1
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Zhu X, Ma S, Wong WH. Genetic effects of sequence-conserved enhancer-like elements on human complex traits. Genome Biol 2024; 25:1. [PMID: 38167462 PMCID: PMC10759394 DOI: 10.1186/s13059-023-03142-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/08/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND The vast majority of findings from human genome-wide association studies (GWAS) map to non-coding sequences, complicating their mechanistic interpretations and clinical translations. Non-coding sequences that are evolutionarily conserved and biochemically active could offer clues to the mechanisms underpinning GWAS discoveries. However, genetic effects of such sequences have not been systematically examined across a wide range of human tissues and traits, hampering progress to fully understand regulatory causes of human complex traits. RESULTS Here we develop a simple yet effective strategy to identify functional elements exhibiting high levels of human-mouse sequence conservation and enhancer-like biochemical activity, which scales well to 313 epigenomic datasets across 106 human tissues and cell types. Combined with 468 GWAS of European (EUR) and East Asian (EAS) ancestries, these elements show tissue-specific enrichments of heritability and causal variants for many traits, which are significantly stronger than enrichments based on enhancers without sequence conservation. These elements also help prioritize candidate genes that are functionally relevant to body mass index (BMI) and schizophrenia but were not reported in previous GWAS with large sample sizes. CONCLUSIONS Our findings provide a comprehensive assessment of how sequence-conserved enhancer-like elements affect complex traits in diverse tissues and demonstrate a generalizable strategy of integrating evolutionary and biochemical data to elucidate human disease genetics.
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Affiliation(s)
- Xiang Zhu
- Department of Statistics, The Pennsylvania State University, 326 Thomas Building, University Park, 16802, PA, USA.
- Huck Institutes of the Life Sciences, The Pennsylvania State University, 201 Huck Life Sciences Building, University Park, 16802, PA, USA.
- Department of Statistics, Stanford University, 390 Jane Stanford Way, Stanford, 94305, CA, USA.
| | - Shining Ma
- Department of Statistics, Stanford University, 390 Jane Stanford Way, Stanford, 94305, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, 1265 Welch Road MC5464, Stanford, 94305, CA, USA
| | - Wing Hung Wong
- Department of Statistics, Stanford University, 390 Jane Stanford Way, Stanford, 94305, CA, USA.
- Department of Biomedical Data Science, Stanford University School of Medicine, 1265 Welch Road MC5464, Stanford, 94305, CA, USA.
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2
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Ben-Zvi I, Karasik D, Ackert-Bicknell CL. Zebrafish as a Model for Osteoporosis: Functional Validations of Genome-Wide Association Studies. Curr Osteoporos Rep 2023; 21:650-659. [PMID: 37971665 DOI: 10.1007/s11914-023-00831-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/02/2023] [Indexed: 11/19/2023]
Abstract
PURPOSE OF REVIEW GWAS, as a largely correlational analysis, requires in vitro or in vivo validation. Zebrafish (Danio rerio) have many advantages for studying the genetics of human diseases. Since gene editing in zebrafish has been highly valuable for studying embryonic skeletal developmental processes that are prenatally or perinatally lethal in mammalian models, we are reviewing pros and cons of this model. RECENT FINDINGS The true power for the use of zebrafish is the ease by which the genome can be edited, especially using the CRISPR/Cas9 system. Gene editing, followed by phenotyping, for complex traits such as BMD, is beneficial, but the major physiological differences between the fish and mammals must be considered. Like mammals, zebrafish do have main bone cells; thus, both in vivo stem cell analyses and in vivo imaging are doable. Yet, the "long" bones of fish are peculiar, and their bone cavities do not contain bone marrow. Partial duplication of the zebrafish genome should be taken into account. Overall, small fish toolkit can provide unmatched opportunities for genetic modifications and morphological investigation as a follow-up to human-first discovery.
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Affiliation(s)
- Inbar Ben-Zvi
- The Musculoskeletal Genetics Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - David Karasik
- The Musculoskeletal Genetics Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel.
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3
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Weichert-Leahey N, Shi H, Tao T, Oldridge DA, Durbin AD, Abraham BJ, Zimmerman MW, Zhu S, Wood AC, Reyon D, Joung JK, Young RA, Diskin SJ, Maris JM, Look AT. Genetic predisposition to neuroblastoma results from a regulatory polymorphism that promotes the adrenergic cell state. J Clin Invest 2023; 133:e166919. [PMID: 37183825 PMCID: PMC10178836 DOI: 10.1172/jci166919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/14/2023] [Indexed: 05/16/2023] Open
Abstract
Childhood neuroblastomas exhibit plasticity between an undifferentiated neural crest-like mesenchymal cell state and a more differentiated sympathetic adrenergic cell state. These cell states are governed by autoregulatory transcriptional loops called core regulatory circuitries (CRCs), which drive the early development of sympathetic neuronal progenitors from migratory neural crest cells during embryogenesis. The adrenergic cell identity of neuroblastoma requires LMO1 as a transcriptional cofactor. Both LMO1 expression levels and the risk of developing neuroblastoma in children are associated with a single nucleotide polymorphism, G/T, that affects a GATA motif in the first intron of LMO1. Here, we showed that WT zebrafish with the GATA genotype developed adrenergic neuroblastoma, while knock-in of the protective TATA allele at this locus reduced the penetrance of MYCN-driven tumors, which were restricted to the mesenchymal cell state. Whole genome sequencing of childhood neuroblastomas demonstrated that TATA/TATA tumors also exhibited a mesenchymal cell state and were low risk at diagnosis. Thus, conversion of the regulatory GATA to a TATA allele in the first intron of LMO1 reduced the neuroblastoma-initiation rate by preventing formation of the adrenergic cell state. This mechanism was conserved over 400 million years of evolution, separating zebrafish and humans.
