Expression of <i>Idh1</i>^R132H in the murine subventricular zone stem cell niche recapitulates features of early gliomagenesis

Isocitrate dehydrogenase 1 mutations drive human gliomagenesis, probably through neomorphic enzyme activity that produces D-2-hydroxyglutarate. To model this disease, we conditionally expressed Idh1(R132H) in the subventricular zone (SVZ) of the adult mouse brain. The mice developed hydrocephalus and grossly dilated lateral ventricles, with accumulation of 2-hydroxyglutarate and reduced α-ketoglutarate. Stem and transit amplifying/progenitor cell populations were expanded, and proliferation increased. Cells expressing SVZ markers infiltrated surrounding brain regions. SVZ cells also gave rise to proliferative subventricular nodules. DNA methylation was globally increased, while hydroxymethylation was decreased. Mutant SVZ cells overexpressed Wnt, cell-cycle and stem cell genes, and shared an expression signature with human gliomas. Idh1(R132H) mutation in the major adult neurogenic stem cell niche causes a phenotype resembling gliomagenesis

Aberrant epithelial GREM1 expression initiates colonic tumorigenesis from cells outside the stem cell niche

Hereditary mixed polyposis syndrome (HMPS) is characterized by the development of mixed-morphology colorectal tumors and is caused by a 40-kb genetic duplication that results in aberrant epithelial expression of the gene encoding mesenchymal bone morphogenetic protein antagonist, GREM1. Here we use HMPS tissue and a mouse model of the disease to show that epithelial GREM1 disrupts homeostatic intestinal morphogen gradients, altering cell fate that is normally determined by position along the vertical epithelial axis. This promotes the persistence and/or reacquisition of stem cell properties in Lgr5-negative progenitor cells that have exited the stem cell niche. These cells form ectopic crypts, proliferate, accumulate somatic mutations and can initiate intestinal neoplasia, indicating that the crypt base stem cell is not the sole cell of origin of colorectal cancer. Furthermore, we show that epithelial expression of GREM1 also occurs in traditional serrated adenomas, sporadic premalignant lesions with a hitherto unknown pathogenesis, and these lesions can be considered the sporadic equivalents of HMPS polyps

Five endometrial cancer risk loci identified through genome-wide association analysis.

We conducted a meta-analysis of three endometrial cancer genome-wide association studies (GWAS) and two follow-up phases totaling 7,737 endometrial cancer cases and 37,144 controls of European ancestry. Genome-wide imputation and meta-analysis identified five new risk loci of genome-wide significance at likely regulatory regions on chromosomes 13q22.1 (rs11841589, near KLF5), 6q22.31 (rs13328298, in LOC643623 and near HEY2 and NCOA7), 8q24.21 (rs4733613, telomeric to MYC), 15q15.1 (rs937213, in EIF2AK4, near BMF) and 14q32.33 (rs2498796, in AKT1, near SIVA1). We also found a second independent 8q24.21 signal (rs17232730). Functional studies of the 13q22.1 locus showed that rs9600103 (pairwise r(2) = 0.98 with rs11841589) is located in a region of active chromatin that interacts with the KLF5 promoter region. The rs9600103[T] allele that is protective in endometrial cancer suppressed gene expression in vitro, suggesting that regulation of the expression of KLF5, a gene linked to uterine development, is implicated in tumorigenesis. These findings provide enhanced insight into the genetic and biological basis of endometrial cancer.I.T. is supported by Cancer Research UK and the Oxford Comprehensive Biomedical Research Centre. T.H.T.C. is supported by the Rhodes Trust and the Nuffield Department of Medicine. Funding for iCOGS infrastructure came from the European Community's Seventh Framework Programme under grant agreement 223175 (HEALTH-F2-2009-223175) (COGS), Cancer Research UK (C1287/A10118, C1287/A10710, C12292/A11174, C1281/A12014, C5047/A8384, C5047/A15007, C5047/A10692 and C8197/A16565), the US National Institutes of Health (R01 CA128978, U19 CA148537, U19 CA148065 and U19 CA148112), the US Department of Defense (W81XWH-10-1-0341), the Canadian Institutes of Health Research (CIHR) for the CIHR Team in Familial Risks of Breast Cancer, the Susan G. Komen Foundation for the Cure, the Breast Cancer Research Foundation and the Ovarian Cancer Research Fund. SEARCH recruitment was funded by a programme grant from Cancer Research UK (C490/A10124). Stage 1 and stage 2 case genotyping was supported by the NHMRC (552402 and 1031333). Control data were generated by the WTCCC, and a full list of the investigators who contributed to the generation of the data is available from the WTCCC website. We acknowledge use of DNA from the British 1958 Birth Cohort collection, funded by UK Medical Research Council grant G0000934 and Wellcome Trust grant 068545/Z/02; funding for this project was provided by the Wellcome Trust under award 085475. NSECG was supported by the European Union's Framework Programme 7 CHIBCHA grant and Wellcome Trust Centre for Human Genetics Core Grant 090532/Z/09Z, and CORGI was funded by Cancer Research UK. BCAC is funded by Cancer Research UK (C1287/A10118 and C1287/A12014). OCAC is supported by a grant from the Ovarian Cancer Research Fund thanks to donations by the family and friends of Kathryn Sladek Smith (PPD/RPCI.07) and the UK National Institute for Health Research Biomedical Research Centres at the University of Cambridge.This is the author accepted manuscript. The final version is available from Nature Publishing Group via http://dx.doi.org/10.1038/ng.356

