Category Archives: Human Genetics

image:The hallmarks of adipose tissue dysfunction view more

Credit: Sakers et al./Cell

Obesity is known to cause cardiometabolic diseases like hypertension and diabetes but attributing these diseases to merely an overabundance of fat is a simplification. On a basic level, fat acts as a receptacle to store energy, but upon a closer look it is an essential actor in vital bodily processes like the immune response, the regulation of insulin sensitivity, and maintenance of body temperature. In a review published in the journal Cell on February 3rd, researchers argue that the negative health effects of obesity stem not simply from an excess of fat but from the decline in its ability to respond to changes, or in other words, its plasticity.

The makeup and functioning of this tissue changes in response to weight fluctuations and aging. As fat declines in plasticity due to aging and obesity, it loses its ability to respond to bodily cues. In the current model of this phenomenon, the rapid growth of adipose tissue outpaces its blood supply, depriving the fat cells of oxygen and causing the accumulation of cells that no longer divide. This leads to insulin resistance, inflammation, and cell death accompanied by the uncontrolled spill of lipids from these cells.

The central role of adipose tissue dysfunction in disease and the incredible plasticity of fat tissue supports the promise of modulating fat tissue phenotypes for therapeutic purposes, write the authors, led by Claudio J. Villanueva (@ClaudioVillanu) from the College of Life Sciences/David Geffen School of Medicine and Patrick Seale (@LabSeale) from Perelman School of Medicine at the University of Pennsylvania. Many questions and opportunities for future discovery remain, which will yield new insights into adipose tissue biology and hopefully lead to improved therapies for human disease.

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Research reported in this publication was supported by NIDDK at the National Institutes of Health, the UCLA Life Sciences Fund, and UCLA Graduate Council Diversity Fellowship. The authors declare no competing interests.

Cell, Sakers et al. Adipose tissue plasticity in health and disease https://www.cell.com/cell/fulltext/S0092-8674(21)01454-9

Cell (@CellCellPress), the flagship journal of Cell Press, is a bimonthly journal that publishes findings of unusual significance in any area of experimental biology, including but not limited to cell biology, molecular biology, neuroscience, immunology, virology and microbiology, cancer, human genetics, systems biology, signaling, and disease mechanisms and therapeutics. Visit: http://www.cell.com/cell. To receive Cell Press media alerts, contact press@cell.com.

Literature review

Not applicable

Adipose-tissue plasticity in health and disease

3-Feb-2022

Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.

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When it comes to obesity, the problem isn't an excess of fat but its loss of function, researchers argue - EurekAlert

Global NGS Sample Preparation Market to Reach $3,279. 3 Million by 2026. Market Report Coverage - NGS Sample Preparation Market Segmentation.

New York, Feb. 02, 2022 (GLOBE NEWSWIRE) -- Reportlinker.com announces the release of the report "NGS Sample Preparation Market - A Global and Regional Analysis: Focus on Product, Workflow, Therapeutic Area, Application, End User, and Region - Analysis and Forecast, 2021-2026" - https://www.reportlinker.com/p06226825/?utm_source=GNW

Product (Consumables, Standalone Automation Instruments, Automated Workstation, Accessories and Components) Workflow (Library Preparation, Target Enrichment, Sample Extraction/Isolation, Fragmentation, Sample Quantification, Library Quantification, Quality Control (QC), and Pooling) Therapeutic Area (Oncology, Infectious Diseases, Human Genetics/Population Genetics, and Others) Application (DNA Sequencing, Whole Genome Sequencing, RNA Sequencing, Methylation Sequencing, and Others) End User (Hospitals and Clinics, Academic and Research Institutions, Pharmaceutical and Biotechnology Companies, and Others)

Regional Segmentation

North America: U.S., Canada Europe: Germany, France, U.K., Italy, Spain, Netherlands, Denmark, Belgium, Switzerland, and Rest-of-Europe Asia-Pacific: China, Japan, India, South Korea, Australia, Singapore, and Rest-of-Asia-Pacific Latin America: Brazil, Mexico, and Rest-of-Latin America Rest-of-the-World

Market Growth Drivers

Increasing Use of NGS for Genetic Disorders Technological Advancements in NGS Sample Preparation Methods Rising Research Funding in the Field of Genomics

Market Challenges

High Cost of Automated NGS Sample Preparation Instruments Dearth of Skilled Professionals and Lack of Infrastructure in Emerging Countries Stringent Regulatory Standards

Market Opportunities

Adoption of Automated NGS Sample Preparation in the Emerging Markets Rising Direct-to-Consumer Testing

Key Companies Profiled

Agilent Technologies, Inc., Aurora Biomed Inc., Danaher, Bio-Rad Laboratories, Inc., Eppendorf SE, Opentrons, BGI Group, Promega Corporation, Oxford Nanopore Technologies plc., F. Hoffmann-La Roche Ltd, Tecan Trading AG, Hamilton Company, PerkinElmer Inc., Illumina, Inc., Thermo Fisher Scientific Inc., New England Biolabs, QIAGEN, Pacific Biosciences of California, Inc.

Key Questions Answered in this Report: How is NGS sample preparation revolutionizing oncology? What are the major market drivers, challenges, and opportunities in the global NGS sample preparation market? What are the underlying structures resulting in the emerging trends within the global NGS sample preparation market? How is the COVID-19 pandemic impacting the global NGS sample preparation ecosystem? What are the key development strategies that are being implemented by the major players in order to sustain themselves in the competitive market? What are the key regulatory implications in developed and developing regions pertaining to the use of NGS sample preparation products? What are the potential entry barriers expected to be faced by the companies willing to enter a particular region?

How is each segment of the market expected to grow during the forecast period 2021-2026, and what is the anticipated revenue to be generated by each of the segments? Following are the segments:o Product (Consumables, Standalone Automation Instruments, Automated Workstation, Accessories and Components)o Workflow (Library Preparation, Target Enrichment, Sample Extraction/Isolation, Fragmentation, Sample Quantification, Library Quantification, Quality Control (QC), and Pooling)o Application (DNA Sequencing, Whole Genome Sequencing, RNA Sequencing, Methylation Sequencing, and Others)o Therapeutic Area (Oncology, Infectious Diseases, Human Genetics/Population Genetics, and Others)o End User (Hospitals and Clinics, Academic and Research Institutions, Pharmaceutical and Biotechnology Companies, and Others)o Region (North America, Europe, Asia-Pacific, Latin America, and Rest-of-the-World) What are the growth opportunities for the NGS sample preparation companies in the region of their operation? Who are the leading players with significant offerings in the global NGS sample preparation market? Which companies are anticipated to be highly disruptive in the future, and why?

Market Overview

The growth of the NGS sample preparation market is expected to be driven by the widespread use of NGS in diagnostic laboratories, which has enhanced the accuracy of genetic diagnostics with high consistency.Advanced genetic diagnostic techniques are being used for predictive genetic testing and prenatal diagnosis.

As the number of people suffering from genetic disorders is increasing, the efficiency and consistency of the diagnostic screening tests are becoming more crucial.Faster results with minimum errors are required to effectively screen a genetic disorder.

The automated NGS sample preparation enhances the consistency and throughput of sample preparation for genetic sequencing. The current market for NGS sample preparation is majorly dominated by manufacturers and service providers such as Thermo Fisher Scientific Inc, Illumina, Inc., BGI Group, Agilent Technologies, Inc., Aurora Biomed, Inc., F. Hoffmann-La Roche Ltd, OPENTRONS, Promega Corporation, Qiagen N.V., Bio-Rad Laboratories, Inc., Eppendorf AG, Oxford Nanopore Technologies plc., Tecan Trading AG , Hamilton Company, New England Biolabs (NEB), Danaher Corporation, and PerkinElmer, Inc.

The global NGS sample preparation market is projected to reach $3,279.3 million by 2026, growing from $1,468.9 million in 2020, at a CAGR of 14.24% during the forecast period 2021-2026.

Improvements in diagnostic methods for the diagnosis of genetic and chronic diseases are highly prioritized all across the globe.There are lots of advancements pertaining to the effective diagnosis of genetic diseases; however, there remains a lack of adoption of technologically advanced equipment in emerging economies.

Most of the developing economies in the world still opt for manual instruments in the field of research and diagnostics on account of financial feasibility.

Competitive Landscape

The growth of the NGS sample preparation market can be majorly attributed to major manufacturers of NGS sample preparation products, along with the service providers, who are actively involved in undertaking significant business strategies to translate success in research and development into the commercial clinical setting.Enterprises, led by the market juggernauts, are frequently updating and developing their respective product and service portfolios with innovative solutions to sustain the high competition in the market.

Additionally, competitors activities also include several partnerships, collaborations, and joint ventures to expand individual product and service portfolios along with the global footprint.Based on region, North America holds the largest share in the market owing to the technological advancements in NGS sample preparation methods, improved healthcare infrastructure, rise in per capita income, and improvised reimbursement policies in the region.

However, the Asia-Pacific region is anticipated to grow at the fastest CAGR during the forecast period 2021-2026.

Countries Covered North America U.S. Canada Europe Germany Italy France U.K. Spain Denmark Netherlands Belgium Switzerland Rest-of-Europe Asia-Pacific China India Singapore Japan Australia South Korea Rest-of-Asia-Pacific Latin America Brazil Mexico Rest-of-Latin America (RoLA) Rest-of-the-World (RoW)Read the full report: https://www.reportlinker.com/p06226825/?utm_source=GNW

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NGS Sample Preparation Market - A Global and Regional Analysis: Focus on Product, Workflow, Therapeutic Area, Application, End User, and Region -...

CommentarymarinasbYesterdayThis image released by ABC shows co-host Whoopi Goldberg on the set of the daytime talk series The View. The network placed Goldberg on a two-week suspension for her comments on Jews and the Holocaust. -

Actress Whoopi Goldberg got herself into very hot water last week for misspeaking on the thorny issue of race. No surprises there because it is almost impossible to talk sensibly about race. It comes down to who is speaking and who is listening or, more likely, not listening.

She said in a public forum that the Holocaust was not about race but about mans inhumanity to man. The second part of her assertion cannot be disputed. It is hard to imagine what goes on in the twisted minds of individuals who dedicate themselves to the murder of millions of undesirable people living across Europe and to the willful extermination of six million Jewish people, rounding them up over the WWII years, like caged animals, and subjecting them to the worst kind of violence and degradation, torture and deprivation. It is unthinkable, yet, the Holocaust happened within living memory and in our lifetimes we have witnessed, most notably, genocide in Yugoslavia and the Rwandan genocide of 1994 in which, during a period of around 100 days, the UN estimates 800,000 members of the Tutsi minority ethnic group, as well as some moderate Hutu and Twa, were slaughtered by armed militias in a state-led genocide, and another two million people fled into exile.

To the average unobservant non-African, Rwandan Hutus and Tutsi might be indistinguishable, lumped together as a single race of black people, but that civil war, like so many of the unending stream of civil wars on that continent, is about the differences between ethnic groups, and about power. The more numerous Hutus, essentially, were dominant in politics and economics and a power-sharing deal with the Tutsis in 1993 angered extremists Hutus, keen to maintain their supremacy. When their presidents plane was shot down by unknown parties, the slaughter began.

Maybe Whoopi Goldberg did not intend to deny the racist element in the Holocaust, which was undeniably the acknowledged reason for the mass extermination, although Hitler resented the formidable economic and cultural power of the Jews. However, she could have been more mindful of the impact of her words, since the Holocaust is itself a taboo subject, with unreconstructed Holocaust deniers everywhere and the present rise in violent attacks upon Jewish people in the US and Europe.

