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Agustinho DP, Fu Y, Menon VK, Metcalf GA, Treangen TJ, Sedlazeck FJ. Unveiling microbial diversity: harnessing long-read sequencing technology. Nat Methods 2024:10.1038/s41592-024-02262-1. [PMID: 38689099 DOI: 10.1038/s41592-024-02262-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 03/29/2024] [Indexed: 05/02/2024]
Abstract
Long-read sequencing has recently transformed metagenomics, enhancing strain-level pathogen characterization, enabling accurate and complete metagenome-assembled genomes, and improving microbiome taxonomic classification and profiling. These advancements are not only due to improvements in sequencing accuracy, but also happening across rapidly changing analysis methods. In this Review, we explore long-read sequencing's profound impact on metagenomics, focusing on computational pipelines for genome assembly, taxonomic characterization and variant detection, to summarize recent advancements in the field and provide an overview of available analytical methods to fully leverage long reads. We provide insights into the advantages and disadvantages of long reads over short reads and their evolution from the early days of long-read sequencing to their recent impact on metagenomics and clinical diagnostics. We further point out remaining challenges for the field such as the integration of methylation signals in sub-strain analysis and the lack of benchmarks.
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Affiliation(s)
- Daniel P Agustinho
- Human Genome Sequencing center, Baylor College of Medicine, Houston, TX, USA
| | - Yilei Fu
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Vipin K Menon
- Human Genome Sequencing center, Baylor College of Medicine, Houston, TX, USA
- Senior research project manager, Human Genetics, Genentech, South San Francisco, CA, USA
| | - Ginger A Metcalf
- Human Genome Sequencing center, Baylor College of Medicine, Houston, TX, USA
| | - Todd J Treangen
- Department of Computer Science, Rice University, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing center, Baylor College of Medicine, Houston, TX, USA.
- Department of Computer Science, Rice University, Houston, TX, USA.
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2
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Chappell CL, Hoffman KL, Lorenzi PL, Tan L, Petrosino J, Gibbs R, Muzny D, Doddapaneni H, Ross MC, Menon VK, Surathu A, Javornik Cregeen SJ, Reyes AG, Okhuysen PC. Tryptophan Metabolites And Their Predicted Microbial Sources In Fecal Samples From Healthy Individuals. bioRxiv 2024:2023.12.20.572622. [PMID: 38187744 PMCID: PMC10769349 DOI: 10.1101/2023.12.20.572622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Gut microbiota produce tryptophan metabolites (TMs) important to homeostasis. However, measuring TM levels in stool and determining their microbial sources can be difficult. Here, we measured TMs from the indole pathway in fecal samples from 21 healthy adults with the goal to: 1) determine fecal TM concentrations in healthy individuals; 2) link TM levels to bacterial abundance using 16S and whole genome shotgun (WGS) sequencing data; and 3) predict likely bacterial sources of TM production. Within our samples, we identified 151 genera (16S) and 592 bacterial species (WGS). Eight TMs were found in ≥17 fecal samples, including four in all persons. To our knowledge, we are the first to report fecal levels for indole-3-lactate, indole-3-propionate, and 3-indoleacrylate levels in healthy persons. Overall, indole, indole-3-acetate (IAA), and skatole accounted for 86% of the eight TMs measured. Significant correlations were found between seven TMs and 29 bacterial species. Predicted multiple TM sources support the notion of a complex network of TM production and regulation. Further, the data suggest key roles for Collinsella aerofaciens and IAA, a metabolite reported to maintain intestinal homeostasis through enhanced barrier integrity and anti-inflammatory/antioxidant activities. These findings extend our understanding of TMs and their relationship to the microbial species that act as effectors and/or regulators in the healthy intestine and may lead to novel strategies designed to manipulate tryptophan metabolism to prevent disease and/or restore health to the dysbiotic gut.
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Holmstrom L, Chaudhary NS, Nakamura K, Chugh H, Uy-Evanado A, Norby F, Metcalf GA, Menon VK, Yu B, Boerwinkle E, Chugh SS, Akdemir Z, Kransdorf EP. Rare Genetic Variants Associated With Sudden Cardiac Arrest in the Young: A Prospective, Population-Based Study. Circ Genom Precis Med 2023; 16:404-405. [PMID: 37194601 PMCID: PMC10524160 DOI: 10.1161/circgen.123.004105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Affiliation(s)
- Lauri Holmstrom
- Center for Cardiac Arrest Prevention, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA (L.H., K.N., H.C., A.U.-E., F.N., S.S.C., E.P.K.)
| | - Ninad S Chaudhary
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston (N.S.C., B.Y., E.B., Z.A.)
| | - Kotoka Nakamura
- Center for Cardiac Arrest Prevention, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA (L.H., K.N., H.C., A.U.-E., F.N., S.S.C., E.P.K.)
| | - Harpriya Chugh
- Center for Cardiac Arrest Prevention, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA (L.H., K.N., H.C., A.U.-E., F.N., S.S.C., E.P.K.)
| | - Audrey Uy-Evanado
- Center for Cardiac Arrest Prevention, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA (L.H., K.N., H.C., A.U.-E., F.N., S.S.C., E.P.K.)
| | - Faye Norby
- Center for Cardiac Arrest Prevention, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA (L.H., K.N., H.C., A.U.-E., F.N., S.S.C., E.P.K.)
| | - Ginger A Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX (G.A.M., V.K.M., E.B.)
| | - Vipin K Menon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX (G.A.M., V.K.M., E.B.)
| | - Bing Yu
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston (N.S.C., B.Y., E.B., Z.A.)
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston (N.S.C., B.Y., E.B., Z.A.)
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX (G.A.M., V.K.M., E.B.)
| | - Sumeet S Chugh
- Center for Cardiac Arrest Prevention, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA (L.H., K.N., H.C., A.U.-E., F.N., S.S.C., E.P.K.)
| | - Zeynep Akdemir
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston (N.S.C., B.Y., E.B., Z.A.)
| | - Evan P Kransdorf
- Center for Cardiac Arrest Prevention, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA (L.H., K.N., H.C., A.U.-E., F.N., S.S.C., E.P.K.)
