included. The median age was 51 years old. Nine were chronic migraine (CM), 22 were episodic migraine and tension-type headaches (EM+TTH), and 12 were chronic TTH. Twenty-seven patients also had medication overuse headaches (MOH). The medians of HIT-6 before, one and three months after treatment were 63, 48, and 40, respectively. Those of MHD were 20, 5, and 2. Those of MMD were 2, 0, and 0. Those of AMD were 15, 0, and 0. Significant reductions in HIT-6, MDH, MMD, and AMD were observed oneand three monthsafter starting Kampo treatment. Similar trends were observed in the EM+TTH and MOH patients as subgroup analyses.

The hybrid medication strategy of Kampo and Western medicines for CDH is safe and effective in terms of both acute and prophylactic medications with rapid efficacy.

A chronic daily headache (CDH) comprises a group of headaches occurring at least 15 days per month for three or more consecutive months. About 5% of the normal population suffers from CDH [1]. The treatment for CDH is difficult because (1) acute medications are ineffective in 25% of patients, which can cause a transformation from episodic to chronic headache [2], medication-overuse headache (MOH) [3,4], and other side effects [5], and (2) prophylactic medications are ineffective in about 50% of patients and have side effects, leading to poor patient adherence, with more than half of the patients stopping treatment within two months [6]. In this context, alternative acute and prophylactic medications for CDH are needed. The ideal medication is a drug that can be used for headache attacks, may not lead to chronic headache and MOH, and can also be used prophylactically with rapid effectiveness.

In Japan, to solve these problems of Western medicine, Japanese traditional herbal Kampo medicine can be used for headache treatment and is also described in the Japanese Clinical Practice Guideline for Headache 2021 [7]. Kampo medicine can be used as both acute [8] and prophylactic therapy [9-12] for headaches. In our hospital, we treated CDH patients with the so-called "hybrid medication strategy of Kampo and Western medicines" [13]. We retrospectively investigated the effectiveness of the CDH treatment strategy using Kampo medicine, including goreisan, goshuyuto, and kakkonto, combined with Western medication.

From the medical records between October 2021 and May 2022, we retrospectively investigated 43 consecutive first-visit CDH patients who presented at our headache-specialized outpatient. All the patients suffered from headaches at least 90 days before the first visit and the Kampo treatment. The headache diagnosis was based on the International Classification of Headache Disorders, 3rd edition (ICHD-3) [14]. Chronic migraine (CM), episodic migraine with tension-type headache (EM+TTH), chronic TTH (CTTH), and MOH were diagnosed.

The hospitals research ethics committee approved this study (approval number 2021-4), and we gained written informed consent for this study from all the patients or patients families. This retrospective study was performed following the Declaration of Helsinki.

After diagnosing the headache based on the ICHD-3, we treated the patients by referring to the Japanese Clinical Practice Guideline for Headache 2021 [7]. Depending on the severity, we prescribed acute medications such as non-steroidal anti-inflammatory drugs (NSAIDs) and triptans. In addition, we also prescribed prophylactic medications, such as lomerizine, propranolol, angiotensin receptor blockers, valproic acid, antidepressants, monoclonal calcitonin gene-related peptide antibodies (CGRP mAbs), and muscle relaxants. If specific prophylactic medications had been used in the past and were ineffective or had side effects, they were not to be prescribed aggressively.

We also prescribed three types of Kampoextract formulations considering the patients symptoms. The choice of a specific Kampo medicine was based on the guidelines [7], experts opinions [15], and previous Japanese reports [7,8,16-18]. For CDH patients with mainly TTH, we prescribed kakkonto [19]. In the case of CDH with migraine, we used two different drugs: goshuyuto for migraines with or without aura [9,20], or for those with sensitivity to cold or the menopausal disorder [21], and goreisan for patients with edema or dehydration (sudoku status; unbalance of water distribution in Kampo medicine theory) [22] or migraines associated with weather conditions [23,24]. All Kampo medications were taken as needed, depending on the patients symptoms. Multiple Kampo medicines were sometimes prescribed, and patients were given a choice depending on the characteristics of their headaches.

Notably, we instructed that the Kampo medicine could be taken prophylactically before a headache occurs or during prodrome symptoms. Besides, Kampo medicine could be taken daily against a headache as a prophylactic medication, with a maximum of three packets per day, in addition to the prescribed Western medicines. We also told the patients that Kampo medicine could be used as an acute medication when the headache was present but not so severe as to use NSAIDs or triptans. When a single Kampo intake could not resolve the headache, Kampo medicine could be used in combination with NSAIDs and triptans. This prescription policy, for Kampo medicine as both acute and prophylactic medication, was based on the fact that Kampo medicine contains a wide variety of substances, not a single active ingredient, and each component acts comprehensively on the entire body to safely produce a therapeutic effect [15]. Such a prescription policy of Kampo medicine as both acute and prophylactic medication is beginning to be widely practiced in Japan [13].

We collected patients characteristics, such as age, sex, comorbidities, and the onset of the headache (years ago). Clinical data reported by paper-based or electronic headache diaries were used. Monthly headache days (MHD), monthly migraine days (MMD), and monthly acute medication intake days (AMD) were defined as the monthly values over the respective observation period of 30 days. A headache day was defined as a day with any kind of headache; a migraine day was defined by patients when they had severe pain, migraine pain characteristics (pulsating, one-sided pain), aura symptoms, vegetative symptoms like phono- or photophobia, nausea, vomiting, need for rest, or when triptans were taken [25]. Headache impact test-6 (HIT-6) [26] was also investigated over the respective observation period. Monthly use days of acute medication and Kampo medicine were also collected from the headache diary. The prescribed prophylactic medications we started with Kampo medicine as the hybrid treatment were also checked. The outcomes were defined as the changes in HIT-6, MHD, MMD, and AMD before treatment and after oneor threemonths.

Results were presented as the median (range). A Friedman's test and a subsequent Wilcoxons test were performed to compare HIT-6, MHD, MMD, and AMD before treatment and after one or three months. We conducted these analyses using version 28.0.0 of SPSS software (IBM, NY, USA). A two-tailed p<0.05 was considered statistically significant. Bonferronis correction for multiple comparisons in each test was applied, but we did not apply it throughout the study [27].

