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Han X, Tian H, Yang L, Ji Y. Bidirectional Mendelian randomization to explore the causal relationships between the gut microbiota and male reproductive diseases. Sci Rep 2024; 14:18306. [PMID: 39112529 PMCID: PMC11306555 DOI: 10.1038/s41598-024-69179-9] [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: 04/18/2024] [Accepted: 08/01/2024] [Indexed: 08/10/2024] Open
Abstract
Gut bacteria might play an important role in male reproductive disorders, such as male infertility and sperm abnormalities; however, their causal role is unclear. Herein, Mendelian randomization (MR)-Egger, weighted median, inverse variance weighting, Simple mode, and Weighted mode were used to test the causal relationship between gut microbes and male reproductive diseases. The MR results were validated using various metrics. The MR results were also consolidated using reverse causality speculation, conducted using two-way MR analysis and Steiger filtering. Biological function was analysed using enrichment analyses. The results suggested that eight intestinal microflorae were causally associated with male infertility. The Eubacterium oxidoreducens group was associated with an increased risk of male infertility, while the family Bacteroidaceae was negatively associated with male reproductive diseases. Eight intestinal microflorae were causally associated with abnormal spermatozoa. The family Streptococcaceae was associated with a high risk of abnormal spermatozoa, whereas the family Porphyromonadaceae was associated with a low risk of abnormal spermatozoa. No pleiotropy was observed, this study identified a high correlation between the gut flora and the likelihood of male reproductive diseases. Future research will attempt to advance microbial-focused treatments for such diseases.
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Affiliation(s)
- Xiaofang Han
- Core Laboratory, Shanxi Provincial People's Hospital (Fifth Hospital of Shanxi Medical University), Taiyuan, China.
| | - Hui Tian
- Core Laboratory, Shanxi Provincial People's Hospital, Shanxi Medical University, Taiyuan, China
| | - Liu Yang
- Core Laboratory, Shanxi Provincial People's Hospital, Shanxi Medical University, Taiyuan, China
| | - Yuanyuan Ji
- Core Laboratory, Shanxi Provincial People's Hospital, Shanxi Medical University, Taiyuan, China
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2
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Wang Y, Tang Y, Liu TH, Shao L, Li C, Wang Y, Tan P. Integrative Multi-omics Analysis to Characterize Herpes Virus Infection Increases the Risk of Alzheimer's Disease. Mol Neurobiol 2024; 61:5337-5352. [PMID: 38191694 DOI: 10.1007/s12035-023-03903-w] [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: 12/06/2022] [Accepted: 12/22/2023] [Indexed: 01/10/2024]
Abstract
Evidence suggests that herpes virus infection is associated with an increased risk of Alzheimer's disease (AD), and innate and adaptive immunity plays an important role in the association. Although there have been many studies, the mechanism of the association is still unclear. This study aims to reveal the underlying molecular and immune regulatory network through multi-omics data and provide support for the study of the mechanism of infection and AD in the future. Here, we found that the herpes virus infection significantly increased the risk of AD. Genes associated with the occurrence and development of AD and genetically regulated by herpes virus infection are mainly enrichment in immune-related pathways. The 22 key regulatory genes identified by machine learning are mainly immune genes. They are also significantly related to the infiltration changes of 3 immune cell in AD. Furthermore, many of these genes have previously been reported to be linked, or potentially linked, to the pathological mechanisms of both herpes virus infection and AD. In conclusion, this study contributes to the study of the mechanisms related to herpes virus infection and AD, and indicates that the regulation of innate and adaptive immunity may be an effective strategy for preventing and treating herpes virus infection and AD. Additionally, the identified key regulatory genes, whether previously studied or newly discovered, may serve as valuable targets for prevention and treatment strategies.
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Affiliation(s)
- Yongheng Wang
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
- Joint International Research Laboratory of Reproductive and Development, Department of Reproductive Biology, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Yaqin Tang
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Tai-Hang Liu
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
- Joint International Research Laboratory of Reproductive and Development, Department of Reproductive Biology, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Lizhen Shao
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Chunying Li
- Chongqing Vocational College of Resources and Environmental Protection, Chongqing, China.
| | - Yingxiong Wang
- Joint International Research Laboratory of Reproductive and Development, Department of Reproductive Biology, School of Public Health, Chongqing Medical University, Chongqing, China.
| | - Pengcheng Tan
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China.
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3
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Darrasse A, Tarkowski ŁP, Briand M, Lalanne D, Chen NWG, Barret M, Verdier J. A stage-dependent seed defense response to explain efficient seed transmission of Xanthomonas citri pv. fuscans to common bean. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39038880 DOI: 10.1111/pce.15037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 06/14/2024] [Accepted: 06/29/2024] [Indexed: 07/24/2024]
Abstract
Although seed represents an important means of plant pathogen dispersion, the seed-pathogen dialogue remains largely unexplored. A multiomic approach was performed at different seed developmental stages of common bean (Phaseolus vulgaris L.) during asymptomatic colonization by Xanthomonas citri pv. fuscans (Xcf), At the early seed developmental stages, we observed high transcriptional changes both in seeds with bacterial recognition and defense signal transduction genes, and in bacteria with up-regulation of the bacterial type 3 secretion system. This high transcriptional activity of defense genes in Xcf-colonized seeds during maturation refutes the widely diffused assumption considering seeds as passive carriers of microbes. At later seed maturation stages, few transcriptome changes indicated a less intense molecular dialogue between the host and the pathogen, but marked by changes in DNA methylation of plant defense genes, in response to Xcf colonization. We showed examples of pathogen-specific DNA methylations in colonized seeds acting as plant defense silencing to repress plant immune response during the germination process. Finally, we propose a novel plant-pathogen interaction model, specific to the seed tissues, highlighting the existence of distinct phases during seed-pathogen interaction with seeds being actively interacting with colonizing pathogens, then both belligerents switching to more passive mode at later stages.
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Affiliation(s)
- Armelle Darrasse
- University Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | | | - Martial Briand
- University Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - David Lalanne
- University Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Nicolas W G Chen
- University Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Matthieu Barret
- University Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Jerome Verdier
- University Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
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4
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Iñiguez-Muñoz S, Llinàs-Arias P, Ensenyat-Mendez M, Bedoya-López AF, Orozco JIJ, Cortés J, Roy A, Forsberg-Nilsson K, DiNome ML, Marzese DM. Hidden secrets of the cancer genome: unlocking the impact of non-coding mutations in gene regulatory elements. Cell Mol Life Sci 2024; 81:274. [PMID: 38902506 DOI: 10.1007/s00018-024-05314-z] [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: 07/06/2023] [Revised: 12/07/2023] [Accepted: 06/06/2024] [Indexed: 06/22/2024]
Abstract
Discoveries in the field of genomics have revealed that non-coding genomic regions are not merely "junk DNA", but rather comprise critical elements involved in gene expression. These gene regulatory elements (GREs) include enhancers, insulators, silencers, and gene promoters. Notably, new evidence shows how mutations within these regions substantially influence gene expression programs, especially in the context of cancer. Advances in high-throughput sequencing technologies have accelerated the identification of somatic and germline single nucleotide mutations in non-coding genomic regions. This review provides an overview of somatic and germline non-coding single nucleotide alterations affecting transcription factor binding sites in GREs, specifically involved in cancer biology. It also summarizes the technologies available for exploring GREs and the challenges associated with studying and characterizing non-coding single nucleotide mutations. Understanding the role of GRE alterations in cancer is essential for improving diagnostic and prognostic capabilities in the precision medicine era, leading to enhanced patient-centered clinical outcomes.