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4
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Carter H, Clark J, Carlin LG, Vaughan E, Rajan A, Olvera A, Yu X, Zeng XL, Kambal A, Holder M, Qin X, Gibbs RA, Petrosino JF, Muzny DM, Doddapaneni H, Menon VK, Hoffman KL, Meng Q, Ross MC, Javornik Cregeen SJ, Metcalf G, Jenq R, Blutt S, Estes MK, Maresso A, Okhuysen PC. Functional Genomics of Gastrointestinal Escherichia coli Isolated from Patients with Cancer and Diarrhea. bioRxiv 2023:2023.05.31.543115. [PMID: 37398483 PMCID: PMC10312547 DOI: 10.1101/2023.05.31.543115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
We describe the epidemiology and clinical characteristics of 29 patients with cancer and diarrhea in whom Enteroaggregative Escherichia coli (EAEC) was initially identified by GI BioFire panel multiplex. E. coli strains were successfully isolated from fecal cultures in 14 of 29 patients. Six of the 14 strains were identified as EAEC and 8 belonged to other diverse E. coli groups of unknown pathogenesis. We investigated these strains by their adherence to human intestinal organoids, cytotoxic responses, antibiotic resistance profile, full sequencing of their genomes, and annotation of their functional virulome. Interestingly, we discovered novel and enhanced adherence and aggregative patterns for several diarrheagenic pathotypes that were not previously seen when co-cultured with immortalized cell lines. EAEC isolates displayed exceptional adherence and aggregation to human colonoids compared not only to diverse GI E. coli , but also compared to prototype strains of other diarrheagenic E. coli . Some of the diverse E. coli strains that could not be classified as a conventional pathotype also showed an enhanced aggregative and cytotoxic response. Notably, we found a high carriage rate of antibiotic resistance genes in both EAEC strains and diverse GI E. coli isolates and observed a positive correlation between adherence to colonoids and the number of metal acquisition genes carried in both EAEC and the diverse E. coli strains. This work indicates that E. coli from cancer patients constitute strains of remarkable pathotypic and genomic divergence, including strains of unknown disease etiology with unique virulomes. Future studies will allow for the opportunity to re-define E. coli pathotypes with greater diagnostic accuracy and into more clinically relevant groupings.
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5
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Behera S, Belyeu JR, Chen X, Paulin LF, Nguyen NQH, Newman E, Mahmoud M, Menon VK, Qi Q, Joshi P, Marcovina S, Rossi M, Roller E, Han J, Onuchic V, Avery CL, Ballantyne CM, Rodriguez CJ, Kaplan RC, Muzny DM, Metcalf GA, Gibbs R, Yu B, Boerwinkle E, Eberle MA, Sedlazeck FJ. Identification of allele-specific KIV-2 repeats and impact on Lp(a) measurements for cardiovascular disease risk. bioRxiv 2023:2023.04.24.538128. [PMID: 37163057 PMCID: PMC10168217 DOI: 10.1101/2023.04.24.538128] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The abundance of Lp(a) protein holds significant implications for the risk of cardiovascular disease (CVD), which is directly impacted by the copy number (CN) of KIV-2, a 5.5 kbp sub-region. KIV-2 is highly polymorphic in the population and accurate analysis is challenging. In this study, we present the DRAGEN KIV-2 CN caller, which utilizes short reads. Data across 166 WGS show that the caller has high accuracy, compared to optical mapping and can further phase ~50% of the samples. We compared KIV-2 CN numbers to 24 previously postulated KIV-2 relevant SNVs, revealing that many are ineffective predictors of KIV-2 copy number. Population studies, including USA-based cohorts, showed distinct KIV-2 CN, distributions for European-, African-, and Hispanic-American populations and further underscored the limitations of SNV predictors. We demonstrate that the CN estimates correlate significantly with the available Lp(a) protein levels and that phasing is highly important.
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Affiliation(s)
- S Behera
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | | | - X Chen
- Illumina Inc., San Diego, CA, USA
| | - L F Paulin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - N Q H Nguyen
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
| | - E Newman
- Illumina Inc., San Diego, CA, USA
| | - M Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - V K Menon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Q Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - P Joshi
- Medpace Reference Laboratories, Cincinnati, OH, USA
| | - S Marcovina
- University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - M Rossi
- Illumina Inc., San Diego, CA, USA
| | - E Roller
- Illumina Inc., San Diego, CA, USA
| | - J Han
- Illumina Inc., San Diego, CA, USA
| | | | - C L Avery
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - C M Ballantyne
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - C J Rodriguez
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - R C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Fred Hutchinson Cancer Center, Public Health Sciences Division, Seattle WA 98109
| | - D M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - G A Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - R Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - B Yu
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
| | - E Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
| | | | - F J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX, USA
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6
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Jun G, English AC, Metcalf GA, Yang J, Chaisson MJP, Pankratz N, Menon VK, Salerno WJ, Krasheninina O, Smith AV, Lane JA, Blackwell T, Kang HM, Salvi S, Meng Q, Shen H, Pasham D, Bhamidipati S, Kottapalli K, Arnett DK, Ashley-Koch A, Auer PL, Beutel KM, Bis JC, Blangero J, Bowden DW, Brody JA, Cade BE, Chen YDI, Cho MH, Curran JE, Fornage M, Freedman BI, Fingerlin T, Gelb BD, Hou L, Hung YJ, Kane JP, Kaplan R, Kim W, Loos RJ, Marcus GM, Mathias RA, McGarvey ST, Montgomery C, Naseri T, Nouraie SM, Preuss MH, Palmer ND, Peyser PA, Raffield LM, Ratan A, Redline S, Reupena S, Rotter JI, Rich SS, Rienstra M, Ruczinski I, Sankaran VG, Schwartz DA, Seidman CE, Seidman JG, Silverman EK, Smith JA, Stilp A, Taylor KD, Telen MJ, Weiss ST, Williams LK, Wu B, Yanek LR, Zhang Y, Lasky-Su J, Gingras MC, Dutcher SK, Eichler EE, Gabriel S, Germer S, Kim R, Viaud-Martinez KA, Nickerson DA, Luo J, Reiner A, Gibbs RA, Boerwinkle E, Abecasis G, Sedlazeck FJ. Structural variation across 138,134 samples in the TOPMed consortium. Res Sq 2023:rs.3.rs-2515453. [PMID: 36778386 PMCID: PMC9915771 DOI: 10.21203/rs.3.rs-2515453/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Ever larger Structural Variant (SV) catalogs highlighting the diversity within and between populations help researchers better understand the links between SVs and disease. The identification of SVs from DNA sequence data is non-trivial and requires a balance between comprehensiveness and precision. Here we present a catalog of 355,667 SVs (59.34% novel) across autosomes and the X chromosome (50bp+) from 138,134 individuals in the diverse TOPMed consortium. We describe our methodologies for SV inference resulting in high variant quality and >90% allele concordance compared to long-read de-novo assemblies of well-characterized control samples. We demonstrate utility through significant associations between SVs and important various cardio-metabolic and hematologic traits. We have identified 690 SV hotspots and deserts and those that potentially impact the regulation of medically relevant genes. This catalog characterizes SVs across multiple populations and will serve as a valuable tool to understand the impact of SV on disease development and progression.