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Affiliation(s)
- Nina Weichert-Leahey
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Division of Pediatric Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Hui Shi
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ting Tao
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- National Clinical Research Center for Child Health, National Children’s Regional Medical Center, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Derek A. Oldridge
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Adam D. Durbin
- Department of Oncology and Comprehensive Cancer Center, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Brian J. Abraham
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Mark W. Zimmerman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Shizhen Zhu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, Minnesota, USA
| | - Andrew C. Wood
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Science, University of Auckland, Auckland, New Zealand
| | - Deepak Reyon
- Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - J. Keith Joung
- Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Richard A. Young
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Biology Department, MIT, Cambridge, Massachusetts, USA
| | - Sharon J. Diskin
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John M. Maris
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - A. Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Division of Pediatric Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts, USA
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4
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Weichert-Leahey N, Shi H, Tao T, Oldridge DA, Durbin AD, Abraham BJ, Zimmerman MW, Zhu S, Wood AC, Reyon D, Joung JK, Young RA, Diskin SJ, Maris JM, Look AT. Genetic Predisposition to Neuroblastoma Results from a Regulatory Polymorphism that Promotes the Adrenergic Cell State. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.28.530457. [PMID: 36909587 PMCID: PMC10002714 DOI: 10.1101/2023.02.28.530457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Childhood neuroblastomas exhibit plasticity between an undifferentiated neural crest-like "mesenchymal" cell state and a more differentiated sympathetic "adrenergic" cell state. These cell states are governed by autoregulatory transcriptional loops called core regulatory circuitries (CRCs), which drive the early development of sympathetic neuronal progenitors from migratory neural crest cells during embryogenesis. The adrenergic cell identity of neuroblastoma requires LMO1 as a transcriptional co-factor. Both LMO1 expression levels and the risk of developing neuroblastoma in children are associated with a single nucleotide polymorphism G/T that affects a G ATA motif in the first intron of LMO1. Here we show that wild-type zebrafish with the G ATA genotype develop adrenergic neuroblastoma, while knock-in of the protective T ATA allele at this locus reduces the penetrance of MYCN-driven tumors, which are restricted to the mesenchymal cell state. Whole genome sequencing of childhood neuroblastomas demonstrates that T ATA/ T ATA tumors also exhibit a mesenchymal cell state and are low risk at diagnosis. Thus, conversion of the regulatory G ATA to a T ATA allele in the first intron of LMO1 reduces the neuroblastoma initiation rate by preventing formation of the adrenergic cell state, a mechanism that is conserved over 400 million years of evolution separating zebrafish and humans.
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5
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Thomas ED, Timms AE, Giles S, Harkins-Perry S, Lyu P, Hoang T, Qian J, Jackson VE, Bahlo M, Blackshaw S, Friedlander M, Eade K, Cherry TJ. Cell-specific cis-regulatory elements and mechanisms of non-coding genetic disease in human retina and retinal organoids. Dev Cell 2022; 57:820-836.e6. [PMID: 35303433 PMCID: PMC9126240 DOI: 10.1016/j.devcel.2022.02.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 12/06/2021] [Accepted: 02/18/2022] [Indexed: 01/05/2023]
Abstract
Cis-regulatory elements (CREs) play a critical role in the development and disease-states of all human cell types. In the retina, CREs have been implicated in several inherited disorders. To better characterize human retinal CREs, we performed single-nucleus assay for transposase-accessible chromatin sequencing (snATAC-seq) and single-nucleus RNA sequencing (snRNA-seq) on the developing and adult human retina and on induced pluripotent stem cell (iPSC)-derived retinal organoids. These analyses identified developmentally dynamic, cell-class-specific CREs, enriched transcription-factor-binding motifs, and putative target genes. CREs in the retina and organoids are highly correlated at the single-cell level, and this supports the use of organoids as a model for studying disease-associated CREs. As a proof of concept, we disrupted a disease-associated CRE at 5q14.3, confirming its principal target gene as the miR-9-2 primary transcript and demonstrating its role in neurogenesis and gene regulation in mature glia. This study provides a resource for characterizing human retinal CREs and showcases organoids as a model to study the function of CREs that influence development and disease.
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Affiliation(s)
- Eric D Thomas
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Andrew E Timms
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Sarah Giles
- Lowy Medical Research Institute, La Jolla, CA 92037, USA; Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sarah Harkins-Perry
- Lowy Medical Research Institute, La Jolla, CA 92037, USA; Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Pin Lyu
- Department of Ophthalmology, Wilmer Eye Institute Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Thanh Hoang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jiang Qian
- Department of Ophthalmology, Wilmer Eye Institute Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Victoria E Jackson
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, VIC, Australia; Department of Medical Biology, The University of Melbourne, Parkville 3052, VIC, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, VIC, Australia; Department of Medical Biology, The University of Melbourne, Parkville 3052, VIC, Australia
| | - Seth Blackshaw
- Department of Ophthalmology, Wilmer Eye Institute Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Martin Friedlander
- Lowy Medical Research Institute, La Jolla, CA 92037, USA; Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kevin Eade
- Lowy Medical Research Institute, La Jolla, CA 92037, USA; Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Timothy J Cherry
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA; Department of Biological Structure, University of Washington School of Medicine, Seattle, WA 98195, USA; Department of Ophthalmology, University of Washington School of Medicine, Seattle, WA 98195, USA; Brotman Baty Institute, Seattle, WA 98195, USA.
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6
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Osman N, Shawky AEM, Brylinski M. Exploring the effects of genetic variation on gene regulation in cancer in the context of 3D genome structure. BMC Genom Data 2022; 23:13. [PMID: 35176995 PMCID: PMC8851830 DOI: 10.1186/s12863-021-01021-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/23/2021] [Indexed: 12/31/2022] Open
Abstract
Background Numerous genome-wide association studies (GWAS) conducted to date revealed genetic variants associated with various diseases, including breast and prostate cancers. Despite the availability of these large-scale data, relatively few variants have been functionally characterized, mainly because the majority of single-nucleotide polymorphisms (SNPs) map to the non-coding regions of the human genome. The functional characterization of these non-coding variants and the identification of their target genes remain challenging. Results In this communication, we explore the potential functional mechanisms of non-coding SNPs by integrating GWAS with the high-resolution chromosome conformation capture (Hi-C) data for breast and prostate cancers. We show that more genetic variants map to regulatory elements through the 3D genome structure than the 1D linear genome lacking physical chromatin interactions. Importantly, the association of enhancers, transcription factors, and their target genes with breast and prostate cancers tends to be higher when these regulatory elements are mapped to high-risk SNPs through spatial interactions compared to simply using a linear proximity. Finally, we demonstrate that topologically associating domains (TADs) carrying high-risk SNPs also contain gene regulatory elements whose association with cancer is generally higher than those belonging to control TADs containing no high-risk variants. Conclusions Our results suggest that many SNPs may contribute to the cancer development by affecting the expression of certain tumor-related genes through long-range chromatin interactions with gene regulatory elements. Integrating large-scale genetic datasets with the 3D genome structure offers an attractive and unique approach to systematically investigate the functional mechanisms of genetic variants in disease risk and progression. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-01021-x.