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Furthermore, identifying themselves as a race is very important to Jewish people. I remember how naive I felt when my sons Jewish godfather told me he identified as a Jew because his mother was Jewish, even though she and he were irreligious and his father was English and, moreover, that he was genetically Jewish. He claimed that Jews belonged to a singular race. That was long before the human genetic code had been sequenced. Jews have done, for a long time, and continue to see Judaism as a biological inheritance, not just a religious or cultural community. According to researchers at Clark and Brown universities, this is particularly true among those who have only one Jewish parent and those who do not belong to a synagogue. For them, Jewishness is inherent and immutable in their genes. This is only now being substantiated, contentiously by genetic analysis.

Read this fascinating article in the UK Guardian which I prefer not to synthesise. https://www.theguardian.com/lifeandstyle/2019/jun/12/what-does-it-mean-to-be-genetically-jewish

It all gets messy when we start talking about genetics because any biologist would tell you that race does not exist except as a social and political construct. After all, race cannot be biologically defined, due to genetic variation among human individuals and populations. In fact, the African race is the most genetically diverse group on earth. Because that gene pool is so vast, a European might have more in common genetically with any African than a fellow European. We get confused, however, because classifications of race are based chiefly on skin colour, with other relevant features such as height, eyes, and hair. Though these physical differences are superficial and dramatic, Harvard magazine assures us that they are determined by only a minute portion of the genome: we as a species have been estimated to share 99.9 per cent of our DNA with each other. The few differences that do exist reflect differences in environments and external factors, not core biology.

This is where ethnicity comes in. Although ethnicity remains primarily a sociocultural category, it turns out to have biological precursors, parameters, and consequences for both individuals and groups. The genetic components of these biological dimensions are also in the process of being identified and quantified. In the meantime and despite the advance in human genetics and clear evidence of negligible difference between ethnic groups, racism and a desire for racial supremacy will continue to be a scourge on our societies witness the antics of Trumpian white supremacists.

I did a DNA test and was fascinated to learn of my predominantly British, surprisingly pan-European and very diverse west African ancestries, but Central and South Asian genes were totally unexpected, and confirmation of indigenous American was welcome. This stellar DNA inheritance gives me no disease markers the great gift of much-maligned racial impurity. We should all desire it.

Read the rest here:
The race taboo - TT Newsday

Significance

The Rab5 GTPase functions in early endosome (EE) fusion in the endocytic pathway. Here, we propose that RAB5B also has a noncanonical vesicular fusion function in the regulated secretion pathway that produces mature surfactant proteins SP-B and SP-C in the lung. This function was revealed from investigation of a proband with interstitial lung disease suggestive of a surfactant dysfunction disorder who carried a de novo Asp136His variant in the RAB5B gene. Our modeling in C. elegans provided information on the genetic and cell biological mechanism, and analyses of proband and normal lung biopsies suggested a function for RAB5B and EEs in surfactant protein processing/trafficking. This work indicates that RAB5B p.Asp136His causes a surfactant dysfunction disorder.

Pathogenic variants in surfactant proteins SP-B and SP-C cause surfactant deficiency and interstitial lung disease. Surfactant proteins are synthesized as precursors (proSP-B, proSP-C), trafficked, and processed via a vesicular-regulated secretion pathway; however, control of vesicular trafficking events is not fully understood. Through the Undiagnosed Diseases Network, we evaluated a child with interstitial lung disease suggestive of surfactant deficiency. Variants in known surfactant dysfunction disorder genes were not found in trio exome sequencing. Instead, a de novo heterozygous variant in RAB5B was identified in the Ras/Rab GTPases family nucleotide binding domain, p.Asp136His. Functional studies were performed in Caenorhabditis elegans by knocking the proband variant into the conserved position (Asp135) of the ortholog, rab-5. Genetic analysis demonstrated that rab-5[Asp135His] is damaging, producing a strong dominant negative gene product. rab-5[Asp135His] heterozygotes were also defective in endocytosis and early endosome (EE) fusion. Immunostaining studies of the probands lung biopsy revealed that RAB5B and EE marker EEA1 were significantly reduced in alveolar type II cells and that mature SP-B and SP-C were significantly reduced, while proSP-B and proSP-C were normal. Furthermore, staining normal lung showed colocalization of RAB5B and EEA1 with proSP-B and proSP-C. These findings indicate that dominant negativeacting RAB5B Asp136His and EE dysfunction cause a defect in processing/trafficking to produce mature SP-B and SP-C, resulting in interstitial lung disease, and that RAB5B and EEs normally function in the surfactant secretion pathway. Together, the data suggest a noncanonical function for RAB5B and identify RAB5B p.Asp136His as a genetic mechanism for a surfactant dysfunction disorder.

Rab5, a member of the Ras/Rab superfamily of small GTPases (1, 2), is a master regulator of the endocytic pathway, controlling early endosome (EE) trafficking in animals (3, 4). Guanosine-5'-triphosphate (GTP)-bound Rab5 is active and associated with the EE membrane via its C-terminal isoprenoid modification. In the endocytic pathway, active Rab5 promotes the heterotypic fusion of nascent endocytic vesicles with EEs and the homotypic fusion of cargo-containing EE vesicles with each other. In contrast, guanosine 5-diphosphate (GDP)-bound Rab5 is inactive and resides in the cytoplasm. Effector proteins promote EE vesicle fusion and cycling between the GTP- and GDP-bound states of Rab5 (57). In addition to its canonical endocytic function, Rab5 has noncanonical functions: for example, in promoting fusion of nascent sorting vesicles with EEs in the regulated secretion pathway in mast cells and in the Drosophila salivary gland (8, 9).

Lung surfactant is a proteinlipid mixture that lines the airliquid surface of the lung alveolar epithelium, reducing surface tension to prevent alveolar collapse and enhance lung compliance during breathing (10, 11). There are four major lung surfactant proteins; hydrophobic SP-B and SP-C function in the formation of the proteinlipid matrix that lines the alveolar epithelium, while hydrophilic SP-A and SP-D are collectin family members that function in innate immunity. The regulated surfactant protein secretion pathway in alveolar type II (AT2) cells commences with translation in the endoplasmic reticulum (ER) of precursor proteins proSP-B and proSP-C, which contain an N-terminal propeptide and a C-terminal mature peptide (1215). proSP-B and proSP-C are trafficked through the Golgi, where they bud into nascent sorting vesicles that progress to the multivesicular body (MVB) and then, transit to the lamellar body. Acidification in the MVB and lamellar body stimulates proteolytic processing to mature SP-B and SP-C and their association with phospholipids. Surfactant proteinlipid complexes are stored in the lamellar body for stimulus-induced secretion. Factors that control the early steps and trafficking of proSP-B and proSP-Ccontaining vesicles to the MVB are not well understood (1618).

Pathogenic variants in the genes that encode SP-B and SP-C (SFTPB and SFTPC) and genes that are involved in surfactant production (ABCA3 and NKX2-1) result in surfactant dysfunction disorders, one of the genetic causes of interstitial lung disease (ILD) (10, 1921). Biallelic loss-of-function variants in SFTPB result in full-term infants with severe respiratory distress syndrome, which is typically lethal within the first few months after birth (22). In contrast, dominant variants in SFTPC result in lung diseases with variable penetrance and expressivity, ranging from neonatal respiratory distress syndrome to ILD in the fifth and sixth decades of life (23). Genetic screening of full-term infants with lethal surfactant dysfunction disorders identified cases that lacked variants in the known causal genes, indicating that there are yet to be identified genes that function in surfactant production (2426), which is not surprising given the complex biology of the regulated surfactant secretion pathway.

Here, we describe a female child identified through the Undiagnosed Diseases Network (UDN) (27) presenting with ILD suggestive of a surfactant dysfunction disorder, dysmorphic features, and global developmental delay. Trio exome sequencing identified that the proband carried a de novo heterozygous c.406G > C [NM_002868.3], p.Asp136His missense variant in RAB5B, a gene not previously associated with disease. We exploited the facile genetics and the well-developed assays for endocytosis and EEs in Caenorhabditis elegans (2830) to assess the functional consequences of the probands RAB5B variant when modeled in the worm ortholog (SI Appendix, Fig. S1). The goals of the functional analysis were to determine if the variant was damaging invivo, to provide insight into the genetic mechanism of the de novo dominant presentation, and to assess alterations in EE biology. We examined the probands lung tissue to understand the basis of the ILD as well as normal donor lung tissue to assess the relationship of RAB5B to the regulated surfactant secretion pathway (SI Appendix, Fig. S1). Our findings indicate that the RAB5B variant disrupts maturation of surfactant proteins B and C, resulting in ILD in the proband, and that RAB5B and EEs function in the regulated lung surfactant secretion pathway.

We identified a female of Pakistani ancestry with global developmental delay, dysmorphic features, and ILD leading to progressive respiratory failure and death at age 2. The proband was born to a 39-y-old mother and a 46-y-old father at 34-wk gestation by Caesarean section and weighed 2.7 kg (91st percentile). She had no respiratory symptoms at birth. Evaluation at 6 mo was significant for hypotonia, a broad nasal bridge with telecanthus, short squared digits, and overlapping second toes. She had profound developmental delay with static encephalopathy. Brain magnetic resonance imaging and electroencephalogram were normal. At 11 mo of age, she had digital clubbing (Fig. 1A) and a chest radiograph that showed hyperinflation and diffuse interstitial opacities (Fig. 1B). A computed tomography scan of the chest demonstrated diffuse ground glass opacities, areas of consolidation, and peripheral cysts, consistent with ILD and suggestive of a surfactant dysfunction disorder (Fig. 1C).

Clinical features of the proband with a de novo variant in RAB5B. (A) Shortened broad fingers with nail clubbing. (B) Hyperinflation of lungs and interstitial opacities by chest radiograph (posterioranterior and lateral views) at 7 mo of age. (C) Computed tomography of the lung at 11 mo of age shows acute and chronic interstitial changes. (D) Lung biopsy stained with hematoxylin and eosin (higher-power details are in insets d1 and d2) shows alveolar filling (d1; asterisk), AT2 cell hyperplasia (d1; bracket), remodeling (d2), and fibrosis (d2). (Scale bars: D, 2.5 mm; d1 and d2, 100 m.) (E) Dideoxy (Sanger) sequencing traces from parents and the proband showing a de novo heterozygous variant in RAB5B, c.406G > C, p.Asp136His. (F) Phylogenetic tree of Rab5 indicating the evolutionary orthologs and human paralogs. Alignment distance values are shown (Clustal Omega). C.e., C. elegans; D.m., D. melanogaster; H.s., Homo sapiens. (G) Alignment of the RAB5B sequence from H.s. residues 121 to 151 with orthologs from indicated species. The location of the variant edited in C. elegans corresponding to the conserved aspartate [D] in the proband is indicated (red arrow). The fourth region of the conserved nucleotide binding domain (NKXD) is indicated (green bars above and below). Identical residues are shaded black; conserved residues are gray (SI Appendix, Fig. S2).

The proband developed chronic tachypnea and had frequent hospitalizations for respiratory distress. At 17 mo of age, she required continuous supplemental oxygen, and a lung biopsy was performed. Histologic examination of lung tissue showed alveolar proteinosis, AT2 cell hyperplasia, lobar remodeling, and early fibrosis, consistent with a chronic disorder of surfactant dysfunction (Fig. 1D). Transmission electron microscopy was not performed. Clinical immunostaining of the lung tissue reported normal levels of ABCA3, TTF-1, SP-D, and proSP-C within AT2 cells but diminished SP-B levels. Despite therapies for ILD, the child died at the age of 2 y from respiratory failure.