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Affiliation(s)
- Goo Jun
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston
| | - Adam C English
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Ginger A Metcalf
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Jianzhi Yang
- University of Southern California, Los Angeles, CA, USA
| | | | | | - Vipin K Menon
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | | | | | - Albert V Smith
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - John A Lane
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Tom Blackwell
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Hyun Min Kang
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Sejal Salvi
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Qingchang Meng
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Hua Shen
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Divya Pasham
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Sravya Bhamidipati
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Kavya Kottapalli
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Donna K. Arnett
- Department of Epidemiology, University of Kentucky College of Public Health
| | - Allison Ashley-Koch
- Department of Medicine, Duke University Medical Center, Durham, NC
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC
| | - Paul L. Auer
- Division of Biostatistics and Cancer Center, Medical College of Wisconsin, Milwaukee WI
| | | | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas, Rio Grande Valley School of Medicine, Brownsville, TX
| | - Donald W. Bowden
- Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Brian E. Cade
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA
| | - Yii-Der Ida Chen
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Joanne E. Curran
- Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX
| | - Barry I. Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Tasha Fingerlin
- Center for Genes, Environment and Health, National Jewish Health, 1400 Jackson St., Denver, CO, 80206, USA
| | - Bruce D. Gelb
- Mindich Child Health and Development Institute and the Departments of Pediatrics and Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai
| | | | - Yi-Jen Hung
- Institute of Preventive Medicine, National Defense Medical Center, Taiwan
| | - John P Kane
- Cardiovascular Research Institute, University of California, San Francisco
| | - Robert Kaplan
- Department of epidemiology and population health, Albert Einstein College of Medicine, Bronx NY USA
| | - Wonji Kim
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Gregory M Marcus
- Division of Cardiology, University of California, San Francisco CA
| | - Rasika A. Mathias
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Stephen T. McGarvey
- Department of Epidemiology, International Health Institute and Department of Anthropology, Brown University
| | - Courtney Montgomery
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation
| | - Take Naseri
- Ministry of Health, Government of Samoa, Apia, Samoa
| | - S. Mehdi Nouraie
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213
| | - Michael H. Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Patricia A. Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI USA
| | | | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA
| | | | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Stephen S. Rich
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI USA
| | - Michiel Rienstra
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins University Bloomberg, School of Public Health, Baltimore, MD, USA
| | - Vijay G. Sankaran
- Division of Hematology/Oncology, Boston Children’s Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | | | - Christine E. Seidman
- Department of Genetics, Harvard Medical School
- Cardiovascular Division, Brigham & Women’s Hospital, Harvard University
- Howard Hughes Medical Institute, Harvard University
| | | | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Jennifer A. Smith
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213
| | - Adrienne Stilp
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Marilyn J. Telen
- Department of Medicine, Duke University Medical Center, Durham, NC
| | - Scott T. Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - L. Keoki Williams
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, Michigan, United States of America
| | - Baojun Wu
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, Michigan, United States of America
| | - Lisa R. Yanek
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Yingze Zhang
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | | | - Susan K. Dutcher
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
| | | | | | - Ryan Kim
- Psomagen, Inc.,Rockville, Maryland, USA
| | | | | | | | - James Luo
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alex Reiner
- Department of Epidemiology, University of Washington, Seattle, WA 98109, USA
| | - Richard A Gibbs
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Goncalo Abecasis
- Regeneron Genetics Center
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Fritz J Sedlazeck
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX, 77005, USA
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7
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Jun G, English AC, Metcalf GA, Yang J, Chaisson MJP, Pankratz N, Menon VK, Salerno WJ, Krasheninina O, Smith AV, Lane JA, Blackwell T, Kang HM, Salvi S, Meng Q, Shen H, Pasham D, Bhamidipati S, Kottapalli K, Arnett DK, Ashley-Koch A, Auer PL, Beutel KM, Bis JC, Blangero J, Bowden DW, Brody JA, Cade BE, Chen YDI, Cho MH, Curran JE, Fornage M, Freedman BI, Fingerlin T, Gelb BD, Hou L, Hung YJ, Kane JP, Kaplan R, Kim W, Loos RJ, Marcus GM, Mathias RA, McGarvey ST, Montgomery C, Naseri T, Nouraie SM, Preuss MH, Palmer ND, Peyser PA, Raffield LM, Ratan A, Redline S, Reupena S, Rotter JI, Rich SS, Rienstra M, Ruczinski I, Sankaran VG, Schwartz DA, Seidman CE, Seidman JG, Silverman EK, Smith JA, Stilp A, Taylor KD, Telen MJ, Weiss ST, Williams LK, Wu B, Yanek LR, Zhang Y, Lasky-Su J, Gingras MC, Dutcher SK, Eichler EE, Gabriel S, Germer S, Kim R, Viaud-Martinez KA, Nickerson DA, Luo J, Reiner A, Gibbs RA, Boerwinkle E, Abecasis G, Sedlazeck FJ. Structural variation across 138,134 samples in the TOPMed consortium. bioRxiv 2023:2023.01.25.525428. [PMID: 36747810 PMCID: PMC9900832 DOI: 10.1101/2023.01.25.525428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Ever larger Structural Variant (SV) catalogs highlighting the diversity within and between populations help researchers better understand the links between SVs and disease. The identification of SVs from DNA sequence data is non-trivial and requires a balance between comprehensiveness and precision. Here we present a catalog of 355,667 SVs (59.34% novel) across autosomes and the X chromosome (50bp+) from 138,134 individuals in the diverse TOPMed consortium. We describe our methodologies for SV inference resulting in high variant quality and >90% allele concordance compared to long-read de-novo assemblies of well-characterized control samples. We demonstrate utility through significant associations between SVs and important various cardio-metabolic and hemotologic traits. We have identified 690 SV hotspots and deserts and those that potentially impact the regulation of medically relevant genes. This catalog characterizes SVs across multiple populations and will serve as a valuable tool to understand the impact of SV on disease development and progression.