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Affiliation(s)
- Sandra Iñiguez-Muñoz
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain
| | - Pere Llinàs-Arias
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain
| | - Miquel Ensenyat-Mendez
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain
| | - Andrés F Bedoya-López
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain
| | - Javier I J Orozco
- Saint John's Cancer Institute, Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Javier Cortés
- International Breast Cancer Center (IBCC), Pangaea Oncology, Quiron Group, 08017, Barcelona, Spain
- Medica Scientia Innovation Research SL (MEDSIR), 08018, Barcelona, Spain
- Faculty of Biomedical and Health Sciences, Department of Medicine, Universidad Europea de Madrid, 28670, Madrid, Spain
| | - Ananya Roy
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- University of Nottingham Biodiscovery Institute, Nottingham, UK
| | - Maggie L DiNome
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Diego M Marzese
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain.
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA.
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Huang HY, Zhang S, Choucha FA, Verdenaud M, Tan FQ, Pichot C, Parsa HS, Slavkovic F, Chen Q, Troadec C, Marcel F, Dogimont C, Quadrana L, Boualem A, Bendahmane A. Harbinger transposon insertion in ethylene signaling gene leads to emergence of new sexual forms in cucurbits. Nat Commun 2024; 15:4877. [PMID: 38849342 PMCID: PMC11161486 DOI: 10.1038/s41467-024-49250-9] [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: 12/12/2023] [Accepted: 05/28/2024] [Indexed: 06/09/2024] Open
Abstract
In flowering plants, the predominant sexual morph is hermaphroditism, and the emergence of unisexuality is poorly understood. Using Cucumis melo (melon) as a model system, we explore the mechanisms driving sexual forms. We identify a spontaneous mutant exhibiting a transition from bisexual to unisexual male flower, and identify the causal mutation as a Harbinger transposon impairing the expression of Ethylene Insensitive 2 (CmEIN2) gene. Genetics and transcriptomic analysis reveal a dual role of CmEIN2 in both sex determination and fruit shape formation. Upon expression of CmACS11, EIN2 is recruited to repress the expression of the carpel inhibitor, CmWIP1. Subsequently, EIN2 is recruited to mediate stamina inhibition. Following the sex determination phase, EIN2 promotes fruit shape elongation. Genome-wide analysis reveals that Harbinger transposon mobilization is triggered by environmental cues, and integrates preferentially in active chromatin, particularly within promoter regions. Characterization of a large collection of melon germplasm points to active transpositions in the wild, compared to cultivated accessions. Our study underscores the association between chromatin dynamics and the temporal aspects of mobile genetic element insertions, providing valuable insights into plant adaptation and crop genome evolution.
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Affiliation(s)
- Hsin-Ya Huang
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif-sur-Yvette, France
| | - Siqi Zhang
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif-sur-Yvette, France
| | - Fadi Abou Choucha
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif-sur-Yvette, France
| | - Marion Verdenaud
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif-sur-Yvette, France
| | - Feng-Quan Tan
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif-sur-Yvette, France
| | - Clement Pichot
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif-sur-Yvette, France
| | - Hadi Shirazi Parsa
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif-sur-Yvette, France
| | - Filip Slavkovic
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif-sur-Yvette, France
| | - Qinghe Chen
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif-sur-Yvette, France
| | - Christelle Troadec
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif-sur-Yvette, France
| | - Fabien Marcel
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif-sur-Yvette, France
| | - Catherine Dogimont
- INRAE, Génétique et Amélioration des Fruits et Légumes (GAFL), 84143, Montfavet, France
| | - Leandro Quadrana
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif-sur-Yvette, France
| | - Adnane Boualem
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif-sur-Yvette, France
| | - Abdelhafid Bendahmane
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif-sur-Yvette, France.
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Sahu M, Vashishth S, Kukreti N, Gulia A, Russell A, Ambasta RK, Kumar P. Synergizing drug repurposing and target identification for neurodegenerative diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 205:111-169. [PMID: 38789177 DOI: 10.1016/bs.pmbts.2024.03.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Despite dedicated research efforts, the absence of disease-curing remedies for neurodegenerative diseases (NDDs) continues to jeopardize human society and stands as a challenge. Drug repurposing is an attempt to find new functionality of existing drugs and take it as an opportunity to discourse the clinically unmet need to treat neurodegeneration. However, despite applying this approach to rediscover a drug, it can also be used to identify the target on which a drug could work. The primary objective of target identification is to unravel all the possibilities of detecting a new drug or repurposing an existing drug. Lately, scientists and researchers have been focusing on specific genes, a particular site in DNA, a protein, or a molecule that might be involved in the pathogenesis of the disease. However, the new era discusses directing the signaling mechanism involved in the disease progression, where receptors, ion channels, enzymes, and other carrier molecules play a huge role. This review aims to highlight how target identification can expedite the whole process of drug repurposing. Here, we first spot various target-identification methods and drug-repositioning studies, including drug-target and structure-based identification studies. Moreover, we emphasize various drug repurposing approaches in NDDs, namely, experimental-based, mechanism-based, and in silico approaches. Later, we draw attention to validation techniques and stress on drugs that are currently undergoing clinical trials in NDDs. Lastly, we underscore the future perspective of synergizing drug repurposing and target identification in NDDs and present an unresolved question to address the issue.
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Affiliation(s)
- Mehar Sahu
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Shrutikirti Vashishth
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Neha Kukreti
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Ashima Gulia
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Ashish Russell
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Rashmi K Ambasta
- Department of Biotechnology and Microbiology, SRM University, Sonepat, Haryana, India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India.
