Showing papers by "Wellcome Trust Centre for Human Genetics published in 2020"
TL;DR: Mendelian randomisation analysis supports causal roles for several HF risk factors, and demonstrates CAD-independent effects for atrial fibrillation, body mass index, and hypertension.
Abstract: Heart failure (HF) is a leading cause of morbidity and mortality worldwide. A small proportion of HF cases are attributable to monogenic cardiomyopathies and existing genome-wide association studies (GWAS) have yielded only limited insights, leaving the observed heritability of HF largely unexplained. We report results from a GWAS meta-analysis of HF comprising 47,309 cases and 930,014 controls. Twelve independent variants at 11 genomic loci are associated with HF, all of which demonstrate one or more associations with coronary artery disease (CAD), atrial fibrillation, or reduced left ventricular function, suggesting shared genetic aetiology. Functional analysis of non-CAD-associated loci implicate genes involved in cardiac development (MYOZ1, SYNPO2L), protein homoeostasis (BAG3), and cellular senescence (CDKN1A). Mendelian randomisation analysis supports causal roles for several HF risk factors, and demonstrates CAD-independent effects for atrial fibrillation, body mass index, and hypertension. These findings extend our knowledge of the pathways underlying HF and may inform new therapeutic strategies.
326 citations
TL;DR: A genome-wide association study including 133,384 breast cancer cases and 113,789 controls plus 18,908 BRCA1 mutation carriers of European ancestry provides an improved understanding of genetic predisposition to breast cancer subtypes and will inform the development of subtype-specific polygenic risk scores.
Abstract: Breast cancer susceptibility variants frequently show heterogeneity in associations by tumor subtype1-3. To identify novel loci, we performed a genome-wide association study including 133,384 breast cancer cases and 113,789 controls, plus 18,908 BRCA1 mutation carriers (9,414 with breast cancer) of European ancestry, using both standard and novel methodologies that account for underlying tumor heterogeneity by estrogen receptor, progesterone receptor and human epidermal growth factor receptor 2 status and tumor grade. We identified 32 novel susceptibility loci (P < 5.0 × 10-8), 15 of which showed evidence for associations with at least one tumor feature (false discovery rate < 0.05). Five loci showed associations (P < 0.05) in opposite directions between luminal and non-luminal subtypes. In silico analyses showed that these five loci contained cell-specific enhancers that differed between normal luminal and basal mammary cells. The genetic correlations between five intrinsic-like subtypes ranged from 0.35 to 0.80. The proportion of genome-wide chip heritability explained by all known susceptibility loci was 54.2% for luminal A-like disease and 37.6% for triple-negative disease. The odds ratios of polygenic risk scores, which included 330 variants, for the highest 1% of quantiles compared with middle quantiles were 5.63 and 3.02 for luminal A-like and triple-negative disease, respectively. These findings provide an improved understanding of genetic predisposition to breast cancer subtypes and will inform the development of subtype-specific polygenic risk scores.
190 citations
TL;DR: It is shown that the common genetic risk for Parkinson’s disease (PD) is associated with dopaminergic neuron (DaN)-specific gene expression, including mitochondrial functioning, protein folding and ubiquitination pathways.
Abstract: We describe a human single-nuclei transcriptomic atlas for the substantia nigra (SN), generated by sequencing approximately 17,000 nuclei from matched cortical and SN samples. We show that the common genetic risk for Parkinson’s disease (PD) is associated with dopaminergic neuron (DaN)-specific gene expression, including mitochondrial functioning, protein folding and ubiquitination pathways. We identify a distinct cell type association between PD risk and oligodendrocyte-specific gene expression. Unlike Alzheimer’s disease (AD), we find no association between PD risk and microglia or astrocytes, suggesting that neuroinflammation plays a less causal role in PD than AD. Beyond PD, we find associations between SN DaNs and GABAergic neuron gene expression and multiple neuropsychiatric disorders. Conditional analysis reveals that distinct neuropsychiatric disorders associate with distinct sets of neuron-specific genes but converge onto shared loci within oligodendrocytes and oligodendrocyte precursors. This atlas guides our aetiological understanding by associating SN cell type expression profiles with specific disease risk. The substantia nigra is important in neurological disease, particularly movement disorders. Here the authors provide a single cell transcriptomic atlas for the human substantia nigra.
141 citations
TL;DR: It is shown that, during homeostasis, the mouse and human meninges contain IgA-secreting plasma cells, which are essential for defending the central nervous system at this vulnerable venous barrier surface.
Abstract: The central nervous system has historically been viewed as an immune-privileged site, but recent data have shown that the meninges—the membranes that surround the brain and spinal cord—contain a diverse population of immune cells1. So far, studies have focused on macrophages and T cells, but have not included a detailed analysis of meningeal humoral immunity. Here we show that, during homeostasis, the mouse and human meninges contain IgA-secreting plasma cells. These cells are positioned adjacent to dural venous sinuses: regions of slow blood flow with fenestrations that can potentially permit blood-borne pathogens to access the brain2. Peri-sinus IgA plasma cells increased with age and following a breach of the intestinal barrier. Conversely, they were scarce in germ-free mice, but their presence was restored by gut re-colonization. B cell receptor sequencing confirmed that meningeal IgA+ cells originated in the intestine. Specific depletion of meningeal plasma cells or IgA deficiency resulted in reduced fungal entrapment in the peri-sinus region and increased spread into the brain following intravenous challenge, showing that meningeal IgA is essential for defending the central nervous system at this vulnerable venous barrier surface. IgA-secreting plasma cells that originate in the intestine are found in the meninges, where they protect the brain against pathogens.
129 citations
TL;DR: The induction of potent and polyclonal antibody responses by RBD-SpyVLP provides strong potential to address clinical and logistic challenges of the COVID-19 pandemic.