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Affiliation(s)
- Goo Jun
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston
| | - Adam C English
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Ginger A Metcalf
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Jianzhi Yang
- University of Southern California, Los Angeles, CA, USA
| | | | | | - Vipin K Menon
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | | | | | - Albert V Smith
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - John A Lane
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Tom Blackwell
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Hyun Min Kang
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Sejal Salvi
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Qingchang Meng
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Hua Shen
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Divya Pasham
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Sravya Bhamidipati
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Kavya Kottapalli
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Donna K. Arnett
- Department of Epidemiology, University of Kentucky College of Public Health
| | - Allison Ashley-Koch
- Department of Medicine, Duke University Medical Center, Durham, NC
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC
| | - Paul L. Auer
- Division of Biostatistics and Cancer Center, Medical College of Wisconsin, Milwaukee WI
| | | | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas, Rio Grande Valley School of Medicine, Brownsville, TX
| | - Donald W. Bowden
- Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Brian E. Cade
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA
| | - Yii-Der Ida Chen
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Joanne E. Curran
- Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX
| | - Barry I. Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Tasha Fingerlin
- Center for Genes, Environment and Health, National Jewish Health, 1400 Jackson St., Denver, CO, 80206, USA
| | - Bruce D. Gelb
- Mindich Child Health and Development Institute and the Departments of Pediatrics and Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai
| | | | - Yi-Jen Hung
- Institute of Preventive Medicine, National Defense Medical Center, Taiwan
| | - John P Kane
- Cardiovascular Research Institute, University of California, San Francisco
| | - Robert Kaplan
- Department of epidemiology and population health, Albert Einstein College of Medicine, Bronx NY USA
| | - Wonji Kim
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Gregory M Marcus
- Division of Cardiology, University of California, San Francisco CA
| | - Rasika A. Mathias
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Stephen T. McGarvey
- Department of Epidemiology, International Health Institute and Department of Anthropology, Brown University
| | - Courtney Montgomery
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation
| | - Take Naseri
- Ministry of Health, Government of Samoa, Apia, Samoa
| | - S. Mehdi Nouraie
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213
| | - Michael H. Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Patricia A. Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI USA
| | | | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA
| | | | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Stephen S. Rich
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI USA
| | - Michiel Rienstra
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins University Bloomberg, School of Public Health, Baltimore, MD, USA
| | - Vijay G. Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | | | - Christine E. Seidman
- Department of Genetics, Harvard Medical School
- Cardiovascular Division, Brigham & Women’s Hospital, Harvard University
- Howard Hughes Medical Institute, Harvard University
| | | | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA
| | - Jennifer A. Smith
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213
| | - Adrienne Stilp
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Marilyn J. Telen
- Department of Medicine, Duke University Medical Center, Durham, NC
| | - Scott T. Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - L. Keoki Williams
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, Michigan, United States of America
| | - Baojun Wu
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, Michigan, United States of America
| | - Lisa R. Yanek
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Yingze Zhang
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Susan K. Dutcher
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
| | | | | | - Ryan Kim
- Psomagen, Inc.,Rockville, Maryland, USA
| | | | | | | | - James Luo
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alex Reiner
- Department of Epidemiology, University of Washington, Seattle, WA 98109, USA
| | - Richard A Gibbs
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Goncalo Abecasis
- Regeneron Genetics Center
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Fritz J Sedlazeck
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX, 77005, USA
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8
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Piedra FA, Henke D, Rajan A, Muzny DM, Doddapaneni H, Menon VK, Hoffman KL, Ross MC, Javornik Cregeen SJ, Metcalf G, Gibbs RA, Petrosino JF, Avadhanula V, Piedra PA. Modeling nonsegmented negative-strand RNA virus (NNSV) transcription with ejective polymerase collisions and biased diffusion. Front Mol Biosci 2023; 9:1095193. [PMID: 36699700 PMCID: PMC9868645 DOI: 10.3389/fmolb.2022.1095193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/19/2022] [Indexed: 01/11/2023] Open
Abstract
Infections by non-segmented negative-strand RNA viruses (NNSV) are widely thought to entail gradient gene expression from the well-established existence of a single promoter at the 3' end of the viral genome and the assumption of constant transcriptional attenuation between genes. But multiple recent studies show viral mRNA levels in infections by respiratory syncytial virus (RSV), a major human pathogen and member of NNSV, that are inconsistent with a simple gradient. Here we integrate known and newly predicted phenomena into a biophysically reasonable model of NNSV transcription. Our model succeeds in capturing published observations of respiratory syncytial virus and vesicular stomatitis virus (VSV) mRNA levels. We therefore propose a novel understanding of NNSV transcription based on the possibility of ejective polymerase-polymerase collisions and, in the case of RSV, biased polymerase diffusion.
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Affiliation(s)
- Felipe-Andrés Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, Unites States,*Correspondence: Felipe-Andrés Piedra,
| | - David Henke
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, Unites States
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, Unites States
| | - Donna M. Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Unites States
| | - Harsha Doddapaneni
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Unites States
| | - Vipin K. Menon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Unites States
| | - Kristi L. Hoffman
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, Unites States
| | - Matthew C. Ross
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Unites States
| | - Sara J. Javornik Cregeen
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, Unites States
| | - Ginger Metcalf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Unites States
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Unites States
| | - Joseph F. Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, Unites States
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, Unites States
| | - Pedro A. Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, Unites States,Department of Pediatrics, Baylor College of Medicine, Houston, TX, Unites States
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9
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English AC, Menon VK, Gibbs RA, Metcalf GA, Sedlazeck FJ. Truvari: refined structural variant comparison preserves allelic diversity. Genome Biol 2022; 23:271. [PMID: 36575487 DOI: 10.1101/2022.02.21.481353] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 12/15/2022] [Indexed: 05/25/2023] Open
Abstract
The fundamental challenge of multi-sample structural variant (SV) analysis such as merging and benchmarking is identifying when two SVs are the same. Common approaches for comparing SVs were developed alongside technologies which produce ill-defined boundaries. As SV detection becomes more exact, algorithms to preserve this refined signal are needed. Here, we present Truvari-an SV comparison, annotation, and analysis toolkit-and demonstrate the effect of SV comparison choices by building population-level VCFs from 36 haplotype-resolved long-read assemblies. We observe over-merging from other SV merging approaches which cause up to a 2.2× inflation of allele frequency, relative to Truvari.
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Affiliation(s)
- Adam C English
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA.
| | - Vipin K Menon
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Richard A Gibbs
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Ginger A Metcalf
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Fritz J Sedlazeck
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
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10
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English AC, Menon VK, Gibbs RA, Metcalf GA, Sedlazeck FJ. Truvari: refined structural variant comparison preserves allelic diversity. Genome Biol 2022; 23:271. [PMID: 36575487 PMCID: PMC9793516 DOI: 10.1186/s13059-022-02840-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 12/15/2022] [Indexed: 12/28/2022] Open
Abstract
The fundamental challenge of multi-sample structural variant (SV) analysis such as merging and benchmarking is identifying when two SVs are the same. Common approaches for comparing SVs were developed alongside technologies which produce ill-defined boundaries. As SV detection becomes more exact, algorithms to preserve this refined signal are needed. Here, we present Truvari-an SV comparison, annotation, and analysis toolkit-and demonstrate the effect of SV comparison choices by building population-level VCFs from 36 haplotype-resolved long-read assemblies. We observe over-merging from other SV merging approaches which cause up to a 2.2× inflation of allele frequency, relative to Truvari.
