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Sun Y, Khan MAAK, Mangiola S, Barrow AD. IL17RB and IL17REL Expression Are Associated with Improved Prognosis in HPV-Infected Head and Neck Squamous Cell Carcinomas. Pathogens 2023; 12:pathogens12040572. [PMID: 37111458 PMCID: PMC10143491 DOI: 10.3390/pathogens12040572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/16/2023] [Accepted: 03/27/2023] [Indexed: 04/29/2023] Open
Abstract
Changes in the cellular secretome are implicated in virus infection, malignancy, and anti-tumor immunity. We analyzed the association between transcriptional signatures (TS) from 24 different immune and stromal cell types on the prognosis of HPV-infected and HPV-free head and neck squamous carcinoma (HNSCC) patients from The Cancer Genome Atlas (TCGA) cohort. We found that HPV-positive HNSCC patients have tumors with elevated immune cell TS and improved prognosis, which was specifically associated with an increased tumor abundance of memory B and activated natural killer (NK) cell TS, compared to HPV-free HNSCC patients. HPV-infected patients upregulated many transcripts encoding secreted factors, such as growth factors, hormones, chemokines and cytokines, and their cognate receptors. Analysis of secretome transcripts and cognate receptors revealed that tumor expression of IL17RB and IL17REL are associated with a higher viral load and memory B and activated NK cell TS, as well as improved prognosis in HPV-infected HNSCC patients. The transcriptional parameters that we describe may be optimized to improve prognosis and risk stratification in the clinic and provide insights into gene and cellular targets that may potentially enhance anti-tumor immunity mediated by NK cells and memory B cells in HPV-infected HNSCC patients.
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Affiliation(s)
- Yuhan Sun
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne 3000, Australia
| | - Md Abdullah Al Kamran Khan
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne 3000, Australia
| | - Stefano Mangiola
- Division of Bioinformatics, Walter and Eliza Hall Institute, Parkville 3052, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne 3010, Australia
| | - Alexander David Barrow
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne 3000, Australia
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Ben-Yosef N, Frampton M, Schiff ER, Daher S, Abu Baker F, Safadi R, Israeli E, Segal AW, Levine AP. Genetic analysis of four consanguineous multiplex families with inflammatory bowel disease. Gastroenterol Rep (Oxf) 2021; 9:521-532. [PMID: 34925849 PMCID: PMC8677555 DOI: 10.1093/gastro/goab007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/03/2020] [Accepted: 11/26/2020] [Indexed: 12/11/2022] Open
Abstract
Background Family studies support a genetic predisposition to inflammatory bowel diseases (IBD), but known genetic variants only partially explain the disease heritability. Families with multiple affected individuals potentially harbour rare and high-impact causal variants. Long regions of homozygosity due to recent inbreeding may increase the risk of individuals bearing homozygous loss-of-function variants. This study aimed to identify rare and homozygous genetic variants contributing to IBD. Methods Four families with known consanguinity and multiple cases of IBD were recruited. In a family-specific analysis, we utilised homozygosity mapping complemented by whole-exome sequencing. Results We detected a single region of homozygosity shared by Crohn's disease cases from a family of Druze ancestry, spanning 2.6 Mb containing the NOD2 gene. Whole-exome sequencing did not identify any potentially damaging variants within the region, suggesting that non-coding variation may be involved. In addition, affected individuals in the families harboured several rare and potentially damaging homozygous variants in genes with a role in autophagy and innate immunity including LRRK1, WHAMM, DENND3, and C5. Conclusion This study examined the potential contribution of rare, high-impact homozygous variants in consanguineous families with IBD. While the analysis was not designed to achieve statistical significance, our findings highlight genes or loci that warrant further research. Non-coding variants affecting NOD2 may be of importance in Druze patients with Crohn's disease.