A chromosomal microarray analysis (Baylor Genetics; CMA-HR+SNP version 11.2) was performed and was nondiagnostic. Trio exome sequencing was performed. No variants, losses, or gains were found in genes known to be involved in surfactant metabolism (SI Appendix, Table S1). Instead, a de novo variant in RAB5B was identified, corresponding to p.Asp136His (p.D136H, c.406G > C, NM_002868.3), and was subsequently confirmed by Sanger sequencing (Fig. 1E). The variant is not found in the sequence database Genome Aggregation Database (gnomAD) of 140,000 individuals (https://gnomad.broadinstitute.org; accessed October 2021) (31). The missense change is predicted to be damaging based on a combined annotation dependent depletion (CADD) score of 29.6 and a MutationTaster score of 81 (32, 33). RAB5B is likely not a haplo-insufficient gene based on tolerance to heterozygous loss-of-function variants, with an observed to expected ratio of 0.19 to 0.75, and probability of being loss-of-function intolerant (pLI) = 0.03 (gnomAD v2.1.1).

In humans, RAB5 has EE vesicular fusion functions mediated by three paralogous genes RAB5A, RAB5B, and RAB5C, compared with single ancestral orthologs in C. elegans (rab-5) and Drosophila melanogaster (Rab5) (34) (Fig. 1F), suggesting redundant and unique functions for the paralogs in humans. The RAB5B residue p.D136 is highly conserved and resides in the fourth region of the small GTPase nucleotide binding domain (Fig. 1G and SI Appendix, Fig. S2A), indicating that the variant may disrupt nucleotide binding, hydrolysis, and/or release. RAS family GTPases have a nearly identical nucleotide binding domain as RAB family GTPases (35). In a forward genetic screen, dominant negative mutations in the C. elegans ortholog of HRAS, let-60, were identified (36). One of these, D119N (allele sy93), is in the fourth region of the nucleotide binding domain of let-60 at the residue corresponding to human RAB5B p.D136 and C. elegans rab-5 D135 (Fig. 1G and SI Appendix, Fig. S2 B and C). These findings led us to propose that the phenotype of the proband results from the de novo heterozygous RAB5B p.D136H variant encoding a dominant negative gene product.

To investigate the functional significance of RAB5B p.D136H and the genetic basis of the dominant presentation, we modeled the probands variant in C. elegans. We generated rab-5[D135H] and the rab-5[D135D] control animals employing CRISPR-Cas9 editing at the endogenous rab-5 locus on chromosome I (SI Appendix, Fig. S3 and Table S2). rab-5 deletion [rab-5(del)] animals were homozygous lethal. Similarly, the rab-5[D135H] homozygous animals were lethal, arrested at the first larval stage (L1). In the variant heterozygotes, we quantitatively assessed organismal phenotypes, including locomotion and size (Fig. 2B). The rab-5(del) and control rab-5[D135D] heterozygous animals were normal compared with wild-type animals. However, the rab-5[D135H] heterozygotes had a >40% reduction in locomotion and a >20% reduction in size at 24 h post-L4 larval stage. D135H is thus damaging to rab-5 function and displays a dominant behavior not observed by rab-5(del), consistent with a dominant negative gene product.

C. elegans rab-5[D135H] produces a dominant negative RAB-5 small GTPase. (A) Illustration of the endogenous rab-5 locus on chromosome I and the single-copy genomic wild-type rab-5 transgene integrated into a safe harbor locus on chromosome II. (B) Mean locomotion speed and worm length on growth media agar plates for the wild-type, rab-5(del) heterozygotes, rab-5[D135D]#1 control edit heterozygotes, rab-5[D135H]#1 heterozygotes, and rab-5[D135H]#2 heterozygotes (tested animals were cross-progeny from mating). (C) Locomotion speed and mean worm length on growth media agar plates. The wild type and the wild type homozygous for the single wild-type copy insertion of rab-5 on chromosome II (light gray) were self-progeny, while rab-5[D135H]#2 heterozygotes with the normal version of chromosome II hemizygous or homozygous for the chromosome II containing a single wild-type copy of rab-5 (dark gray) were cross-progeny from mating. Allele designations for independent edits (#1, #2) are in SI Appendix, Table S2. Three independent biological replicates were combined for each genotype. n 46 per condition, except for rab-5[D135H]#2 heterozygotes in C (n = 29). Scatterplots showing mean and SD are presented for locomotion speed. Filled circles indicate the average speed per animal for up to 1 min. Box plots indicate the mean and first and third quartiles, and whiskers indicate the 5th and 95th percentiles for measures of animal length. Differences between groups were determined by the Students t test. ns, not significant. ***P < 0.001.

By definition, the phenotype of an antimorphic or dominant negative mutation is suppressed by additional copies of the wild-type gene product (37). To test for a dominant negative genetic mechanism of rab-5[D135H], we introduced a genomic wild-type rab-5 single-copy transgene into a chromosome II safe harbor site (Fig. 2A) and assessed the effect of gene dosage on phenotype. We first confirmed that the wild-type single-copy transgene behaves like the endogenous locus based on the evidence that 1) two copies of rab-5 transgene fully rescued rab-5(del) homozygotes in locomotion (SI Appendix, Fig. S3A), 2) transcript read counts from the endogenous locus and the transgene were comparable (SI Appendix, Fig. S3B), and 3) RAB-5 protein level was increased approximately twofold in semiquantitative western blots (SI Appendix, Fig. S3 G and H). We found that animals with wild-type rab-5 at the endogenous locus and homozygous (two copies) for the chromosome II rab-5 transgene (i.e., having four copies of wild-type rab-5) were slightly longer but normal with respect to locomotion (Fig. 2C). For the rab-5[D135H] heterozygous animals, one copy of the rab-5 transgene partially rescued length and locomotion defects, while two copies of the rab-5 transgene fully rescued the rab-5[D135H] heterozygotes in both length and locomotion (Fig. 2C). Combined, these results demonstrate that C. elegans rab-5[D135H] has a strong dominant negative effect, requiring three copies of the wild-type gene to suppress the variants poisonous effect. By extension, we propose that the human RAB5B p.D136H is damaging, producing a dominant negative poisonous gene product and resulting in the probands phenotype.

During endocytosis in animal cells, RAB5 mediates the heterotypic fusion of nascent endocytic vesicles with EEs and the homotypic fusion of EEs to become large ring-shaped EEs when visualized in cross-section by confocal microscopy. We first assessed the effect of rab-5[D135H] on endocytic uptake, measuring fluid-phase endocytosis via clearance of secreted soluble green fluorescent protein (ssGFP) in the body cavity by coelomocytes and receptor-mediated uptake of yolk protein by oocytes (28, 38, 39). C. elegans coelomocytes are scavenger cells that nonspecifically endocytose fluid from the body cavity (pseudocoelom) (Fig. 3A). Under normal conditions, ssGFP in the body cavity, secreted from muscle cells, is efficiently endocytosed and cleared by the coelomocytes. As expected, in wild-type animals and control rab-5[D135D] heterozygotes, the majority of ssGFP was in the coelomocytes (Fig. 3A and SI Appendix, Fig. S4A). In contrast, rab-5[D135H] heterozygous animals failed to clear ssGFP from the body cavity, indicating a blockage of endocytic trafficking (Fig. 3B and SI Appendix, Fig. S4A). Similarly, rab-5[D135H] heterozygotes failed to accumulate yolk protein, synthesized by the intestine, into oocytes, indicating a blockage of receptor-mediated yolk protein endocytosis (SI Appendix, Fig. S4 BE). In both assays, rab-5(del) heterozygotes were not significantly different from wild-type animals, corroborating the organismal length and locomotion data and indicating that rab-5 is not haploinsufficient in C. elegans.

Defective endocytic uptake and fusion in C. elegans rab-5[D135H] heterozygotes. (A) Steady-state ssGFP level imaged in rab-5[D135D]#1 control edit heterozygous animals 24 h post-L4. Schematic (Left) and confocal (Right) image showing rapid endocytic uptake of ssGFP from the body cavity into coelomocytes. (B) Steady-state ssGFP level imaged in rab-5[D135H]#1 heterozygous animals 24 h post-L4. Schematic (Left) and confocal (Right) image showing accumulation of ssGFP in the body cavity with limited uptake in coelomocytes. Arrowheads indicate ssGFP in coelomocytes. Quantification of the staining pattern data is in SI Appendix, Fig. S4A. (Scale bars: 50 m.) (CE) 2xFYVE::GFP-labeled EEs imaged in coelomocytes of rab-5(del) heterozygotes (C), rab-5[D135D]#1 control edited heterozygotes (D), and rab-5[D135H]#1 heterozygotes (E). Arrows indicate large ring-shaped EE. Arrowheads indicate small puncta-sized EE. (Scale bars: 10 m.) (F) Quantification of ring-shaped large EE and puncta-sized EE in coelomocytes of rab-5(del) heterozygotes, rab-5[D135D]#1 heterozygotes, and rab-5[D135H]#1 and rab-5[D135H]#2 heterozygotes as in CE. n 18 coelomocytes from at least five animals per genotype. Allele designations for independent edits (#1, #2) are in SI Appendix, Table S2. Coelomocytes are very large professional cells specialized in endocytic uptake and thus, have large EE, facilitating analysis. ns, not significant. **P < 0.005; ***P < 0.001 determined by the MannWhitney U test.

We next assessed the effect of rab-5[D135H] on EE fusion by visualizing the size of EEs in coelomocytes using the marker 2xFYVE::GFP, which binds to phosphatidylinositol-3-phosphate (PI(3)P)-modified lipids on EEs (40, 41). rab-5(del) and control rab-5[D135D] heterozygous animals contained various stages of EEs, ranging from small-sized puncta to large ring-shaped structures (Fig. 3 C, D, and F), suggesting continuous endosomal trafficking in these animals. In contrast, EEs in rab-5[D135H] heterozygotes were all puncta sized and failed to mature into larger ring-shaped EEs (Fig. 3 E and F), presumably due to the dominant negative RAB-5 D135H disrupting EE fusion. We conclude that rab-5[D135H] is defective in EE fusion events, leading to multi-cell type defects in endocytic uptake and EE function. By extension, we suggest that RAB5B p.D136H produces a dominant negative RAB5B GTPase that disrupts EE fusion events. However, as humans have three RAB5 paralogs, there is likely additional biological complexity that arises from potential genetic redundancy and possible paralog-specific RAB5B function.

We next sought to connect the de novo dominant negative RAB5B p.D136H allele identified in the proband with ILD and features of a surfactant dysfunction disorder (Fig. 1). From the proband lung biopsy, fixed tissue was available for antibody staining; unfortunately, lung tissue was not available for transmission electron microscopy or western blotting. We first assessed whether RAB5B messenger RNA (mRNA) (as well as RAB5A and RAB5C) was expressed in normal infant lung AT2 cells, the site of surfactant synthesis, from the LungMAP human single-cell RNA sequencing (RNA-seq) dataset (42). The AT2 cell Uniform Manifold Approximation and Projection (UMAP) clusters from day-1 and 21-mo datasets were identified using marker genes SFTPB and SFTPC (SI Appendix, Figs. S5 and S6). For both day 1 and 21 mo, RAB5B, RAB5A, and RAB5C were all expressed in AT2 cells as well as other lung cell types (SI Appendix, Fig. S7), with RAB5A expression lower than RAB5B and RAB5C. Detection of RAB5B mRNA in these postnatal cells is consistent with the RAB5B p.D136H allele affecting AT2 cell function. We propose that RAB5B dysfunction leads to a defect in surfactant protein trafficking/processing, resulting in the childs ILD (Figs. 1D and 4A).