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Affiliation(s)
- Adam C. English
- grid.39382.330000 0001 2160 926XBaylor College of Medicine Human Genome Sequencing Center, Houston, TX USA
| | - Vipin K. Menon
- grid.39382.330000 0001 2160 926XBaylor College of Medicine Human Genome Sequencing Center, Houston, TX USA
| | - Richard A. Gibbs
- grid.39382.330000 0001 2160 926XBaylor College of Medicine Human Genome Sequencing Center, Houston, TX USA
| | - Ginger A. Metcalf
- grid.39382.330000 0001 2160 926XBaylor College of Medicine Human Genome Sequencing Center, Houston, TX USA
| | - Fritz J. Sedlazeck
- grid.39382.330000 0001 2160 926XBaylor College of Medicine Human Genome Sequencing Center, Houston, TX USA
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11
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Blobner BM, Kirabo A, Kashlan OB, Sheng S, Arnett DK, Becker LC, Boerwinkle E, Carlson JC, Gao Y, Gibbs RA, He J, Irvin MR, Kardia SLR, Kelly TN, Kooperberg C, McGarvey ST, Menon VK, Montasser ME, Naseri T, Redline S, Reiner AP, Reupena MS, Smith JA, Sun X, Vaidya D, Viaud-Martinez KA, Weeks DE, Yanek LR, Zhu X, Minster RL, Kleyman TR. Rare Variants in Genes Encoding Subunits of the Epithelial Na + Channel Are Associated With Blood Pressure and Kidney Function. Hypertension 2022; 79:2573-2582. [PMID: 36193739 PMCID: PMC9669116 DOI: 10.1161/hypertensionaha.121.18513] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 07/31/2022] [Indexed: 11/16/2022]
Abstract
BACKGROUND The epithelial Na+ channel (ENaC) is intrinsically linked to fluid volume homeostasis and blood pressure. Specific rare mutations in SCNN1A, SCNN1B, and SCNN1G, genes encoding the α, β, and γ subunits of ENaC, respectively, are associated with extreme blood pressure phenotypes. No associations between blood pressure and SCNN1D, which encodes the δ subunit of ENaC, have been reported. A small number of sequence variants in ENaC subunits have been reported to affect functional transport in vitro or blood pressure. The effects of the vast majority of rare and low-frequency ENaC variants on blood pressure are not known. METHODS We explored the association of low frequency and rare variants in the genes encoding ENaC subunits, with systolic blood pressure, diastolic blood pressure, mean arterial pressure, and pulse pressure. Using whole-genome sequencing data from 14 studies participating in the Trans-Omics in Precision Medicine Whole-Genome Sequencing Program, and sequence kernel association tests. RESULTS We found that variants in SCNN1A and SCNN1B were associated with diastolic blood pressure and mean arterial pressure (P<0.00625). Although SCNN1D is poorly expressed in human kidney tissue, SCNN1D variants were associated with systolic blood pressure, diastolic blood pressure, mean arterial pressure, and pulse pressure (P<0.00625). ENaC variants in 2 of the 4 subunits (SCNN1B and SCNN1D) were also associated with estimated glomerular filtration rate (P<0.00625), but not with stroke. CONCLUSIONS Our results suggest that variants in extrarenal ENaCs, in addition to ENaCs expressed in kidneys, influence blood pressure and kidney function.
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Affiliation(s)
- Brandon M Blobner
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Annet Kirabo
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ossama B Kashlan
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Shaohu Sheng
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Donna K Arnett
- College of Public Health, University of Kentucky, Lexington, KY, USA
| | - Lewis C Becker
- GeneSTAR Research Program, Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jenna C Carlson
- Department of Biostatistics, University of Pittsburgh Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yan Gao
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
- Tulane University Translational Science Institute, New Orleans, LA, USA
| | - Marguerite R Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sharon LR Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Tanika N Kelly
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
- Tulane University Translational Science Institute, New Orleans, LA, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stephen T McGarvey
- Department of Epidemiology and International Health Institute, Brown University School of Public Health, Providence, RI, USA
| | - Vipin K Menon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - May E Montasser
- Department of Medicine, University of Maryland, Baltimore, MD, USA
| | - Take Naseri
- Department of Epidemiology and International Health Institute, Brown University School of Public Health, Providence, RI, USA
- Ministry of Health, Apia, Samoa
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Alexander P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Xiao Sun
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Dhananjay Vaidya
- GeneSTAR Research Program, Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Daniel E Weeks
- Department of Biostatistics, University of Pittsburgh Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lisa R Yanek
- GeneSTAR Research Program, Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | | | - Ryan L Minster
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Thomas R Kleyman
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Cell Biology, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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12
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Othman M, Menon VK. The prevalence of Schmorl's nodes in osteoporotic vs normal patients: a Middle Eastern population study. Osteoporos Int 2022; 33:1493-1499. [PMID: 35175396 DOI: 10.1007/s00198-022-06316-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 01/19/2022] [Indexed: 10/19/2022]
Abstract
UNLABELLED The study was conducted to establish the association of Schmorl's nodes and osteoporosis in a Middle Eastern cohort. The prevalence of SN in this sample was 41.1%. It was most frequent in the lumbar spine typically solitary central lesions. Over 88% Schmorl's node cases were osteoporotic/osteopenic and only 11.6% normal. INTRODUCTION This study aims to identify the prevalence of Schmorl's nodes (SNs) in a cohort of Omani nationals, and also to determine any relation between osteoporosis and Schmorl's nodes. METHODS This retrospective observational study was conducted on Omani nationals. One thousand three hundred and forty-eight DEXA scan patients were included. Of these, 545 patients had complete X-rays and MRI scans that would help determine the SN status. The X-rays and sagittal, coronal, and axial T2-weighted MR images were used to identify the presence and exact location of the Schmorl nodes by one orthopedic trainee and confirmed by the senior author. The correlation of each parameter with the presence of SN was analyzed by the independent-samples T test and one-way ANOVA. RESULTS The overall prevalence of SN in this population sample appeared to be 41.1%. Over 88% of the SN-positive cases were either osteopenic or frankly osteoporotic by the WHO definition. Vast majority of SNs (87.1%) occurred in the lumbar spine and were central in location and mostly solitary. Statistical analysis of the data revealed significant correlation between osteopenia or osteoporosis and the presence of SNs. CONCLUSIONS The prevalence of SN in the sample of Omanis studied was 41.1% and was most frequently seen in older men in the lumbar spine. It is strongly associated with osteoporosis/osteopenia (88.4%) and frequently presents as solitary central lesions.