Abstract: There is dire need for an effective and affordable vaccine against SARS-CoV-2 to tackle the ongoing pandemic. In this study, we describe a modular virus-like particle vaccine candidate displaying the SARS-CoV-2 spike glycoprotein receptor-binding domain (RBD) using SpyTag/SpyCatcher technology (RBD-SpyVLP). Low doses of RBD-SpyVLP in a prime-boost regimen induced a strong neutralising antibody response in mice and pigs that was superior to convalescent human sera. We evaluated antibody quality using ACE2 blocking and neutralisation of cell infection by pseudovirus or wild-type SARS-CoV-2. Using competition assays with a monoclonal antibody panel, we showed that RBD-SpyVLP induced a polyclonal antibody response that recognised all key epitopes on the RBD, reducing the likelihood of selecting neutralisation-escape mutants. The induction of potent and polyclonal antibody responses by RBD-SpyVLP provides strong potential to address clinical and logistic challenges of the COVID-19 pandemic. Moreover, RBD-SpyVLP is highly resilient, thermostable and can be lyophilised without losing immunogenicity, to facilitate global distribution and reduce cold-chain dependence.
121 citations
TL;DR: The cost of genome sequencing is underestimated if only sequencing costs are considered, and likely surpasses $1000/genome in a single laboratory if consumable costs are considerably reduced and sequencing is performed at scale.
120 citations
TL;DR: This work genetically and structurally characterized β-propiolactone-inactivated viruses from a propagated and purified clinical strain of SARS-CoV-2 and observed that the virus particles are roughly spherical or moderately pleiomorphic, thus resembling a postfusion state.
119 citations
TL;DR: An unbiased atlas of human colonic CD8+ T cell phenotypes in health and ulcerative colitis is compiled using single-cell transcriptomics with T-cell receptor repertoire analysis and mass cytometry to identify and characterize terminally differentiated dysfunctional UC CD8 + T cells expressing IL-26.
Abstract: Colonic antigen-experienced lymphocytes such as tissue-resident memory CD8+ T cells can respond rapidly to repeated antigen exposure. However, their cellular phenotypes and the mechanisms by which they drive immune regulation and inflammation remain unclear. Here we compiled an unbiased atlas of human colonic CD8+ T cells in health and ulcerative colitis (UC) using single-cell transcriptomics with T-cell receptor repertoire analysis and mass cytometry. We reveal extensive heterogeneity in CD8+ T-cell composition, including expanded effector and post-effector terminally differentiated CD8+ T cells. While UC-associated CD8+ effector T cells can trigger tissue destruction and produce tumor necrosis factor (TNF)-α, post-effector cells acquire innate signatures to adopt regulatory functions that may mitigate excessive inflammation. Thus, we identify colonic CD8+ T-cell phenotypes in health and UC, define their clonal relationships and characterize terminally differentiated dysfunctional UC CD8+ T cells expressing IL-26, which attenuate acute colitis in a humanized IL-26 transgenic mouse model. Multimodal single-cell profiling reveals heterogeneity of colonic CD8+ T cells in patients with ulcerative colitis, including expansion of a chronically activated IL-26-expressing subpopulation with innate-like features.
104 citations
Broad Institute1, Harvard University2, Vanderbilt University3, University of Helsinki4, University of Mississippi Medical Center5, Technische Universität München6, University of Ottawa7, University of Oxford8, Wellcome Trust Centre for Human Genetics9, University of Vic10, University of Leicester11, Icahn School of Medicine at Mount Sinai12, University of Lübeck13, Wellcome Trust Sanger Institute14, University of Cambridge15, University of Pennsylvania16, Veterans Health Administration17, University of Texas Health Science Center at Houston18
TL;DR: A common missense variant in the Mitochondrial Amidoxime Reducing Component 1 gene (MARC1 p.A165T) that associates with protection from all-cause cirrhosis is identified suggesting that deficiency of the MARC1 enzyme may lower blood cholesterol levels and protect against Cirrhosis.
Abstract: Analyzing 12,361 all-cause cirrhosis cases and 790,095 controls from eight cohorts, we identify a common missense variant in the Mitochondrial Amidoxime Reducing Component 1 gene (MARC1 p.A165T) that associates with protection from all-cause cirrhosis (OR 0.91, p = 2.3*10-11). This same variant also associates with lower levels of hepatic fat on computed tomographic imaging and lower odds of physician-diagnosed fatty liver as well as lower blood levels of alanine transaminase (-0.025 SD, 3.7*10-43), alkaline phosphatase (-0.025 SD, 1.2*10-37), total cholesterol (-0.030 SD, p = 1.9*10-36) and LDL cholesterol (-0.027 SD, p = 5.1*10-30) levels. We identified a series of additional MARC1 alleles (low-frequency missense p.M187K and rare protein-truncating p.R200Ter) that also associated with lower cholesterol levels, liver enzyme levels and reduced risk of cirrhosis (0 cirrhosis cases for 238 R200Ter carriers versus 17,046 cases of cirrhosis among 759,027 non-carriers, p = 0.04) suggesting that deficiency of the MARC1 enzyme may lower blood cholesterol levels and protect against cirrhosis.
90 citations
TL;DR: It is shown that binding sites are widely dispersed, but neutralizing epitopes highly focused, in human monoclonal antibodies recognizing the viral spike, and by mapping antigenic sites using a unique computational methodology and comparing with inhibitory activity.
Abstract: Antibodies are crucial to immune protection against SARS-CoV-2 with some in emergency use as therapeutics. Here we identified 377 human monoclonal antibodies (mAbs) recognizing the viral spike, and focused on 80 which bind the receptor binding domain (RBD). By mapping antigenic sites using a unique computational methodology and comparing with inhibitory activity, we show that binding sites are widely dispersed, but neutralizing epitopes highly focused. Nearly all highly potent neutralizing mAbs (IC50< 0.1mg/ml) block receptor interaction, although one binds a unique epitope in the N-terminal domain. Many mAbs use public V-genes and are close to germline, boding well for vaccine responses. 19 Fab-antigen structures, some as RBD complexed with two Fabs, reveal two novel modes of engagement for potently inhibitory mAbs. Several Fabs are glycosylated, enhancing neutralisation for three, for two of which the sugar contacts the antigen. The most potent mAbs protect, prophylactically or therapeutically, in animal models.