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Affiliation(s)
- Noha Osman
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.,Department of Cell Biology, National Research Centre, Giza, 12622, Egypt.,Department of Medicine, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Abd-El-Monsif Shawky
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Michal Brylinski
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA. .,Center for Computation and Technology, Louisiana State University, Baton Rouge, LA, 70803, USA.
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7
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Functional Validation of Osteoporosis Genetic Findings Using Small Fish Models. Genes (Basel) 2022; 13:genes13020279. [PMID: 35205324 PMCID: PMC8872034 DOI: 10.3390/genes13020279] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 12/11/2022] Open
Abstract
The advancement of human genomics has revolutionized our understanding of the genetic architecture of many skeletal diseases, including osteoporosis. However, interpreting results from human association studies remains a challenge, since index variants often reside in non-coding regions of the genome and do not possess an obvious regulatory function. To bridge the gap between genetic association and causality, a systematic functional investigation is necessary, such as the one offered by animal models. These models enable us to identify causal mechanisms, clarify the underlying biology, and apply interventions. Over the past several decades, small teleost fishes, mostly zebrafish and medaka, have emerged as powerful systems for modeling the genetics of human diseases. Due to their amenability to genetic intervention and the highly conserved genetic and physiological features, fish have become indispensable for skeletal genomic studies. The goal of this review is to summarize the evidence supporting the utility of Zebrafish (Danio rerio) for accelerating our understanding of human skeletal genomics and outlining the remaining gaps in knowledge. We provide an overview of zebrafish skeletal morphophysiology and gene homology, shedding light on the advantages of human skeletal genomic exploration and validation. Knowledge of the biology underlying osteoporosis through animal models will lead to the translation into new, better and more effective therapeutic approaches.
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8
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Dhar S, Mridha S, Bhattacharjee P. Mutational Landscape Screening Through Comprehensive In Silico Analysis for Polycystic Ovarian Syndrome-Related Genes. Reprod Sci 2021; 29:480-496. [PMID: 34697776 DOI: 10.1007/s43032-021-00752-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/25/2021] [Indexed: 12/14/2022]
Abstract
Polycystic ovary syndrome (PCOS) is a multifactorial endocrinopathy of indistinguishable etiopathogenesis that is liable to entail genetic and environmental machinery synergistically interacting with its phenotypic expression. It has been hypothesized that the environment secondarily interacts with genes to define the quantifiable phenotype in a primary, genetically determined, hyper-androgenic ovarian defect. The severity and prevalence of the disease are escalating due to uncontrolled diet and lifestyle, the influence of multiple environmental factors as well as genetic disorders. Many candidate genes have been identified to be one of the causes of PCOS. Different studies have been carried out to find the genetic correlation of PCOS. The mutational landscape analysis scans the entire genes for SNPs which usually occurs more frequently in patients and not in healthy individuals. In this study, an extensive computational analysis of all reported nsSNPs of the 27 selected PCOS-related genes was performed to infer the most pathogenic forms associated with PCOS. As a result, 28 genetic variants from 11 genes were predicted to be most harmful. Results of the present study can be useful for building an integrative genotype-phenotype database for further studies.
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Affiliation(s)
- Shrinjana Dhar
- Department of Environmental Science, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Saptarshi Mridha
- Department of Environmental Science, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
- Department of Biotechnology, St. Xavier's College (Autonomous), 30, Mother Teresa Sarani, Kolkata, 700016, India
| | - Pritha Bhattacharjee
- Department of Environmental Science, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India.
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Prabhu BN, Kanchamreddy SH, Sharma AR, Bhat SK, Bhat PV, Kabekkodu SP, Satyamoorthy K, Rai PS. Conceptualization of functional single nucleotide polymorphisms of polycystic ovarian syndrome genes: an in silico approach. J Endocrinol Invest 2021; 44:1783-1793. [PMID: 33506367 PMCID: PMC8285346 DOI: 10.1007/s40618-021-01498-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 01/02/2021] [Indexed: 12/24/2022]
Abstract
PURPOSE Polycystic ovarian syndrome (PCOS) is a multi-faceted endocrinopathy frequently observed in reproductive-aged females, causing infertility. Cumulative evidence revealed that genetic and epigenetic variations, along with environmental factors, were linked with PCOS. Deciphering the molecular pathways of PCOS is quite complicated due to the availability of limited molecular information. Hence, to explore the influence of genetic variations in PCOS, we mapped the GWAS genes and performed a computational analysis to identify the SNPs and their impact on the coding and non-coding sequences. METHODS The causative genes of PCOS were searched using the GWAS catalog, and pathway analysis was performed using ClueGO. SNPs were extracted using an Ensembl genome browser, and missense variants were shortlisted. Further, the native and mutant forms of the deleterious SNPs were modeled using I-TASSER, Swiss-PdbViewer, and PyMOL. MirSNP, PolymiRTS, miRNASNP3, and SNP2TFBS, SNPInspector databases were used to find SNPs in the miRNA binding site and transcription factor binding site (TFBS), respectively. EnhancerDB and HaploReg were used to characterize enhancer SNPs. Linkage Disequilibrium (LD) analysis was performed using LDlink. RESULTS 25 PCOS genes showed interaction with 18 pathways. 7 SNPs were predicted to be deleterious using different pathogenicity predictions. 4 SNPs were found in the miRNA target site, TFBS, and enhancer sites and were in LD with reported PCOS GWAS SNPs. CONCLUSION Computational analysis of SNPs residing in PCOS genes may provide insight into complex molecular interactions among genes involved in PCOS pathophysiology. It may also aid in determining the causal variants and consequently contributing to predicting disease strategies.