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Affiliation(s)
- M Othman
- Oman Medical Speciality Board, Muscat, Oman
| | - V K Menon
- Department of Spine Surgery, Bharati Vidyapeeth Medical College Hospital, Pune, India.
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13
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Menon VK, Okhuysen PC, Chappell CL, Mahmoud M, Mahmoud M, Meng Q, Doddapaneni H, Vee V, Han Y, Salvi S, Bhamidipati S, Kottapalli K, Weissenberger G, Shen H, Ross MC, Hoffman KL, Cregeen SJ, Muzny DM, Metcalf GA, Gibbs RA, Petrosino JF, Sedlazeck FJ. Fully resolved assembly of Cryptosporidium parvum. Gigascience 2022; 11:6528769. [PMID: 35166336 PMCID: PMC8848321 DOI: 10.1093/gigascience/giac010] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/07/2021] [Accepted: 01/20/2022] [Indexed: 11/17/2022] Open
Abstract
Background Cryptosporidium parvum is an apicomplexan parasite commonly found across many host species with a global infection prevalence in human populations of 7.6%. Understanding its diversity and genomic makeup can help in fighting established infections and prohibiting further transmission. The basis of every genomic study is a high-quality reference genome that has continuity and completeness, thus enabling comprehensive comparative studies. Findings Here, we provide a highly accurate and complete reference genome of Cryptosporidium parvum. The assembly is based on Oxford Nanopore reads and was improved using Illumina reads for error correction. We also outline how to evaluate and choose from different assembly methods based on 2 main approaches that can be applied to other Cryptosporidium species. The assembly encompasses 8 chromosomes and includes 13 telomeres that were resolved. Overall, the assembly shows a high completion rate with 98.4% single-copy BUSCO genes. Conclusions This high-quality reference genome of a zoonotic IIaA17G2R1 C. parvum subtype isolate provides the basis for subsequent comparative genomic studies across the Cryptosporidium clade. This will enable improved understanding of diversity, functional, and association studies.
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Affiliation(s)
- Vipin K Menon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Pablo C Okhuysen
- Department of Infectious Diseases, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Cynthia L Chappell
- Center for Infectious Diseases, The University of Texas School of Public Health, Houston, TX 77030, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Vanesa Vee
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yi Han
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sejal Salvi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sravya Bhamidipati
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kavya Kottapalli
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - George Weissenberger
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hua Shen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew C Ross
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Kristi L Hoffman
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Sara Javornik Cregeen
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ginger A Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
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14
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Criss ZK, Bhasin N, Di Rienzi SC, Rajan A, Deans-Fielder K, Swaminathan G, Kamyabi N, Zeng XL, Doddapaneni H, Menon VK, Chakravarti D, Estrella C, Yu X, Patil K, Petrosino JF, Fleet JC, Verzi MP, Christakos S, Helmrath MA, Arimura S, DePinho RA, Britton RA, Maresso AW, Grande-Allen KJ, Blutt SE, Crawford SE, Estes MK, Ramani S, Shroyer NF. Drivers of transcriptional variance in human intestinal epithelial organoids. Physiol Genomics 2021; 53:486-508. [PMID: 34612061 DOI: 10.1152/physiolgenomics.00061.2021] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Human intestinal epithelial organoids (enteroids and colonoids) are tissue cultures used for understanding the physiology of the human intestinal epithelium. Here, we explored the effect on the transcriptome of common variations in culture methods, including extracellular matrix substrate, format, tissue segment, differentiation status, and patient heterogeneity. RNA-sequencing datasets from 276 experiments performed on 37 human enteroid and colonoid lines from 29 patients were aggregated from several groups in the Texas Medical Center. DESeq2 and gene set enrichment analysis (GSEA) were used to identify differentially expressed genes and enriched pathways. PERMANOVA, Pearson's correlation, and dendrogram analysis of the data originally indicated three tiers of influence of culture methods on transcriptomic variation: substrate (collagen vs. Matrigel) and format (3-D, transwell, and monolayer) had the largest effect; segment of origin (duodenum, jejunum, ileum, colon) and differentiation status had a moderate effect; and patient heterogeneity and specific experimental manipulations (e.g., pathogen infection) had the smallest effect. GSEA identified hundreds of pathways that varied between culture methods, such as IL1 cytokine signaling enriched in transwell versus monolayer cultures and E2F target genes enriched in collagen versus Matrigel cultures. The transcriptional influence of the format was furthermore validated in a synchronized experiment performed with various format-substrate combinations. Surprisingly, large differences in organoid transcriptome were driven by variations in culture methods such as format, whereas experimental manipulations such as infection had modest effects. These results show that common variations in culture conditions can have large effects on intestinal organoids and should be accounted for when designing experiments and comparing results between laboratories. Our data constitute the largest RNA-seq dataset interrogating human intestinal epithelial organoids.
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Affiliation(s)
- Zachary K Criss
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Nobel Bhasin
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Sara C Di Rienzi
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Kali Deans-Fielder
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | | | | | - Xi-Lei Zeng
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Vipin K Menon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Deepavali Chakravarti
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Clarissa Estrella
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Xiaomin Yu
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Ketki Patil
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Joseph F Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - James C Fleet
- Department of Nutrition Sciences, The University of Texas, Austin, Texas
| | - Michael P Verzi
- Department of Genetics, Rutgers University, Piscataway, New Jersey
| | - Sylvia Christakos
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers-New Jersey Medical School, Newark, New Jersey
| | - Michael A Helmrath
- Department of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Sumimasa Arimura
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Ronald A DePinho
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Robert A Britton
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Anthony W Maresso
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | | | - Sarah E Blutt
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Sue E Crawford
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Sasirekha Ramani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Noah F Shroyer
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas
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15
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Menon VK, Gottumukkala RS, Chen J, Su X, Mistry N, Majumdar A, Shin JH, Li S, Shetty K, Wu X, Weston B, Miller E, Stroehlein JR, Davila ML, Shafi MA, Rashid A, Kallakury BV, Thirumurthi S, McMurray JS, Lin SH, Jogunoori W, Mishra L. Abstract 67: Genomic and mutational profiling of human colon adenomas reveals early driver mutations and a TGF-β-CEA regulated profile. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-67] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Colorectal cancer (CRC) is the third most commonly diagnosed cancer in the world with 143,700 newly diagnosed cases in 2012. The rapid development of cancers in small, sessile adenomas could be a contributing factor that may have been overlooked. Identifying high risk patients through genomic analysis of adenomas could potentially lead to an early intervention therapy.