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Affiliation(s)
- Noam Ben-Yosef
- Centre for Molecular Medicine, Division of Medicine, University College London, London, UK
- Institute of Gastroenterology and Liver disease, Hadassah Medical Center, Jerusalem, Israel
| | - Matthew Frampton
- Centre for Molecular Medicine, Division of Medicine, University College London, London, UK
| | - Elena R Schiff
- Institute of Ophthalmology, Moorfields Eye Hospital, University College London, London, UK
| | - Saleh Daher
- Institute of Gastroenterology and Liver disease, Hadassah Medical Center, Jerusalem, Israel
| | - Fadi Abu Baker
- Institue of Gastroenterology and Hepatology, Hillel Yaffe Medical Center, Hadera, Israel
| | - Rifaat Safadi
- Institute of Gastroenterology and Liver disease, Hadassah Medical Center, Jerusalem, Israel
| | - Eran Israeli
- Institute of Gastroenterology and Liver disease, E. Wolfson Medical Center, Holon, Israel
| | - Anthony W Segal
- Centre for Molecular Medicine, Division of Medicine, University College London, London, UK
| | - Adam P Levine
- Centre for Molecular Medicine, Division of Medicine, University College London, London, UK
- Department of Pathology, University College London, London, UK
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Abstract
Zusammenfassung
Häufige Krankheiten, die sog. Volkskrankheiten, sind in der Regel multifaktoriell verursacht, d. h. zu ihrer Entwicklung tragen sowohl genetische Faktoren als auch nicht-genetische Umgebungseinflüsse bei. Die geschätzte Gesamterblichkeit (‑heritabilität) reicht von moderat bis vergleichsweise hoch. Die genetische Architektur ist komplex und kann das gesamte allelische Spektrum, von häufigen Varianten mit niedriger Penetranz bis hin zu seltenen Varianten mit höherer Penetranz, sowie alle möglichen Kombinationen umfassen. Während häufige Varianten seit mehreren Jahren mit großem Erfolg durch genomweite Assoziationsstudien (GWAS) identifiziert werden, war bisher die Identifizierung seltener Varianten, insbesondere aufgrund der großen Zahl beitragender Gene, nur begrenzt erfolgreich. Dies ändert sich derzeit dank der Anwendung von Hochdurchsatz-Sequenziertechnologien („next-generation sequencing“, NGS) und der daraus resultierenden zunehmenden Verfügbarkeit von exom- und genomweiten Sequenzdaten großer Kollektive. In diesem Artikel geben wir einen Überblick über die Bedeutung seltener Varianten bei häufigen Erkrankungen sowie den aktuellen Stand in Bezug auf deren Identifizierung mittels NGS. Wir betrachten insbesondere die folgenden Fragen: Bei welchen häufigen Krankheiten ist ein Beitrag seltener Varianten zu erwarten, wie können diese Varianten identifiziert werden, und welches Potenzial bieten seltene Varianten für das Verständnis biologischer Prozesse bzw. für die Translation in die klinische Praxis?
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Affiliation(s)
- Kerstin U. Ludwig
- Aff2 0000 0000 8786 803X grid.15090.3d Emmy-Noether-Gruppe „Kraniofaziale Genomik“, Institut für Humangenetik U ni ver si täts kli ni kum Bonn Venusberg-Campus 1, Gebäude 76 53127 Bonn Deutschland
| | - Franziska Degenhardt
- Aff1 0000 0000 8786 803X grid.15090.3d Institut für Humangenetik Universitätsklinikum Bonn Bonn Deutschland
| | - Markus M. Nöthen
- Aff1 0000 0000 8786 803X grid.15090.3d Institut für Humangenetik Universitätsklinikum Bonn Bonn Deutschland
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Swaidani S, Liu C, Zhao J, Bulek K, Li X. TRAF Regulation of IL-17 Cytokine Signaling. Front Immunol 2019; 10:1293. [PMID: 31316496 PMCID: PMC6610456 DOI: 10.3389/fimmu.2019.01293] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 05/21/2019] [Indexed: 01/23/2023] Open
Abstract
Tumor necrosis factor receptor (TNFR)-associated factors or (TRAFs) are important mediators of Interleukin-17 (IL-17) cytokine signaling and contribute to driving tissue responses that are crucial for protective immunity but are often implicated in immunopathology. By amplifying tissue immune activity, IL-17 cytokine pathways contribute to maintaining barrier function as well as activation of innate and adaptive immunity necessary for host defense. IL-17 receptors signaling is orchestrated in part, by the engagement of TRAFs and the subsequent unlocking of downstream cellular machinery that can promote pathogen clearance or contribute to immune dysregulation, chronic inflammation, and disease. Originally identified as signaling adaptors for TNFR superfamily, TRAF proteins can mediate the signaling of a variety of intercellular and extracellular stimuli and have been shown to regulate the downstream activity of many cytokine receptors including receptors for IL-1β, IL-2, IL-6, IL-17, IL-18, IL-33, type I IFNs, type III IFNs, GM-CSF, M-CSF, and TGF-β Toll-like receptors (TLRs), NOD-like receptors (NLRs), RIG-I- like receptors, and C-type lectin receptors. This review will focus on discussing studies that reveal our current understanding of how TRAFs mediate and regulate biochemical activities downstream of the IL-17 cytokines signaling.