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Li Z, Liu S, Liu F, Dai N, Liang R, Lv S, Bao L. Gut microbiota and autism spectrum disorders: a bidirectional Mendelian randomization study. Front Cell Infect Microbiol 2023; 13:1267721. [PMID: 38156319 PMCID: PMC10753022 DOI: 10.3389/fcimb.2023.1267721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 11/22/2023] [Indexed: 12/30/2023] Open
Abstract
Background In recent years, observational studies have provided evidence supporting a potential association between autism spectrum disorder (ASD) and gut microbiota. However, the causal effect of gut microbiota on ASD remains unknown. Methods We identified the summary statistics of 206 gut microbiota from the MiBioGen study, and ASD data were obtained from the latest Psychiatric Genomics Consortium Genome-Wide Association Study (GWAS). We then performed Mendelian randomization (MR) to determine a causal relationship between the gut microbiota and ASD using the inverse variance weighted (IVW) method, simple mode, MR-Egger, weighted median, and weighted model. Furthermore, we used Cochran's Q test, MR-Egger intercept test, Mendelian Randomization Pleiotropy RESidual Sum and Outlier (MR-PRESSO), and leave-one-out analysis to identify heterogeneity and pleiotropy. Moreover, the Benjamin-Hochberg approach (FDR) was employed to assess the strength of the connection between exposure and outcome. We performed reverse MR analysis on the gut microbiota that were found to be causally associated with ASD in the forward MR analysis to examine the causal relationships. The enrichment analyses were used to analyze the biological function at last. Results Based on the results of IVW results, genetically predicted family Prevotellaceae and genus Turicibacter had a possible positive association with ASD (IVW OR=1.14, 95% CI: 1.00-1.29, P=3.7×10-2), four gut microbiota with a potential protective effect on ASD: genus Dorea (OR=0.81, 95% CI: 0.69-0.96, P=1.4×10-2), genus Ruminiclostridium5 (OR=0.81, 95% CI: 0.69-0.96, P=1.5×10-2), genus Ruminococcus1 (OR=0.83, 95% CI: 0.70-0.98, P=2.8×10-2), and genus Sutterella (OR=0.82, 95% CI: 0.68-0.99, P=3.6×10-2). After FDR multiple-testing correction we further observed that there were two gut microbiota still have significant relationship with ASD: family Prevotellaceae (IVW OR=1.24; 95% CI: 1.09-1.40, P=9.2×10-4) was strongly positively correlated with ASD and genus RuminococcaceaeUCG005 (IVW OR=0.78, 95% CI: 0.67-0.89, P=6.9×10-4) was strongly negatively correlated with ASD. The sensitivity analysis excluded the influence of heterogeneity and horizontal pleiotropy. Conclusion Our findings reveal a causal association between several gut microbiomes and ASD. These results deepen our comprehension of the role of gut microbiota in ASD's pathology, providing the foothold for novel ideas and theoretical frameworks to prevent and treat this patient population in the future.
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Affiliation(s)
- Zhi Li
- Department of Pediatrics, Hebei Medical University, Shijiazhuang, Hebei, China
- Department of Pediatrics, Bethune International Peace Hospital, Shijiazhuang, Hebei, China
| | - Shuai Liu
- Department of Cancer Epidemiology Division, University of Hawaii Cancer Center, Honolulu, HI, United States
| | - Fang Liu
- Department of Pediatrics, Hebei Medical University, Shijiazhuang, Hebei, China
- Department of Pediatrics, Bethune International Peace Hospital, Shijiazhuang, Hebei, China
| | - Nannan Dai
- Department of Clinical Laboratory, The ECO-City Hospital of Tianjin Fifth Central Hospital, Tianjin, China
| | - Rujia Liang
- Department of Pediatrics, Bethune International Peace Hospital, Shijiazhuang, Hebei, China
| | - Shaoguang Lv
- Department of Pediatrics, Bethune International Peace Hospital, Shijiazhuang, Hebei, China
| | - Lisha Bao
- Department of Pediatrics, Bethune International Peace Hospital, Shijiazhuang, Hebei, China
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Chanasongkhram K, Damkliang K, Sangket U. DisVar: an R library for identifying variants associated with diseases using large-scale personal genetic information. PeerJ 2023; 11:e16086. [PMID: 37790633 PMCID: PMC10542659 DOI: 10.7717/peerj.16086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/22/2023] [Indexed: 10/05/2023] Open
Abstract
Background Genetic variants may potentially play a contributing factor in the development of diseases. Several genetic disease databases are used in medical research and diagnosis but the web applications used to search these databases for disease-associated variants have limitations. The application may not be able to search for large-scale genetic variants, the results of searches may be difficult to interpret and variants mapped from the latest reference genome (GRCH38/hg38) may not be supported. Methods In this study, we developed a novel R library called "DisVar" to identify disease-associated genetic variants in large-scale individual genomic data. This R library is compatible with variants from the latest reference genome version. DisVar uses five databases of disease-associated variants. Over 100 million variants can be simultaneously searched for specific associated diseases. Results The package was evaluated using 24 Variant Call Format (VCF) files (215,054 to 11,346,899 sites) from the 1000 Genomes Project. Disease-associated variants were detected in 298,227 hits across all the VCF files, taking a total of 63.58 m to complete. The package was also tested on ClinVar's VCF file (2,120,558 variants), where 20,657 hits associated with diseases were identified with an estimated elapsed time of 45.98 s. Conclusions DisVar can overcome the limitations of existing tools and is a fast and effective diagnostic and preventive tool that identifies disease-associated variations from large-scale genetic variants against the latest reference genome.
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Affiliation(s)
- Khunanon Chanasongkhram
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Kasikrit Damkliang
- Division of Computational Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Unitsa Sangket
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
- Center for Genomics and Bioinformatics Research, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
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9
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Fang T, Liu S, Chen L, Ren Y, Lu D, Yao X, Hong T, Zhang X, Xie Z, Yang K, Wang X. Whole-genome bisulfite sequencing identified the key role of the Src family tyrosine kinases and related genes in systemic lupus erythematosus. Genes Genomics 2023; 45:1187-1196. [PMID: 37300789 DOI: 10.1007/s13258-023-01407-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/18/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND As a multisystemic autoimmune illness, the basic mechanisms behind the pathophysiology of systemic lupus erythematosus (SLE) remain poorly understood. OBJECTIVE We aimed to investigate the possible significance of SLE's DNA methylation and gain further insight into potential SLE-related biomarkers and therapeutic targets. METHODS We used whole genome bisulfite sequencing (WGBS) method to analyze DNA methylation in 4 SLE patients and 4 healthy people. RESULTS 702 differentially methylated regions (DMRs) were identified, and 480 DMR-associated genes were annotated. We found the majority of the DMR-associated elements were enriched in repeat and gene bodies. The top 10 hub genes identified were LCK, FYB, PTK2B, LYN, CTNNB1, MAPK1, GNAQ, PRKCA, ABL1, and CD247. Compared to the control group, LCK and PTK2B had considerably decreased levels of mRNA expression in the SLE group. Receiver operating characteristic (ROC) curve suggested that LCK and PTK2B may be potential candidate biomarkers to predict SLE. CONCLUSIONS Our study improved comprehension of the DNA methylation patterns of SLE and identified potential biomarkers and therapeutic targets for SLE.
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Affiliation(s)
- Ting Fang
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Suyi Liu
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Liying Chen
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Yating Ren
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Dingqi Lu
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Xinyi Yao
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Tao Hong
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Xvfeng Zhang
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Zhimin Xie
- Department of Rheumatology, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Kepeng Yang
- Department of Rheumatology, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Xinchang Wang
- Department of Rheumatology, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, People's Republic of China.