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Affiliation(s)
- B N Prabhu
- Department of Biotechnology, Manipal School of Life Sciences, MAHE, Manipal, Karnataka, India
| | - S H Kanchamreddy
- Department of Biotechnology, Manipal School of Life Sciences, MAHE, Manipal, Karnataka, India
| | - A R Sharma
- Department of Biotechnology, Manipal School of Life Sciences, MAHE, Manipal, Karnataka, India
| | - S K Bhat
- Department of Obstetrics and Gynaecology, Dr. T.M.A Pai Hospital, MMMC, MAHE, Manipal, Karnataka, India
| | - P V Bhat
- Department of Obstetrics and Gynaecology, Dr. T.M.A Pai Hospital, MMMC, MAHE, Manipal, Karnataka, India
| | - S P Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, MAHE, Manipal, Karnataka, India
| | - K Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, MAHE, Manipal, Karnataka, India
| | - P S Rai
- Department of Biotechnology, Manipal School of Life Sciences, MAHE, Manipal, Karnataka, India.
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10
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Abstract
We developed dbCNS (http://yamasati.nig.ac.jp/dbcns), a new database for conserved noncoding sequences (CNSs). CNSs exist in many eukaryotes and are assumed to be involved in protein expression control. Version 1 of dbCNS, introduced here, includes a powerful and precise CNS identification pipeline for multiple vertebrate genomes. Mutations in CNSs may induce morphological changes and cause genetic diseases. For this reason, many vertebrate CNSs have been identified, with special reference to primate genomes. We integrated ∼6.9 million CNSs from many vertebrate genomes into dbCNS, which allows users to extract CNSs near genes of interest using keyword searches. In addition to CNSs, dbCNS contains published genome sequences of 161 species. With purposeful taxonomic sampling of genomes, users can employ CNSs as queries to reconstruct CNS alignments and phylogenetic trees, to evaluate CNS modifications, acquisitions, and losses, and to roughly identify species with CNSs having accelerated substitution rates. dbCNS also produces links to dbSNP for searching pathogenic single-nucleotide polymorphisms in human CNSs. Thus, dbCNS connects morphological changes with genetic diseases. A test analysis using 38 gnathostome genomes was accomplished within 30 s. dbCNS results can evaluate CNSs identified by other stand-alone programs using genome-scale data.
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Affiliation(s)
- Jun Inoue
- Population Genetics Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan.,Center for Earth Surface System Dynamics, Atmosphere and Ocean Research Institute, University of Tokyo, Kashiwa, Japan
| | - Naruya Saitou
- Population Genetics Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan.,Department of Okinawa Bioinformation Bank, Faculty of Medicine, University of the Ryukyus, Okinawa, Japan
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11
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Leypold NA, Speicher MR. Evolutionary conservation in noncoding genomic regions. Trends Genet 2021; 37:903-918. [PMID: 34238591 DOI: 10.1016/j.tig.2021.06.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/25/2021] [Accepted: 06/07/2021] [Indexed: 12/28/2022]
Abstract
Humans may share more genomic commonalities with other species than previously thought. According to current estimates, ~5% of the human genome is functionally constrained, which is a much larger fraction than the ~1.5% occupied by annotated protein-coding genes. Hence, ~3.5% of the human genome comprises likely functional conserved noncoding elements (CNEs) preserved among organisms, whose common ancestors existed throughout hundreds of millions of years of evolution. As whole-genome sequencing emerges as a standard procedure in genetic analyses, interpretation of variations in CNEs, including the elucidation of mechanistic and functional roles, becomes a necessity. Here, we discuss the phenomenon of noncoding conservation via four dimensions (sequence, regulatory conservation, spatiotemporal expression, and structure) and the potential significance of CNEs in phenotype variation and disease.
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Affiliation(s)
- Nicole A Leypold
- Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, 8010 Graz, Austria.
| | - Michael R Speicher
- Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, 8010 Graz, Austria; BioTechMed-Graz, Graz, Austria.
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12
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Efentakis P, Molitor M, Kossmann S, Bochenek ML, Wild J, Lagrange J, Finger S, Jung R, Karbach S, Schäfer K, Schulz A, Wild P, Münzel T, Wenzel P. Tubulin-folding cofactor E deficiency promotes vascular dysfunction by increased endoplasmic reticulum stress. Eur Heart J 2021; 43:488-500. [PMID: 34132336 PMCID: PMC8830526 DOI: 10.1093/eurheartj/ehab222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 10/29/2020] [Accepted: 03/26/2021] [Indexed: 12/14/2022] Open
Abstract
AIMS Assessment of endothelial function in humans by measuring flow-mediated dilation (FMD) risk-stratifies individuals with established cardiovascular disease, whereas its predictive value is limited in primary prevention. We therefore aimed to establish and evaluate novel markers of FMD at the population level. METHODS AND RESULTS In order to identify novel targets that were negatively correlated with FMD and investigate their contribution to vascular function, we performed a genome-wide association study (GWAS) of 4175 participants of the population based Gutenberg Health Study. Subsequently, conditional knockout mouse models deleting the gene of interest were generated and characterized. GWAS analysis revealed that single-nucleotide polymorphisms (SNPs) in the tubulin-folding cofactor E (TBCE) gene were negatively correlated with endothelial function and TBCE expression. Vascular smooth muscle cell (VSMC)-targeted TBCE deficiency was associated with endothelial dysfunction, aortic wall hypertrophy, and endoplasmic reticulum (ER) stress-mediated VSMC hyperproliferation in mice, paralleled by calnexin up-regulation and exacerbated by the blood pressure hormone angiotensin II. Treating SMMHC-ERT2-Cre+/-TBCEfl/fl mice with the ER stress modulator tauroursodeoxycholic acid amplified Raptor/Beclin-1-dependent autophagy and reversed vascular dysfunction. CONCLUSION TBCE and tubulin homeostasis seem to be novel predictors of vascular function and offer a new drug target to ameliorate ER stress-dependent vascular dysfunction.