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Affiliation(s)
- Shadi Swaidani
- Department of Inflammation and Immunity, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, United States.,Department of Cardiovascular & Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, United States
| | - Caini Liu
- Department of Inflammation and Immunity, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, United States
| | - Junjie Zhao
- Department of Inflammation and Immunity, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, United States
| | - Katarzyna Bulek
- Department of Inflammation and Immunity, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, United States
| | - Xiaoxia Li
- Department of Inflammation and Immunity, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, United States
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Dovrolis N, Filidou E, Kolios G. Systems biology in inflammatory bowel diseases: on the way to precision medicine. Ann Gastroenterol 2019; 32:233-246. [PMID: 31040620 PMCID: PMC6479645 DOI: 10.20524/aog.2019.0373] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/25/2019] [Indexed: 02/07/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are chronic and recurrent inflammatory disorders of the gastrointestinal tract. The elucidation of their etiopathology requires complex and multiple approaches. Systems biology has come to fulfill this need in approaching the pathogenetic mechanisms of IBD and its etiopathology, in a comprehensive way, by combining data from different scientific sources. In combination with bioinformatics and network medicine, it uses principles from computer science, mathematics, physics, chemistry, biology, medicine and computational tools to achieve its purposes. Systems biology utilizes scientific sources that provide data from omics studies (e.g., genomics, transcriptomics, etc.) and clinical observations, whose combined analysis leads to network formation and ultimately to a more integrative image of disease etiopathogenesis. In this review, we analyze the current literature on the methods and the tools utilized by systems biology in order to cover an innovative and exciting field: IBD-omics.
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Affiliation(s)
- Nikolas Dovrolis
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Eirini Filidou
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - George Kolios
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
- Correspondence to: Prof. George Kolios, MD PhD, Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Dragana, Alexandroupolis, 68100, Greece, e-mail:
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Zhang H, Zeng Z, Mukherjee A, Shen B. Molecular diagnosis and classification of inflammatory bowel disease. Expert Rev Mol Diagn 2018; 18:867-886. [PMID: 30152711 DOI: 10.1080/14737159.2018.1516549] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Traditional diagnosis and classification of inflammatory bowel diseases (IBDs) have been based on clinical evaluation, laboratory testing, endoscopy, imaging, and histological examinations. With the advancement of medical technology, an increasing number of molecular surrogates are playing a key role in diagnosis, differential diagnosis, assessment of disease activity, prediction of clinical course, and therapeutic response of IBD. Areas covered: The authors review roles of both existing and emerging surrogates including genetic, serological, histologic, and fecal markers in diagnosis and classification of IBD. Comparisons in advantages and disadvantages of different markers have also been discussed. In addition, this review underscores controversial and unclear aspects which need further study. Expert commentary: IBD is characteristic of chronicity, relapse-remission and destructiveness. It is of great importance for clinicians to make an accurate diagnosis and classification. Current and new molecular markers perform well with acceptable sensitivity and specificity. The use of molecular markers in clinical practice needs to be further explored and then generalized. More work is warranted to identify novel useful markers and elucidate how to apply them together with current markers in clinical settings.