Table 1 shows the characteristics of 43 CDH patients. Thirty-six women and seven men were included. The median age was 51 (15-99) years old. Of the 43 patients, 9 were CM, 22 were EM+TTH, and 12 were CTTH. Twenty-seven patients also had MOH. The median past years from the first repetitive headache was 20 (1-70) years. Goreisan, goshuyuto, and kakkonto were prescribed depending on the patients headache characteristics. Twenty-six patients also had prophylactic medications. The median use days of goreisan in the first month of treatment were 15 (0-30) days, those of goshuyuto were 4 (0-30) days, and those of kakkonto were 5 (0-30) days, with a maximum intake of three packets per day. Other details and characteristics of each headache type were also described in Table 1.

Of all the 43 CDH patients, the median HIT-6 before, oneand three months after treatment were 63 (44-78), 48 (36-78), and 40 (36-78), respectively. MHD before, oneand three months after treatment were 20 (15-30), 5 (0-30), and 2 (0-30), respectively. Those about MMD were 2 (0-16), 0 (0-7), and 0 (0-5). Those about AMD were 15 (0-30), 0 (0-30), and 0 (0-30).

Regarding all the 43 CDH patients, significant reductions in HIT-6, MDH, MMD, and AMD were observed one month after starting Kampo treatment. These trends were also confirmed after three months. Similar trends were observed in the 22 EM+TTH patients and 27 MOH patients. In the 9 CM patients and 12 CTTH patients, a significant decrease in AMD at oneand three months were observed, but those of HIT-6, MDH, and MMD were confirmed only at three months (Figure 1). Laboratory tests and physical examinations over three months confirmed no side effects of Kampo medicines, such as liver dysfunction, interstitial pneumonia, and pseudoaldosteronism.

We herein describe the results of our hybrid therapy for CDH using Kampo and Western medicines. Kampo medicine may act as both acute and prophylactic medications, leading to the rapid decrease of HIT-6, MHD, MMD, and AMD, especially in EM+TTH and MOH patients. In addition, there were no side effects from Kampo medicine.

The standard CDH treatment is not established. However, the main treatment strategies are (1) to discontinue the current regimen of analgesic medications, (2) to rotate and select appropriate analgesic medicine specific to the headache characteristics, and (3) to initiate a prophylactic medication regimen to reduce the frequency and intensity of both the chronic headaches and the acute exacerbations [28].

About (1) and (2), in approximately 77% of CDH patients, discontinuation of the overused medication alone will result in the return to an episodic form of headache that can then be more easily managed [29]. However, some patients have withdrawal headaches or continuous headaches during this process, and bridging analgesics are needed [7,30]. Therefore, our results show that AMD and HIT-6 decreased rapidly by using Kampo medicine as an alternative acute medication [8] can help resolve the withdrawal headache or continuous headache and stop the medication overuse.

About (3), the consideration of the duration of prophylactic therapy as well as tapering and discontinuation of the therapy also depends on the severity of headache-induced disability before the prophylactic therapy, and no uniform criteria can be applied. However, it takes at least two months before the effectiveness of prophylactic therapy can be evaluated [7,31]. While determining efficacy during the two months, it is possible that CDH could recur. Some medications act rapidly, such as amitriptyline [32] and CGRP mAbs [25,33]. Kampo medicine can be a prophylactic medication that rapidly acts [7,18] and has long-term effects [10]. Furthermore, Kampo medicine does not have a side effect of drowsiness, which is often confirmed by using amitriptyline. Also, Kampo medicine is not as expensive as CGRP mAbs. Our results showed the possibility that Kampo medicine can be prescribed as a prophylactic medication for CDH.

Kampo medicine is empirically used for headache treatment. However, it cannot be denied that scientific evidence, such as basic and clinical research, remains insufficient. In addition to goreisan, goshuyuto, and kakkonto, keishininjinto, and chotosan are introduced in the Japanese guidelines [7]. Many other Kampo medicines are also prescribed for headache treatment. Therefore, further studies with a strong evidence level should be needed, using placebos or case cross-over studies. There are some studies with strong evidence of Kampo medicines' utility in other clinical faculties. Yokukansan is effective for the behavioral and psychological symptoms of dementia [34]. Daikenchuto prevents postoperative ileus after abdominal surgery [35]. Goreisan prevents postoperative recurrence of some types of chronic subdural hematomas [36]. Like these clinical trials, a large prospective study for headache treatment using Kampo medicine is needed.

Kampo medicine has side effects. The major side effects are pseudoaldosteronism, interstitial pneumonia, liver dysfunction, and allergy. Of the three types of Kampo medicines we used, kakkonto contains kanzo, which sometimes causes pseudoaldosteronism. Since long-term use of kakkonto may result in pseudoaldosteronism, other appropriate treatment modalities, such as physical therapy for TTH, are essential. Also, laboratory tests, X-rays, and physical examinations should be considered appropriately.

First, the sample size was small, and this study was performed in a single hospital with a single arm. Second, we did not compare to the control arm, so the true therapeutic effects of Kampo medicine were unknown. Third, the follow-up period differed for each patient, and side effects can occur in the long term. Therefore, we should follow up with the patients carefully. Fourth, we could not check the medication compliance rate of Kampo medicine other than the first month because some patients' headache diaries became less accurate as their symptoms improved. Finally, it was difficult to assess whether the improvement was due to the Western medication, a placebo effect, or spontaneous remission. Further studies using a control arm and placebo are considered in future research.

The hybrid medication strategy of Kampo and Western medicines for CDH is safe and effective in terms of both acute and prophylactic medications with rapid efficacy. The decrease of HIT-6, MHD, MMD, and AMD, especially in EM+TTH and MOH patients, was observed. Goreisan, goshuyuto, and kakkonto can be used as alternative medicines for CDH treatment combined with Western medicine. Further studies are needed to establish the efficacy of Kampo medicine for headaches.

Continued here:
The Efficacy of Japanese Herbal Kampo Medicine as an Acute and Prophylactic Medication to Treat Chronic Daily Headache and Medication Overuse...

Dr. Erika Kube| Special to The Columbus Dispatch USA TODAY NETWORK

Doug came to the emergency department in the middle of the night complaining of chest pain. He was in his 60s and had a history of diabetes and high blood pressure.

He was vague in describing his symptoms and said his pain had been going on for a couple of days, but seemed worse at night. He came to the hospitalbecause he couldnt sleep.

He rated the pain as a mild 3 out of 10 burning pain that crossed the front of his chest. He didn'thave any shortness of breath or nausea, and he hadn'ttaken anything for his symptoms.