As an initial evaluation, we stained normal (transplant donor) and proband lung sections with an antibody that reacts with RAB5A, RAB5B, and RAB5C (pan-RAB5) together with an RAB5B-specific antibody (SI Appendix, SI Materials and Methods and Fig. S8 have assessment of the specificity of the RAB5 antibodies). The pan-RAB5 antibody stained both normal and proband lung tissue (Fig. 4 B and D), although immunofluorescent staining was more extensive in the proband due to AT2 cell hyperplasia (AT2 cells were identified by proSP-B, proSP-C, and ABCA3 immunostaining [SI Appendix, Figs. S13 and S14]). In contrast, while RAB5B-specific staining was observed in the normal lung, the fluorescent signal was significantly reduced in the probands lung tissue. Quantification indicated an 80% reduction in RAB5B staining in the proband vs. normal AT2 cells, while pan-RAB5 staining showed an 20% reduction in proband vs. normal lung (Fig. 4 C and D). In contrast, there was no obvious change in RAB5B staining in lung tissues and AT2 cells in patients with surfactant protein dysfunction disorders resulting from pathogenic variants in SFTPB, SFTPC, or ABCA3 (SI Appendix, Figs. S9S11 and S14; variants information is in SI Appendix, SI Materials and Methods), indicating that the reduction in RAB5B staining in the proband is not a consequence of a surfactant dysfunction disorder. The reduction in RAB5B staining in AT2 cells is consistent with the dominant negative RAB5B p.D136H allele contributing to the probands ILD.

Loss of RAB5B and mature SP-B and SP-C in the proband lung. Lung sections from normal donor and proband lung tissue are stained as indicated. (A) AT2 cell hyperplasia in the proband (hematoxylin and eosin). (B) Immunostaining for pan-RAB5 and RAB5B (SI Appendix, Figs. S13 and S14). Differential interference contrast (DIC) microscopy, together with staining, shows lung structure, with a pentagonal alveolar organization in the normal donor and hyperplastic disorganization in the proband. (C) Quantification of immunostaining from B. (D) Confocal microscopy images of single lung cells with pan-RAB5 and RAB5B antibodies showing colocalization in cytoplasmic puncta (arrows). (E) proSP-C and mature SP-C staining and (G) proSP-B and mature SP-B staining in single cells. (Scale bars: A and B, 20 m; D, E, and G, 5 m.) (F and H) Quantification of immunostaining from low-magnification staining for proSP-C, mature SP-C, proSP-B, and mature SP-B. (I and J) ABCA3 and mature SP-C staining and ABCA3 and mature SP-B staining, respectively, in individual cells. Images in A, B, D, E, G, I, and J are representative of n = 3 to 4 normal donor lungs. Nuclei were stained with 4,6-diamidino-2-phenylindole (DAPI). Shown in C, F, and H are plots of relative fluorescent intensity of cells from n = 4 to 6 images from each condition analyzed by the two-tailed Students t test. ns, not significant. ***P < 0.001.

The reduction of RAB5B staining in the proband could be because the dominant negative RAB5B variant leads to the degradation of RAB5B or leads to reduced GTP binding, resulting in diffuse cytoplasmic staining. To address this possibility in the absence of a suitable proband lung sample for western blot, we assessed the level of RAB-5 protein in C. elegans by western blotting employing an antiRAB-5 antibody preparation (43). The RAB-5 band was identified by its substantial knockdown following rab-5 RNA interference (RNAi) feeding and its molecular weight (SI Appendix, Fig. S3C). We found that the RAB-5 level was significantly reduced in rab-5[D135H] heterozygotes compared with control edit rab-5[D135D] heterozygotes, with a similar or slightly greater decrease relative to rab-5(del) heterozygotes (SI Appendix, Fig. S3 E and F). The decrease in RAB-5 level in variant heterozygotes, in contrast to deletion heterozygotes, is likely a result of protein degradation. Unfortunately, we were unable to evaluate the subcellular distribution of RAB-5 and RAB-5[D135H] as the antibody staining in the intestine of the wild type was not altered following rab-5 RNAi. This result may be due to cross-reaction with C. elegans proteins larger and/or smaller than RAB-5 observed in the western blot (Materials and Methods and SI Appendix, Fig. S3C). The C. elegans results with the RAB-5[D135H] heterozygous strains suggest that the reduced RAB5B staining in proband AT2 cells is, at least in part, due to protein degradation.

To more thoroughly investigate and provide insight into the possible disorder of surfactant dysfunction, we immunostained normal and proband lung sections for proSP-B or mature SP-B as well as proSP-C or mature SP-C (Fig. 4 EH and SI Appendix, Fig. S13; SI Appendix, Figs. S9S12 show assessment of the specificity of the surfactant protein antibodies). proSP-B and proSP-C staining signal intensity per cell was similar in normal and proband lung tissue, with more extensive staining in the proband lung due to AT2 cell hyperplasia. In contrast, the mature SP-B and SP-C staining signal was significantly reduced by 66% in the proband vs. normal AT2 cells. The presence of the precursor proteins but not the mature SP-B and SP-C indicates that there is a defect in trafficking/processing in the vesicular pathway for production of mature SP-B and SP-C. These results are consistent with the decreased levels of mature SP-B and SP-C causing a disorder of surfactant dysfunction and ILD in the proband.

ABCA3 is an ABC transporter family member that transports phospholipids into the lamellar body to generate the functional surfactant proteinlipid complex. ABCA3, like proSP-B and proSP-C, is synthesized in the ER and trafficked to the lamellar body, potentially by the same vesicular pathway used for the surfactant protein trafficking. To address this possibility, we stained normal donor and proband lung sections for ABCA3 (Fig. 4 I and J and SI Appendix, Figs. S12, S13, and S15). We observed the previously reported ring-like ABCA3 stained structures (44, 45), with similar intensity and organization, in both normal and proband AT2 cells, while mature SP-B and SP-C staining was significantly reduced only in the proband. The typical staining of ABCA3 in the proband suggests that ABCA3 is trafficked by a different pathway, at least at the level of RAB5, from the surfactant proteins proSP-B and proSP-C. Additionally, the staining showed that lamellar body organization, at least relative to the distribution of ABCA3 immunostaining, was similar in the proband and normal lung.

How might RAB5B function in the accumulation of mature SP-B and SP-C while not necessary for the accumulation of proSP-B and proSP-C? RAB5B and EEs have recently been found to have a noncanonical function in the regulated secretion pathways in mammalian mast cells and the Drosophila salivary gland (8, 9). RAB5B-associated EEs may similarly fuse with small sorting vesicles containing proSP-B and proSP-C in the surfactant secretion pathway. Alternatively, it is known that extracellular mature SP-B and SP-C are recycled by AT2 cells for repackaging into the lamellar body or trafficked to the lysosomes for degradation (46, 47), presumably through the canonical RAB5B-dependent endocytic pathway. If RAB5B and EEs have a noncanonical function in the regulated secretion pathway for surfactant, we predict that in normal lung, proSP-B and proSP-C would colocalize with RAB5B and EE marker EEA1, and that colocalization with EEA1 would be lost in the proband lung. In contrast, if RAB5B functions only in endocytic recycling/degradation of extracellular mature SP-B and SP-C, colocalization of RAB5B with proSP-B and proSP-C is not expected. Significantly, staining for RAB5B and for proSP-B or proSP-C showed colocalization in normal lung (Fig. 5A). Furthermore, proSP-B or proSP-C and EEA1 also showed colocalization in normal lung (Fig. 5 D and E). While proSP-B and proSP-C staining was similar between normal and proband AT2 cells, EEA1 staining was significantly reduced in the proband lung (Fig. 5 B and C), precluding assessment of colocalization in proband AT2 cells. Since EE localization of EEA1 is dependent on activated RAB5B, the decreased staining of EEA1 in the proband lung is likely due to the dominant negative RAB5B p.D136H. The colocalization of RAB5B with proSP-B and proSP-C, as well as of EEA1 with proSP-B and proSP-C in normal lung, is consistent with RAB5B-dependent fusion of nascent sorting vesicles containing proSP-B and proSP-C with EEs to form small sorting vesicles in the regulated surfactant secretion pathway.

Colocalization of proSP-B and proSP-C with RAB5B and EEA1 in donor AT2 cells. Tissue sections from normal donor lung were immunostained with antibodies for the indicated protein. (A) Colocalization of RAB5B and proSP-C or RAB5B and proSP-B (arrows) in single cells. (B) EEA1 staining. (Upper) Normal donor. (Lower) Proband. (Left) Low-power image; arrowheads indicate a subset of AT2 cells. (Right) Single-cell confocal micrographs are shown. (C) Quantification of EEA1 staining from low-power images in B. ***P < 0.001, two-tailed Students t test. (D and E) Normal donor lung EEA1 and proSP-C or mature SP-C and EEA1 with proSP-B or mature SP-B, respectively, in single cells. (F) Pan-RAB5, RAB5B, and mature SP-C in normal lung. Arrows in A, D, E, and F indicate colocalization of markers in cytoplasm. Images in A, B, D, E, and F are representative images of n = 3 to 4 normal donor lungs. Nuclei were stained with DAPI. Shown in C is the mean fluorescent intensity of immunostained cells from n = 4 images for each condition. (Scale bars: A, B, Right, D, E, and F, 5 m; B, Left, 20 m.)

We also examined canonical endocytic recycling of mature SP-B and SP-C. In normal lung, EEA1 colocalized with mature SP-B and SP-C (Fig. 5 D and E). Mature SP-C staining also showed colocalization with pan-RAB5 and RAB5B (Fig. 5F). These results suggest that RAB5B, as well as RAB5A and RAB5C, functions in endocytic recycling of extracellular mature surfactant proteins and is consistent with RAB5B and RAB5C being identified in the lamellar body proteome (48). A function in endocytic recycling of mature SP-B and SP-C (Fig. 5 DF) provides an explanation of why some RAB5B did not colocalize with proSP-B and proSP-C (Fig. 5A) in the regulated surfactant secretion pathway.

The above analysis suggests that RAB5B may specifically function in a noncanonical EE fusion event with proSP-B and proSP-Ccontaining nascent early sorting vesicles in surfactant trafficking/processing. Accordingly, we performed Rab5b-specific knockdown using short hairpin RNAs (shRNAs) in MLE-15 cells. The MLE-15 cell line has AT2 characteristics, was derived from a transgenic mouse with an SV40 transformed lung, and has previously been employed to investigate the processing of proSP-B (49) (SI Appendix, Fig. S16). For two different shRNAs, RAB5B protein, but not total RAB5 protein, was significantly knocked down (Fig. 6A and SI Appendix, Fig. S16). In a western blot assay to distinguish between precursor and processed SP-B, Rab5b shRNA knockdown did not result in a significant change in proSP-B compared with control shRNA treatment (Fig. 6). In contrast, Rab5b knockdown resulted in a significant reduction in the mature SP-B band (Fig. 6). The RAB5B-specific knockdown in MLE-15 cells recapitulates the failure to generate mature SP-B from proSP-B observed in the RAB5B p.D136H proband lung, likely due to an EE vesicular trafficking defect. Together, these results support that RAB5B has an essential function in the regulated secretion pathway for lung surfactant.

Rab5b knockdown in MLE-15 cells decreases mature SP-B production. MEL-15 cells were transduced with lentiviruses that express nontargeted control shRNA or Rab5b-specific shRNA sequences (shRNA1, shRNA2) after selection for 5 d in puromycin. (A) Western blot analysis of transduced MLE-15 cells using antibodies to detect RAB5B, pan-RAB5 (total RAB5), mature SP-B, proSP-B, and ACTIN. (B) Quantification of the western blot signal for RAB5B, total RAB5, mature SP-B, and proSP-B from MLE-15 cells transduced with control shRNA, Rab5b shRNA1, and Rab5b shRNA2 from four independent transductions. Multiple medians were compared using the KruskalWallis test followed by Dunns multiple comparison. ns, not significant. ***P < 0.001.