Ethical Approval: Patients were recruited into the Sepsis Immunomics project [Oxford REC
C, reference:19/SC/0296] ISARIC/WHO Clinical Characterisation Protocol
for Severe Emerging Infections [Oxford REC C, reference 13/SC/0149].
Animal studies were carried out in accordance with the recommendations
in the Guide for the Care and Use of Laboratory Animals of the
National Institutes of Health. The protocols were approved by the
Institutional Animal Care and Use Committee at the Washington
University School of Medicine (assurance number A3381–01).
Funding: The Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Science (CIFMS), China (ID: 2018-I2M-2-002); Medical Research Council, UK. National Institute for Health Research Biomedical Research Centre Funding Scheme (to G.R.S.), the Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Science (CIFMS), China (grant number: 2018-I2M-2-002) to D.I.S. and G.R.S., and G.R.S. is supported as a Wellcome Trust Senior Investigator (grant 095541/A/11/Z). H.M.E.D. and J.Ren are supported by the Wellcome Trust (101122/Z/13/Z), Y.Z. by Cancer Research UK (C375/A17721) and D.I.S. by the UK Medical Research Council (MR/N00065X/1). D.I.S. and GRS are Jenner Investigators. N.M.K is supported by T32AI007172. The National Institute for Health Research Biomedical Research Centre Funding Scheme supports G.R.S. We are also grateful for a Fast Grant from Fast Grants, Mercatus Center to support the isolation of human monoclonal antibodies to SARS-2 and Schmidt Futures for support of this work. G.R.S. is also supported as a Wellcome Trust Senior Investigator (grant 095541/A/11/Z). This is a contribution from the UK Instruct-ERIC Centre. The Wellcome Centre for Human Genetics is supported by the Wellcome Trust (grant 090532/Z/09/Z). We acknowledge Diamond Light Source for time on Beamline I03 under Proposal lb27009 and for electron microscope time at the UK national electron bio-imaging centre (eBIC), Proposal BI26983. Computational aspects were supported by the Wellcome Trust Core Award Grant Number 203141/Z/16/Z and the NIHR Oxford BRC. This study was supported by grants from NIH (R01 AI157155) and the Defense Advanced Research Project Agency (HR001117S0019). J.B.C. is supported by a Helen Hay Whitney Foundation postdoctoral fellowship.
Competing Interest: M.S.D. is a consultant for Inbios, Vir Biotechnology, NGM
Biopharmaceuticals, Carnival Corporation and on the Scientific Advisory Boards of Moderna and Immunome. The M.S.D. laboratory has received unrelated funding support in sponsored research agreements from Moderna, Vir Biotechnology, and Emergent BioSolutions. GRS sits
on the GSK Vaccines Scientific Advisory Board.
78 citations
TL;DR: In this paper, the phase of a rotavirus and immature HIV-1 virus-like particles were recovered using phase contrast imaging at high defocus to improve information transfer at low spatial frequencies at the expense of higher spatial frequencies.
Abstract: Cryo-electron microscopy is an essential tool for high-resolution structural studies of biological systems. This method relies on the use of phase contrast imaging at high defocus to improve information transfer at low spatial frequencies at the expense of higher spatial frequencies. Here we demonstrate that electron ptychography can recover the phase of the specimen with continuous information transfer across a wide range of the spatial frequency spectrum, with improved transfer at lower spatial frequencies, and as such is more efficient for phase recovery than conventional phase contrast imaging. We further show that the method can be used to study frozen-hydrated specimens of rotavirus double-layered particles and HIV-1 virus-like particles under low-dose conditions (5.7 e/A2) and heterogeneous objects in an Adenovirus-infected cell over large fields of view (1.14 × 1.14 μm), thus making it suitable for studies of many biologically important structures. Cryo-electron microscopy is widely employed in structural biology and uses phase contrast imaging. Here, the authors employ electron ptychography, a quantitative phase retrieval method for high-contrast, low-dose phase imaging of cryo-state rotavirus and immature HIV-1 virus-like particles, and show that electron ptychography is more efficient for phase recovery than conventional phase contrast imaging.
University of Hong Kong1, Li Ka Shing Faculty of Medicine, University of Hong Kong2, University of North Carolina at Chapel Hill3, Johns Hopkins University4, University of Cambridge5, Monash University, Clayton campus6, Cancer Council Victoria7, University of Melbourne8, Laval University9, Karolinska Institutet10, The Cyprus Institute of Neurology and Genetics11, Netherlands Cancer Institute12, German Cancer Research Center13, University of Hamburg14, QIMR Berghofer Medical Research Institute15, American Cancer Society16, Fred Hutchinson Cancer Research Center17, University of Southern California18, University of Virginia19, Wellcome Trust Centre for Human Genetics20, University of Birmingham21, Brigham and Women's Hospital22, Harvard University23, University of Leeds24, French Institute of Health and Medical Research25, University of Western Australia26, Baylor College of Medicine27, Institute of Cancer Research28, University of California, San Francisco29, Umeå University30, Case Western Reserve University31, International Agency for Research on Cancer32, University of Utah33, Mayo Clinic34, Duke University35, Cedars-Sinai Medical Center36, University of Michigan37, Emory University38, Roswell Park Cancer Institute39, National Institutes of Health40, Yale University41, University of Texas MD Anderson Cancer Center42, Copenhagen University Hospital43, Technical University of Denmark44, University of Pennsylvania45
TL;DR: It is shown that PRS have potential for risk stratification for cancers of breast, colon and prostate, but less so for others because of modest heritability and lower incidence, and the utility of polygenic risk scores may vary depending on cancer type.