Dougs EKG was normal, andI asked him to tell me about his symptoms. In my head I was running down the list of causes of chest pain, trying to figure out what was going on with him.Chest pain is alwaysconcerning, especially given Dougs risk factors for heart disease, but he didnt have the classic symptoms of a heart attack. I ordered lab tests and a chest X-ray and gave him medication for acid reflux to see if that would help.

I asked him if there was anything else going on with him or his health, and he initially said no, but called me back to the room a few minutes later to tell me that he had noticed a lump on his chest. He had been meaning to see his family doctor about it, but never got around to it. I asked Doug if I could pull down his gown to look at the area, and I immediately noticed his right breast had a mass the size of a walnut and the nipplewas distorted. I examined his armpit and felt a few small swollen lymph nodes, which heightened my concern.

Doug could see the concern in my eyes as I was examining him, and hestarted to look worried. I asked him about his family history, and he said that his parents and siblings had diabetes and high blood pressure, like he did. I asked specifically about cancer, and he said that almost all the women in his family had had breast cancer. His eyes grew wider as he realized why I was asking the questions I was asking. I told him we would await theresults of the tests already taken and then further discuss how to work up his breast mass.

As I was leaving the room, he asked me if it was even possible for a man to have breast cancer.

Dougs labs came back normal; his chest X-ray didnt show any specific abnormalities. He was feeling better after he received the medications.I was glad his chest pain symptoms seemed to be mostly related to acid reflux, but I was worried about the mass and wanted to admit him to the hospital. I reviewed his results with him, and he agreed to stay in the hospital to get some answers. He was very quiet and kept shaking his head in disbelief.

Doug was admitted to the hospital and underwent a biopsy of his breast mass.

Unfortunately, this confirmed that Doug had a form of breast cancer, and it had spread to his lymph nodes.He met with a breast surgeon and oncologist while in the hospital. They recommended he undergo surgical removal of the mass followed by chemotherapy and radiation.

While breast cancer is not common in men, approximately 1 in 100 diagnosed breast cancers in the United States are in men.Because it is less common and not screened for like breast cancer in women, it is often more advanced when it is finally diagnosed.

The types of breast cancers seen in men are the same as found in women. Risk factorsinclude advanced age, family history of breast cancer, genetic mutations, use of hormonal therapies like estrogen that can be used to treat prostate cancer, obesityand liver disease.

Like women, breast cancer treatment in men depends on the size of the tumor and whether it has spread outside of the breast. Treatment can include surgery, chemotherapy, radiation therapy and hormonal therapies.

Doug hadsurgery to remove the breast tumor before he left the hospital. Chemotherapy was scheduled to start a few weeks later, and radiation would start once his surgical wounds had healed. The oncologist recommended genetic testing for Doug and his family members, as there are certain inherited gene mutations that can increase cancer risk.

There are two genes, known as BRCA1 and BRCA2 (breast cancer 1 and breast cancer 2 genes), that are the most commonly affected in hereditary breast and ovarian cancer.

Approximately 3% of breast cancers and 10% of ovarian cancers result in inherited mutations in the BRCA1 and BRCA2 genes. These genes normally protect you from getting certain cancers, but when mutated, they can increase your risk of developing cancer.

Dougs oncologist was hopeful Doug would continue to do well with his cancer treatments and have many healthy years ahead. Dougs children met with a genetic counselor after hehad gone through genetic testing, and they made specific cancer screening recommendations for Dougs family in hopes of preventing or finding cancer at an earlier and more treatable stage.

Read more here:
Breast cancer in man unexpectedly diagnosed after chest pain - The Columbus Dispatch

During foetal development, before the biological clock starts ticking on its own, genes respond to rhythmic behaviour in the mother. The hypothalamus's suprachiasmatic nuclei (SCN) are the body's timekeepers. Rhythmic gene activity in SCN cells governs the activity of many other genes locally and throughout the body, influencing circadian rhythmic behaviour such as feeding and sleeping. But rhythmic gene activity begins late in foetal development, raising the question of whether maternal influences entrain SCN gene activity before birth.

The authors compared gene activity in SCN tissue from pregnant rats kept in the dark under two conditions. Lesioned rats had disrupted SCNs and limited food access to impose a circadian rhythm in their activity that their SCNs could not sustain. Control rats had intact SCNs and free access to food.

They found that, within the SCNs of both sets of fetuses, there was a very small set of genes whose timing patterns differed between the two groups and a much larger set whose activity oscillated in sync with each other.

The study reveals that distinct maternal signals rhythmically control a variety of neuronal processes in the fetal rat suprachiasmatic nuclei before they begin to operate as the central circadian clock. The results indicate the importance of a well-functioning maternal biological clock in providing a rhythmic environment during fetal brain development.

Continued here:
While the fetal clock develops, moms behaviour tells the time - The Daily Star

First companion diagnostic claim for Illumina's TruSight Oncology Comprehensive (EU) test enables targeted therapy with Bayer's VITRAKVI (larotrectinib) for patients with NTRK fusion cancer

SAN DIEGO, May 24, 2022 /PRNewswire/ -- Illumina, Inc. (NASDAQ: ILMN), a global leader in DNA sequencing and array-based technologies, today announced the addition of a companion diagnostic (CDx) indication to its CE-marked in vitro diagnostic TruSight Oncology (TSO) Comprehensive (EU) test. This single test kit, recently launched across Europe, assesses multiple tumor genes and biomarkers to reveal the specific molecular profile of a patient's cancer. The CDx pan-cancer indication will allow identification of cancer patients with solid tumors who are positive for neurotrophic tyrosine receptor kinase (NTRK) gene fusions including NTRK1, NTRK2 or NTRK3, and may benefit from targeted therapy with Bayer's VITRAKVI (larotrectinib), in accordance with the approved therapeutic labeling.

TSO Comprehensive (EU) is a comprehensive genomic profiling (CGP) test which combines less prevalent biomarkers with more prevalent ones in the same test, using a single biopsy specimen. This helps maximize the chances of identifying an actionable alteration so that patients can be treated with a targeted therapy or enrolled into a clinical trial based on their unique tumor genomic profile. The addition of this first CDx claim specific to NTRK gene fusions, a rare but highly actionable biomarker, helps provide patients harboring this genetic alteration with an opportunity to benefit from larotrectinib, a genomically matched treatment.