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10
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Tavares V, Assis J, Pinto R, Freitas-Silva M, Medeiros R. Venous thromboembolism-related genetic determinant F11 rs4253417 is a potential prognostic factor in ischaemic stroke. Mol Cell Probes 2023; 70:101917. [PMID: 37364690 DOI: 10.1016/j.mcp.2023.101917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 06/23/2023] [Accepted: 06/24/2023] [Indexed: 06/28/2023]
Abstract
Ischaemic stroke (IS) and venous thromboembolism (VTE) are two forms of thromboembolism that, although distinct, seem to share numerous risk factors. Concerning genetic risk factors, while many VTE genetic markers have been reported, inclusively by genome-wide association studies (GWAS), the identification and validation of genetic determinants underlying IS pathogenesis have been challenging. Considering that IS and VTE shared biological pathways and aetiological factors, the severity of IS might be also influenced by VTE-related genetic variants. Thus, the present study was designed to analyse the impact of six VTE GWAS-identified genetic variants on the clinical outcome of 363 acute IS patients. Results revealed that the single-nucleotide polymorphism (SNP) F11 rs4253417 was an independent predictor of the 5-year risk of death among patients with total anterior circulation infarct (TACI). Namely, the ones carrying the SNP C allele presented a fourfold increase in the 5-year risk of death compared to TT genotype carriers (CC/CT vs. TT; adjusted HR, 4.240; 95% CI, 1.260-14.270; P = 0.020). This SNP is known to be associated with coagulation factor XI (FXI) levels, thus with implications in haemostasis and inflammation. As such, F11 rs4253417 might be a promising prognostic biomarker among TACI patients to aid in clinical decision-making. However, additional investigation is required to confirm the study's results and dissect the underlying mechanisms.
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Affiliation(s)
- Valéria Tavares
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP), Pathology and Laboratory Medicine Dep., Clinical Pathology SV, RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center (Porto.CCC), 4200-072, Porto, Portugal; ICBAS, Abel Salazar Institute for the Biomedical Sciences, 4050-313, Porto, Portugal; FMUP, Faculty of Medicine, University of Porto, 4200-072, Porto, Portugal
| | - Joana Assis
- Clinical Research Unit, Research Center of IPO Porto (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center (Porto.CCC), 4200-072, Porto, Portugal
| | - Ricardo Pinto
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP), Pathology and Laboratory Medicine Dep., Clinical Pathology SV, RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center (Porto.CCC), 4200-072, Porto, Portugal
| | - Margarida Freitas-Silva
- FMUP, Faculty of Medicine, University of Porto, 4200-072, Porto, Portugal; Department of Medicine, Centro Hospitalar São João, Porto, Portugal
| | - Rui Medeiros
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP), Pathology and Laboratory Medicine Dep., Clinical Pathology SV, RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center (Porto.CCC), 4200-072, Porto, Portugal; ICBAS, Abel Salazar Institute for the Biomedical Sciences, 4050-313, Porto, Portugal; FMUP, Faculty of Medicine, University of Porto, 4200-072, Porto, Portugal; Research Department, Portuguese League Against Cancer (NRNorte), 4200-172, Porto, Portugal; CEBIMED, Faculty of Health Sciences, Fernando Pessoa University, 4200-150, Porto, Portugal.
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11
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Sun D, Song M, Zeng C, Chen H, Zhang J, Liu F, Luo S, Liao Q, Xiao Y, Xu W, Zeng D, Tan Z, Tian F, Huang X. Associations of vitamin D-related single nucleotide polymorphisms with post-stroke depression among ischemic stroke population. Front Psychiatry 2023; 14:1148047. [PMID: 37404714 PMCID: PMC10317012 DOI: 10.3389/fpsyt.2023.1148047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/11/2023] [Indexed: 07/06/2023] Open
Abstract
Objective To investigate the relationship between single nucleotide polymorphisms (SNPs) related to vitamin D (VitD) metabolism and post-stroke depression (PSD) in patients with ischemic stroke. Methods A total of 210 patients with ischemic stroke were enrolled at the Department of Neurology in Xiangya Hospital, Central South University, from July 2019 to August 2021. SNPs in the VitD metabolic pathway (VDR, CYP2R1, CYP24A1, and CYP27B1) were genotyped using the SNPscan™ multiplex SNP typing kit. Demographic and clinical data were collected using a standardized questionnaire. Multiple genetic models including dominant, recessive, and over-dominant models were utilized to analyze the associations between SNPs and PSD. Results In the dominant, recessive, and over-dominant models, no significant association was observed between the selected SNPs in the CYP24A1 and CYP2R1 genes and PSD. However, univariate and multivariate logistic regression analysis revealed that the CYP27B1 rs10877012 G/G genotype was associated with a decreased risk of PSD (OR: 0.41, 95% CI: 0.18-0.92, p = 0.030 and OR: 0.42, 95% CI: 0.18-0.98, p = 0.040, respectively). Furthermore, haplotype association analysis indicated that rs11568820-rs1544410-rs2228570-rs7975232-rs731236 CCGAA haplotype in the VDR gene was associated with a reduced risk of PSD (OR: 0.14, 95% CI: 0.03-0.65, p = 0.010), whereas no significant association was observed between haplotypes in the CYP2R1 and CYP24A1 genes and PSD. Conclusion Our findings suggest that the polymorphisms of VitD metabolic pathway genes VDR and CYP27B1 may be associated with PSD in patients with ischemic stroke.
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Affiliation(s)
- Dongren Sun
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Mingyu Song
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Chang Zeng
- Health Management Center, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hengshu Chen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Jingyuan Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Fan Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Shihang Luo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Qiao Liao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yeqing Xiao
- Department of Neurology, Hengyang Central Hospital, Hengyang, Hunan, China
| | - Weiye Xu
- Department of Human Anatomy and Neurobiology, School of Basic Medicine, Central South University, Changsha, Hunan, China
| | - Danfeng Zeng
- Department of Neurology, Xiangtan Central Hospital, Xiangtan, Hunan, China
| | - Zheren Tan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Fafa Tian
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Xia Huang
- Department of Critical Care Medicine, The First People’s Hospital of Huaihua, Huaihua, Hunan, China
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12
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Zhang Y, Wei Y, Meng J, Wang Y, Nie S, Zhang Z, Wang H, Yang Y, Gao Y, Wu J, Li T, Liu X, Zhang H, Gu L. Chromosome-scale de novo genome assembly and annotation of three representative Casuarina species: C. equisetifolia, C. glauca, and C. cunninghamiana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:1490-1505. [PMID: 36971060 DOI: 10.1111/tpj.16201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 02/15/2023] [Accepted: 03/13/2023] [Indexed: 06/17/2023]
Abstract
Australian pine (Casuarina spp.) is extensively planted in tropical and subtropical regions for wood production, shelterbelts, environmental protection, and ecological restoration due to their superior biological characteristics, such as rapid growth, wind and salt tolerance, and nitrogen fixation. To analyze the genomic diversity of Casuarina, we sequenced the genomes and constructed de novo genome assemblies of the three most widely planted Casuarina species: C. equisetifolia, C. glauca, and C. cunninghamiana. We generated chromosome-scale genome sequences using both Pacific Biosciences (PacBio) Sequel sequencing and chromosome conformation capture technology (Hi-C). The total genome sizes for C. equisetifolia, C. glauca, and C. cunninghamiana are 268 942 579 bp, 296 631 783 bp, and 293 483 606 bp, respectively, of which 25.91, 27.15, and 27.74% were annotated as repetitive sequences. We annotated 23 162, 24 673, and 24 674 protein-coding genes in C. equisetifolia, C. glauca, and C. cunninghamiana, respectively. We then collected branchlets from male and female individuals for whole-genome bisulfite sequencing (BS-seq) to explore the epigenetic regulation of sex determination in these three species. Transcriptome sequencing (RNA-seq) revealed differential expression of phytohormone-related genes between male and female plants. In summary, we generated three chromosome-level genome assemblies and comprehensive DNA methylation and transcriptome datasets from both male and female material for three Casuarina species, providing a basis for the comprehensive investigation of genomic diversity and functional gene discovery of Casuarina in the future.