Methods: Whole Genome Sequence (WGS) and Whole Exome Sequence (WES) analyses were performed for 4 pairs of normal controls (two from proximal colon and two from the distal colon) and colorectal adenomas (2 sessile serrated (SSA) and 2 tubulovillous adenomas (TVA) less than 1 cm in size). Transcriptome sequence analysis was performed in seven pairs of control-test matched adenomas (6 TVA and 1 SSA). Expression level of CEA and TGF-β pathway members were carried out on 30 non dysplastic adenomas and normal colon tissues by immunohistochemistry.
Results: 1. Hyper-mutator profiles were observed in two of the samples (1 SSA and 1 TVA) by WGS with 1709 mutations after normalization with normal paired samples. 2. The samples showed an average mutation frequency of 0.55 mutations per 106 bases. 3. Aberrant mutational profiles was detected in seven of the eleven adenomas, with distinct mutational signatures among the samples, two with high, two intermediate and three low mutational rates. 4. Six of the eleven adenomas (1 SSA and 4 TVAs) showed alteration in the Wnt and p53 pathway. 5. Transitional single nucleotide substitutions of C:T>G:A in the mutational spectrum were observed in 37% of the samples. 6. Subtle localized hyper mutation (kataegis) was observed among two of the samples. 7. Five out of eleven adenomas showed mutations in the TGF-β (transforming growth factor-β) and CEA pathways members, overlapping with Wnt/p53 mutations in four adenomas. 8. Analyses of expression level of CEA and TGF-β pathway members in 30 non dysplastic tissues revealed a marked increase (over 8 fold) in CEA expression in 25% of adenoma samples which was linked to concomitant loss of TGF-β signaling. 9. Further functional studies revealed that CEA associated with TGF-β Type I receptor and disruption of TGF-β tumor suppressor signaling with activation of STAT3.
Conclusions: Our studies indicate that small adenomas both TVAs and SSAs can resemble CRCs in genomic profiling and may reflect a high risk population. Genetic and mechanistic analyses reveal that disruption of CEA/TGF-β pathway in early adenomas may reflect a new and early role for these pathways in CRC. This study further supports the biomarker driven targeting of CEA/TGF-β in high risk adenomas and can be used as a prognostic marker for early detection of aggressive adenoma-CRC progression.
Citation Format: Vipin K. Menon, Raju S. Gottumukkala, Jian Chen, Xiaoping Su, Nipun Mistry, Avijit Majumdar, Ji-Hyun Shin, Shulin Li, Kirti Shetty, Xifeng Wu, Brian Weston, Ethan Miller, John R. Stroehlein, Marta L. Davila, Mehnaz A. Shafi, Asif Rashid, Bhaskar V. Kallakury, Selvi Thirumurthi, John S. McMurray, Sue-Hwa Lin, Wilma Jogunoori, Lopa Mishra. Genomic and mutational profiling of human colon adenomas reveals early driver mutations and a TGF-β-CEA regulated profile. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 67. doi:10.1158/1538-7445.AM2015-67
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Affiliation(s)
| | | | - Jian Chen
- 1MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | - Shulin Li
- 1MD Anderson Cancer Center, Houston, TX
| | - Kirti Shetty
- 2Johns Hopkins Medical Institutions, Baltimore, MD
| | - Xifeng Wu
- 1MD Anderson Cancer Center, Houston, TX
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Abstract
PURPOSE Noroviruses (NoV) are increasingly recognized as an important cause for acute gastroenteritis, worldwide. Reverse transcription polymerase chain reaction (RT-PCR) and sequencing are the methods of choice for the detection of NoVs, but there is currently no consensus about the primers to be used in these assays. MATERIALS AND METHODS In this study, five published primer sets were evaluated for the detection of genogroup II (GII) NoVs in India. The primers target different regions of the NoV genome. Three primer sets detect an NoV in a single round RT-PCR platform, while the remaining two primer sets are based on a nested RT-PCR platform. RESULT A panel of 100 samples from previous studies on norovirus diarrhoea in children were tested by all five primer sets. Of them, 74 samples were identified as positive for NoV, by at least one primer set. Subsets of positive amplicons were sequenced to check for specificity. CONCLUSION The most sensitive primer set was Girish 2002, which detected GII NoV by nested RT-PCR, and was modified from the previously published primers. This study demonstrates that higher detection can be obtained by either using multiple primer sets or using a sensitive nested RT-PCR assay. It also demonstrates the differences in primer sensitivity for detection of Genogroup II (GII) NoVs in India.
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Affiliation(s)
- S George
- Department of Gastrointestinal Sciences, Christian Medical College, Vellore - 632 004, India
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17
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Ajjampur SSR, Sarkar R, Sankaran P, Kannan A, Menon VK, Muliyil J, Ward H, Kang G. Symptomatic and asymptomatic Cryptosporidium infections in children in a semi-urban slum community in southern India. Am J Trop Med Hyg 2010; 83:1110-5. [PMID: 21036847 DOI: 10.4269/ajtmh.2010.09-0644] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Cryptosporidium is a leading cause of childhood diarrhea in developing countries. We investigated symptomatic and asymptomatic cryptosporidiosis in 20 children less than two years of age in a semi-urban slum in southern India. All surveillance (conducted every two weeks) and diarrheal samples from 20 children (n = 1,036) with cryptosporidial diarrhea previously identified by stool microscopy were tested by polymerase chain reaction-restriction fragment length polymorphism for species and subgenotype determination. Thirty-five episodes of cryptosporidiosis were identified in 20 children, of which 25 were diarrheal. Fifteen episodes were associated with prolonged oocyst shedding. Multiple episodes of cryptosporidiosis occurred in 40% of the children. Most infections were with C. hominis, subtype Ia. Children with multiple infections had significantly lower weight-for-age and height-for-age Z scores at 24 months but had scores comparable with children with a single episode by 36 months. Multiple symptomatic Cryptosporidium infections associated with prolonged oocyst shedding occur frequently in this disease-endemic area and may contribute to the long-term effects of cryptosporidiosis on physical growth in these children.
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Affiliation(s)
- Sitara S R Ajjampur
- Department of Gastrointestinal Sciences, Christian Medical College, Vellore, India.