Abstract: Genome-wide association studies (GWAS) have led to the identification of hundreds of susceptibility loci across cancers, but the impact of further studies remains uncertain. Here we analyse summary-level data from GWAS of European ancestry across fourteen cancer sites to estimate the number of common susceptibility variants (polygenicity) and underlying effect-size distribution. All cancers show a high degree of polygenicity, involving at a minimum of thousands of loci. We project that sample sizes required to explain 80% of GWAS heritability vary from 60,000 cases for testicular to over 1,000,000 cases for lung cancer. The maximum relative risk achievable for subjects at the 99th risk percentile of underlying polygenic risk scores (PRS), compared to average risk, ranges from 12 for testicular to 2.5 for ovarian cancer. We show that PRS have potential for risk stratification for cancers of breast, colon and prostate, but less so for others because of modest heritability and lower incidence.
TL;DR: It is found that monoclonal antibody CR3022 binds the RBD tightly, neutralising SARS-CoV-2 and the crystal structure at 2.4 A of the Fab/RBD complex is reported, suggesting the highly conserved, structure-stabilising,CR3022 epitope is inaccessible in the prefusion Spike, suggesting that CR30 22 binding would facilitate conversion to the fusion-incompetent post-fusion state.
Abstract: There are as yet no licenced therapeutics for the COVID-19 pandemic. The causal coronavirus (SARS-CoV-2) binds host cells via a trimeric Spike whose receptor binding domain (RBD) recognizes angiotensin-converting enzyme 2 (ACE2), initiating conformational changes that drive membrane fusion. We find that monoclonal antibody CR3022 binds the RBD tightly, neutralising SARS-CoV-2 and report the crystal structure at 2.4 A of the Fab/RBD complex. Some crystals are suitable for screening for entry-blocking inhibitors. The highly conserved, structure-stabilising, CR3022 epitope is inaccessible in the prefusion Spike, suggesting that CR3022 binding would facilitate conversion to the fusion-incompetent post-fusion state. Cryo-EM analysis confirms that incubation of Spike with CR3022 Fab leads to destruction of the prefusion trimer. Presentation of this cryptic epitope in an RBD-based vaccine might advantageously focus immune responses. Binders at this epitope may be useful therapeutically, possibly in synergy with an antibody blocking receptor attachment.
Funding: This work was supported by a grant from the CAMS-Oxford Institute to D.I.S. E.E.F and J.Ren are supported by the Wellcome Trust (101122/Z/13/Z), Y.Z. by Cancer Research UK (C375/A17721) and D.I.S. and E.E.F. by the UK Medical Research Council (MR/N00065X/1). J.H. is supported by a grant from the EPA Cephalosporin Fund. PPUK is funded by the Rosalind Franklin Institute EPSRC Grant no. EP/S025243/1. The National Institute for Health Research Biomedical Research Centre Funding Scheme supports G.R.S. together with the Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Science (CIFMS), China (grant number: 2018-I2M-2-002), which also supports D.I.S. G.R.S. is also supported as a Wellcome Trust Senior Investigator (grant 095541/A/11/Z). T.M. is supported by Cancer Research UK grants C20724/A14414 and C20724/A26752 to Christian Siebold. This is a contribution from the UK Instruct-ERIC Centre. The Wellcome Centre for Human Genetics is supported by the Wellcome Trust (grant 090532/Z/09/Z). Virus used for the neutralisation assays was a gift from Julian Druce, Doherty Centre, Melbourne, Australia.
Conflict of Interest: The authors declare no competing interests.
TL;DR: This review will investigate the molecular processes of wound healing and scar tissue formation, the process of electrospinning, and examine how electrospun biomaterials can be utilized and adapted to wound repair in the hope of reducing Scar tissue formation and conferring an enhanced tensile strength of the skin.
Abstract: Electrospinning is a promising method for the rapid and cost-effective production of nanofibers from a wide variety of polymers given the high surface area morphology of these nanofibers, they make excellent wound dressings, and so have significant potential in the prevention and treatment of scars. Wound healing and the resulting scar formation are exceptionally well-characterized on a molecular and cellular level. Despite this, novel effective anti-scarring treatments which exploit this knowledge are still clinically absent. As the process of electrospinning can produce fibers from a variety of polymers, the treatment avenues for scars are vast, with therapeutic potential in choice of polymers, drug incorporation, and cell-seeded scaffolds. It is essential to show the new advances in this field; thus, this review will investigate the molecular processes of wound healing and scar tissue formation, the process of electrospinning, and examine how electrospun biomaterials can be utilized and adapted to wound repair in the hope of reducing scar tissue formation and conferring an enhanced tensile strength of the skin. Future directions of the research will explore potential novel electrospun treatments, such as gene therapies, as targets for enhanced tissue repair applications. With this class of biomaterial gaining such momentum and having such promise, it is necessary to refine our understanding of its process to be able to combine this technology with cutting-edge therapies to relieve the burden scars place on world healthcare systems.
TL;DR: It is suggested that IFITM3 oligomers inhibit virus-cell fusion by promoting membrane rigidity by driving protein oligomerization from within a GxxxG motif.
Abstract: The interferon-inducible transmembrane (IFITM) proteins belong to the Dispanin/CD225 family and inhibit diverse virus infections. IFITM3 reduces membrane fusion between cells and virions through a poorly characterized mechanism. Mutation of proline-rich transmembrane protein 2 (PRRT2), a regulator of neurotransmitter release, at glycine-305 was previously linked to paroxysmal neurological disorders in humans. Here, we show that glycine-305 and the homologous site in IFITM3, glycine-95, drive protein oligomerization from within a GxxxG motif. Mutation of glycine-95 (and to a lesser extent, glycine-91) disrupted IFITM3 oligomerization and reduced its antiviral activity against Influenza A virus. An oligomerization-defective variant was used to reveal that IFITM3 promotes membrane rigidity in a glycine-95-dependent and amphipathic helix-dependent manner. Furthermore, a compound which counteracts virus inhibition by IFITM3, Amphotericin B, prevented the IFITM3-mediated rigidification of membranes. Overall, these data suggest that IFITM3 oligomers inhibit virus-cell fusion by promoting membrane rigidity.