We present evidence that the de novo heterozygous RAB5B p.D136H variant results in a disorder of surfactant dysfunction. The p.D136H variant is not found in gnomAD, is bioinformatically predicted to be damaging, and based on crystal structure, resides in the fourth nucleotide binding domain of Rab/Ras family small GTPases. However, RAB5B is not a haplo-insufficient gene. Functional studies with the C. elegans ortholog demonstrated that the variant was damaging invivo, resulting from the production of a strong dominant negative gene product and providing a genetic mechanism for the de novo dominant presentation. Worm studies also showed that the variant was defective in endocytosis, was defective in heterotypic nascent endocytic/sorting vesicleEE fusion and/or homotypic EE fusion, and led to degradation of the RAB-5 protein. Defects in RAB5B and EEA1 in the proband as a result of the p.D136H variant were supported by histological analysis of the probands lung biopsy showing that RAB5B and EEA1 staining was significantly reduced. The reduction in RAB5B was shown not to be an effect of ILD, as it was not observed in other cases with pathogenic variants in known surfactant dysfunction disorder genes. Notably, proband lung staining revealed a disruption in the generation of mature SP-B and SP-C from proSP-B and proSP-C, respectively. Importantly, a requirement for RAB5B function in the production of mature SP-B was recapitulated in cell culture. Furthermore, in normal lung, RAB5B and EEA1 colocalized with proSP-B and proSP-C, indicating a role for RAB5B and EEs in normal surfactant biogenesis. This function appears to be unique to RAB5B, but not coexpressed paralogs RAB5A and RAB5C, in AT2 cells. RAB5 paralogspecific functions have been reported for other aspects of biology: for example, epidermal growth factor receptor (EGFR) trafficking (50), RAC GTPase-mediated cell motility (51), and hematopoietic stem and progenitor cell development (52).

The lung phenotype of the proband was less pronounced than that of infants with biallelic loss-of-function variants in SFTPB who present with lethal neonatal respiratory distress syndrome and more similar to patients with SFTPC dominant variants (10, 19, 20) who demonstrate variable age of ILD onset, severity, and progression. This difference suggests that in the RAB5B p.D136H heterozygous proband, there was partial production of mature surfactant protein B through the regulated surfactant secretion pathway, which was sufficient at birth but ultimately, inadequate and led to lung injury in early life. While this work provides evidence for a direct role of the RAB5B p.D136H variant in the trafficking/processing of SP-B and SP-C, it does not address the dysmorphic features or neurological phenotype of the proband. However, given the widespread expression including the brain (https://gtexportal.org/home/gene/RAB5B) and the recent finding that RAB5C functions in hematopoietic stem and progenitor cell development (52), RAB5B may have analogous paralog-specific functions in facial, digit, and/or neural development.

The production of mature SP-B and SP-C in AT2 cells by the regulated surfactant secretion pathway has been described (1216) (Fig. 7). We propose, as a refinement of this pathway, that the nascent sorting vesicles containing proSP-B or proSP-C undergo RAB5B-dependent fusion with EEs, which then mature into MVBs en route to lamellar bodies. This proposal is consistent with colocalization of proSP-B and proSP-C with RAB5B and EEA1, with subsequent acidification during vesicular progression through the regulated secretion pathway resulting in proteolytic processing to form mature SP-B and SP-C and with recent reports of Rab5 and EEs functioning in vesicular progression in mammalian mast cells and the Drosophila salivary glandregulated secretion pathways (8, 9). We further propose that in the proband lung, productive fusion of EEs with the nascent sorting vesicles containing proSP-B or proSP-C is disrupted because of the RAB5B p.D136H variant, resulting in a failure to traffic prosurfactant proteins to the MVBs/lamellar bodies (Fig. 7). In contrast, ABCA3 trafficking and formation of the ABCA3 compartment of the lamellar body appear to be normal in the proband. Thus, the failure to produce mature SP-B and SP-C is proposed to be a result of defective vesicular trafficking rather than a failure in protein processing per se. We note that while we observe a defect in the production of both mature SP-B and SP-C in the proband, SP-B function is needed for the generation of mature SP-C (17, 22, 53), so it is possible that only proSP-B trafficking is disrupted by the RAB5B D136H variant protein.

Potential role for RAB5B in the surfactant proteinregulated secretion pathway. A model showing the regulated secretion pathway for surfactant in AT2 cells. Surfactant protein precursors proSP-B and proSP-C are translated in the ER and trafficked to the Golgi, where they bud off as cargo in nascent sorting vesicles. We propose that RAB5B-associated EEs fuse with prosurfactant containing nascent sorting vesicles to form small sorting vesicles, which subsequently fuse with the MVB, and then progress to the lamellar body for maturation and storage. Acidification during vesicular trafficking results in processing of proSP-B and proSP-C to mature SP-B and SP-C in the MVB/lamellar body. We further propose that dominant negative RAB5B p.D136H in the proband led to aberrant EEs that were defective in productive fusion with prosurfactant containing nascent sorting vesicles to generate functional small sorting vesicles (indicated by red X). We speculate that aberrant EEs containing RAB5B D136H, potentially as arrested fusion intermediates with nascent sorting vesicles containing proSP-B or proSP-C, are degraded. Such a mechanism would provide an explanation for reduced RAB5B as well as reduced EEA1 and the significant reduction of mature SP-B and SP-C. It is unknown if proSP-B and proSP-C are trafficked in the same or separate vesicles.

The C. elegans experiments revealed that RAB-5 protein is degraded in rab-5[D135H] heterozygous animals. However, the gene dosage studies demonstrated that it is not the reduced levels of RAB-5 causing the heterozygous mutant phenotypes but the dominant negative poisonous D135H gene product, which requires three wild-type rab-5 copies to fully restore normal phenotypes. Instead, the degradation of RAB-5 is likely a secondary effect of the dominant negative protein. By extension, the significantly reduced RAB5B level in proband AT2 cells is likely due to protein degradation, a secondary effect of the dominant negative RAB5B p.D136H gene product. RAB5B D136H could be removed by a ubiquitin-mediated degradation process. Alternatively, aberrant EEs containing RAB5B D136H, possibly engaged in defective fusion with proSP-B or proSP-C containing nascent sorting vesicles, could be recognized as abnormal and removed through autophagy (54). This latter possibility is intriguing as it could also explain both the reduced levels of EEA1 and the ultimate fate of the surfactant proteins as well as why levels of proSP-B and proSP-C did not build up in proband AT2 cells when vesicular trafficking was disrupted.

A limitation of this work is that proband lung tissue samples for transmission electron microscopy to assess vesicular and lamellar body ultrastructure and for western blotting to assess processing of the endogenous surfactant proteins were not available. Mouse knock-in models of Rab5B p.D136H as well as Rab5B AT2 cell conditional knockout should allow testing of the model (Fig. 7) and assessment of whether the other phenotypes in the proband (e.g., neurological phenotypes) are also caused by the dominant negative RAB5B variant.

In summary, we have used modeling in C. elegans, knockdown studies in MLE-15 cells, and staining of proband lung tissue to provide evidence that the de novo heterozygous RAB5B p.D136H allele is a genetic mechanism causing surfactant dysfunction that was previously unknown. Currently, this is a single case, however, it is likely other RAB5B variants, especially dominant negative variants or compound heterozygous variants, may cause disease. We suggest that for infants and children with ILD consistent with a disorder of surfactant dysfunction in whom a pathogenic variant in the established surfactant disease genes is not found, the RAB5B locus be sequenced.

The SI Appendix has more details.

Written consent for genetic studies, for use of tissue for research, and to publish photographs was obtained from the probands parents. Genetic and tissue studies were approved by the institutional review boards (IRBs) at Washington University in St. Louis and Baylor College of Medicine. The UDN protocol, 15-HG-0130, was approved by the National Human Genome Research Institute IRB. Nondiseased control lungs were those donated but unsuitable for transplantation. Lung sections from individuals with disorders of surfactant dysfunction due to pathogenic variants in SFTPB, SFTPC, and ABCA3 were used for comparisons with the immunostaining from the proband. Parents provided written consent, and the study was approved by the IRB at Washington University School of Medicine in St. Louis.

C. elegans strains were cultured on standard nematode growth media seeded with OP50 Escherichia coli and grown at 20C (55). rab-5[D135H] heterozygous animals showed significant cold sensitivity, although they can be very slowly propagated at 15C; we, therefore, maintained all rab-5[D135H] and corresponding control strains at 22C and assayed them at 20C. Strains and alleles used in this study are listed in SI Appendix, Table S2.

Single-nucleotide changes were introduced by editing the VC2010 animals with CRISPR-Cas9 (56, 57) (SI Appendix, Table S3). A single-copy rab-5 transgene was integrated at Mos1 transposon insertion site ttTi5605 on chromosome II (II: 0.77cM) (58) through CRISPR-Cas9 using the self-excising cassette method (59). All CRISPR-edited strains were backcrossed at least twice.

Crawling assays were performed using the WormLab system (MBF Bioscience) for individual worm tracking and analysis. Age/stage-matched young adults were analyzed for locomotion and size (60). Assays for endocytosis were performed by crossing into various marker strains and tested in cross-progeny. Images were analyzed using LASX (Leica Microsystems) and Volocity (v6.3; Quorum Technologies).

Tissue sections were processed and immunostained using primary antibodies as in SI Appendix, Table S4. Images for lung sections were acquired using an epifluorescent or laser scanning confocal microscope and were then analyzed for fluorescent intensity in FIJI (61).

Control nontargeted (SHC002; Sigma-Aldrich) and mouse Rab5b-specific shRNAs (Sigma-Aldrich) (SI Appendix, Table S5) were used to produce lentivirus and transduce MLE-15 cells similar to the methods previously described (62).

Proteins from MLE-15 cells were separated onto 4 to 12% gradient polyacrylamide gels. Membranes were incubated with the primary and secondary antibodies in SI Appendix, Table S4. The density of bands was quantified relative to ACTIN in FIJI.

Statistical analysis was performed using GraphPad Prism (version 6.07). Differences between two groups were compared using the two-tailed Students t test or the MannWhitney U test. Multiple medians were compared using the KruskalWallis test followed by Dunns multiple comparison. P < 0.01 indicates statistically significant difference, unless otherwise stated. Box plots show the median, a box representing the first and third quartiles, and whiskers at the 5th and 95th percentiles.

All study data are included in the article and/or SI Appendix.

We thank Ping Yang and Barth Grant for their helpful discussions, Anne Spang for the antiRAB-5 antibody preparation, and the reviewers for helpful comments. Dr. R. Paul Guillerman assisted in reviewing and obtaining radiographic images. Research reported in this manuscript was supported by the NIH Common Fund through Office of Strategic Coordination/Office of the NIH Director Award U54 NS108251 (T.S. and Lila Solnica-Krezel) and Grant U01 HG007709. Funding was also provided by the St. Louis Childrens Hospital Foundation (G.A.S. and S.C.P.), the Childrens Discovery Institute (J.A.W.), the Barnes Jewish Hospital Foundation (S.L.B.), and NIH Grant R01 GM100756 (T.S.). Some strains were provided by the Caenorhabditis Genetics Center, which is funded by NIH Office of Research Infrastructure Programs Grant P40 OD010440. The LungMAP consortium and the LungMAP Data Coordinating Center Grants U01HL122642 and 1U01HL122638 are funded by the National Heart, Lung, and Blood Institute. The content of this manuscript is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.

Author contributions: H.H., S.C.P., S.L.B., and T.S. designed research; H.H., J.P., A.M., T.H., A.G.L., H.K., J.C., S.A.M., Z.D.D., and A.Z.H. performed research; U.D.N. contributed new reagents/analytic tools; H.H., J.P., D.R.S., N.A.H., D.A.S., L.C.B., H.D., D.M., J.A.R., A.M., A.G.L., H.K., J.C., A.R., S.A.M., Z.D.D., E.T., G.A.S., D.B., S.C.P., S.L.B., and T.S. analyzed data; and H.H., J.A.W., S.C.P., S.L.B., and T.S. wrote the paper.