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Affiliation(s)
- Panagiotis Efentakis
- Department of Cardiology, University Medical Center Mainz, Langenbeckstraße 1, 55131 Mainz, Germany.,Center for Thrombosis and Hemostasis, University Medical Center Mainz, Langenbeckstraße 1, 55131 Mainz, Germany
| | - Michael Molitor
- Department of Cardiology, University Medical Center Mainz, Langenbeckstraße 1, 55131 Mainz, Germany.,Center for Thrombosis and Hemostasis, University Medical Center Mainz, Langenbeckstraße 1, 55131 Mainz, Germany.,German Center for Cardiovascular Research (DZHK)-Partner site Rhine-Main, University Medical Center Mainz, Langenbeckstraße 1, 55131 Mainz, Germany
| | - Sabine Kossmann
- Department of Cardiology, University Medical Center Mainz, Langenbeckstraße 1, 55131 Mainz, Germany.,Center for Thrombosis and Hemostasis, University Medical Center Mainz, Langenbeckstraße 1, 55131 Mainz, Germany
| | - Magdalena L Bochenek
- Department of Cardiology, University Medical Center Mainz, Langenbeckstraße 1, 55131 Mainz, Germany.,Center for Thrombosis and Hemostasis, University Medical Center Mainz, Langenbeckstraße 1, 55131 Mainz, Germany.,German Center for Cardiovascular Research (DZHK)-Partner site Rhine-Main, University Medical Center Mainz, Langenbeckstraße 1, 55131 Mainz, Germany
| | - Johannes Wild
- Department of Cardiology, University Medical Center Mainz, Langenbeckstraße 1, 55131 Mainz, Germany.,Center for Thrombosis and Hemostasis, University Medical Center Mainz, Langenbeckstraße 1, 55131 Mainz, Germany
| | - Jeremy Lagrange
- Department of Cardiology, University Medical Center Mainz, Langenbeckstraße 1, 55131 Mainz, Germany.,Center for Thrombosis and Hemostasis, University Medical Center Mainz, Langenbeckstraße 1, 55131 Mainz, Germany
| | - Stefanie Finger
- Center for Thrombosis and Hemostasis, University Medical Center Mainz, Langenbeckstraße 1, 55131 Mainz, Germany
| | - Rebecca Jung
- Center for Thrombosis and Hemostasis, University Medical Center Mainz, Langenbeckstraße 1, 55131 Mainz, Germany
| | - Susanne Karbach
- Department of Cardiology, University Medical Center Mainz, Langenbeckstraße 1, 55131 Mainz, Germany.,Center for Thrombosis and Hemostasis, University Medical Center Mainz, Langenbeckstraße 1, 55131 Mainz, Germany.,German Center for Cardiovascular Research (DZHK)-Partner site Rhine-Main, University Medical Center Mainz, Langenbeckstraße 1, 55131 Mainz, Germany
| | - Katrin Schäfer
- Department of Cardiology, University Medical Center Mainz, Langenbeckstraße 1, 55131 Mainz, Germany.,German Center for Cardiovascular Research (DZHK)-Partner site Rhine-Main, University Medical Center Mainz, Langenbeckstraße 1, 55131 Mainz, Germany
| | - Andreas Schulz
- Department of Cardiology-Preventive Cardiology and Medical Prevention, University Medical Center Mainz, Langenbeckstraße 1, 55131 Mainz, Germany
| | - Philipp Wild
- Center for Thrombosis and Hemostasis, University Medical Center Mainz, Langenbeckstraße 1, 55131 Mainz, Germany.,German Center for Cardiovascular Research (DZHK)-Partner site Rhine-Main, University Medical Center Mainz, Langenbeckstraße 1, 55131 Mainz, Germany.,Department of Cardiology-Preventive Cardiology and Medical Prevention, University Medical Center Mainz, Langenbeckstraße 1, 55131 Mainz, Germany
| | - Thomas Münzel
- Department of Cardiology, University Medical Center Mainz, Langenbeckstraße 1, 55131 Mainz, Germany.,Center for Thrombosis and Hemostasis, University Medical Center Mainz, Langenbeckstraße 1, 55131 Mainz, Germany.,German Center for Cardiovascular Research (DZHK)-Partner site Rhine-Main, University Medical Center Mainz, Langenbeckstraße 1, 55131 Mainz, Germany
| | - Philip Wenzel
- Department of Cardiology, University Medical Center Mainz, Langenbeckstraße 1, 55131 Mainz, Germany.,Center for Thrombosis and Hemostasis, University Medical Center Mainz, Langenbeckstraße 1, 55131 Mainz, Germany.,German Center for Cardiovascular Research (DZHK)-Partner site Rhine-Main, University Medical Center Mainz, Langenbeckstraße 1, 55131 Mainz, Germany
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13
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Bonelli R, Ansell BRE, Lotta L, Scerri T, Clemons TE, Leung I, Peto T, Bird AC, Sallo FB, Langenberg C, Bahlo M. Genetic disruption of serine biosynthesis is a key driver of macular telangiectasia type 2 aetiology and progression. Genome Med 2021; 13:39. [PMID: 33750426 PMCID: PMC7945323 DOI: 10.1186/s13073-021-00848-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 02/08/2021] [Indexed: 11/12/2022] Open
Abstract
Background Macular telangiectasia type 2 (MacTel) is a rare, heritable and largely untreatable retinal disorder, often comorbid with diabetes. Genetic risk loci subtend retinal vascular calibre and glycine/serine/threonine metabolism genes. Serine deficiency may contribute to MacTel via neurotoxic deoxysphingolipid production; however, an independent vascular contribution is also suspected. Here, we use statistical genetics to dissect the causal mechanisms underpinning this complex disease. Methods We integrated genetic markers for MacTel, vascular and metabolic traits, and applied Mendelian randomisation and conditional and interaction genome-wide association analyses to discover the causal contributors to both disease and spatial retinal imaging sub-phenotypes. Results Genetically induced serine deficiency is the primary causal metabolic driver of disease occurrence and progression, with a lesser, but significant, causal contribution of type 2 diabetes genetic risk. Conversely, glycine, threonine and retinal vascular traits are unlikely to be causal for MacTel. Conditional regression analysis identified three novel disease loci independent of endogenous serine biosynthetic capacity. By aggregating spatial retinal phenotypes into endophenotypes, we demonstrate that SNPs constituting independent risk loci act via related endophenotypes. Conclusions Follow-up studies after GWAS integrating publicly available data with deep phenotyping are still rare. Here, we describe such analysis, where we integrated retinal imaging data with MacTel and other traits genomics data to identify biochemical mechanisms likely causing this disorder. Our findings will aid in early diagnosis and accurate prognosis of MacTel and improve prospects for effective therapeutic intervention. Our integrative genetics approach also serves as a useful template for post-GWAS analyses in other disorders. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00848-4.