TL;DR: It is demonstrated that the epigenetic regulator CREBBP/EP300 is a critical determinant of the profibrotic phenotype, and collagen VI is identified to be a key downstream target of CRE BBP/ EP300 and reveal valuable insights in the role it plays in key profib Rotic functions, including contractile force, chemotaxis, and wound healing, and hence its potential as a therapeutic target.
Abstract: Fibrotic diseases remain a major cause of morbidity and mortality, yet there are few effective therapies. The underlying pathology of all fibrotic conditions is the activity of myofibroblasts. Using cells from freshly excised disease tissue from patients with Dupuytren's disease (DD), a localized fibrotic disorder of the palm, we sought to identify new therapeutic targets for fibrotic disease. We hypothesized that the persistent activity of myofibroblasts in fibrotic diseases might involve epigenetic modifications. Using a validated genetics-led target prioritization algorithm (Pi) of genome wide association studies (GWAS) data and a broad screen of epigenetic inhibitors, we found that the acetyltransferase CREBBP/EP300 is a major regulator of contractility and extracellular matrix production via control of H3K27 acetylation at the profibrotic genes, ACTA2 and COL1A1 Genomic analysis revealed that EP300 is highly enriched at enhancers associated with genes involved in multiple profibrotic pathways, and broad transcriptomic and proteomic profiling of CREBBP/EP300 inhibition by the chemical probe SGC-CBP30 identified collagen VI (Col VI) as a prominent downstream regulator of myofibroblast activity. Targeted Col VI knockdown results in significant decrease in profibrotic functions, including myofibroblast contractile force, extracellular matrix (ECM) production, chemotaxis, and wound healing. Further evidence for Col VI as a major determinant of fibrosis is its abundant expression within Dupuytren's nodules and also in the fibrotic foci of idiopathic pulmonary fibrosis (IPF). Thus, Col VI may represent a tractable therapeutic target across a range of fibrotic disorders.
TL;DR: This study provides a systematic characterisation of the specific immune environment in the peritoneal cavity and identifies cell immune signatures associated with endometriosis, suggesting that both the innate and the adaptive immune system play roles in endometRIosis.
Abstract: Endometriosis is a gynaecological condition characterised by immune cell infiltration and distinct inflammatory signatures found in the peritoneal cavity. In this study, we aim to characterise the immune microenvironment in samples isolated from the peritoneal cavity in patients with endometriosis. We applied mass cytometry (CyTOF), a recently developed multiparameter single-cell technique, in order to characterise and quantify the immune cells found in peritoneal fluid and peripheral blood from endometriosis and control patients. Our results demonstrate the presence of more than 40 different distinct immune cell types within the peritoneal cavity. This suggests that there is a complex and highly heterogeneous inflammatory microenvironment underpinning the pathology of endometriosis. Stratification by clinical disease stages reveals a dynamic spectrum of cell signatures suggesting that adaptations in the inflammatory system occur due to the severity of the disease. Notably, among the inflammatory microenvironment in peritoneal fluid (PF), the presence of CD69+ T cell subsets is increased in endometriosis when compared to control patient samples. On these CD69+ cells, the expression of markers associated with T cell function are reduced in PF samples compared to blood. Comparisons between CD69+ and CD69− populations reveal distinct phenotypes across peritoneal T cell lineages. Taken together, our results suggest that both the innate and the adaptive immune system play roles in endometriosis. This study provides a systematic characterisation of the specific immune environment in the peritoneal cavity and identifies cell immune signatures associated with endometriosis. Overall, our results provide novel insights into the specific cell phenotypes governing inflammation in patients with endometriosis. This prospective study offers a useful resource for understanding disease pathology and opportunities for identifying therapeutic targets.
TL;DR: In Chinese adults, both red meat and fish, but not poultry, intake were positively associated with diabetes risk, particularly among urban participants, adding new evidence linking red meat, poultry and fish intake with cardiometabolic diseases.
Abstract: Previous evidence linking red meat consumption with diabetes risk mainly came from western countries, with little evidence from China, where patterns of meat consumption are different. Moreover, global evidence remains inconclusive about the associations of poultry and fish consumption with diabetes. Therefore we investigated the associations of red meat, poultry and fish intake with incidence of diabetes in a Chinese population. The prospective China Kadoorie Biobank recruited ~512,000 adults (59% women, mean age 51 years) from ten rural and urban areas across China in 2004–2008. At the baseline survey, a validated interviewer-administered laptop-based questionnaire was used to collect information on the consumption frequency of major food groups including red meat, poultry, fish, fresh fruit and several others. During ~9 years of follow-up, 14,931 incidences of new-onset diabetes were recorded among 461,036 participants who had no prior diabetes, cardiovascular diseases or cancer at baseline. Cox regression analyses were performed to calculate adjusted HRs for incident diabetes associated with red meat, poultry and fish intake. At baseline, 47.0%, 1.3% and 8.9% of participants reported a regular consumption (i.e. ≥4 days/week) of red meat, poultry and fish, respectively. After adjusting for adiposity and other potential confounders, each 50 g/day increase in red meat and fish intake was associated with 11% (HR 1.11 [95% CI 1.04, 1.20]) and 6% (HR 1.06 [95% CI 1.00, 1.13]) higher risk of incident diabetes, respectively. For both, the associations were more pronounced among men and women from urban areas, with an HR (95% CI) of 1.42 (1.15, 1.74) and 1.18 (1.03, 1.36), respectively, per 50 g/day red meat intake and 1.15 (1.02, 1.30) and 1.11 (1.01, 1.23), respectively, per 50 g/day fish intake. There was no significant association between diabetes and poultry intake, either overall (HR 0.96 [95% CI 0.83, 1.12] per 50 g/day intake) or in specific population subgroups. In Chinese adults, both red meat and fish, but not poultry, intake were positively associated with diabetes risk, particularly among urban participants. Our findings add new evidence linking red meat and fish intake with cardiometabolic diseases. Details of how to access the China Kadoorie Biobank data and rules of China Kadoorie Biobank data release are available from www.ckbiobank.org/site/Data+Access.