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Affiliation(s)
- Hu Zhang
- a Center for Inflammatory Bowel Disease & Department of Gastroenterology , West China Hospital, Sichuan University , Chengdu , China
| | - Zhen Zeng
- a Center for Inflammatory Bowel Disease & Department of Gastroenterology , West China Hospital, Sichuan University , Chengdu , China
| | - Arjudeb Mukherjee
- b West China School of Medicine , Sichuan University , Chengdu , China
| | - Bo Shen
- c Center for Inflammatory Bowel Disease, Digestive Disease and Surgery Institute, The Cleveland Clinic Foundation , Cleveland , Ohio , USA
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Kwon YC, Kim JJ, Yun SW, Yu JJ, Yoon KL, Lee KY, Kil HR, Kim GB, Han MK, Song MS, Lee HD, Ha KS, Sohn S, Ebata R, Hamada H, Suzuki H, Ito K, Onouchi Y, Hong YM, Jang GY, Lee JK. Male-specific association of the FCGR2A His167Arg polymorphism with Kawasaki disease. PLoS One 2017; 12:e0184248. [PMID: 28886140 PMCID: PMC5590908 DOI: 10.1371/journal.pone.0184248] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/17/2017] [Indexed: 01/18/2023] Open
Abstract
Kawasaki disease (KD) is an acute systemic vasculitis that can potentially cause coronary artery aneurysms in some children. KD occurs approximately 1.5 times more frequently in males than in females. To identify sex-specific genetic variants that are involved in KD pathogenesis in children, we performed a sex-stratified genome-wide association study (GWAS), using the Illumina HumanOmni1-Quad BeadChip data (249 cases and 1,000 controls) and a replication study for the 34 sex-specific candidate SNPs in an independent sample set (671 cases and 3,553 controls). Male-specific associations were detected in three common variants: rs1801274 in FCGR2A [odds ratio (OR) = 1.40, P = 9.31 × 10-5], rs12516652 in SEMA6A (OR = 1.87, P = 3.12 × 10-4), and rs5771303 near IL17REL (OR = 1.57, P = 2.53 × 10-5). The male-specific association of FCGR2A, but not SEMA6A and IL17REL, was also replicated in a Japanese population (OR = 1.74, P = 1.04 × 10-4 in males vs. OR = 1.22, P = 0.191 in females). In a meta-analysis with 1,461 cases and 5,302 controls, a very strong association of KD with the nonsynonymous SNP rs1801274 (p.His167Arg, previously assigned as p.His131Arg) in FCGR2A was confirmed in males (OR = 1.48, P = 1.43 × 10-7), but not in the females (OR = 1.17, P = 0.055). The present study demonstrates that p.His167Arg, a KD-associated FCGR2A variant, acts as a susceptibility gene in males only. Overall, the gender differences associated with FCGR2A in KD provide a new insight into KD susceptibility.
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Affiliation(s)
- Young-Chang Kwon
- Asan Institute for Life Sciences, University of Ulsan College of Medicine, Seoul, Korea
| | - Jae-Jung Kim
- Asan Institute for Life Sciences, University of Ulsan College of Medicine, Seoul, Korea
| | - Sin Weon Yun
- Department of Pediatrics, Chung-Ang University Hospital, Seoul, Korea
| | - Jeong Jin Yu
- Department of Pediatrics, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
| | - Kyung Lim Yoon
- Department of Pediatrics, Kyung Hee University Hospital at Gangdong, Seoul, Korea
| | - Kyung-Yil Lee
- Department of Pediatrics, The Catholic University of Korea, Daejeon St. Mary’s Hospital, Daejeon, Korea
| | - Hong-Ryang Kil
- Department of Pediatrics, Chungnam National University Hospital, Daejeon, Korea
| | - Gi Beom Kim
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea
| | - Myung-Ki Han
- Department of Pediatrics, University of Ulsan, Gangneung Asan Hospital, Gangneung, Korea
| | - Min Seob Song
- Department of Pediatrics, Inje University Haeundae Paik Hospital, Busan, Korea
| | - Hyoung Doo Lee
- Department of Pediatrics, Pusan National University Hospital, Busan, Korea
| | - Kee-Soo Ha
- Department of Pediatrics, Korea University Hospital, Seoul, Korea
| | - Sejung Sohn
- Department of Pediatrics, Ewha Womans University Hospital, Seoul, Korea
| | - Ryota Ebata
- Department of Pediatrics, Chiba-University Graduate School of Medicine, Chiba, Japan
| | - Hiromichi Hamada
- Department of Pediatrics, Tokyo Women’s Medical University Yachiyo Medical Center, Yachiyo, Japan
| | - Hiroyuki Suzuki
- Department of Pediatrics, Wakayama Medical University, Wakayama, Japan
| | - Kaoru Ito
- Laboratory for Cardiovascular diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoshihiro Onouchi
- Laboratory for Cardiovascular diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Public Health, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Young Mi Hong