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Affiliation(s)
- Roberto Bonelli
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3052, Australia.,Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Brendan R E Ansell
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3052, Australia.,Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Luca Lotta
- MRC Epidemiology Unit, University of Cambridge, Cambridge, CB2 0SL, UK
| | - Thomas Scerri
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3052, Australia.,Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | | | - Irene Leung
- Department of Research and Development, Moorfields Eye Hospital NHS Foundation Trust, London, EC1V 2PD, UK
| | | | - Tunde Peto
- Department of Ophthalmology, Queen's University, Belfast, BT7 1NN, UK
| | - Alan C Bird
- Inherited Eye Disease, Moorfields Eye Hospital NHS Foundation Trust, London, EC1V 2PD, UK
| | - Ferenc B Sallo
- Department of Ophthalmology, Hôpital Ophtalmique Jules-Gonin, Fondation Asile des Aveugles, University of Lausanne, Lausanne, Switzerland
| | | | - Melanie Bahlo
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3052, Australia. .,Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia.
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14
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Bonelli R, Jackson VE, Prasad A, Munro JE, Farashi S, Heeren TFC, Pontikos N, Scheppke L, Friedlander M, Egan CA, Allikmets R, Ansell BRE, Bahlo M. Identification of genetic factors influencing metabolic dysregulation and retinal support for MacTel, a retinal disorder. Commun Biol 2021; 4:274. [PMID: 33654266 PMCID: PMC7925591 DOI: 10.1038/s42003-021-01788-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 01/27/2021] [Indexed: 01/31/2023] Open
Abstract
Macular Telangiectasia Type 2 (MacTel) is a rare degenerative retinal disease with complex genetic architecture. We performed a genome-wide association study on 1,067 MacTel patients and 3,799 controls, which identified eight novel genome-wide significant loci (p < 5 × 10-8), and confirmed all three previously reported loci. Using MAGMA, eQTL and transcriptome-wide association analysis, we prioritised 48 genes implicated in serine-glycine biosynthesis, metabolite transport, and retinal vasculature and thickness. Mendelian randomization indicated a likely causative role of serine (FDR = 3.9 × 10-47) and glycine depletion (FDR = 0.006) as well as alanine abundance (FDR = 0.009). Polygenic risk scoring achieved an accuracy of 0.74 and was associated in UKBiobank with retinal damage (p = 0.009). This represents the largest genetic study on MacTel to date and further highlights genetically-induced systemic and tissue-specific metabolic dysregulation in MacTel patients, which impinges on retinal health.
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Affiliation(s)
- Roberto Bonelli
- grid.1042.7Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Parkville, VIC Australia
| | - Victoria E. Jackson
- grid.1042.7Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Parkville, VIC Australia
| | - Aravind Prasad
- grid.1042.7Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Parkville, VIC Australia
| | - Jacob E. Munro
- grid.1042.7Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Parkville, VIC Australia
| | - Samaneh Farashi
- grid.1042.7Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Parkville, VIC Australia
| | - Tjebo F. C. Heeren
- grid.436474.60000 0000 9168 0080Moorfields Eye Hospital NHS Foundation Trust, London, UK ,grid.83440.3b0000000121901201University College London Institute of Ophthalmology, London, UK
| | - Nikolas Pontikos
- grid.436474.60000 0000 9168 0080Moorfields Eye Hospital NHS Foundation Trust, London, UK ,grid.83440.3b0000000121901201University College London Institute of Ophthalmology, London, UK
| | - Lea Scheppke
- grid.489357.4The Lowy Medical Research Institute, La Jolla, CA USA
| | - Martin Friedlander
- grid.489357.4The Lowy Medical Research Institute, La Jolla, CA USA ,grid.214007.00000000122199231Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA USA
| | | | - Catherine A. Egan
- grid.436474.60000 0000 9168 0080Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Rando Allikmets
- grid.21729.3f0000000419368729Department of Ophthalmology, Columbia University, New York, NY USA ,grid.21729.3f0000000419368729Department of Pathology and Cell Biology, Columbia University, New York, NY USA
| | - Brendan R. E. Ansell
- grid.1042.7Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Parkville, VIC Australia
| | - Melanie Bahlo
- grid.1042.7Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Parkville, VIC Australia
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15
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Osman N, Shawky A, Brylinski M. Exploring the effects of genetic variation on gene regulation in cancer in the context of 3D genome structure.. [DOI: 10.1101/2020.10.06.328567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
AbstractNumerous genome-wide association studies (GWAS) conducted to date revealed genetic variants associated with various diseases, including breast and prostate cancers. Despite the availability of these large-scale data, relatively few variants have been functionally characterized, mainly because the majority of single-nucleotide polymorphisms (SNPs) map to the non-coding regions of the human genome. The functional characterization of these non-coding variants and the identification of their target genes remain challenging. In this communication, we explore the potential functional mechanisms of non-coding SNPs by integrating GWAS with the high-resolution chromosome conformation capture (Hi-C) data for breast and prostate cancers. We show that more genetic variants map to regulatory elements through the 3D genome structure than the 1D linear genome lacking physical chromatin interactions. Importantly, the association of enhancers, transcription factors, and their target genes with breast and prostate cancers tends to be higher when these regulatory elements are mapped to high-risk SNPs through spatial interactions compared to simply using a linear proximity. Finally, we demonstrate that topologically associating domains (TADs) carrying high-risk SNPs also contain gene regulatory elements whose association with cancer is generally higher than those belonging to control TADs containing no high-risk variants. Our results suggest that many SNPs may contribute to the cancer development by affecting the expression of certain tumor-related genes through long-range chromatin interactions with gene regulatory elements. Integrating large-scale genetic datasets with the 3D genome structure offers an attractive and unique approach to systematically investigate the functional mechanisms of genetic variants in disease risk and progression.