Competing interest statement: The Department of Molecular and Human Genetics at Baylor College of Medicine receives revenue from clinical genetic testing conducted at Baylor Genetics Laboratories.

This article is a PNAS Direct Submission.

This article contains supporting information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.2105228119/-/DCSupplemental.

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A dominant negative variant of RAB5B disrupts maturation of surfactant protein B and surfactant protein C - pnas.org

Core data science skills are needed for all kinds of scientific research. While many excellent resources are available, putting together a skills training programme suitable for your research institute is a challenge. Interdisciplinary research programmes attract students and staff with a wide range of background knowledge and skills. Graduate students are funded by a hodgepodge of schemes with different training requirements and support. Training of postdocs and early career researchers can be neglected, and many struggle to build the skills they need to progress their research and careers. Students and staff alike can start any time of year, though there is often a cohort of new students each autumn.

We are leading a UKRI-funded programme called Ed-DaSH, developing new training workshop materials available to the whole research community. We are working with The Carpentries, an inclusive community teaching coding and data skills, whose pedagogical model of collaborative hands-on learning we have adopted in our workshops. The workshop topics include statistics, Fair (findability,accessibility,interoperability andreuse) principles of data management, and workflow management systems. Starting in autumn 2021, our institutes began using these new materials in core data science training programmes, focused initially on the PhD student intake but available to all staff and students.

What does your audience need to learn to fulfil their potential as researchers? Surveys are a good start, especially if these are short and easy to complete. For example, a survey of the MRC Human Genetics Units parent Institute of Genetics and Cancer regarding statistical training needs and support found high demand for both one-to-one training and workshops.

However, surveying can only capture what you ask about, and what people know they need right now. Future needs must also be looked after, especially for early career researchers. Observations from experts need to be factored in: what is the bleeding edge doing? We could observe a sea change towards workflow management systems in health and bioscience research and a lack of training to incorporate these into everyday usage.

What is your institute offering? And how is that related to the training needs youve identified? Your survey can tell you what training has helped in the past, and it is also helpful to collate existing post-training surveys. If training is offered via your institutes graduate research programme, is it open only to the students on that programme, or could it be made more widely available? We had a number of locally developed workshops, such as an introduction to our university computer cluster and an introduction to genome browsers, that were well received and in high demand.

What training and resources have other people developed that you can use? Dont waste time reinventing the wheel. Training material developed by others in the research community is often freely available, adaptable and high quality. Even better, academic research communities will generally welcome contributions and feedback.

We believe that to foster a living curriculum, it is worth letting go of some control over its content. Data science is in the fortunate position of having access to the open source Carpentries workshop material. We use lessons from the Software Carpentry and Data Carpentry suites, covering the basics of the Unix shell, Python and R.

Dont be afraid to adapt: we previously offered an internally developed genomics workshop, but we have replaced this with a more up-to-date Carpentries lesson. Lessons developed with the input of the wider research community are tested and updated by hundreds of instructors worldwide, making them easier to share across institutes. Our local Edinburgh Carpentries community facilitates collaboration.

Looking back at your training needs, what is missing? In our case, it was statistics, data management and workflow management systems that we felt most needed new material. If you have the capacity to begin right away and are interested in making your new material a community effort, talk to the Carpentries about their Incubator scheme, and take a look at their Curriculum Development Handbook. For funding, as well as UKRI, the Software Sustainability Institute generally and Elixirspecifically for biosciences may have relevant schemes.

When, where and how do you want to deliver your new training programme?

Data science is here for the long term, and your programme will need to evolve with changing needs. Collecting feedback and, more importantly, acting on it will keep your programme relevant and effective. Community-developed materials help to spread the burden of keeping your lessons current, and you can pay it forward by contributing fixes and updates based on your experiences.

Alison Meynert is a senior research fellow and bioinformatics analysis core manager in the MRC Human Genetics Unit, and Edward Wallace is a Sir Henry Dale fellow in the School of Biological Sciences, both at the University of Edinburgh.

If you found this interesting and want advice and insight from academics and university staff delivered directly to your inbox each week,sign up for theTHE Campusnewsletter.

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Core data science skills: filling the gaps with community developed workshops - Times Higher Education (THE)

In the last 10 years, developments in DNA analysis have completely revolutionized how we see the human past. Working with archaeologists, anthropologists, and language experts, weve discovered some mind-blowing stuff just in the last few years that have changed how we see our species.

Here is some of the coolest research on DNA from our human past from 2020 and 2021.

Related: 10 Unexpected Results Of The Genealogy DNA Craze

Before we started analyzing ancient DNA, we used to think that early human migrations were way simpler. But discoveries in the last few years have shown just how wrong we were. Were still learning how and when people first arrived in the Americas. In 2021, archaeologists in New Mexico found human footprints dating to 21,00023,000 years ago, pushing back the date for the colonization of the Americas by thousands of years!

Analysis of the DNA from native Australians has already shown that a group, referred to as the Y population, shares some common ancestry with native people living in the Amazon todaybut not Northern or Central America. A study published in 2021 uses one of the largest databases of South American DNA to work on this problem. They discovered that the ancestors of South Americans and Australians met and had children somewhere in East Asia before some of their descendants entered the Americas and traveled to the Amazon along the Pacific coastline. This would mean that humans entered the Americas from Asia at least twice.[1]

Genetic Consequences of the Transatlantic Slave Trade Part 1

DNA analysis has also helped us understand more about one of the darkest periods of recent human history. The Trans-Atlantic slave trade was the largest forced migration in history; 12.5 million people were transported in slave ships in just a few hundred years. New analysis using data from the 23&Me database has helped us understand more about how it played out.

What the researchers learned backs up historical records and reinforces what we know about the brutality of the slave trade. For example, people from what is now Senegal and Gambia were prayed upon by slave traders for centuries. But their descendants are massively under-represented in the USA today. This is probably due to the high mortality rates experienced in plantations. The study also shows geographical differences in how Africans mixed and married with other people. African descendants from Latin America, where enslaved Africans often had children with native people, tend to have fewer African descendants than people in North America, where there was more segregation.[2]

Neanderthal genes found in Africans

Were all familiar with the out-of-Africa theory: the idea that most non-Africans today are descended from a small group of people that left the continent around 60,00070,000 years ago. Along the way, those humans met other human groups like Neanderthals and Denisovans and had some babies.

Because all this mixing happened outside of Africa, previous studies assumed that Africans had no Neanderthal ancestry. Some geneticists even treat African DNA as a control sample when measuring how much Neanderthal or Denisovan ancestry other populations may have. But this study suggests that people also migrated back into Africa, bringing with them the Neanderthal genes and spreading them into the African gene pool through a process called gene flow.

As a result, the study suggests that we may have over-estimated the diversity of Neanderthal ancestry in non-African populations, basically meaning that all humans may have more or less the same amount of Neanderthal DNA. This study complements archaeological work around the Arabian peninsula published in 2021 that has shown just how many people would have moved across this region and back and forth between the Middle East and Africa, spreading genes and culture as they went.[3]

Worlds oldest family tree reconstructed from Stone Age tomb

The British Neolithic period is known for its large megaliths, cairns, and other stone structures, often featuring many people buried together. Until now, it has been unclear what relationship, if any, the human remains in a monument might have with each other. Now we know that they were probably family tombs. A study using data from 35 people buried together in a long cairn in Hazleton, UK, showed that they were five generations of a single extended family. Scientists have used the relationships between these individuals to recreate the worlds oldest family tree.

The reconstructed family tree shows a direct biological relationship between male members. One male skeleton appeared to be the father, grandfather, or great-grandfather of almost everyone else in the tomb. His children and grandchildren by two different women were buried with him. The two women and their children were actually buried in separate areas of the tomb, suggesting that the difference in lineages was recognized even after several generations.

Many of the female skeletons appeared to be from elsewhere and may have joined the family through marriage, coming to live with their male partners. This suggests that early Neolithic farmers practiced what we call female exomany, a system where women move in with their partners and where family identity is inherited from the father. This is much like how we often take on our fathers surname in the modern world. The burial also included several people who had no biological relationship with the rest of the family, leading researchers to suggest that people could become family through different kinds of connections, such as adopting step-children.[4]

Reaction to News Story about Transeurasion Languages Origin Theories

This study combines genetics with linguistics. The spread of language families across the globe is another area of study that works with archaeology and history, often with confusing and contradictory results.

The Transeurasian language family covers the whole Asian continent and includes Japanese, Mongolian, and Turkish. The spread of languages over such a large area has been hotly contested by scholars who cannot agree whether the language was spread by farmers, pastoralists, or Bronze Age migrations.

Scientists used ancient DNA, language study, and archaeological remains to find a solution. The study concluded that the homeland of the Transeurasian language family can be traced back to early millet farmers in northeast Asia. It then spread out in two phases. The first phase involved the gradual expansion of millet farmers into new territory, bringing their language with them. Transeurasian people then split into five daughter groups after the late Neolithic and intermingled with other Eurasian peoples, exchanging partners and linguistic terms and learning new subsistence techniques like wheat farming.[5]

Polynesian Origins: DNA, Migrations and History

Like the Americas, the way that humans settled Polynesia is a controversial subject. Remember that this is an island region that spreads across the biggest ocean in the world, and people were moving from place to place in open canoes. For a long time, scientists couldnt agree on whether Polynesia was settled by South Americans or Australasians, or both!

This study used the genomes of 430 modern people from 21 islands. They found that the settlement of Polynesia started around the 11th century from Samoa, where people spread eastward, perhaps colonizing islands that had only existed for a few hundred years. They finally arrived at Easter Island around the year 1200. They would have made the trip in small groups, less than 200 people at a time, navigating using the stars and leaving behind them the huge statues that Easter Island is famous for today.[6]

Denisovan DNA In The Philippines

Reading this list, you can see how ancient DNA has shown us how complex and full of surprises ancient human migrations were. The Denisovans were first discovered in a cave in Siberia back in 2010. When their genome was compared with people alive today, we found out they share the most common ancestry with people living in modern Southeast Asia!

This study builds on previous work and concludes that a native group called the Ayta Magbukon, who live in what is now the Northern Philippines has the most Denisovan DNA, up to 5% of their genome! The scientists conclude that Denisovans must have been present in the islands of Southeast Asia at least 50,000 years ago.

The Philippines are beginning to get a lot of attention. In 2019 researchers also announced the discovery of a new species of small hominid, Homo luzonensis, that lived in the north of the islands around 60,000 years ago. It now looks like the Philippines and the rest of Southeast Asia were busy places back in the day, with lots of different types of humans living in the same area and meeting each other.[7]

Ancient Coronavirus Infected Ancestors of East Asians

You thought coronavirus was new? Ancient viruses can leave a mark on our DNA that can be analyzed by researchers. The scientists in this study found that humans have been dealing with variants of the coronavirus since the Stone Age! They also support previous research that suggests that intermixing with Neanderthals made Europeans more vulnerable to the coronavirus.

The earliest corona epidemic emerged in East Asia around 20,000 years or 900 human generations ago. It lasted several generations, long enough to create what scientists call a selective pressure on humans. The first strain was probably more dangerous than the modern Covid-19 variant, becoming less deadly over time. Although the researchers note that it doesnt appear to have made modern East Asians any more or less vulnerable to the virus, evolutionary medicine, as this field is called, may still be useful in helping us find cures or fight future outbreaks.[8]

Earliest modern humans in Europe were in Bacho Kiro 45,000 years ago

As youve probably realized by now, ancient DNA has thrown up a few surprises as we discover how complicated human movements actually are. It can also give some real darn confusing results. For example, two recent papers analyzed the genome of people living in Bacho Kiro cave in Bulgaria around 45,00042,000 years ago. These skeletons are also the oldest Homo sapiens remains in Europe.