10 Jan 2020
TL;DR: Cryo-electron tomography and sub-tomogram averaging are used to examine the structure of the core-signalling units of E. coli chemotaxis arrays at subnanometer resolution, finding multiple distinct conformations of the critical CheA kinase domain, offering new insights into CheA signalling.
Abstract: To enable the processing of chemical gradients, chemotactic bacteria possess large arrays of transmembrane chemoreceptors, the histidine kinase CheA, and the adaptor protein CheW, organized as coupled core-signaling units (CSU). Despite decades of study, important questions surrounding the molecular mechanisms of sensory signal transduction remain unresolved, owing especially to the lack of a high-resolution CSU structure. Here, we use cryo-electron tomography and sub-tomogram averaging to determine a structure of the Escherichia coli CSU at sub-nanometer resolution. Based on our experimental data, we use molecular simulations to construct an atomistic model of the CSU, enabling a detailed characterization of CheA conformational dynamics in its native structural context. We identify multiple, distinct conformations of the critical P4 domain as well as asymmetries in the localization of the P3 bundle, offering several novel insights into the CheA signaling mechanism.
TL;DR: Two independent RSPO3 signals that associate with body fat distribution are described, fine-mapping is performed and the function of RSPo3 is explored in human adipocyte biology and bodyfat distribution in zebrafish is identified.
Abstract: Fat distribution is an independent cardiometabolic risk factor. However, its molecular and cellular underpinnings remain obscure. Here we demonstrate that two independent GWAS signals at RSPO3, which are associated with increased body mass index-adjusted waist-to-hip ratio, act to specifically increase RSPO3 expression in subcutaneous adipocytes. These variants are also associated with reduced lower-body fat, enlarged gluteal adipocytes and insulin resistance. Based on human cellular studies RSPO3 may limit gluteofemoral adipose tissue (AT) expansion by suppressing adipogenesis and increasing gluteal adipocyte susceptibility to apoptosis. RSPO3 may also promote upper-body fat distribution by stimulating abdominal adipose progenitor (AP) proliferation. The distinct biological responses elicited by RSPO3 in abdominal versus gluteal APs in vitro are associated with differential changes in WNT signalling. Zebrafish carrying a nonsense rspo3 mutation display altered fat distribution. Our study identifies RSPO3 as an important determinant of peripheral AT storage capacity.
TL;DR: It is found that monoclonal antibody CR3022 binds the RBD tightly, neutralising SARS-CoV-2 and the crystal structure at 2.4 Å of the Fab/RBD complex is reported, suggesting this epitope may be useful therapeutically, possibly in synergy with an antibody blocking receptor attachment.
Abstract: Summary There are as yet no licenced therapeutics for the COVID-19 pandemic. The causal coronavirus (SARS-CoV-2) binds host cells via a trimeric Spike whose receptor binding domain (RBD) recognizes angiotensin-converting enzyme 2 (ACE2), initiating conformational changes that drive membrane fusion. We find that monoclonal antibody CR3022 binds the RBD tightly, neutralising SARS-CoV-2 and report the crystal structure at 2.4 A of the Fab/RBD complex. Some crystals are suitable for screening for entry-blocking inhibitors. The highly conserved, structure-stabilising, CR3022 epitope is inaccessible in the prefusion Spike, suggesting that CR3022 binding would facilitate conversion to the fusion-incompetent post-fusion state. Cryo-EM analysis confirms that incubation of Spike with CR3022 Fab leads to destruction of the prefusion trimer. Presentation of this cryptic epitope in an RBD-based vaccine might advantageously focus immune responses. Binders at this epitope may be useful therapeutically, possibly in synergy with an antibody blocking receptor attachment. Highlights CR3022 neutralises SARS-CoV-2 Neutralisation is by destroying the prefusion SPIKE conformation This antibody may have therapeutic potential alone or with one blocking receptor attachment
TL;DR: While the evolution of seroprevalence points to a high effectiveness of containment measures, the data highlight that antibody waning warrants a continuous seromonitoring to reliably estimate the prevalence in a population.
Abstract: Serological assays can detect anti-SARS-CoV-2 antibodies, but their sensitivity often comes at the expense of specificity. Here we developed a Tripartite Automated Blood Immunoassay (TRABI) to assess the IgG response against SARS-CoV-2. Calibration was performed with 90 prepandemic and 55 virologically and clinically confirmed COVID-19 samples. Posterior probabilities were calculated from 3x8 measurements of logarithmically diluted samples against the ectodomain and the receptor-binding domain of the spike protein and the nucleocapsid protein. We then performed 9489528 assays on 59503 prepandemic and 349019 copandemic samples from hospital patients and healthy blood donors. The seroprevalence increased in March 2020 (0.3%; CI95%: 0.1% - 0.5%) among hospital patients but plateaued in April at 1.1-1.3%, and dropped to 0.3-0.7% in July. A dynamic transmission model describing SARS-CoV-2 transmission and seroconversion in the general population of the Canton of Zurich yielded an infection fatality ratio of 0.6% (CI95%: 0.4%-0.8%), similarly to other European areas. While the evolution of seroprevalence points to a high effectiveness of containment measures, our data highlight that antibody waning warrants a continuous seromonitoring to reliably estimate the prevalence in a population.