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16
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Yevshin I, Sharipov R, Kolmykov S, Kondrakhin Y, Kolpakov F. GTRD: a database on gene transcription regulation-2019 update. Nucleic Acids Res 2020; 47:D100-D105. [PMID: 30445619 PMCID: PMC6323985 DOI: 10.1093/nar/gky1128] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 10/26/2018] [Indexed: 01/16/2023] Open
Abstract
The current version of the Gene Transcription Regulation Database (GTRD; http://gtrd.biouml.org) contains information about: (i) transcription factor binding sites (TFBSs) and transcription coactivators identified by ChIP-seq experiments for Homo sapiens, Mus musculus, Rattus norvegicus, Danio rerio, Caenorhabditis elegans, Drosophila melanogaster, Saccharomyces cerevisiae, Schizosaccharomyces pombe and Arabidopsis thaliana; (ii) regions of open chromatin and TFBSs (DNase footprints) identified by DNase-seq; (iii) unmappable regions where TFBSs cannot be identified due to repeats; (iv) potential TFBSs for both human and mouse using position weight matrices from the HOCOMOCO database. Raw ChIP-seq and DNase-seq data were obtained from ENCODE and SRA, and uniformly processed. ChIP-seq peaks were called using four different methods: MACS, SISSRs, GEM and PICS. Moreover, peaks for the same factor and peak calling method, albeit using different experiment conditions (cell line, treatment, etc.), were merged into clusters. To reduce noise, such clusters for different peak calling methods were merged into meta-clusters; these were considered to be non-redundant TFBS sets. Moreover, extended quality control was applied to all ChIP-seq data. Web interface to access GTRD was developed using the BioUML platform. It provides browsing and displaying information, advanced search possibilities and an integrated genome browser.
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Affiliation(s)
- Ivan Yevshin
- BIOSOFT.RU, LLC, Novosibirsk 630090, Russian Federation
| | - Ruslan Sharipov
- BIOSOFT.RU, LLC, Novosibirsk 630090, Russian Federation.,Institute of Computational Technologies SB RAS, Novosibirsk 630090, Russian Federation.,Novosibirsk State University, Novosibirsk 630090, Russian Federation
| | - Semyon Kolmykov
- BIOSOFT.RU, LLC, Novosibirsk 630090, Russian Federation.,Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russian Federation
| | - Yury Kondrakhin
- BIOSOFT.RU, LLC, Novosibirsk 630090, Russian Federation.,Institute of Computational Technologies SB RAS, Novosibirsk 630090, Russian Federation
| | - Fedor Kolpakov
- BIOSOFT.RU, LLC, Novosibirsk 630090, Russian Federation.,Institute of Computational Technologies SB RAS, Novosibirsk 630090, Russian Federation
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17
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Cherry TJ, Yang MG, Harmin DA, Tao P, Timms AE, Bauwens M, Allikmets R, Jones EM, Chen R, De Baere E, Greenberg ME. Mapping the cis-regulatory architecture of the human retina reveals noncoding genetic variation in disease. Proc Natl Acad Sci U S A 2020; 117:9001-9012. [PMID: 32265282 PMCID: PMC7183164 DOI: 10.1073/pnas.1922501117] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The interplay of transcription factors and cis-regulatory elements (CREs) orchestrates the dynamic and diverse genetic programs that assemble the human central nervous system (CNS) during development and maintain its function throughout life. Genetic variation within CREs plays a central role in phenotypic variation in complex traits including the risk of developing disease. We took advantage of the retina, a well-characterized region of the CNS known to be affected by pathogenic variants in CREs, to establish a roadmap for characterizing regulatory variation in the human CNS. This comprehensive analysis of tissue-specific regulatory elements, transcription factor binding, and gene expression programs in three regions of the human visual system (retina, macula, and retinal pigment epithelium/choroid) reveals features of regulatory element evolution that shape tissue-specific gene expression programs and defines regulatory elements with the potential to contribute to Mendelian and complex disorders of human vision.
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Affiliation(s)
- Timothy J Cherry
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98101;
- Department of Ophthalmology, University of Washington School of Medicine, Seattle, WA 98101
- Department of Biological Structure, University of Washington School of Medicine, Seattle, WA 98101
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101
| | - Marty G Yang
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115
- Program in Neuroscience, Harvard Medical School, Boston, MA 02115
| | - David A Harmin
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115
| | - Peter Tao
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115
| | - Andrew E Timms
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101
| | - Miriam Bauwens
- Center for Medical Genetics, Ghent University and Ghent University Hospital, 9000 Ghent, Belgium
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, NY 10032
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032
| | - Evan M Jones
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030-3411
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030-3411
| | - Rui Chen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030-3411
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030-3411
| | - Elfride De Baere
- Center for Medical Genetics, Ghent University and Ghent University Hospital, 9000 Ghent, Belgium
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18
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Abstract
Sarcopenia – the accelerated age-related loss of muscle mass and function – is an under-diagnosed condition, and is central to deteriorating mobility, disability and frailty in older age. There is a lack of treatment options for older adults at risk of sarcopenia. Although sarcopenia's pathogenesis is multifactorial, its major phenotypes – muscle mass and muscle strength – are highly heritable. Several genome-wide association studies of muscle-related traits were published recently, providing dozens of candidate genes, many with unknown function. Therefore, animal models are required not only to identify causal mechanisms, but also to clarify the underlying biology and translate this knowledge into new interventions. Over the past several decades, small teleost fishes had emerged as powerful systems for modeling the genetics of human diseases. Owing to their amenability to rapid genetic intervention and the large number of conserved genetic and physiological features, small teleosts – such as zebrafish, medaka and killifish – have become indispensable for skeletal muscle genomic studies. The goal of this Review is to summarize evidence supporting the utility of small fish models for accelerating our understanding of human skeletal muscle in health and disease. We do this by providing a basic foundation of the (zebra)fish skeletal muscle morphology and physiology, and evidence of muscle-related gene homology. We also outline challenges in interpreting zebrafish mutant phenotypes and in translating them to human disease. Finally, we conclude with recommendations on future directions to leverage the large body of tools developed in small fish for the needs of genomic exploration in sarcopenia. Summary: Zebrafish and other small fish have become powerful disease models. Here, we summarize the evidence for the utility of small teleost models for genetic research in sarcopenia – the age-related loss of muscle mass and function.