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Affiliation(s)
- Yong Zhang
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Yongcheng Wei
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Jingxiang Meng
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Yujiao Wang
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Sen Nie
- Fujian Academy of Forestry Sciences, Fuzhou, Fujian, 350012, China
| | - Zeyu Zhang
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huiyuan Wang
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yongkang Yang
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yubang Gao
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ji Wu
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Tuhe Li
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xuqing Liu
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hangxiao Zhang
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lianfeng Gu
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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13
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Zhang M, Chen R, Zheng S, Wang Z. Acquired crizotinib-resistant pulmonary adenocarcinoma and subsequent primary gallbladder cancer: A case report. Medicine (Baltimore) 2023; 102:e33162. [PMID: 36930086 PMCID: PMC10019204 DOI: 10.1097/md.0000000000033162] [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] [Received: 01/19/2023] [Accepted: 02/13/2023] [Indexed: 03/18/2023] Open
Abstract
RATIONALE Proto-oncogene-oriented targeted therapy has limited benefits in elderly patients with multiple primary tumors. PATIENT CONCERNS A woman with anaplastic lymphoma kinase-positive lung adenocarcinoma developed acquired resistance after 3 years of targeted therapy with crizotinib. DIAGNOSES Diagnosis of unexpected subsequent primary gallbladder tumor. INTERVENTIONS Lenvatinib was administered therapeutically. Meanwhile, next-generation sequencing results before and after crizotinib treatment were analyzed by comparing the tumor-driving mutation genes with bioinformatics methods. OUTCOMES The patient died of ascites and liver failure. Furthermore, bypass activation was found to be the main reason for acquired drug resistance for this patient, and the abnormal expression of tumor suppressor genes and senescence-related genes was the likely cause of the second primary tumor. LESSONS A bioinformatic comparison of pre- and post-treatment sequencing in elderly oncology patients is of interest. CONCLUSIONS For diagnosing, precision bioinformatics analysis and repeat biopsy are equally valuable. For therapy, potential therapy such as p53 gene replacement therapy and CAR-T therapy need to be practiced for senescence-related conditions.
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Affiliation(s)
- Min Zhang
- The First Clinical Medical College, Zhejiang Chinese Medicine University, HangZhou, China
| | - Ruilin Chen
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Zhejiang Chinese Medicine University, Hangzhou, China
| | - Suqun Zheng
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Zhejiang Chinese Medicine University, Hangzhou, China
| | - Zhen Wang
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Zhejiang Chinese Medicine University, Hangzhou, China
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14
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An autoimmune pleiotropic SNP modulates IRF5 alternative promoter usage through ZBTB3-mediated chromatin looping. Nat Commun 2023; 14:1208. [PMID: 36869052 PMCID: PMC9984425 DOI: 10.1038/s41467-023-36897-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 02/22/2023] [Indexed: 03/05/2023] Open
Abstract
Genetic sharing is extensively observed for autoimmune diseases, but the causal variants and their underlying molecular mechanisms remain largely unknown. Through systematic investigation of autoimmune disease pleiotropic loci, we found most of these shared genetic effects are transmitted from regulatory code. We used an evidence-based strategy to functionally prioritize causal pleiotropic variants and identify their target genes. A top-ranked pleiotropic variant, rs4728142, yielded many lines of evidence as being causal. Mechanistically, the rs4728142-containing region interacts with the IRF5 alternative promoter in an allele-specific manner and orchestrates its upstream enhancer to regulate IRF5 alternative promoter usage through chromatin looping. A putative structural regulator, ZBTB3, mediates the allele-specific loop to promote IRF5-short transcript expression at the rs4728142 risk allele, resulting in IRF5 overactivation and M1 macrophage polarization. Together, our findings establish a causal mechanism between the regulatory variant and fine-scale molecular phenotype underlying the dysfunction of pleiotropic genes in human autoimmunity.
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15
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Stikker BS, Hendriks RW, Stadhouders R. Decoding the genetic and epigenetic basis of asthma. Allergy 2023; 78:940-956. [PMID: 36727912 DOI: 10.1111/all.15666] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/17/2023] [Accepted: 01/30/2023] [Indexed: 02/03/2023]
Abstract
Asthma is a complex and heterogeneous chronic inflammatory disease of the airways. Alongside environmental factors, asthma susceptibility is strongly influenced by genetics. Given its high prevalence and our incomplete understanding of the mechanisms underlying disease susceptibility, asthma is frequently studied in genome-wide association studies (GWAS), which have identified thousands of genetic variants associated with asthma development. Virtually all these genetic variants reside in non-coding genomic regions, which has obscured the functional impact of asthma-associated variants and their translation into disease-relevant mechanisms. Recent advances in genomics technology and epigenetics now offer methods to link genetic variants to gene regulatory elements embedded within non-coding regions, which have started to unravel the molecular mechanisms underlying the complex (epi)genetics of asthma. Here, we provide an integrated overview of (epi)genetic variants associated with asthma, focusing on efforts to link these disease associations to biological insight into asthma pathophysiology using state-of-the-art genomics methodology. Finally, we provide a perspective as to how decoding the genetic and epigenetic basis of asthma has the potential to transform clinical management of asthma and to predict the risk of asthma development.
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Affiliation(s)
- Bernard S Stikker
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Rudi W Hendriks
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Ralph Stadhouders
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.,Department of Cell Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
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16
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Babushkina NP, Kucher AN. Regulatory Potential of SNP Markers in Genes of DNA Repair Systems. Mol Biol 2023. [DOI: 10.1134/s002689332301003x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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17
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Lazure F, Farouni R, Sahinyan K, Blackburn DM, Hernández-Corchado A, Perron G, Lu T, Osakwe A, Ragoussis J, Crist C, Perkins TJ, Jahani-Asl A, Najafabadi HS, Soleimani VD. Transcriptional reprogramming of skeletal muscle stem cells by the niche environment. Nat Commun 2023; 14:535. [PMID: 36726011 PMCID: PMC9892560 DOI: 10.1038/s41467-023-36265-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 01/23/2023] [Indexed: 02/03/2023] Open
Abstract
Adult stem cells are indispensable for tissue regeneration, but their function declines with age. The niche environment in which the stem cells reside plays a critical role in their function. However, quantification of the niche effect on stem cell function is lacking. Using muscle stem cells (MuSC) as a model, we show that aging leads to a significant transcriptomic shift in their subpopulations accompanied by locus-specific gain and loss of chromatin accessibility and DNA methylation. By combining in vivo MuSC transplantation and computational methods, we show that the expression of approximately half of all age-altered genes in MuSCs from aged male mice can be restored by exposure to a young niche environment. While there is a correlation between gene reversibility and epigenetic alterations, restoration of gene expression occurs primarily at the level of transcription. The stem cell niche environment therefore represents an important therapeutic target to enhance tissue regeneration in aging.