- Department of Pediatrics, Ewha Womans University Hospital, Seoul, Korea
| | - Gi Young Jang
- Department of Pediatrics, Korea University Hospital, Seoul, Korea
| | - Jong-Keuk Lee
- Asan Institute for Life Sciences, University of Ulsan College of Medicine, Seoul, Korea
- * E-mail:
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Uhlig HH, Muise AM. Clinical Genomics in Inflammatory Bowel Disease. Trends Genet 2017; 33:629-641. [PMID: 28755896 DOI: 10.1016/j.tig.2017.06.008] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 06/25/2017] [Accepted: 06/27/2017] [Indexed: 12/19/2022]
Abstract
Genomic technologies inform the complex genetic basis of polygenic inflammatory bowel disease (IBD) as well as Mendelian disease-associated IBD. Aiming to diagnose patients that present with extreme phenotypes due to monogenic forms of IBD, genomics has progressed from 'orphan disease' research towards an integrated standard of clinical care. Advances in diagnostic clinical genomics are increasingly complemented by pathway-specific therapies that aim to correct the consequences of genetic defects. This highlights the exceptional potential for personalized precision medicine. IBD is nevertheless a challenging example for genomic medicine because the overall fraction of patients with Mendelian defects is low, the number of potential candidate genes is high, and interventional evidence is still emerging. We discuss requirements and prospects of explanatory and predictive clinical genomics in IBD.
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Affiliation(s)
- Holm H Uhlig
- Translational Gastroenterology Unit, University of Oxford, UK; Department of Paediatrics, University of Oxford, UK.
| | - Aleixo M Muise
- Program in Cell Biology, Research Institute, Hospital for Sick Children, Toronto, ON, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, Canada; SickKids Inflammatory Bowel Disease Centre and Division of Gastroenterology, Hepatology, and Nutrition, Department of Paediatrics, University of Toronto, Hospital for Sick Children, Toronto, ON, Canada
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Abernathy J, Brezas A, Snekvik KR, Hardy RW, Overturf K. Integrative functional analyses using rainbow trout selected for tolerance to plant diets reveal nutrigenomic signatures for soy utilization without the concurrence of enteritis. PLoS One 2017; 12:e0180972. [PMID: 28723948 PMCID: PMC5517010 DOI: 10.1371/journal.pone.0180972] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 06/24/2017] [Indexed: 12/13/2022] Open
Abstract
Finding suitable alternative protein sources for diets of carnivorous fish species remains a major concern for sustainable aquaculture. Through genetic selection, we created a strain of rainbow trout that outperforms parental lines in utilizing an all-plant protein diet and does not develop enteritis in the distal intestine, as is typical with salmonids on long-term plant protein-based feeds. By incorporating this strain into functional analyses, we set out to determine which genes are critical to plant protein utilization in the absence of gut inflammation. After a 12-week feeding trial with our selected strain and a control trout strain fed either a fishmeal-based diet or an all-plant protein diet, high-throughput RNA sequencing was completed on both liver and muscle tissues. Differential gene expression analyses, weighted correlation network analyses and further functional characterization were performed. A strain-by-diet design revealed differential expression ranging from a few dozen to over one thousand genes among the various comparisons and tissues. Major gene ontology groups identified between comparisons included those encompassing central, intermediary and foreign molecule metabolism, associated biosynthetic pathways as well as immunity. A systems approach indicated that genes involved in purine metabolism were highly perturbed. Systems analysis among the tissues tested further suggests the interplay between selection for growth, dietary utilization and protein tolerance may also have implications for nonspecific immunity. By combining data from differential gene expression and co-expression networks using selected trout, along with ontology and pathway analyses, a set of 63 candidate genes for plant diet tolerance was found. Risk loci in human inflammatory bowel diseases were also found in our datasets, indicating rainbow trout selected for plant-diet tolerance may have added utility as a potential biomedical model.