Netherlands Cancer Institute1, Erasmus University Rotterdam2, University of Cambridge3, Leiden University Medical Center4, Technion – Israel Institute of Technology5, Lunenfeld-Tanenbaum Research Institute6, University of California, Irvine7, Queen's University8, Lund University9, University of Hamburg10, University of Erlangen-Nuremberg11, German Cancer Research Center12, Russian Academy of Sciences13, Hannover Medical School14, Copenhagen University Hospital15, European Institute of Oncology16, University of Tübingen17, National Institutes of Health18, QIMR Berghofer Medical Research Institute19, Seoul National University20, University of Sydney21, Erasmus University Medical Center22, Mayo Clinic23, University of Sheffield24, Karolinska Institutet25, Fox Chase Cancer Center26, University of London27, University of Westminster28, University of Southampton29, Manchester Academic Health Science Centre30, University of California, Los Angeles31, University of California, San Diego32, Hospital Clínico San Carlos33, University of Melbourne34, University of Utah35, University of Southern California36, National University of Singapore37, Kaohsiung Medical University Chung-Ho Memorial Hospital38, University of Manchester39, Nagoya University40, Laboratory of Molecular Biology41, Stanford University42, New Generation University College43, Oslo University Hospital44, University of Hong Kong45, Katholieke Universiteit Leuven46, University of Hawaii47, Genome Institute of Singapore48, Karolinska University Hospital49, Pomeranian Medical University50, University of Eastern Finland51, Ludwig Maximilian University of Munich52, University Health Network53, University of Helsinki54, Beckman Research Institute55, University of North Carolina at Chapel Hill56, King's College London57, University of Oulu58, University College Hospital59, University of Cologne60, The Breast Cancer Research Foundation61, Academia Sinica62, Vanderbilt University63, University of Twente64, University of British Columbia65, University of Western Australia66, Columbia University67, Wellcome Trust Centre for Human Genetics68
TL;DR: PRS313 is an independent factor associated with CBC risk and can be incorporated into CBC risk prediction models to help improve stratification and optimize surveillance and treatment strategies.
Abstract: Previous research has shown that polygenic risk scores (PRSs) can be used to stratify women according to their risk of developing primary invasive breast cancer. This study aimed to evaluate the association between a recently validated PRS of 313 germline variants (PRS313) and contralateral breast cancer (CBC) risk. We included 56,068 women of European ancestry diagnosed with first invasive breast cancer from 1990 onward with follow-up from the Breast Cancer Association Consortium. Metachronous CBC risk (N = 1,027) according to the distribution of PRS313 was quantified using Cox regression analyses. We assessed PRS313 interaction with age at first diagnosis, family history, morphology, ER status, PR status, and HER2 status, and (neo)adjuvant therapy. In studies of Asian women, with limited follow-up, CBC risk associated with PRS313 was assessed using logistic regression for 340 women with CBC compared with 12,133 women with unilateral breast cancer. Higher PRS313 was associated with increased CBC risk: hazard ratio per standard deviation (SD) = 1.25 (95%CI = 1.18-1.33) for Europeans, and an OR per SD = 1.15 (95%CI = 1.02-1.29) for Asians. The absolute lifetime risks of CBC, accounting for death as competing risk, were 12.4% for European women at the 10th percentile and 20.5% at the 90th percentile of PRS313. We found no evidence of confounding by or interaction with individual characteristics, characteristics of the primary tumor, or treatment. The C-index for the PRS313 alone was 0.563 (95%CI = 0.547-0.586). In conclusion, PRS313 is an independent factor associated with CBC risk and can be incorporated into CBC risk prediction models to help improve stratification and optimize surveillance and treatment strategies.
Wellcome Trust Sanger Institute1, University of Oxford2, Mahosot Hospital3, University of Health Sciences Antigua4, Harvard University5, Mahidol University6, National Institutes of Health7, Chittagong Medical College Hospital8, World Health Organization9, University of Kinshasa10, Aix-Marseille University11, Royal Society12, Midnapore College13, National Institute of Malaria Research14, Wellcome Trust Centre for Human Genetics15
TL;DR: GenRe-Mekong, a platform for genetic surveillance of malaria in the Greater Mekong Subregion, enables NMCPs to conduct large-scale surveillance project in endemic regions by integrating simple sample collection procedures in the routine operations of public health facilities.
Abstract: The use of parasite genetic data by National Malaria Control Programmes (NMCPs) is currently limited, and typically focused on specific genetic features or a small number of study sites. We have developed GenRe-Mekong, a platform for genetic surveillance of malaria in the Greater Mekong Subregion (GMS). By integrating simple sample collection procedures in the routine operations of public health facilities, GenRe-Mekong enables NMCPs to conduct large-scale surveillance project in endemic regions. Samples are processed by the SpotMalaria platform, which uses high-throughput technologies to produce a broad set of genotypes, including most known drug resistance markers, species markers and a genomic barcode. Through the application of heuristics based on published evidence, GenRe-Mekong delivers Genetic Report Cards, a compendium of genotypes and phenotype predictions that are used to map prevalence of resistance to multiple drugs. To date, GenRe-Mekong has worked with NMCPs in five countries, and with several large-scale research projects, processing 9,645 samples from clinical cases. The monitoring of resistance markers has been especially valuable for NMCPs tracking the recent rapid spread of DHA-piperaquine resistant parasites across the region. In Vietnam and Laos, data from GenRe-Mekong have provided novel knowledge about the spread of these resistant strains in provinces previously thought to be unaffected. GenRe-Mekong facilitates data sharing by aggregating at regional level results from different countries, providing cross-border views of the spread of resistant strains.
TL;DR: The current understanding on the genetic basis of T2D is reviewed focusing on approaches which have facilitated the identification of causal variants and their effector transcripts in human islets and examples of functional studies based on animal and conventional cellular systems are presented.
TL;DR: Ternary Automated Blood Im-munoassay (TRABI) identifies seropositive individuals in large unselected cohorts, discriminates be-tween SARS2 immunity and low-affinity crossreactivity, and is therefore suitable for large-scale nationwide screening campaigns.