"This CDx claim, developed in partnership with Bayer, is the first of a series under development, building upon Illumina's broad portfolio of oncology partnerships with industry leaders to advance cancer diagnostics and precision medicine," said Paula Dowdy, Senior Vice President and General Manager of Illumina for Europe, the Middle East, and Africa. "We continue to focus on unlocking the potential of new biomarkers to identify those most likely to benefit from precision medicines so that no patient is left behindwe don't want anyone to miss the opportunity to have their biomarker detected and gain access to a potentially life-saving therapy."

Across most solid cancer tumor types, NTRK gene fusions can have a rare prevalence of 0.1-3% and can be challenging to detect as these genes fuse with many different partners, many of them previously unknown. Most CDx tests are specific to one type of cancer, but the NTRK claim is pan-cancer, enabling TSO Comprehensive (EU) to target multiple solid tumor types and a broad range of known and novel gene fusion partners across all three NTRK genes. This helps maximize the chances of finding actionable information from each patient's biopsy, to inform treatment with larotrectinib.

"Since it launched four years ago, VITRAKVI has demonstrated high response rates and highly durable responses in adults and children with TRK fusion cancer," said Christine Roth, Member of the Executive Committee of Bayer's Pharmaceuticals Division and Head of Bayer's Oncology Strategic Business Unit. "The CE marking of Illumina's TSO Comprehensive (EU) assay inclusive of NTRK gene fusion detection for VITRAKVI is an important advance in enabling precision oncology for patients in Europe. Assays that enable precision oncology through comprehensive genomic testing are crucial for informing optimal treatment plans and help to ensure the best possible outcomes for cancer patients. We look forward to continuing to collaborate with Illumina to ensure that more patients are evaluated comprehensively inclusive of NTRK gene fusions."

The performance of TSO Comprehensive (EU) with NTRK fusions was assessed by analytical and clinical validation studies. Pooled data from three clinical trials, LOXO-TRK-14001 (NCT02122913), NAVIGATE (NCT02576431) and SCOUT (NCT02637687), were used to demonstrate the clinical effectiveness and safety of TSO Comprehensive (EU) in identifying NTRK1, NTRK2 and NTRK3 gene fusion positive patients who may be eligible for treatment with larotrectinib. The primary endpoint was the overall response rate (ORR), measured as the patient presenting either a complete response, a surgical complete response or partial response, to larotrectinib.

"We were delighted to be the clinical study partner for Illumina in this significant achievement of the first CDx claim for the TSO Comprehensive (EU) panel," said Professor Richard Kennedy, Global VP of Biomarker Development & Medical Director, Almac Diagnostic Services. "TSO Comprehensive (EU) represents a powerful and versatile platform with a broad range of cancer-relevant content, and we recognize its value to our biopharma partners, for the development and delivery of companion diagnostics to further precision medicines."

Illumina has a growing pipeline of CDx claims under development through partnerships with pharmaceutical companies, which will be added to TSO Comprehensive (EU) following appropriate regulatory approvals. These CDx claims will help unlock groundbreaking targeted therapies and immunotherapies to make a difference in the lives of cancer patients. As Illumina continues to expand its broad portfolio of oncology partnerships with industry leaders, the company aims to advance cancer diagnostics and precision medicine.

About TruSight Oncology Comprehensive (EU)

TruSight Oncology Comprehensive is an in vitro diagnostic test that uses targeted next generation sequencing to detect variants in 517 genes using nucleic acids extracted from formalin-fixed, paraffin embedded (FFPE) tumor tissue samples from cancer patients with solid malignant neoplasms using the Illumina NextSeq 550Dx instrument. The test can be used to detect single nucleotide variants, multi-nucleotide variants, insertions, deletions and gene amplifications from DNA, and gene fusions and splice variants from RNA. The test also reports a Tumor Mutational Burden (TMB) score and Microsatellite Instability (MSI) status.

The test is intended as a companion diagnostic to identify cancer patients for treatment with the targeted therapy listed in Table 1, in accordance with the approved therapeutic product labeling. In addition, the test is intended to provide tumor profiling information for use by qualified healthcare professionals in accordance with professional guidelines and is not conclusive or prescriptive for labeled use of any specific therapeutic product.

Table 1: Companion Diagnostics Indication

Tumor Type

Biomarkers

Targeted Therapy

Solid Tumors

NTRK1, NTRK2, and NTRK3

Gene Fusions

VITRAKVI (larotrectinib)

To learn more about TruSight Oncology Comprehensive, click here.

About VITRAKVI (larotrectinib)

VITRAKVI (larotrectinib), a first-in-class oral TRK inhibitor, was exclusively designed to treat tumors that have an NTRK gene fusion. The compound has demonstrated high response rates and highly durable responses of over four years in adults and children with TRK fusion cancer, including central nervous system (CNS) tumors. To date, it has the largest dataset and longest follow-up data of any TRK inhibitor. The trials are still ongoing, with the latest dataset presented at the European Society for Medical Oncology (ESMO) Congress 2021 and additional updates planned to be presented at upcoming scientific meetings.

Larotrectinib is approved under the brand name Vitrakvi in more than 40 countries around the world, including the U.S., countries of the European Union (EU), and most recently in China. Filings in other regions are underway or planned. In the EU, the product is approved for the treatment of adult and pediatric patients with solid tumors that harbor a Neurotrophic Tyrosine Receptor Kinase (NTRK) gene fusion, who have a disease that is locally advanced, metastatic or where surgical resection is likely to result in severe morbidity, and who have no satisfactory treatment options.

Use of forward-looking statements

This release may contain forward-looking statements that involve risks and uncertainties. Among the important factors to which our business is subject that could cause actual results to differ materially from those in any forward-looking statements are: (i) our ability to manufacture robust instrumentation and consumables; (ii) challenges inherent in developing, manufacturing, and launching new products and services; (iii) our ability to obtain regulatory approval for our products from government agencies and reimbursement from payors; (iv) our ability to successfully partner with other companies and organizations to develop new products, expand markets, and grow our business, together with other factors detailed in our filings with the Securities and Exchange Commission, including our most recent filings on Forms 10-K and 10-Q, or in information disclosed in public conference calls, the date and time of which are released beforehand. We undertake no obligation, and do not intend, to update these forward-looking statements, to review or confirm analysts' expectations, or to provide interim reports or updates on the progress of the current quarter.

About Bayer

Bayer is a global enterprise with core competencies in the life science fields of health care and nutrition. Its products and services are designed to help people and planet thrive by supporting efforts to master the major challenges presented by a growing and aging global population. Bayer is committed to drive sustainable development and generate a positive impact with its businesses. At the same time, the Group aims to increase its earning power and create value through innovation and growth. The Bayer brand stands for trust, reliability and quality throughout the world. In fiscal 2021, the Group employed around 100,000 people and had sales of 44.1 billion euros. R&D expenses before special items amounted to 5.3 billion euros. For more information, go to http://www.bayer.com.