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Affiliation(s)
- Jason Abernathy
- Hagerman Fish Culture Experiment Station, USDA-ARS, Hagerman, Idaho, United States of America
| | - Andreas Brezas
- Aquaculture Research Institute, University of Idaho, Hagerman, Idaho, United States of America
| | - Kevin R. Snekvik
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, United States of America
| | - Ronald W. Hardy
- Aquaculture Research Institute, University of Idaho, Hagerman, Idaho, United States of America
| | - Ken Overturf
- Hagerman Fish Culture Experiment Station, USDA-ARS, Hagerman, Idaho, United States of America
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Genetic architecture differences between pediatric and adult-onset inflammatory bowel diseases in the Polish population. Sci Rep 2016; 6:39831. [PMID: 28008999 PMCID: PMC5180213 DOI: 10.1038/srep39831] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 11/29/2016] [Indexed: 12/15/2022] Open
Abstract
Most inflammatory bowel diseases (IBDs) are classic complex disorders represented by common alleles. Here we aimed to define the genetic architecture of pediatric and adult-onset IBDs for the Polish population. A total of 1495 patients were recruited, including 761 patients with Crohn’s disease (CD; 424 pediatric), 734 patients with ulcerative colitis (UC; 390 pediatric), and 934 healthy controls. Allelotyping employed a pooled-DNA genome-wide association study (GWAS) and was validated by individual genotyping. Whole exome sequencing (WES) was performed on 44 IBD patients diagnosed before 6 years of age, 45 patients diagnosed after 40 years of age, and 18 healthy controls. Altogether, out of 88 selected SNPs, 31 SNPs were replicated for association with IBD. A novel BRD2 (rs1049526) association reached significance of P = 5.2 × 10−11 and odds ratio (OR) = 2.43. Twenty SNPs were shared between pediatric and adult patients; 1 and 7 were unique to adult-onset and pediatric-onset IBD, respectively. WES identified numerous rare and potentially deleterious variants in IBD-associated or innate immunity-associated genes. Deleterious alleles in both groups were over-represented among rare variants in affected children. Our GWAS revealed differences in the polygenic architecture of pediatric- and adult-onset IBD. A significant accumulation of rare and deleterious variants in affected children suggests a contribution by yet unexplained genetic components.
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Abstract
Atrial fibrillation (AF) is a morbid and heritable arrhythmia. Over 35 genes have been reported to underlie AF, most of which were described in small candidate gene association studies. Replication remains lacking for most, and therefore the contribution of coding variation to AF susceptibility remains poorly understood. We examined whole exome sequencing data in a large community-based sample of 1,734 individuals with and 9,423 without AF from the Framingham Heart Study, Cardiovascular Health Study, Atherosclerosis Risk in Communities Study, and NHLBI-GO Exome Sequencing Project and meta-analyzed the results. We also examined whether genetic variation was enriched in suspected AF genes (N = 37) in AF cases versus controls. The mean age ranged from 59 to 73 years; 8,656 (78%) were of European ancestry. None of the 99,404 common variants evaluated was significantly associated after adjusting for multiple testing. Among the most significantly associated variants was a common (allele frequency = 86%) missense variant in SYNPO2L (rs3812629, p.Pro707Leu, [odds ratio 1.27, 95% confidence interval 1.13-1.43, P = 6.6x10-5]) which lies at a known AF susceptibility locus and is in linkage disequilibrium with a top marker from prior analyses at the locus. We did not observe significant associations between rare variants and AF in gene-based tests. Individuals with AF did not display any statistically significant enrichment for common or rare coding variation in previously implicated AF genes. In conclusion, we did not observe associations between coding genetic variants and AF, suggesting that large-effect coding variation is not the predominant mechanism underlying AF. A coding variant in SYNPO2L requires further evaluation to determine whether it is causally related to AF. Efforts to identify biologically meaningful coding variation underlying AF may require large sample sizes or populations enriched for large genetic effects.