Researchers found that these people had Neanderthal ancestors just a few generations back, suggesting that hooking up with our Neanderthal neighbors was probably pretty common. Scientists then compared the Bacho Kiro genomes with people alive today to see what modern populations they might be related to. Surprisingly, they found out that they were the ancestors of Native Americans and East Asians. The paper also found that human remains from the same site but dating to a later part of the Paleolithic were more closely related to modern Europeans, showing that populations were always mixing and moving.[1]

Head Lice on South American Mummies Shed Light on Ancient Virus Spread

Although it doesnt tell us anything new about the human past per se, we just couldnt help including this delightful bit of news about how human DNA might be analyzed in the future, Jurassic Park style. Apparently, human DNA can be preserved in the cement that head-lice use to glue their eggs to our hair! The scientists behind this technique sampled the hair from Argentinian mummies that died 1,5002,000 years ago. Can you imagine going through an ancient mummys hair with a nit-comb?

As well as being revolutionary (and maybe just a little bit gross), this technique may be a more sustainable way of extracting ancient human DNA. Current techniques which extract DNA from bones or teeth actually destroy the original sample. So obviously, many archaeologists are reluctant to conduct DNA analysis on their rarer specimens. This technique could also represent a way of sampling DNA from countries that might be reluctant to allow Western scientists to export human remains.[10]

fact checked by Darci Heikkinen

Continued here:
10 Awesome New Discoveries About the Human Past from DNA - nation.lk - The Nation Newspaper

The Genetics Society of America (GSA)selected former Princeton University President Shirley M. Tilghman as the 2022 winner of the George W. Beadle Award for outstanding contributions to the community of genetics researchers.

The award citation lauded Tilghman's "exemplary contributions to the genetics community and society with service on the National Advisory Council for the Human Genome Project Initiative and advocacy for transparent, equitable policies, openness in data sharing and publicly available databases, and sustainable funding policies. The award also recognizes pioneering contributions to mammalian imprinting."

I am deeply grateful to the Genetics Society of America, and my colleagues who nominated me for this wonderful honor, said Tilghman, who is an emerita professor of molecular biology and public affairs in addition to having served as University president from 2001 to 2013. Having an award named after one of the 20thcenturys greatest geneticists is truly meaningful to me.

A native of Canada, Tilghman received her Honors B.Sc. in chemistry from Queens University in Kingston, Ontario, in 1968. After two years of secondary school teaching in Sierra Leone, West Africa, she obtained her Ph.D. in biochemistry from Temple University in Philadelphia.

Tilghman came to Princeton in 1986 as the Howard A. Prior Professor of the Life Sciences. In 1998, she became the founding director of Princetons Lewis-Sigler Institute for Integrative Genomics. She was a member of the National Research Councils committee that set the blueprint for the U.S. effort in the Human Genome Project, as well as one of the founding members of the National Advisory Council of the Human Genome Project for the National Institutes of Health.

She is renowned not only for her pioneering research, but for her national leadership on behalf of women in science and for promoting efforts to make the early careers of young scientists as meaningful and productive as possible.

Her other awards and honors include being named a Howard Hughes Medical Institute Investigator in 1988, winning the LOral-UNESCO Award for Women in Science in 2002, receiving the Lifetime Achievement Award from the Society for Developmental Biology in 2003 and receiving the GSA Medal in 2007. She is a member of the American Philosophical Society, the National Academy of Sciences, the Institute of Medicine and the Royal Society of London.

The Beadle Award is awarded annually to someone who the GSA determines has contributed to the genetics community beyond an exemplary research career, for example by creating an invaluable technique or tool, helping the community adopt a model system, being a voice for the community in public or political forums, or maintaining active leadership roles. GSA established the award in 1999 in honor of George W. Beadle (1903-1989), an outstanding scientist and a respected academic and public servant who won the 1958 Nobel Prize in Physiology or Medicine.

Tilghman and the recipients of the GSA's other awards will present their work in a lecture series to be held online during 2022.

Read the rest here:
Shirley Tilghman wins award for 'exemplary contributions to the genetics community and society' - Princeton University

Assessment of viable retinal cells is made by combining the information derived from the clinical assessment including BCVA, OCT, visual field assessment, visual electrophysiology (including full field scotopic threshold testing and patient reported outcomes). The assessment will include a combination of all the investigations, and this will vary from patient to patient.

IRD management is similar to other complex conditions. The management around this process is critical to ensure that patients receive the appropriate ophthalmic and genetic advice.56-58Patients are best managed in a multi-disciplinary clinic with ophthalmologists experienced in IRD diagnostic steps and management, and with access to clinical geneticists and genetic counsellor expertise

The four steps outlined in this review will lead to improved patient care with streamlined ophthalmic diagnosis, molecular diagnosis and counselling, management of visual dysfunction and preparation for clinical trials and therapies.

The complexity of IRDs requires input from both ophthalmology and clinical genetics.44 The benefits of modern genetic diagnostics and counselling supports the introduction of equitable genetic testing for patients with presumed genetically-caused retinal diseases.5

NOTE: Some of the material has been adapted from the RANZCO Guidelines for the assessment and management of patients with inherited retinal diseases, which Profs Grigg and Jamieson co-authored with seven other experts.

References

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3. Hanany M, Rivolta C, Sharon D. Worldwide carrier frequency and genetic prevalence of autosomal recessive inherited retinal diseases. Proc Natl Acad Sci U S A 2020; 117: 2710-6.

4. Liew G, Michaelides M, Bunce C. A comparison of the causes of blindness certifications in England and Wales in working age adults (16-64 years), 1999-2000 with 2009-2010. BMJ open 2014; 4: e004015.

5. Holtan JP, Selmer KK, Heimdal KR et al. Inherited retinal disease in Norway a characterization of current clinical and genetic knowledge. Acta Ophthalmol 2019.

6. Thompson DA, Ali RR, Banin E et al. Advancing therapeutic strategies for inherited retinal degeneration: recommendations from the Monaciano Symposium. Investigative Ophthalmology & Visual Science 2015; 56: 918-31.

7. Schieppati A, Henter JI, Daina E et al. Why rare diseases are an important medical and social issue. Lancet 2008; 371: 2039-41.

8. Walker CE, Mahede T, Davis G et al. The collective impact of rare diseases in Western Australia: an estimate using a population-based cohort. Genet Med 2017; 19: 546-52.

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10. Khachatryan N, Pistilli M, Maguire MG et al. A Review of Studies of the Association of Vision-Related Quality of Life with Measures of Visual Function and Structure in Patients with Glaucoma in the United States. Ophthalmic Epidemiol 2021; 28: 265-76.

11. Halioua-Haubold C-L, Jolly JK, Smith JA et al. Potential lifetime quality of life benefits of choroideremia gene therapy: projections from a clinically informed decision model. Eye 2019; 33: 1215-23.

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13. Russell S, Bennett J, Wellman JA et al. Efficacy and safety of voretigene neparvovec (AAV2-hRPE65v2) in patients with RPE65-mediated inherited retinal dystrophy: a randomised, controlled, open-label, phase 3 trial. Lancet 2017; 390: 849-60.

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15. Lee YJ, Joo K, Seong MW et al. Congenital Stationary Night Blindness due to Novel TRPM1 Gene Mutations in a Korean Patient. Korean J Ophthalmol 2020; 34: 170-2.

16. Grigg J, Jamieson R, Chen F et al. Guidelines for the assessment and management of patients with inherited retinal diseases (IRD) 2020: 1-14.

17. Quality of Care Secretariat Hoskins Center for Quality Eye Care. Recommendations on Clinical Assessment of Patients with Inherited Retinal Degenerations [Internet]. San Francisco: American Academy of Ophthalmology; 2016 [cited 2021 Dec 7]. Available from: https://www.aao.org/clinical-statement/recommendations-on-clinical-assessment-of-patients.

18. Gill JS, Georgiou M, Kalitzeos A et al. Progressive cone and cone-rod dystrophies: clinical features, molecular genetics and prospects for therapy. Br J Ophthalmol 2019; 24: 24.

19. Verbakel SK, van Huet RAC, Boon CJF et al. Non-syndromic retinitis pigmentosa. Progress in Retinal & Eye Research 2018; 66: 157-86.

20. Kumaran N, Moore AT, Weleber RG et al. Leber congenital amaurosis/early-onset severe retinal dystrophy: clinical features, molecular genetics and therapeutic interventions. Br J Ophthalmol 2017; 101: 1147-54.

21. Na KH, Kim HJ, Kim KH et al. Prevalence, Age at Diagnosis, Mortality, and Cause of Death in Retinitis Pigmentosa in Korea-A Nationwide Population-based Study. Am J Ophthalmol 2017; 176: 157-65.

22. Prokudin I, Li D, He S et al. Value of whole exome sequencing for syndromic retinal dystrophy diagnosis in young patients. Clin Experiment Ophthalmol 2014; 43: 132-8.

23. Stone EM, Andorf JL, Whitmore SS et al. Clinically Focused Molecular Investigation of 1000 Consecutive Families with Inherited Retinal Disease. Ophthalmology 2017; 124: 1314-31.

24. Hafler BP. Clinical Progress in Inherited Retinal Degenerations: Gene Therapy Clinical Trials and Advances in Genetic Sequencing. Retina 2017; 37: 417-23.

25. Thompson JA, De Roach JN, McLaren TL et al. The genetic profile of Leber congenital amaurosis in an Australian cohort. Molecular genetics & genomic medicine 2017; 5: 652-67.

26. Stone EM, Aldave AJ, Drack AV et al. Recommendations for genetic testing of inherited eye diseases: report of the American Academy of Ophthalmology task force on genetic testing. Ophthalmology 2012; 119: 2408-10.

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28. Barwell J, Snape K, Wedderburn S. The new genomic medicine service and implications for patients. Clinical Medicine 2019; 19: 273-7.

29. Flannery DB. Challenges and opportunities for effective delivery of clinical genetic services in the U.S. healthcare system. Current Opinion in Pediatrics 2018; 30: 740-5.

30. Murray A, Jain V. Clinical genetics: a guide to a career in the specialty. Bmj 2015; 350: h2532.

31. James C, Worthington S, Colley A. The Genetic Counseling WorkplaceAn Australasian Perspective. A National Study of Workplace Issues for Genetic Counselors and Associate Genetic Counselors. J Genet Couns 2003; 12: 439-56.

32. BarlowStewart K, Dunlop KL, Fleischer R et al. The NSW Genetic Counselling Workforce: Background information paper an evidence check rapid review brokered by the Sax Institute for the Centre for the NSW Ministry of Health [Internet]. Sydney: Sax Institute for the NSW Ministry of Health; 2015 [cited 2021 Dec 7]. Available from: https://www.saxinstitute.org.au/wp-content/uploads/The-NSW-Genetic-Counselling-Workforce_June2016.pdf.

33. Dwarte T, Barlow-Stewart K, OShea R et al. Role and practice evolution for genetic counseling in the genomic era: The experience of Australian and UK genetics practitioners. J Genet Couns 2019; 28: 378-87.

34. Braverman G, Shapiro ZE, Bernstein JA. Ethical Issues in Contemporary Clinical Genetics. Mayo Clin Proc Innov Qual Outcomes 2018; 2: 81-90.

35. Richards S, Aziz N, Bale S et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med 2015; 17: 405-24.

36. Gonzalez-Cordero A, Kruczek K, Naeem A et al. Recapitulation of Human Retinal Development from Human Pluripotent Stem Cells Generates Transplantable Populations of Cone Photoreceptors. Stem Cell Reports 2017; 9: 820-37.