About Illumina

Illumina is improving human health by unlocking the power of the genome. Our focus on innovation has established us as a global leader in DNA sequencing and array-based technologies, serving customers in the research, clinical and applied markets. Our products are used for applications in the life sciences, oncology, reproductive health, agriculture and other emerging segments. To learn more, visit http://www.illumina.com and connect with us on Twitter, Facebook, LinkedIn, Instagram, and YouTube.

Investors:

Salli Schwartz858.291.6421IR@illumina.com

Media:

Adi RavalUS: 202.629.8172PR@illumina.com

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SOURCE Illumina, Inc.

Company Codes: NASDAQ-NMS:ILMN

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Illumina Introduces New Pan-Cancer Companion Diagnostic to Match Patients with Rare Genetic Mutations to Targeted Therapy - BioSpace

CAMBRIDGE, Mass.--(BUSINESS WIRE)--Foundation Medicine, Inc., a pioneer in molecular profiling for cancer, today announced that the company and its collaborators will present a total of 26 abstracts at the 2022 American Society of Clinical Oncology (ASCO) Annual Meeting held virtually and in person in Chicago from June 3-7, 2022.

Presentations focus on the power of genomic research to provide physicians and researchers with the latest insights on innovative treatment strategies for patients, including those with early-stage cancers, and cancers with rare or complex alterations. Highlights of this data include:

At Foundation Medicine, we provide doctors and researchers with tools to help them find answers and take action on treatment options for patients across cancer types and stages. At this years ASCO, we will demonstrate the expanded capacity of our tests to detect actionable complex biomarkers and alterations in earlier stages of cancer to support care decisions for patients, said Priti Hegde, PhD, chief scientific officer at Foundation Medicine. We are proud of our many collaborations on this research with partners across the oncology community. These collaborations reinforce Foundation Medicines role as an essential partner with the scientific expertise and real-world data to support efficient progress for equitable patient care.

The Value of Liquid Biopsy in Identifying Actionable Alterations

LCMC LEADER neoadjuvant screening trial: LCMC4 evaluation of actionable drivers in early stage lung cancers. Abstract #TPS8596.

In collaboration with the Lung Cancer Research Foundation, the Lung Cancer Mutation Consortium, and Memorial Sloan Kettering Cancer Center, this Trial in Progress abstract details the umbrella trial design of the LCMC4 Evaluation of Actionable Drivers in EaRly-Stage Lung Cancer (LEADER) clinical trial. Foundation Medicines tissue-based CGP test, FoundationOneCDx, and its blood-based CGP test, FoundationOneLiquidCDx, will both be used in the LEADER trial to screen for 10 actionable driver mutations in 1,000 patients with high-risk, resectable NSCLC who are candidates for neoadjuvant therapy. Results will enable selection of neoadjuvant therapy and enrollment onto independent therapeutic trials with genomically matched neoadjuvant treatment, standard therapies, or other trials if no driver is detected.

CtDNA shed as a tool to select immune checkpoint inhibitors (ICPI) with or without chemotherapy for patients (pts) with advanced non-small cell lung cancer (aNSCLC). Abstract #9045.

Using the CGDB, this study with Gustave Roussy Cancer Center investigated circulating tumor DNA (ctDNA) shed as an indicator to support treatment selection for patients with advanced NSCLC. Researchers found that elevated plasma tumor fraction (TF) can identify patients at risk of early progression on immune checkpoint inhibitors (ICPI) who may benefit from chemotherapy in addition to an ICPI. In patients with low/intermediate TF, the study found that outcomes on ICPIs alone are similar to those receiving both chemotherapy and ICPI treatment, suggesting TFs ability as a non-invasive tool to identify patients for single-agent ICPI.

Genomic landscape of acquired resistance to targeted therapies in patients with solid tumors: a study from the National Center for Precision Medicine (PRISM). Abstract #3016.

Researchers from Gustave Roussy Cancer Center and Institut Bergoni set up a study using FoundationOneLiquid CDx to detect ctDNA in an effort to characterize the landscape of secondary resistance mechanisms in patients with solid tumors. While many targeted therapies are approved for treatment in solid tumors, acquired resistance to these therapies remains as a barrier limiting the ultimate effectiveness of these treatments. Researchers reported that polyclonal secondary genomic alterations represent a frequent clinical resistance mechanism that may explain the low rate of sustained complete remission for patients treated with targeted therapies.

The Power of Real-World Genomic Data to Shape the Future of Cancer Care

A real-world (rw) evidence study quantifying the clinical value of multi-gene testing in early-stage lung adenocarcinoma (LUAD). Abstract #8525.

In collaboration with Cleveland Clinic Cancer Center and Flatiron Health, this study used the CGDB to assess the potential value of CGP in early-stage lung adenocarcinoma (LUAD). Researchers found that CGP of early-stage LUAD can identify EGFR, ALK, ROS1, RET and other drivers and enable appropriate selection of targeted therapies and timely use of effective first line therapy at recurrence. By avoiding the use of ICPIs in patients unlikely to respond, CGP could represent a way to avoid ineffective treatment and risk of tyrosine kinase inhibitor (TKI)-associated toxicity.

Biomarker associations of immune checkpoint inhibitor versus chemotherapy effectiveness in first-line metastatic endometrial carcinomas: A real-world study. Abstract #5596.

Using real world data from the CGDB, this study in partnership with the Yale School of Medicine evaluated TMB greater than 10 mutations per megabase and MSI-high as predictive biomarkers for ICPI benefit in comparison to standard of care chemotherapy in first line metastatic endometrial cancer (mEC). More favorable time to next treatment and overall survival were observed on ICPI versus chemotherapy in first line treatment among those with high TMB and/or MSI-high, but not those without. The results of this study suggest that a randomized controlled trial in this setting using these biomarkers has a favorable chance of success to develop a chemotherapy-sparing first line option for patients with mEC.

Clinical and genomic characteristics of pts with durable benefit from immune checkpoint inhibitors (ICPI) in advanced non-small cell lung cancer (aNSCLC). Abstract #9048.