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Affiliation(s)
- Felicia Lazure
- Department of Human Genetics, McGill University, 3640 rue University, Montréal, QC, H3A 0C7, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T 1E2, Canada
| | - Rick Farouni
- Department of Human Genetics, McGill University, 3640 rue University, Montréal, QC, H3A 0C7, Canada.,McGill Genome Centre, Victor Phillip Dahdaleh Institute of Genomic Medicine, 740 Dr Penfield Avenue, Montreal, QC, H3A 0G1, Canada
| | - Korin Sahinyan
- Department of Human Genetics, McGill University, 3640 rue University, Montréal, QC, H3A 0C7, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T 1E2, Canada
| | - Darren M Blackburn
- Department of Human Genetics, McGill University, 3640 rue University, Montréal, QC, H3A 0C7, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T 1E2, Canada
| | - Aldo Hernández-Corchado
- Department of Human Genetics, McGill University, 3640 rue University, Montréal, QC, H3A 0C7, Canada.,McGill Genome Centre, Victor Phillip Dahdaleh Institute of Genomic Medicine, 740 Dr Penfield Avenue, Montreal, QC, H3A 0G1, Canada
| | - Gabrielle Perron
- Department of Human Genetics, McGill University, 3640 rue University, Montréal, QC, H3A 0C7, Canada.,McGill Genome Centre, Victor Phillip Dahdaleh Institute of Genomic Medicine, 740 Dr Penfield Avenue, Montreal, QC, H3A 0G1, Canada
| | - Tianyuan Lu
- Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T 1E2, Canada.,Quantitative Life Sciences, McGill University, Montreal, Canada
| | - Adrien Osakwe
- Quantitative Life Sciences, McGill University, Montreal, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, 3640 rue University, Montréal, QC, H3A 0C7, Canada.,McGill Genome Centre, Victor Phillip Dahdaleh Institute of Genomic Medicine, 740 Dr Penfield Avenue, Montreal, QC, H3A 0G1, Canada
| | - Colin Crist
- Department of Human Genetics, McGill University, 3640 rue University, Montréal, QC, H3A 0C7, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T 1E2, Canada
| | - Theodore J Perkins
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, ON, K1H 8L6, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Arezu Jahani-Asl
- Department of Cellular and Molecular Medicine and University of Ottawa Brain and Mind Research Institute, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
| | - Hamed S Najafabadi
- Department of Human Genetics, McGill University, 3640 rue University, Montréal, QC, H3A 0C7, Canada. .,McGill Genome Centre, Victor Phillip Dahdaleh Institute of Genomic Medicine, 740 Dr Penfield Avenue, Montreal, QC, H3A 0G1, Canada. .,Quantitative Life Sciences, McGill University, Montreal, Canada.
| | - Vahab D Soleimani
- Department of Human Genetics, McGill University, 3640 rue University, Montréal, QC, H3A 0C7, Canada. .,Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T 1E2, Canada.
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18
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Lai PMR, Ryu JY, Park SC, Gross BA, Dickinson LD, Dagen S, Aziz-Sultan MA, Boulos AS, Barrow DL, Batjer HH, Blackburn S, Chang EF, Chen PR, Colby GP, Cosgrove GR, David CA, Day AL, Frerichs KU, Niemela M, Ojemann SG, Patel NJ, Shi X, Valle-Giler EP, Wang AC, Welch BG, Zusman EE, Weiss ST, Du R. Somatic Variants in SVIL in Cerebral Aneurysms. Neurol Genet 2022; 8:e200040. [PMID: 36475054 PMCID: PMC9720733 DOI: 10.1212/nxg.0000000000200040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 09/12/2022] [Indexed: 11/30/2022]
Abstract
Background and ObjectivesWhile somatic mutations have been well-studied in cancer, their roles in other complex traits are much less understood. Our goal is to identify somatic variants that may contribute to the formation of saccular cerebral aneurysms.MethodsWe performed whole-exome sequencing on aneurysm tissues and paired peripheral blood. RNA sequencing and the CRISPR/Cas9 system were then used to perform functional validation of our results.ResultsSomatic variants involved in supervillin (SVIL) or its regulation were found in 17% of aneurysm tissues. In the presence of a mutation in theSVILgene, the expression level of SVIL was downregulated in the aneurysm tissue compared with normal control vessels. Downstream signaling pathways that were induced by knockdown ofSVILvia the CRISPR/Cas9 system in vascular smooth muscle cells (vSMCs) were determined by evaluating changes in gene expression and protein kinase phosphorylation. We found thatSVILregulated the phenotypic modulation of vSMCs to the synthetic phenotype via Krüppel-like factor 4 and platelet-derived growth factor and affected cell migration of vSMCs via the RhoA/ROCK pathway.DiscussionWe propose that somatic variants form a novel mechanism for the development of cerebral aneurysms. Specifically, somatic variants inSVILresult in the phenotypic modulation of vSMCs, which increases the susceptibility to aneurysm formation. This finding suggests a new avenue for the therapeutic intervention and prevention of cerebral aneurysms.