37. Aghaizu ND, Kruczek K, Gonzalez-Cordero A et al. Pluripotent stem cells and their utility in treating photoreceptor degenerations. Prog Brain Res 2017; 231: 191-223.

38. Chen FK, McLenachan S, Edel M et al. iPS Cells for Modelling and Treatment of Retinal Diseases. Journal of Clinical Medicine 2014; 3: 1511-41.

39. Gonzalez-Cordero A, West EL, Pearson RA et al. Photoreceptor precursors derived from three-dimensional embryonic stem cell cultures integrate and mature within adult degenerate retina. Nat biotechnol 2013; 31: 741-7.

40. Bobba S, Di Girolamo N, Munsie M et al. The current state of stem cell therapy for ocular disease. Exp Eye Res 2018; 177: 65-75.

41. Guo Y, Wang P, Ma JH et al. Modeling Retinitis Pigmentosa: Retinal Organoids Generated From the iPSCs of a Patient With the USH2A Mutation Show Early Developmental Abnormalities. Front Cell Neurosci 2019; 13: 361.

42. Hung SSC, McCaughey T, Swann O et al. Genome engineering in ophthalmology: Application of CRISPR/Cas to the treatment of eye disease. Progress in Retinal & Eye Research 2016; 53: 1-20.

43. Wynn J, Lewis K, Amendola LM et al. Clinical providers experiences with returning results from genomic sequencing: an interview study. BMC Med Genomics 2018; 11: 45.

44. Moore T, Burton H. Genetic Ophthalmology in Focus: A Needs Assessment and Review of Specialist Services for Genetic Eye Disorders [Internet]. Cambridge: PHG Foundation; 2011. Available from: https://phgfoundation.org/media/188/download/ophthalmology_in_focus_summary.pdf?v=1&inline=1.

45. Ramsden SC, OGrady A, Fletcher T et al. A clinical molecular genetic service for United Kingdom families with choroideraemia. European journal of medical genetics 2013; 56: 432-8.

46. Sergouniotis PI. Inherited Retinal Disorders: Using Evidence as a Driver for Implementation. Ophthalmologica Journal international dophtalmologie International journal of ophthalmology Zeitschrift fur Augenheilkunde 2019: 1-8.

47. Lee JJY, van Karnebeek CDM, Wasserman WW. Development and user evaluation of a rare disease gene prioritization workflow based on cognitive ergonomics. J Am Med Inform Assoc 2019; 26: 124-33.

48. Kumaran N, Rubin GS, Kalitzeos A et al. A Cross-Sectional and Longitudinal Study of Retinal Sensitivity in RPE65-Associated Leber Congenital Amaurosis. Investigative Ophthalmology & Visual Science 2018; 59: 3330-9.

49. Jacobson SG, Cideciyan AV, Sumaroka A et al. Outcome Measures for Clinical Trials of Leber Congenital Amaurosis Caused by the Intronic Mutation in the CEP290 GeneCEP290-LCA Outcomes. Investigative Ophthalmology & Visual Science 2017; 58: 2609-22.

50. Aleman TS, Han G, Serrano LW et al. Natural History of the Central Structural Abnormalities in Choroideremia: A Prospective Cross-Sectional Study. Ophthalmology 2017; 124: 359-73.

51. Strauss RW, Ho A, Munoz B et al. The Natural History of the Progression of Atrophy Secondary to Stargardt Disease (ProgStar) Studies: Design and Baseline Characteristics: ProgStar Report No. 1. Ophthalmology 2016; 123: 817-28.

52. Scholl, H.P.N. The natural history of the progression of atrophy secondary to stargardt disease (ProgStar) studies: Design and Baseline characteristics: Progstar Report No. 1. Ophthalmology 2016; 123: 817-28.

53. Lenassi E, Saihan Z, Cipriani V et al. Natural history and retinal structure in patients with Usher syndrome type 1 owing to MYO7A mutation. Ophthalmology 2014; 121: 580-7.

54. Fujinami K, Lois N, Davidson AE et al. A longitudinal study of stargardt disease: clinical and electrophysiologic assessment, progression, and genotype correlations. Am J Ophthalmol 2013; 155: 1075-88.e13.

55. Shaberman B, Durham T. The Foundation Fighting Blindness Plays an Essential and Expansive Role in Driving Genetic Research for Inherited Retinal Diseases. Genes (Basel) 2019; 10: 06.

56. Thorogood A, Dalp G, Knoppers BM. Return of individual genomic research results: are laws and policies keeping step? European Journal of Human Genetics 2019; 27: 535-46.

57. Eckstein L, Otlowski M. Strategies to Guide the Return of Genomic Research Findings: An Australian Perspective. J Bioeth Inq 2018; 15: 403-15.

58. Souzeau E, Burdon KP, Mackey DA et al. Ethical Considerations for the Return of Incidental Findings in Ophthalmic Genomic Research. Transl 2016; 5: 3.

59. Moore AT. Genetic Testing for Inherited Retinal Disease. Ophthalmology 2017; 124: 1254-5.

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Inherited retinal diseases the patient journey - Insight News

Four professors join the biological sciences, chemistry, Earth sciences, and quantitative and computational biology departments. [2 min read]

Clockwise from upper left, Laura Melissa Guzman, Jazlyn Mooney, Elias Picazo and Sam Silva are the newest USC Dornsife faculty members. (Photos: Courtesy of Guzman, Mooney, Picazo and Silva.)

A new cohort of faculty arrive at the USC Dornsife College of Letters, Arts and Sciences this spring, ready to tackle urgent problems, such as declining bee populations, invent new chemical reactions and untangle questions surrounding our genetics.

Laura Melissa Guzman| Gabilan Assistant Professor ofBiological Sciences

Academic Focus:In my research, I use quantitative and computational tools to learn about biodiversity and to inform potential conservation actions. Right now, Im working on modeling the distribution of native bees in North America and determining whether native bees have been declining across the continent. Im also identifying potential causes of that decline.

What do you like to do in your spare time? I am an avid fan of fiber arts. I love crocheting, cross-stitching, sewing, etc. I also love dog training; my dog and I do competitive dog sports.

Favorite book youve read lately? My Brilliant Friendseries by Elena Ferrante.

What food or condiments will we always find in your kitchen? Everything! I love cooking and have an overflowing pantry with every type of spice I can get my hands on.

Jazlyn Mooney| Assistant Professor ofQuantitative and Computational Biology

Academic Focus:My work focuses on deciphering a populations history using genomic data. Once we understand a populations history, we use that information to learn about variation in the genome and disease.

What do you like to do in your spare time?Look for vinyl (records), especially Japanese pressings of records.

If you could invite one person to dinner, living or dead, who would you select?What would be on the menu?Amy Winehouse, for New Mexican food.

Favorite book youve read lately? Sabriel by Garth Nix.

Elias Picazo | Assistant Professor ofChemistry

Academic Focus:Nearly 80% of new pharmaceuticals and most new materials are prepared synthetically. My group invents chemical reactions to enable the synthesis and characterization of novel pharmaceuticals and materials. We pay close attention to the abundance and toxicity profiles of the reactions chemical ingredients to improve pharmaceutical and material affordability, utility and application.

What do you like to do in your spare time?I like to exercise! I enjoy running.

If you could invite one person to dinner, living or dead, who would you select? What would be on the menu? My wife, for pizza Fridays.

What food or condiments will we always find in your kitchen?Fruit!

Sam Silva| Assistant Professor ofEarth Sciences

Academic Focus:My work is all about improving our understanding of air quality and climate change. I am specifically focused on studying the chemical composition of the atmosphere using computer modeling, data science and artificial intelligence techniques.

What do you like to do in your spare time?I have two kids under 2. That keeps me busy these days!

Where is your favorite place to travel?Tucson, Arizona. I love all things Sonoran Desert!

What food or condiments will we always find in your kitchen? Realistically? Mustard and a way-to-hot hot sauce that I ambitiously bought and cant actually handle.

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New faculty bring expertise in native bees, air quality, human genetics and chemical synthesis to USC Dornsife > News > USC Dornsife - USC...

SUNNYVALE, Calif., Jan. 27, 2022 (GLOBE NEWSWIRE) -- 23andMe Holding Co. (Nasdaq: ME) (23andMe), a leading consumer genetics and research company, announced today that it will report financial results for the fiscal year 2022 (FY2022) third quarter after the market closes on Thursday, February 10, 2022. The Company will webcast a conference call at 4:30 p.m. Eastern Time to discuss the quarters financial results and report on business progress.

The webcast can be accessed on the day of the event at https://investors.23andme.com/news-events/events-presentations. A webcast replay will be available at the same address for a limited time within 24 hours after the event.

In addition, 23andMe will use the Say Technologies platform to allow retail and institutional shareholders to submit and upvote questions to management. Starting today, shareholders can submit questions ahead of earnings by visiting https://app.saytechnologies.com/23andme-2022-q3. The Q&A platform will remain open until 24 hours before the earnings call.

About 23andMe23andMe, headquartered in Sunnyvale, CA, is a leading consumer genetics and research company. Founded in 2006, the Companys mission is to help people access, understand, and benefit from the human genome. 23andMe has pioneered direct access to genetic information as the only company with multiple FDA authorizations for genetic health risk reports. The Company has created the worlds largest crowdsourced platform for genetic research, with 80 percent of its customers electing to participate. The 23andMe research platform has generated more than 180 publications on the genetic underpinnings of a wide range of diseases, conditions, and traits. The platform also powers the 23andMe Therapeutics group, currently pursuing drug discovery programs rooted in human genetics across a spectrum of disease areas, including oncology, respiratory, and cardiovascular diseases, in addition to other therapeutic areas. More information is available at http://www.23andMe.com.

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Forward-Looking StatementsThis press release contains forward-looking statements within the meaning of Section 27A of the Securities Act of 1933, as amended, and Section 21E of the Securities Exchange Act of 1934, as amended, including statements regarding the future performance of 23andMes businesses in consumer genetics and therapeutics and the growth and potential of its proprietary research platform. All statements, other than statements of historical fact, included or incorporated in this press release, including statements regarding 23andMes strategy, financial position, funding for continued operations, cash reserves, projected costs, plans, and objectives of management, are forward-looking statements. The words "believes," "anticipates," "estimates," "plans," "expects," "intends," "may," "could," "should," "potential," "likely," "projects," "continue," "will," schedule, and "would" or, in each case, their negative or other variations or comparable terminology, are intended to identify forward-looking statements, although not all forward-looking statements contain these identifying words. These forward-looking statements are predictions based on 23andMes current expectations and projections about future events and various assumptions. 23andMe cannot guarantee that it will actually achieve the plans, intentions, or expectations disclosed in its forward-looking statements and you should not place undue reliance on 23andMes forward-looking statements. These forward-looking statements involve a number of risks, uncertainties (many of which are beyond the control of 23andMe), or other assumptions that may cause actual results or performance to be materially different from those expressed or implied by these forward-looking statements. The forward-looking statements contained herein are also 8-K filed with the Securities and Exchange Commission (SEC) on June 21, 2021 and in 23andMes Current Report on Form 10-Q filed with the SEC on November 10, 2021, as well as other filings made by 23andMe with the SEC from time to time. Investors are cautioned not to place undue reliance on any such forward-looking statements, which speak only as of the date they are made. Except as required by law, 23andMe does not undertake any obligation to update or revise any forward-looking statements whether as a result of new information, future events, or otherwise.

Investor Relations Contact: investors@23andMe.comMedia Contact: press@23andMe.com

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23andMe to Report FY2022 Third Quarter Financial Results - Yahoo Finance