In collaboration with Dana-Farber Cancer Institute, this study queried the CGDB to better understand patients with advanced NSCLC who had a durable response to ICPIs. The two-year mark has increasingly become a milestone in progression-free patients with advanced NSCLC, with a subset experiencing ongoing disease control even after discontinuing active treatment. In a cohort of 4,030 advanced NSCLC patients, 4.6% were free of progression or treatment failure at 24 months, with a median overall survival of almost 5 years. 41% of those patients stopped immunotherapy usage before the two-year mark. Researchers also found that elevated TMB was associated with durable benefit on ICPIs, as well as prolonged progression-free survival after the 2-year mark and deserves further investigation as a biomarker for prolonged benefit from ICPIs in advanced NSCLC.

Ancestry-based differences in gene alterations in non-small cell lung cancer: Real-world data using genetic ancestry analysis. Abstract #9125.

In this study, researchers investigated alteration prevalence in a large real-world NSCLC cohort, stratified by genetic ancestry. Together with Juntendo University Graduate School of Medicine and others, the study looked at FoundationCore, Foundation Medicines robust real-world dataset, to reveal ancestry-associated differences in genomic alterations in NSCLC. Age and sex were also associated with differences in prevalence of gene alterations and immunotherapy-associated biomarkers, such as high TMB status.

Real-world (rw) analysis of quantitative MET copy number (CN) as a biomarker in advanced NSCLC (aNSCLC). Abstract #9123.

Researchers used real-world data from the CGDB to explore the genomic landscape of MET amplification in NSCLC and its association with outcomes to MET TKIs. In partnership with the University of Colorado, CGP results from 64,521 tissue and 5,177 blood-based NSCLC samples were queried for MET amplification, which was detected in 3.3% of tissue samples and 3.2% of high TF blood samples. MET amplification was found to be associated with response to MET TKIs. In TKI-nave patients, MET copy number was negatively correlated with the presence of a concurrent NSCLC driver, suggesting that further studies evaluating MET copy number as a predicative biomarker for MET TKIs, and as an indicator of MET dependence to aid therapy section, are warranted.

Activating MET kinase domain mutations define a novel molecular subtype of non-small cell lung cancer that is clinically targetable with the MET inhibitor elzovantinib (TPX-0022). Abstract #9124.

In this study conducted in partnership with Dana-Farber Cancer Institute and Turning Point Therapeutics, researchers investigated a novel, actionable subtype of NSCLC characterized by activating MET tyrosine kinase domain (MET-TKD) mutations in the absence of METex14 mutations. Looking at a multi-institutional dataset of cancers that underwent genomic profiling, including FoundationCore, researchers found that potentially actionable MET-TKD mutations represent a novel genomic subtype in 0.6-0.9% of NSCLC and occur in the absence of other known drivers in a subset of cases.

The following is a list of select abstracts that will be presented at the meeting. To access all abstracts being presented by Foundation Medicine and its collaborators, please visit: meetinglibrary.asco.org.

Follow Foundation Medicine on Twitter and LinkedIn for more updates from #ASCO22 and visit us in person at Booth #13019.

Abstract #

Title

Collaborator

Product

Poster Discussions

Abstract 3016,Sunday, June 5, 2022, 8:00 AM-11:00 AM CDT

Genomic landscape of acquired resistance to targeted therapies in patients with solid tumors: A study from the National Center for Precision Medicine (PRISM)

National Center for Precision Medicine, Gustave Roussy Cancer Center, Institut Bergoni

FoundationOneLiquid CDx

Abstract LBA9023,Monday, June 6, 2022, 8:00 AM-11:00 AM CDT

Efficacy/safety of entrectinib in patients (pts) with ROS1-positive (ROS1+) advanced/metastatic NSCLC from the Blood First Assay Screening Trial (BFAST)

Roche/Genentech

Clinical trial assay based on FoundationOneLiquid CDx

Poster Presentations

Abstract 5596,Saturday, June 4, 2022, 1:15 PM-4:15 PM CDT

Biomarker associations of immune checkpoint inhibitor versus chemotherapy effectiveness in first-line metastatic endometrial carcinomas: A real-world study

Yale School of Medicine, Flatiron Health

Flatiron Health-Foundation Medicine Clinico-Genomic Database (CGDB)

Abstract 4102,Saturday, June 4, 2022, 8:00 AM-11:00 AM CDT

Conquer Cancer Merit Award Winner: Genomic profile of intrahepatic cholangiocarcinoma with MTAP loss

MD Anderson Cancer Center

FoundationCore

Abstract 3130,Sunday, June 5, 2022, 8:00 AM-11:00 AM CDT

Increasing targeted therapy options for patients with relapsed cancer with broader somatic gene panel analysis from the primary tumor: The Profiler02 randomized phase II trial

Roche

FoundationOneCDx

Abstract TPS8596,Monday, June 6, 2022, 8:00 AM-11:00 AM CDT

LCMC LEADER neoadjuvant screening trial: LCMC4 evaluation of actionable drivers in early stage lung cancers

Lung Cancer Research Foundation, Lung Cancer Mutation Consortium, Memorial Sloan Kettering Cancer Center

FoundationOneCDx & FoundationOneLiquid CDx

Abstract 9045,Monday, June 6, 2022, 8:00 AM-11:00 AM CDT

CtDNA shed as a tool to select immune checkpoint inhibitors (ICPI) with or without chemotherapy for patients (pts) with advanced non-small cell lung cancer (aNSCLC)

Gustave Roussy Cancer Center, Flatiron Health

Flatiron Health-Foundation Medicine Clinico-Genomic Database (CGDB)

Abstract 8525,Monday, June 6, 2022, 8:00 AM-11:00 AM CDT

A real-world (rw) evidence study quantifying the clinical value of multi-gene testing in early-stage lung adenocarcinoma (LUAD)

Cleveland Clinic Cancer Center, Flatiron Health

Flatiron Health-Foundation Medicine Clinico-Genomic Database (CGDB)

Abstract 9048,Monday, June 6, 2022, 8:00 AM-11:00 AM CDT

Clinical and genomic characteristics of pts with durable benefit from immune checkpoint inhibitors (ICI) in advanced non-small cell lung cancer (aNSCLC)

Dana-Farber Cancer Institute

Flatiron Health-Foundation Medicine Clinico-Genomic Database (CGDB)

Abstract 9125,Monday, June 6, 2022, 8:00 AM-11:00 AM CDT

Conquer Cancer Merit Award Winner: Ancestry-based differences in gene alterations in non-small cell lung cancer: Real-world data using genetic ancestry analysis