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Bimber BN, Raboin MJ, Letaw J, Nevonen KA, Spindel JE, McCouch SR, Cervera-Juanes R, Spindel E, Carbone L, Ferguson B, Vinson A. Whole-genome characterization in pedigreed non-human primates using genotyping-by-sequencing (GBS) and imputation. BMC Genomics 2016; 17:676. [PMID: 27558348 PMCID: PMC4997765 DOI: 10.1186/s12864-016-2966-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Accepted: 07/22/2016] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Rhesus macaques are widely used in biomedical research, but the application of genomic information in this species to better understand human disease is still in its infancy. Whole-genome sequence (WGS) data in large pedigreed macaque colonies could provide substantial experimental power for genetic discovery, but the collection of WGS data in large cohorts remains a formidable expense. Here, we describe a cost-effective approach that selects the most informative macaques in a pedigree for 30X WGS, followed by low-cost genotyping-by-sequencing (GBS) at 30X on the remaining macaques in order to generate sparse genotype data at high accuracy. Dense variants from the selected macaques with WGS data are then imputed into macaques having only sparse GBS data, resulting in dense genome-wide genotypes throughout the pedigree. RESULTS We developed GBS for the macaque genome using a digestion with PstI, followed by sequencing of size-selected fragments at 30X coverage. From GBS sequence data collected on all individuals in a 16-member pedigree, we characterized high-confidence genotypes at 22,455 single nucleotide variant (SNV) sites that were suitable for guiding imputation of dense sequence data from WGS. To characterize dense markers for imputation, we performed WGS at 30X coverage on nine of the 16 individuals, yielding 10,193,425 high-confidence SNVs. To validate the use of GBS data for facilitating imputation, we initially focused on chromosome 19 as a test case, using an optimized panel of 833 sparse, evenly-spaced markers from GBS and 5,010 dense markers from WGS. Using the method of "Genotype Imputation Given Inheritance" (GIGI), we evaluated the effects on imputation accuracy of 3 different strategies for selecting individuals for WGS, including 1) using "GIGI-Pick" to select the most informative individuals, 2) using the most recent generation, or 3) using founders only. We also evaluated the effects on imputation accuracy of using a range of from 1 to 9 WGS individuals for imputation. We found that the GIGI-Pick algorithm for selection of WGS individuals outperformed common heuristic approaches, and that genotype numbers and accuracy improved very little when using >5 WGS individuals for imputation. Informed by our findings, we used 4 macaques with WGS data to impute variants at up to 7,655,491 sites spanning all 20 autosomes in the 12 remaining macaques, based on their GBS genotypes at only 17,158 loci. Using a strict confidence threshold, we imputed an average of 3,680,238 variants per individual at >99 % accuracy, or an average 4,458,883 variants per individual at a more relaxed threshold, yielding >97 % accuracy. CONCLUSIONS We conclude that an optimal tradeoff between genotype accuracy, number of imputed genotypes, and overall cost exists at the ratio of one individual selected for WGS using the GIGI-Pick algorithm, per 3-5 relatives selected for GBS. This approach makes feasible the collection of accurate, dense genome-wide sequence data in large pedigreed macaque cohorts without the need for more expensive WGS data on all individuals.
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Affiliation(s)
- Benjamin N Bimber
- Primate Genetics Section, Oregon National Primate Research Center, Beaverton, OR, USA.,Oregon Health & Science University, Portland, OR, USA
| | - Michael J Raboin
- Primate Genetics Section, Oregon National Primate Research Center, Beaverton, OR, USA.,Oregon Health & Science University, Portland, OR, USA
| | - John Letaw
- Primate Genetics Section, Oregon National Primate Research Center, Beaverton, OR, USA.,Oregon Health & Science University, Portland, OR, USA
| | - Kimberly A Nevonen
- Primate Genetics Section, Oregon National Primate Research Center, Beaverton, OR, USA.,Oregon Health & Science University, Portland, OR, USA
| | - Jennifer E Spindel
- Section of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, USA
| | - Susan R McCouch
- Section of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, USA
| | - Rita Cervera-Juanes
- Primate Genetics Section, Oregon National Primate Research Center, Beaverton, OR, USA.,Oregon Health & Science University, Portland, OR, USA
| | - Eliot Spindel
- Primate Genetics Section, Oregon National Primate Research Center, Beaverton, OR, USA.,Oregon Health & Science University, Portland, OR, USA
| | - Lucia Carbone
- Primate Genetics Section, Oregon National Primate Research Center, Beaverton, OR, USA.,Oregon Health & Science University, Portland, OR, USA
| | - Betsy Ferguson
- Primate Genetics Section, Oregon National Primate Research Center, Beaverton, OR, USA.,Oregon Health & Science University, Portland, OR, USA
| | - Amanda Vinson
- Primate Genetics Section, Oregon National Primate Research Center, Beaverton, OR, USA. .,Oregon Health & Science University, Portland, OR, USA.
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