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Affiliation(s)
- Pui Man Rosalind Lai
- Department of Neurosurgery (P.M.R.L., J.-Y.R., S.-C.P., S.D., M.A.A.-S., G.R.C., K.U.F., N.J.P., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Artificial Intelligence and Robotics Laboratory (S.-C.P.), Myongji Hospital, Goyang, Korea; Department of Neurosurgery (B.A.G.), University of Pittsburgh, PA; Department of Neurosurgery (L.D.D., E.E.Z.), Sutter Health, Danville, CA; Department of Neurosurgery (A.S.B.), Albany Medical Center, NY; Department of Neurosurgery (D.L.B.), Emory University, Atlanta, GA; Department of Neurosurgery (H.H.B., B.G.W.), University of Texas Southwestern, Dallas, TX; Department of Neurosurgery (S.B., P.R.C., A.L.D.), University of Texas Health Science Center, Houston; Department of Neurosurgery (E.F.C.), University of California San Francisco, CA; Department of Neurosurgery (G.P.C., A.C.W.), University of California Los Angeles; Department of Neurosurgery (C.A.D.), Lahey Hospital and Medical Center, Burlington, MA; Department of Neurosurgery (M.N.), Helsinki University and Helsinki University Hospital, Finland; Department of Neurosurgery (S.G.O.), University of Colorado, Denver; Department of Neurosurgery (X.S.), Affiliated Fuxing Hospital, Capital Medical University, Beijing, China; Department of Neurosurgery (E.P.V.-G.), Ochsner Medical Center, New Orleans, LA; and Channing Division of Network Medicine (S.T.W., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Jee-Yeon Ryu
- Department of Neurosurgery (P.M.R.L., J.-Y.R., S.-C.P., S.D., M.A.A.-S., G.R.C., K.U.F., N.J.P., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Artificial Intelligence and Robotics Laboratory (S.-C.P.), Myongji Hospital, Goyang, Korea; Department of Neurosurgery (B.A.G.), University of Pittsburgh, PA; Department of Neurosurgery (L.D.D., E.E.Z.), Sutter Health, Danville, CA; Department of Neurosurgery (A.S.B.), Albany Medical Center, NY; Department of Neurosurgery (D.L.B.), Emory University, Atlanta, GA; Department of Neurosurgery (H.H.B., B.G.W.), University of Texas Southwestern, Dallas, TX; Department of Neurosurgery (S.B., P.R.C., A.L.D.), University of Texas Health Science Center, Houston; Department of Neurosurgery (E.F.C.), University of California San Francisco, CA; Department of Neurosurgery (G.P.C., A.C.W.), University of California Los Angeles; Department of Neurosurgery (C.A.D.), Lahey Hospital and Medical Center, Burlington, MA; Department of Neurosurgery (M.N.), Helsinki University and Helsinki University Hospital, Finland; Department of Neurosurgery (S.G.O.), University of Colorado, Denver; Department of Neurosurgery (X.S.), Affiliated Fuxing Hospital, Capital Medical University, Beijing, China; Department of Neurosurgery (E.P.V.-G.), Ochsner Medical Center, New Orleans, LA; and Channing Division of Network Medicine (S.T.W., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Sang-Cheol Park
- Department of Neurosurgery (P.M.R.L., J.-Y.R., S.-C.P., S.D., M.A.A.-S., G.R.C., K.U.F., N.J.P., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Artificial Intelligence and Robotics Laboratory (S.-C.P.), Myongji Hospital, Goyang, Korea; Department of Neurosurgery (B.A.G.), University of Pittsburgh, PA; Department of Neurosurgery (L.D.D., E.E.Z.), Sutter Health, Danville, CA; Department of Neurosurgery (A.S.B.), Albany Medical Center, NY; Department of Neurosurgery (D.L.B.), Emory University, Atlanta, GA; Department of Neurosurgery (H.H.B., B.G.W.), University of Texas Southwestern, Dallas, TX; Department of Neurosurgery (S.B., P.R.C., A.L.D.), University of Texas Health Science Center, Houston; Department of Neurosurgery (E.F.C.), University of California San Francisco, CA; Department of Neurosurgery (G.P.C., A.C.W.), University of California Los Angeles; Department of Neurosurgery (C.A.D.), Lahey Hospital and Medical Center, Burlington, MA; Department of Neurosurgery (M.N.), Helsinki University and Helsinki University Hospital, Finland; Department of Neurosurgery (S.G.O.), University of Colorado, Denver; Department of Neurosurgery (X.S.), Affiliated Fuxing Hospital, Capital Medical University, Beijing, China; Department of Neurosurgery (E.P.V.-G.), Ochsner Medical Center, New Orleans, LA; and Channing Division of Network Medicine (S.T.W., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Bradley A Gross
- Department of Neurosurgery (P.M.R.L., J.-Y.R., S.-C.P., S.D., M.A.A.-S., G.R.C., K.U.F., N.J.P., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Artificial Intelligence and Robotics Laboratory (S.-C.P.), Myongji Hospital, Goyang, Korea; Department of Neurosurgery (B.A.G.), University of Pittsburgh, PA; Department of Neurosurgery (L.D.D., E.E.Z.), Sutter Health, Danville, CA; Department of Neurosurgery (A.S.B.), Albany Medical Center, NY; Department of Neurosurgery (D.L.B.), Emory University, Atlanta, GA; Department of Neurosurgery (H.H.B., B.G.W.), University of Texas Southwestern, Dallas, TX; Department of Neurosurgery (S.B., P.R.C., A.L.D.), University of Texas Health Science Center, Houston; Department of Neurosurgery (E.F.C.), University of California San Francisco, CA; Department of Neurosurgery (G.P.C., A.C.W.), University of California Los Angeles; Department of Neurosurgery (C.A.D.), Lahey Hospital and Medical Center, Burlington, MA; Department of Neurosurgery (M.N.), Helsinki University and Helsinki University Hospital, Finland; Department of Neurosurgery (S.G.O.), University of Colorado, Denver; Department of Neurosurgery (X.S.), Affiliated Fuxing Hospital, Capital Medical University, Beijing, China; Department of Neurosurgery (E.P.V.-G.), Ochsner Medical Center, New Orleans, LA; and Channing Division of Network Medicine (S.T.W., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Lawrence D Dickinson
- Department of Neurosurgery (P.M.R.L., J.-Y.R., S.-C.P., S.D., M.A.A.-S., G.R.C., K.U.F., N.J.P., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Artificial Intelligence and Robotics Laboratory (S.-C.P.), Myongji Hospital, Goyang, Korea; Department of Neurosurgery (B.A.G.), University of Pittsburgh, PA; Department of Neurosurgery (L.D.D., E.E.Z.), Sutter Health, Danville, CA; Department of Neurosurgery (A.S.B.), Albany Medical Center, NY; Department of Neurosurgery (D.L.B.), Emory University, Atlanta, GA; Department of Neurosurgery (H.H.B., B.G.W.), University of Texas Southwestern, Dallas, TX; Department of Neurosurgery (S.B., P.R.C., A.L.D.), University of Texas Health Science Center, Houston; Department of Neurosurgery (E.F.C.), University of California San Francisco, CA; Department of Neurosurgery (G.P.C., A.C.W.), University of California Los Angeles; Department of Neurosurgery (C.A.D.), Lahey Hospital and Medical Center, Burlington, MA; Department of Neurosurgery (M.N.), Helsinki University and Helsinki University Hospital, Finland; Department of Neurosurgery (S.G.O.), University of Colorado, Denver; Department of Neurosurgery (X.S.), Affiliated Fuxing Hospital, Capital Medical University, Beijing, China; Department of Neurosurgery (E.P.V.-G.), Ochsner Medical Center, New Orleans, LA; and Channing Division of Network Medicine (S.T.W., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Sarajune Dagen