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18
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Hou YJ, Yu AC, Garcia JM, Aotaki-Keen A, Lee YL, Eng LF, Hjelmeland LJ, Menon VK. Astrogliosis in culture. IV. Effects of basic fibroblast growth factor. J Neurosci Res 1995; 40:359-70. [PMID: 7745630 DOI: 10.1002/jnr.490400310] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Previous studies have shown that the mechanical wounding of 3-week-old cultured rat astrocytes results in cell proliferation and hypertrophy resembling astrocyte responses to a brain injury in vivo. We now report the effects of basic fibroblast growth factor (bFGF) and an anti-bFGF antibody on astrocyte morphology, proliferation, and migration following in vitro wounding of confluent secondary cultures. Addition of bFGF (20 ng/ml) to wounded cultures induced morphological changes characteristic of differentiation in wounded and nonwounded areas of the culture. Combined treatment with bFGF and an anti-bFGF antibody (100 micrograms/ml) prevented this effect. Astrocyte proliferation along the edges of a scratch wound was at maximum 24 hr after wounding in cells growing in Eagle's minimum essential medium (EMEM) containing 10% serum. Low serum concentration and treatment with dibutyryl cyclic adenosine monophosphate (dbc-AMP) reduced injury-associated astrocyte proliferation. Addition of bFGF to cultures in EMEM with serum increased astrocyte proliferation at 18 and 24 hr after wounding. This effect was reduced considerably by treatment of cultures with bFGF in combination with an anti-bFGF antibody. The combined treatment and the antibody alone reduced cell division to a level lower than in control cultures. Twenty-four hr following wounding, astrocytes along the edges of the wound exhibited extension of thick, flat processes into the wound area. At 3 and 5 days after wounding, a bodily migration of astrocytes into the wounded area was observed. Addition of bFGF significantly increased astrocyte migration 1 day after wounding, with maximum effect on day 3 and no subsequent increase on day 5. A combination of bFGF and anti-bFGF antibody as well as the antibody alone reduced astrocyte migration to a level lower than in controls. Immunohistochemical localization and isoform pattern of bFGF in astrocytes did not change with dbc-AMP treatment or wounding. We conclude that mechanically wounded confluent astrocytes respond to bFGF added to the culture medium by enhancing cell division, differentiation, and migration. In addition, the results of the antibody treatment also suggest a role for endogenous bFGF in astrocyte proliferation and migration elicited by wounding in vitro. These results support the notion that in vivo, both bFGF released by injury and endogenous bFGF synthesized by astrocytes, contribute to the cellular responses that lead to astrogliosis.
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Affiliation(s)
- Y J Hou
- Department of Cell Biology and Human Anatomy, University of California, Davis 95616, USA
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19
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Abstract
A traumatic injury to the rat brain is known to induce astrocyte proliferation and hypertrophy leading to astrogliosis. In addition, trauma also induces microglial proliferation in the brain. Since basic fibroblast growth factor (bFGF) is believed to play a role in mediating glial responses to brain injury, we examined the effects of bFGF administration on astrocyte and microglial proliferation and astrocyte hypertrophy resulting from a traumatic injury to the rat brain. Intracerebroventricular infusion of bFGF for 2 days prior to and following injury failed to alter glial reactivity. In contrast, a single intralesion injection of bFGF immediately after injury increased total cell division 2 and 5 days later, with an exclusive effect on glial fibrillary acidic protein-negative glia which consisted mostly of cells of macrophage-microglial phenotype. In addition, bFGF also enhanced injury-induced astrocyte hypertrophy. These results support a role for bFGF in macrophage-microglia proliferation and astrocyte hypertrophy following brain injury. They also suggest that alteration of injury responses of nonneuronal cells of the brain may be a potential side effect of intracerebral administration of bFGF.
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Affiliation(s)
- V K Menon
- Department of Cell Biology and Human Anatomy, School of Medicine, University of California, Davis 95616
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20
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Abstract
This paper describes a method for the rapid isolation of phycobilisomes using a cationic detergent, CTAB (cetyltrimethylammonium bromide). The method has distinct advantages over those currently in use in that (i) release of intact phycobilisomes from cells in the presence of CTAB occurs in 40 s (as compared to 40-60 min of incubation required with Triton X-100), thereby reducing the chances of proteolysis of the component phycobiliproteins; and (ii) these phycobilisome preparations have reduced chlorophyll contamination in the initial stages. In addition this method also helps retain the structural and functional properties, as evidenced by spectroscopy and sodium dodecyl sulfate-polyacrylamide gel analysis.
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Affiliation(s)
- V K Menon
- Microbiology Unit, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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21
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Flannigan SA, Smolensky MH, Harrist R, Brown RL, Menon VK, McGovern JP. Scapular reactivity to contact irritants: application-time and area variations. Chronobiologia 1984; 11:93-107. [PMID: 6745010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Twenty-two diurnally active, fair-skinned, male volunteers were repeatedly patch tested with 10, 15 and 20% lapyrium chloride (LC) and 0.3 and 0.5% sodium lauryl sulfate (SLS) for 5 consecutive days. A series of 5 patches containing SLS and LC were placed vertically once daily for 6 h on different sites of the scapula: paravertebral, lateral and medial. The sites of application were randomized over subjects for patch testing once a day per area at either 08%, 16% or 00%. Each patch was left in place 6 h; scoring of each site, using a 13-point scale, was done 2, 10 and 18 h after removal. The cutaneous reactivity varied in a statistically significant manner according to the time and area of patch application. For each day except the first, LC scores exhibited highest and lowest responses at 16% and 00%, respectively. For SLS, a statistically significant application-time difference in reactivity was detected only for the readings of day 2 when scores were highest at 00% and lowest at 16%. Intraregional variations in scapular reactivity were also exhibited. Strongest reactions to LC occurred in the center of each scapula; weakest reactions were elicited on either the lateral or paravertebral sites. For SLS, statistically significant intraregional differences in reactivity were detected only for the second day of patching, with strongest responses near the spinal column and weakest near the axilla.
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22
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Menon VK, Alurkar VM, Durairaj M. Anomalous origin of the coronary artery in Marfan's syndrome. Indian Heart J 1983; 35:176-7. [PMID: 6629392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
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23
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Menon VK, Jaiprakash MP, Ayier PS, Srinivas K. Successful revival and follow-up of primary ventricular fibrillation. J Assoc Physicians India 1983; 31:118. [PMID: 6885708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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24
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Srinivas K, Ramachandran U, Menon VK, Ramasekar K. Infective polyneuritis with complete external ophthalmoplegia. Indian Pediatr 1983; 20:61-3. [PMID: 6862606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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25
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Abstract
ATP-sulphurylase from an unicellular blue-green alga, Spirulina platensis was localized in the soluble fractions of cell-free homogenate, and it was stable for over 3 weeks at -6 degrees C.
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