Juntendo University, Stanford University, Chugai, Ohio State University

FoundationCore

Abstract 9123,Monday, June 6, 2022, 8:00 AM-11:00 AM CDT

Conquer Cancer Merit Award Winner: Real-world (rw) analysis of quantitative MET copy number (CN) as a biomarker in NSCLC

University of Colorado

Flatiron Health-Foundation Medicine Clinico-Genomic Database (CGDB)

Abstract 9124,Monday, June 6, 2022, 8:00 AM-11:00 AM CDT

Activating MET kinase domain mutations define a novel molecular subtype of non-small cell lung cancer that is clinically targetable with the MET inhibitor elzovantinib (TPX-0022)

Dana-Farber Cancer Institute, Turning Point Therapeutics

FoundationCore

Abstract 8587,Monday, June 6, 2022, 8:00 AM-11:00 AM CDT

Conquer Cancer Merit Award Winner: Genomic characterization of thymic epithelial tumor from real-world data

Juntendo University, Stanford University, Chugai, Ohio State University

FoundationCore

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Foundation Medicine is a pioneer in molecular profiling for cancer, working to shape the future of clinical care and research. We collaborate with a broad range of partners across the cancer community and strive to set the standard for quality, scientific excellence, and regulatory leadership. Our deep understanding of cancer biology helps physicians make informed treatment decisions for their patients and empowers researchers to develop new medicines. Every day, we are driven to help our partners find answers and take action, enabling more people around the world to benefit from precision cancer care. For more information, please visit http://www.FoundationMedicine.com and follow us on Twitter and LinkedIn.

About FoundationOneCDx

FoundationOne CDx is a next-generation sequencing based in vitro diagnostic device for detection of substitutions, insertion and deletion alterations (indels), and copy number alterations (CNAs) in 324 genes and select gene rearrangements, as well as genomic signatures including microsatellite instability (MSI) and tumor mutational burden (TMB) using DNA isolated from formalin-fixed, paraffin-embedded (FFPE) tumor tissue specimens. FoundationOne CDx is for prescription use only and is intended as a companion diagnostic to identify patients who may benefit from treatment with certain targeted therapies in accordance with their approved therapeutic product labeling. Additionally, FoundationOne CDx is intended to provide tumor mutation profiling to be used by qualified health care professionals in accordance with professional guidelines in oncology for patients with solid malignant neoplasms. Use of the test does not guarantee a patient will be matched to a treatment. A negative result does not rule out the presence of an alteration. Some patients may require a biopsy. For a full list of targeted therapies for which FoundationOne CDx is indicated as a companion diagnostic, please visit http://www.F1CDxLabel.com.

About FoundationOneLiquid CDx

FoundationOne Liquid CDx is a qualitative next generation sequencing based in vitro diagnostic test for prescription use only that uses targeted high throughput hybridization-based capture technology to analyze 324 genes utilizing circulating cell-free DNA (cfDNA) isolated from plasma derived from anti-coagulated peripheral whole blood of advanced cancer patients. The test is FDA-approved to report short variants in over 300 genes and is a companion diagnostic to identify patients who may benefit from treatment with specific therapies (listed in Table 1 of the Intended Use) in accordance with the approved therapeutic product labeling. Additional genomic findings may be reported and are not prescriptive or conclusive for labeled use of any specific therapeutic product. Use of the test does not guarantee a patient will be matched to a treatment. A negative result does not rule out the presence of an alteration. Patients who are negative for companion diagnostic mutations should be reflexed to tumor tissue testing and mutation status confirmed using an FDA-approved tumor tissue test, if feasible. For the complete label, including companion diagnostic indications and complete risk information, please visit http://www.F1LCDxLabel.com.

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Foundation Medicine and Collaborators to Share More Than 20 Abstracts Featuring New Data at the 2022 American Society of Clinical Oncology Annual...

SINGAPORE - The Republic is embarking on a mission to map the DNA and the complete set of genes of 100,000 Singaporeans - to unravel clues that will further the population's health and well-being.

By scrutinising genes and dissecting biological processes at the molecular level, doctors and researchers can pinpoint the underlying causes of cancer and chronic ailments, and identify new ways to prevent or slow down disease progression.

This would help to pave the way for new drugs, faster diagnostics and targeted treatments through precision medicine, said Professor Patrick Tan, executive director of Precision Health Research, Singapore (Precise), the entity that will helm the population study.

Over the next three years, the whole genomes of 100,000 healthy Singaporeans - between the ages of 30 and 80 - will be sequenced and analysed to create one of Singapore's largest research data sets.

Malay and Indian participants will comprise 40 per cent of the 100,000, and the rest will be Chinese.

The project, called SG100K, will end up as one of Asia's leading reference genome databases since Singapore's ethnic diversity captures more than 80 per cent of Asia's diversity.

On Thursday (May 26), Precise and genomics technology leader Illumina inked a partnership agreement to kick-start the SG100K effort.

The whole genome sequences will amount to 20 petabytes of data - which is equivalent to about 200,000 high-definition movies. The human brain can store around 2.5 petabytes of memory.

To date, the project has enrolled 70,000 participants from existing cohort studies, and is working towards recruiting the remaining 30,000 participants at a rate of 300 participants per week, said Deputy Prime Minister Heng Swee Keat, who attended the signing ceremony and toured Illumina's premises in Woodlands on Thursday.

Mr Heng added that Precise has in place robust safeguards to protect the privacy and security of data collected from people.

For one, Illumina has invested heavily in safeguarding its software, and researchers need approval to access the anonymised data, said Prof Tan.

The remaining 30,000 participants will be recruited mainly through referrals from the healthcare clusters, and from those who sign up for The Health For Life In Singapore population cohort study, led by Lee Kong Chian School of Medicine.

Under the SG100K project, participants' blood samples will be sent for whole genome sequencing.

The genomic data will also be linked to other physical health measurements taken from the participants. This means that participants have to undergo a whole day of tests, which includemeasuring blood sugar and cholesterol levels, a fitness test using trackers, and answer a questionnaire on their lifestyle.

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Project SG100K: DNA of 100000 Singaporeans to be mapped to identify new ways to prevent diseases - The Straits Times

image:Mitochondria being engulfed by autophagosome view more

Credit: Jlio C. B. Ferreira/USP

A study by Brazilian scientists points to the probable biological mechanism that modulates the accumulation of mutant mitochondrial DNA in cells during aging, especially in the liver. The mechanism is called autophagy, a process of cellular cleansing that destroys organelles, including mitochondria, and recycles their components. The findings resolve a paradigm in the field and raise a hypothesis for the emergence of diseases associated with mitochondrial DNA, paving the way for the development of therapies.