A communal catalogue reveals Earth's multiscale microbial diversity

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.Peer reviewe

A communal catalogue reveals Earth’s multiscale microbial diversity

Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity

Mortality and pulmonary complications in patients undergoing surgery with perioperative SARS-CoV-2 infection: an international cohort study

Background: The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on postoperative recovery needs to be understood to inform clinical decision making during and after the COVID-19 pandemic. This study reports 30-day mortality and pulmonary complication rates in patients with perioperative SARS-CoV-2 infection. Methods: This international, multicentre, cohort study at 235 hospitals in 24 countries included all patients undergoing surgery who had SARS-CoV-2 infection confirmed within 7 days before or 30 days after surgery. The primary outcome measure was 30-day postoperative mortality and was assessed in all enrolled patients. The main secondary outcome measure was pulmonary complications, defined as pneumonia, acute respiratory distress syndrome, or unexpected postoperative ventilation. Findings: This analysis includes 1128 patients who had surgery between Jan 1 and March 31, 2020, of whom 835 (74·0%) had emergency surgery and 280 (24·8%) had elective surgery. SARS-CoV-2 infection was confirmed preoperatively in 294 (26·1%) patients. 30-day mortality was 23·8% (268 of 1128). Pulmonary complications occurred in 577 (51·2%) of 1128 patients; 30-day mortality in these patients was 38·0% (219 of 577), accounting for 81·7% (219 of 268) of all deaths. In adjusted analyses, 30-day mortality was associated with male sex (odds ratio 1·75 [95% CI 1·28–2·40], p\textless0·0001), age 70 years or older versus younger than 70 years (2·30 [1·65–3·22], p\textless0·0001), American Society of Anesthesiologists grades 3–5 versus grades 1–2 (2·35 [1·57–3·53], p\textless0·0001), malignant versus benign or obstetric diagnosis (1·55 [1·01–2·39], p=0·046), emergency versus elective surgery (1·67 [1·06–2·63], p=0·026), and major versus minor surgery (1·52 [1·01–2·31], p=0·047). Interpretation: Postoperative pulmonary complications occur in half of patients with perioperative SARS-CoV-2 infection and are associated with high mortality. Thresholds for surgery during the COVID-19 pandemic should be higher than during normal practice, particularly in men aged 70 years and older. Consideration should be given for postponing non-urgent procedures and promoting non-operative treatment to delay or avoid the need for surgery. Funding: National Institute for Health Research (NIHR), Association of Coloproctology of Great Britain and Ireland, Bowel and Cancer Research, Bowel Disease Research Foundation, Association of Upper Gastrointestinal Surgeons, British Association of Surgical Oncology, British Gynaecological Cancer Society, European Society of Coloproctology, NIHR Academy, Sarcoma UK, Vascular Society for Great Britain and Ireland, and Yorkshire Cancer Research

Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

AbstractUnderstanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and following a national lockdown. Transmission clusters were largely segregated within the university or the community. Our study highlights key determinants of SARS-CoV-2 transmission and effective interventions in a higher education setting that will inform public health policy during pandemics.</jats:p