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Affiliation(s)
- Alon Daya
- The Faculty of Marine Sciences, Ruppin Academic Center, Michmoret 40297, Israel
| | - Rajashekar Donaka
- The Musculoskeletal Genetics Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 130010, Israel
| | - David Karasik
- The Musculoskeletal Genetics Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 130010, Israel .,Hebrew SeniorLife, Hinda and Arthur Marcus Institute for Aging Research, Boston, MA 02131, USA
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19
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Kwon RY, Watson CJ, Karasik D. Using zebrafish to study skeletal genomics. Bone 2019; 126:37-50. [PMID: 30763636 PMCID: PMC6626559 DOI: 10.1016/j.bone.2019.02.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/20/2019] [Accepted: 02/09/2019] [Indexed: 12/26/2022]
Abstract
While genome-wide association studies (GWAS) have revolutionized our understanding of the genetic architecture of skeletal diseases, animal models are required to identify causal mechanisms and to translate underlying biology into new therapies. Despite large-scale knockout mouse phenotyping efforts, the skeletal functions of most genes residing at GWAS-identified loci remain unknown, highlighting a need for complementary model systems to accelerate gene discovery. Over the past several decades, zebrafish (Danio rerio) has emerged as a powerful system for modeling the genetics of human diseases. In this review, our goal is to outline evidence supporting the utility of zebrafish for accelerating our understanding of human skeletal genomics, as well as gaps in knowledge that need to be filled for this purpose. We do this by providing a basic foundation of the zebrafish skeletal morphophysiology and phenotypes, and surveying evidence of skeletal gene homology and the use of zebrafish for post-GWAS analysis in other tissues and organs. We also outline challenges in translating zebrafish mutant phenotypes. Finally, we conclude with recommendations of future directions and how to leverage the large body of tools and knowledge of skeletal genetics in zebrafish for the needs of human skeletal genomic exploration. Due to their amenability to rapid genetic approaches, as well as the large number of conserved genetic and phenotypic features, there is a strong rationale supporting the use of zebrafish for human skeletal genomic studies.
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Affiliation(s)
- Ronald Y Kwon
- Department of Orthopaedics and Sports Medicine, University of Washington, Seattle, WA, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA; Department of Mechanical Engineering, University of Washington, Seattle, WA, USA.
| | - Claire J Watson
- Department of Orthopaedics and Sports Medicine, University of Washington, Seattle, WA, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - David Karasik
- The Musculoskeletal Genetics Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel; Hebrew SeniorLife, Hinda and Arthur Marcus Institute for Aging Research, Boston, MA, USA.
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20
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Paone C, Diofano F, Park DD, Rottbauer W, Just S. Genetics of Cardiovascular Disease: Fishing for Causality. Front Cardiovasc Med 2018; 5:60. [PMID: 29911105 PMCID: PMC5992778 DOI: 10.3389/fcvm.2018.00060] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/15/2018] [Indexed: 01/08/2023] Open
Abstract
Cardiovascular disease (CVD) is still the leading cause of death in all western world countries and genetic predisposition in combination with traditional risk factors frequently mediates their manifestation. Genome-wide association (GWA) studies revealed numerous potentially disease modifying genetic loci often including several SNPs and associated genes. However, pure genetic association does not prove direct or indirect relevance of the modifier region on pathogenesis, nor does it define within the associated region the exact genetic driver of the disease. Therefore, the relevance of the identified genetic disease associations needs to be confirmed either in monogenic traits or in experimental in vivo model system by functional genomic studies. In this review, we focus on the use of functional genomic approaches such as gene knock-down or CRISPR/Cas9-mediated genome editing in the zebrafish model to validate disease-associated genomic loci and to identify novel cardiovascular disease genes. We summarize the benefits of the zebrafish for cardiovascular research and highlight examples demonstrating the successful combination of GWA studies and functional genomics in zebrafish to broaden our knowledge on the genetic and molecular underpinnings of cardiovascular diseases.
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Affiliation(s)
- Christoph Paone
- Molecular Cardiology, Department of Internal Medicine II, University of Ulm, Ulm, Germany
| | - Federica Diofano
- Molecular Cardiology, Department of Internal Medicine II, University of Ulm, Ulm, Germany
| | - Deung-Dae Park
- Molecular Cardiology, Department of Internal Medicine II, University of Ulm, Ulm, Germany
| | | | - Steffen Just
- Molecular Cardiology, Department of Internal Medicine II, University of Ulm, Ulm, Germany
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21
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Abstract
Functional genomics encompasses diverse disciplines in molecular biology and bioinformatics to comprehend the blueprint, regulation, and expression of genetic elements that define the physiology of an organism. The deluge of sequencing data in the postgenomics era has demanded the involvement of computer scientists and mathematicians to create algorithms, analytical software, and databases for the storage, curation, and analysis of biological big data. In this chapter, we discuss on the concept of functional genomics in the context of systems biology and provide examples of its application in human genetic disease studies, molecular crop improvement, and metagenomics for antibiotic discovery. An overview of transcriptomics workflow and experimental considerations is also introduced. Lastly, we present an in-house case study of transcriptomics analysis of an aromatic herbal plant to understand the effect of elicitation on the biosynthesis of volatile organic compounds.
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Affiliation(s)
- Hoe-Han Goh
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia.
| | - Chyan Leong Ng
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia
| | - Kok-Keong Loke
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia
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