Abstract: Serological assays can detect anti-SARS-CoV-2 (SARS2) antibodies, but their sensitivity often comes at the expense of specificity. Here we used a Ternary Automated Blood Im-munoassay (TRABI) to assess the IgG response against SARS2 in 3,815 prepandemic plasma samples and 126 virologically and/or clinically confirmed COVID-19 samples. Posterior probabilities were calculated from 3x8 measurements of logarithmically diluted samples against the ectodomain and the receptor-binding domain of the spike protein and the nucleoprotein. We then performed 429,624 assays on 17,901 blood samples from patients of the University Hospital Zurich and from healthy blood donors. We found se-ropositivity in 44 of 8,591 patients and in 26 of 5,388 blood donors from December 2019 to May 2020. Western blotting confirmed seropositivity in COVID samples but in none of the prepandemic samples. Solution-equilibrium measurements revealed immunodominant antibodies with nanomolar affinity in COVID samples, whereas prepandemic plasma showed lower affinities despite similar titers for individual SARS2 antigens. Hence, TRABI identifies seropositive individuals in large unselected cohorts, discriminates be-tween SARS2 immunity and low-affinity crossreactivity, and is therefore suitable for large-scale nationwide screening campaigns.
Northwestern University1, Meharry Medical College2, Columbia University3, Vanderbilt University Medical Center4, University of Washington5, University of Cambridge6, University of Pennsylvania7, Children's Hospital of Philadelphia8, Cincinnati Children's Hospital Medical Center9, University of Cincinnati Academic Health Center10, Marshfield Clinic11, Cedars-Sinai Medical Center12, Wellcome Trust Centre for Human Genetics13, Erasmus University Rotterdam14
TL;DR: This study has expanded the methodological utility of PRS in patient stratification and risk prediction, especially in a multifactorial condition like PCOS, across different genetic origins.
Abstract: Context As many as 75% of patients with polycystic ovary syndrome (PCOS) are estimated to be unidentified in clinical practice. Objective Utilizing polygenic risk prediction, we aim to identify the phenome-wide comorbidity patterns characteristic of PCOS to improve accurate diagnosis and preventive treatment. Design, patients, and methods Leveraging the electronic health records (EHRs) of 124 852 individuals, we developed a PCOS risk prediction algorithm by combining polygenic risk scores (PRS) with PCOS component phenotypes into a polygenic and phenotypic risk score (PPRS). We evaluated its predictive capability across different ancestries and perform a PRS-based phenome-wide association study (PheWAS) to assess the phenomic expression of the heightened risk of PCOS. Results The integrated polygenic prediction improved the average performance (pseudo-R2) for PCOS detection by 0.228 (61.5-fold), 0.224 (58.8-fold), 0.211 (57.0-fold) over the null model across European, African, and multi-ancestry participants respectively. The subsequent PRS-powered PheWAS identified a high level of shared biology between PCOS and a range of metabolic and endocrine outcomes, especially with obesity and diabetes: "morbid obesity", "type 2 diabetes", "hypercholesterolemia", "disorders of lipid metabolism", "hypertension", and "sleep apnea" reaching phenome-wide significance. Conclusions Our study has expanded the methodological utility of PRS in patient stratification and risk prediction, especially in a multifactorial condition like PCOS, across different genetic origins. By utilizing the individual genome-phenome data available from the EHR, our approach also demonstrates that polygenic prediction by PRS can provide valuable opportunities to discover the pleiotropic phenomic network associated with PCOS pathogenesis.
TL;DR: This review describes the recent discovery of numerous Evasins produced by ticks, their classification into two structural and functional classes, and the efficacy of EvAsins in animal models of inflammatory diseases.
TL;DR: A novel pan-genome graph structure and algorithms implemented in the software pandora, which approximates a sequenced genome as a recombinant of reference genomes, detects novel variation and thenPan-genotypes multiple samples, and provides a stable framework for analysing diverse samples without reference bias is presented.
Abstract: Bacterial genomes follow a U-shaped frequency distribution whereby most genomic loci are either rare (accessory) or common (core) - the alignable fraction of two genomes from a single species might be only 50%. Standard tools therefore analyse mutations only in the core genome, ignoring accessory mutations. We present a novel pan-genome graph structure and algorithms implemented in the software pandora, which approximates a sequenced genome as a recombinant of reference genomes, detects novel variation and then pan-genotypes multiple samples. Constructing a reference graph from 578 E. coli genomes, we analyse a diverse set of 20 E. coli isolates. We show, for rare variants, pandora recovers at least 13k more SNPs than single-reference based tools, achieving equal or better error rates with Nanopore as with Illumina data, and providing a stable framework for analysing diverse samples without reference bias. This is a significant step towards comprehensive analyses of bacterial genetic variation.
TL;DR: Structural, biochemical, and chemical evidence is reported that benzoxazole biosynthesis proceeds through an ester generated by an ATP‐dependent adenylating enzyme, which is a shunt product and not, as previously thought, an intermediate in the pathway.
Abstract: Heterocycles, a class of molecules that includes oxazoles, constitute one of the most common building blocks in current pharmaceuticals and are common in medicinally important natural products. The antitumor natural product nataxazole is a model for a large class of benzoxazole-containing molecules that are made by a pathway that is not characterized. We report structural, biochemical, and chemical evidence that benzoxazole biosynthesis proceeds through an ester generated by an ATP-dependent adenylating enzyme. The ester rearranges via a tetrahedral hemiorthoamide to yield an amide, which is a shunt product and not, as previously thought, an intermediate in the pathway. A second zinc-dependent enzyme catalyzes the formation of hemiorthoamide from the ester but, by shuttling protons, the enzyme eliminates water, a reverse hydrolysis reaction, to yield the benzoxazole and avoids the amide. These insights have allowed us to harness the pathway to synthesize a series of novel halogenated benzoxazoles.