Germline determinants of colorectal cancer risk and outcome

Colorectal cancer (CRC) is the third most common global cancer. Approximately one fifth of phenotypic variance in CRC is attributable to additive genetic inputs: the disease risk is heritable. The nature and location of these genetic inputs has been the preoccupation of association studies over the last decade. Variation at some 30 genomic loci influences sporadic CRC risk. However, in Mendelian disorders this risk is almost absolute. Such cancer syndromes include Lynch syndrome, caused by defective DNA mismatch repair, and serrated polyposis syndrome, which has no confirmed genetic cause. The aim of this thesis was to continue exploring how common and rare germline genetics influence CRC liability. A reexamination of the chromosome 15 GREM1 locus in seven imputed UK case-control cohorts revealed a new, genome-wide significant risk polymorphism at rs17816465, independent of previously reported associations. This polymorphism lies near to conserved regulatory elements within the FMN1 gene and had allele-specific luciferase activity. Similar fine-mapping at the POLD3 locus showed a large haplotype carrying CRC risk, making further refinement of the signal difficult. A risk score incorporating a correlate of this haplotype and all other independently CRC-associated polymorphisms was significantly higher in cases than in controls, but did not predict patient survival. Instead, the risk score anticorrelated with tumour driver mutation burden in publically available colorectal cancer data. This thesis also reports the mapping and calling of the whole-genome sequences of 299 UK CRC and adenoma patients. Rare variants within this cohort were shown to be shared beyond expectation in geographic clines not visible to principal component analysis. Future rare variant association studies will need to correct for cryptic population structure using other statistical tools. In contravention of recruitment criteria, known polyposis syndrome genes were often deleteriously mutant within the genomes. Also, filtering on phenotype or gene subsets revealed potentially pathogenic variants in either whole-genome or whole-exome sequences in EXO1, RPA4, and LNX1. One individual displayed homozygous mutation of the mismatch repair gene MSH3. This was the second account of a germline MSH3 change causing tetranucleotide-unstable CRC. Lastly, a family suffering serrated polyposis was shown to carry a heterozygous RNF43 frameshift that segregated with the disease. This thesis improves our account of both sporadic and Mendelian CRC risk. It identifies a new genome-wide significant association with sporadic CRC at the GREM1 locus and provides a haplotypic account of risk at POLD3. It also describes two rare germline causes of Mendelian CRC: MSH3 and RNF43 loss of function.</p

Germline determinants of colorectal cancer risk and outcome

Colorectal cancer (CRC) is the third most common global cancer. Approximately one fifth of phenotypic variance in CRC is attributable to additive genetic inputs: the disease risk is heritable. The nature and location of these genetic inputs has been the preoccupation of association studies over the last decade. Variation at some 30 genomic loci influences sporadic CRC risk. However, in Mendelian disorders this risk is almost absolute. Such cancer syndromes include Lynch syndrome, caused by defective DNA mismatch repair, and serrated polyposis syndrome, which has no confirmed genetic cause. The aim of this thesis was to continue exploring how common and rare germline genetics influence CRC liability. A reexamination of the chromosome 15 GREM1 locus in seven imputed UK case-control cohorts revealed a new, genome-wide significant risk polymorphism at rs17816465, independent of previously reported associations. This polymorphism lies near to conserved regulatory elements within the FMN1 gene and had allele-specific luciferase activity. Similar fine-mapping at the POLD3 locus showed a large haplotype carrying CRC risk, making further refinement of the signal difficult. A risk score incorporating a correlate of this haplotype and all other independently CRC-associated polymorphisms was significantly higher in cases than in controls, but did not predict patient survival. Instead, the risk score anticorrelated with tumour driver mutation burden in publically available colorectal cancer data. This thesis also reports the mapping and calling of the whole-genome sequences of 299 UK CRC and adenoma patients. Rare variants within this cohort were shown to be shared beyond expectation in geographic clines not visible to principal component analysis. Future rare variant association studies will need to correct for cryptic population structure using other statistical tools. In contravention of recruitment criteria, known polyposis syndrome genes were often deleteriously mutant within the genomes. Also, filtering on phenotype or gene subsets revealed potentially pathogenic variants in either whole-genome or whole-exome sequences in EXO1, RPA4, and LNX1. One individual displayed homozygous mutation of the mismatch repair gene MSH3. This was the second account of a germline MSH3 change causing tetranucleotide-unstable CRC. Lastly, a family suffering serrated polyposis was shown to carry a heterozygous RNF43 frameshift that segregated with the disease. This thesis improves our account of both sporadic and Mendelian CRC risk. It identifies a new genome-wide significant association with sporadic CRC at the GREM1 locus and provides a haplotypic account of risk at POLD3. It also describes two rare germline causes of Mendelian CRC: MSH3 and RNF43 loss of function.</p