The study was supported by FAPESP and is reported in an articlepublishedin the journalAutophagy.

Mitochondria are responsible for cellular respiration, processing substrates to supply energy to the organism. They have their own genome inherited solely from the mother, unlike the DNA found in cell nuclei, which is inherited from both parents. Mitochondrial DNA is also subject to mutations, some of which can lead to diseases. According to estimates, disorders caused by mitochondrial DNA mutations affect at least one in every 5,000 people worldwide. One of these disorders is MELAS syndrome (Mitochondrial Encephalopathy, Lactic Acidosis, and Stroke-like episodes), which can cause seizures, pain, altered consciousness and focal neurological deficits, among other symptoms.

Besides the disorders due directly to mitochondrial DNA mutations, there are others to which mutations contribute at least partly, saidMarcos Chiaratti, last author of the article. These include diabetes, Parkinsons and Alzheimers, he added, indicating that the study could pave the way for treatments involving autophagy in the context of different diseases.

Chiaratti is a professor in the Department of Genetics and Evolution at the Federal University of So Carlos (UFSCar) in So Paulo state. The other authors of the article are researchers affiliated with UFSCar and the University of So Paulo (USP) in Brazil, and with Cedars-Sinai Medical Center and Stanford University in the United States. The study was led by Chiaratti and supported by FAPESP via seven projects (16/07868-4,17/05899-2,17/04372-0,18/20028-0,20/15412-6,19/25049-9, and12/50231-6).

Aging

Research has shown that mitochondrial DNA mutations build up as part of aging. One of the oldest questions in biomedicine is why this is so, Chiaratti said. Theories that blame mitochondrial DNA replication or cell proliferation have been ruled out by previous studies. Given the importance of autophagy in the life cycle of cells and mitochondrial recycling, Chiaratti and colleagues decided to see if it played a role in mitochondrial DNA mutations. Autophagy is in vogue. The scientific literature on the topic is growing, he said. The 2016 Nobel Prize in Physiology or Medicine was awarded to Japanese cell biologist Yoshinori Ohsumi for his discoveries relating to autophagy mechanisms.

Methodology

Practically all humans have a small amount of mutant DNA. The coexistence of mutant and wild-type (non-mutant) mitochondrial DNA in a cell is called heteroplasmy. In this study, Chiaratti et al. used mice with heteroplasmy at 30%: a mutant strain known as NZB/BINJ (or NZB) accounted for 30% of their mitochondrial genome, while the rest was C57BL/6N (or BL6), considered normal.

The researchers cross-bred these mice with others that lacked the geneatg7specifically in the liver. Without this gene, the requisite machinery to make autophagy possible simply disappears. We spent almost a year just on breeding, Chiaratti said.

After this period, they had two groups of mice: a control group with NZB mitochondrial DNA and the geneatg7; and a group with NZB but without the geneatg7in liver cells, so that autophagy in the liver was impossible (liver-specificatg7knockout).

Experiments were conducted to see if autophagy affected the buildup of mutant mitochondrial DNA over time. Ten days after birth, similar levels of NZB were found in the tissue of both groups of mice, but after 21 days NZB began to accumulate in the livers of the control animals, while the knockout group had the same proportion as before. After 100 days, when mice are considered adults, the controls had even higher levels of NZB while the knockouts had practically the same levels as when they were born, making the difference between the two groups even more evident and suggesting that autophagy plays a role in the age-related buildup of mutant mitochondrial DNA.

The researchers then set out to validate this finding by conducting an experiment with mice that lacked the genePrkn, which is responsible for a specific stage of autophagy. InPrknknockout mice, autophagy occurred but was defective. We again compared these mice with the controls, Chiaratti said. Although thePrknknockout mice did eventually accumulate NZB mitochondrial DNA, the buildup was smaller than for the control group. This reinforced the theory that autophagy is involved since manipulation of another gene associated with it led to changes in the data.

The researchers also found that autophagy mostly cleared BL6 mitochondrial DNA in controls, which presumably explained the higher levels of NZB. On exploring this possibility further, they discovered that the presence of NZB enhanced mitochondrial respiratory capacity in liver cells. We, therefore, postulated that autophagy might help eliminate less functional mitochondria while conserving the fittest, which of course would be positive, Chiaratti said.

Another stage of the study entailed isolation of fibroblasts, a type of connective tissue cell, from the mice, and the in vitro observation that NZB mitochondrial DNA levels in them fell over time. However, when drugs that stimulated autophagy were applied, the decline was reversed. This was further evidence of the importance of autophagy to mitochondrial DNA regulation, Chiaratti said.

Next steps

While NZB was considered mutant in the mice involved in these experiments, the results show that it is not detrimental to the liver. On the contrary, it enhances mitochondrial respiratory capacity in liver cells, as already noted. Now we need to investigate the phenomenon with different mitochondrial DNAs that are known to be pathological, Chiaratti said.

If autophagy also proves relevant in this context, the researchers can begin to test treatments that stimulate the cell cleansing mechanism against diseases affected by the functioning of mitochondria. Other possibilities for future research, Chiaratti added, will include the role of autophagy in mitochondrial DNA accumulation in tissue elsewhere in the body apart from the liver and isolated fibroblasts.

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About So Paulo Research Foundation (FAPESP)

The So Paulo Research Foundation (FAPESP) is a public institution with the mission of supporting scientific research in all fields of knowledge by awarding scholarships, fellowships and grants to investigators linked with higher education and research institutions in the State of So Paulo, Brazil. FAPESP is aware that the very best research can only be done by working with the best researchers internationally. Therefore, it has established partnerships with funding agencies, higher education, private companies, and research organizations in other countries known for the quality of their research and has been encouraging scientists funded by its grants to further develop their international collaboration. You can learn more about FAPESP atwww.fapesp.br/enand visit FAPESP news agency atwww.agencia.fapesp.br/ento keep updated with the latest scientific breakthroughs FAPESP helps achieve through its many programs, awards and research centers. You may also subscribe to FAPESP news agency athttp://agencia.fapesp.br/subscribe.

Autophagy deficiency abolishes liver mitochondrial DNA segregation

27-Feb-2022

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Study reveals potential target for treatment of diseases associated with mitochondrial DNA mutations - EurekAlert