- Department of Neurosurgery (P.M.R.L., J.-Y.R., S.-C.P., S.D., M.A.A.-S., G.R.C., K.U.F., N.J.P., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Artificial Intelligence and Robotics Laboratory (S.-C.P.), Myongji Hospital, Goyang, Korea; Department of Neurosurgery (B.A.G.), University of Pittsburgh, PA; Department of Neurosurgery (L.D.D., E.E.Z.), Sutter Health, Danville, CA; Department of Neurosurgery (A.S.B.), Albany Medical Center, NY; Department of Neurosurgery (D.L.B.), Emory University, Atlanta, GA; Department of Neurosurgery (H.H.B., B.G.W.), University of Texas Southwestern, Dallas, TX; Department of Neurosurgery (S.B., P.R.C., A.L.D.), University of Texas Health Science Center, Houston; Department of Neurosurgery (E.F.C.), University of California San Francisco, CA; Department of Neurosurgery (G.P.C., A.C.W.), University of California Los Angeles; Department of Neurosurgery (C.A.D.), Lahey Hospital and Medical Center, Burlington, MA; Department of Neurosurgery (M.N.), Helsinki University and Helsinki University Hospital, Finland; Department of Neurosurgery (S.G.O.), University of Colorado, Denver; Department of Neurosurgery (X.S.), Affiliated Fuxing Hospital, Capital Medical University, Beijing, China; Department of Neurosurgery (E.P.V.-G.), Ochsner Medical Center, New Orleans, LA; and Channing Division of Network Medicine (S.T.W., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Mohammad Ali Aziz-Sultan
- Department of Neurosurgery (P.M.R.L., J.-Y.R., S.-C.P., S.D., M.A.A.-S., G.R.C., K.U.F., N.J.P., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Artificial Intelligence and Robotics Laboratory (S.-C.P.), Myongji Hospital, Goyang, Korea; Department of Neurosurgery (B.A.G.), University of Pittsburgh, PA; Department of Neurosurgery (L.D.D., E.E.Z.), Sutter Health, Danville, CA; Department of Neurosurgery (A.S.B.), Albany Medical Center, NY; Department of Neurosurgery (D.L.B.), Emory University, Atlanta, GA; Department of Neurosurgery (H.H.B., B.G.W.), University of Texas Southwestern, Dallas, TX; Department of Neurosurgery (S.B., P.R.C., A.L.D.), University of Texas Health Science Center, Houston; Department of Neurosurgery (E.F.C.), University of California San Francisco, CA; Department of Neurosurgery (G.P.C., A.C.W.), University of California Los Angeles; Department of Neurosurgery (C.A.D.), Lahey Hospital and Medical Center, Burlington, MA; Department of Neurosurgery (M.N.), Helsinki University and Helsinki University Hospital, Finland; Department of Neurosurgery (S.G.O.), University of Colorado, Denver; Department of Neurosurgery (X.S.), Affiliated Fuxing Hospital, Capital Medical University, Beijing, China; Department of Neurosurgery (E.P.V.-G.), Ochsner Medical Center, New Orleans, LA; and Channing Division of Network Medicine (S.T.W., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Alan S Boulos
- Department of Neurosurgery (P.M.R.L., J.-Y.R., S.-C.P., S.D., M.A.A.-S., G.R.C., K.U.F., N.J.P., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Artificial Intelligence and Robotics Laboratory (S.-C.P.), Myongji Hospital, Goyang, Korea; Department of Neurosurgery (B.A.G.), University of Pittsburgh, PA; Department of Neurosurgery (L.D.D., E.E.Z.), Sutter Health, Danville, CA; Department of Neurosurgery (A.S.B.), Albany Medical Center, NY; Department of Neurosurgery (D.L.B.), Emory University, Atlanta, GA; Department of Neurosurgery (H.H.B., B.G.W.), University of Texas Southwestern, Dallas, TX; Department of Neurosurgery (S.B., P.R.C., A.L.D.), University of Texas Health Science Center, Houston; Department of Neurosurgery (E.F.C.), University of California San Francisco, CA; Department of Neurosurgery (G.P.C., A.C.W.), University of California Los Angeles; Department of Neurosurgery (C.A.D.), Lahey Hospital and Medical Center, Burlington, MA; Department of Neurosurgery (M.N.), Helsinki University and Helsinki University Hospital, Finland; Department of Neurosurgery (S.G.O.), University of Colorado, Denver; Department of Neurosurgery (X.S.), Affiliated Fuxing Hospital, Capital Medical University, Beijing, China; Department of Neurosurgery (E.P.V.-G.), Ochsner Medical Center, New Orleans, LA; and Channing Division of Network Medicine (S.T.W., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Daniel L Barrow
- Department of Neurosurgery (P.M.R.L., J.-Y.R., S.-C.P., S.D., M.A.A.-S., G.R.C., K.U.F., N.J.P., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Artificial Intelligence and Robotics Laboratory (S.-C.P.), Myongji Hospital, Goyang, Korea; Department of Neurosurgery (B.A.G.), University of Pittsburgh, PA; Department of Neurosurgery (L.D.D., E.E.Z.), Sutter Health, Danville, CA; Department of Neurosurgery (A.S.B.), Albany Medical Center, NY; Department of Neurosurgery (D.L.B.), Emory University, Atlanta, GA; Department of Neurosurgery (H.H.B., B.G.W.), University of Texas Southwestern, Dallas, TX; Department of Neurosurgery (S.B., P.R.C., A.L.D.), University of Texas Health Science Center, Houston; Department of Neurosurgery (E.F.C.), University of California San Francisco, CA; Department of Neurosurgery (G.P.C., A.C.W.), University of California Los Angeles; Department of Neurosurgery (C.A.D.), Lahey Hospital and Medical Center, Burlington, MA; Department of Neurosurgery (M.N.), Helsinki University and Helsinki University Hospital, Finland; Department of Neurosurgery (S.G.O.), University of Colorado, Denver; Department of Neurosurgery (X.S.), Affiliated Fuxing Hospital, Capital Medical University, Beijing, China; Department of Neurosurgery (E.P.V.-G.), Ochsner Medical Center, New Orleans, LA; and Channing Division of Network Medicine (S.T.W., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - H Hunt Batjer
- Department of Neurosurgery (P.M.R.L., J.-Y.R., S.-C.P., S.D., M.A.A.-S., G.R.C., K.U.F., N.J.P., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Artificial Intelligence and Robotics Laboratory (S.-C.P.), Myongji Hospital, Goyang, Korea; Department of Neurosurgery (B.A.G.), University of Pittsburgh, PA; Department of Neurosurgery (L.D.D., E.E.Z.), Sutter Health, Danville, CA; Department of Neurosurgery (A.S.B.), Albany Medical Center, NY; Department of Neurosurgery (D.L.B.), Emory University, Atlanta, GA; Department of Neurosurgery (H.H.B., B.G.W.), University of Texas Southwestern, Dallas, TX; Department of Neurosurgery (S.B., P.R.C., A.L.D.), University of Texas Health Science Center, Houston; Department of Neurosurgery (E.F.C.), University of California San Francisco, CA; Department of Neurosurgery (G.P.C., A.C.W.), University of California Los Angeles; Department of Neurosurgery (C.A.D.), Lahey Hospital and Medical Center, Burlington, MA; Department of Neurosurgery (M.N.), Helsinki University and Helsinki University Hospital, Finland; Department of Neurosurgery (S.G.O.), University of Colorado, Denver; Department of Neurosurgery (X.S.), Affiliated Fuxing Hospital, Capital Medical University, Beijing, China; Department of Neurosurgery (E.P.V.-G.), Ochsner Medical Center, New Orleans, LA; and Channing Division of Network Medicine (S.T.W., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Spiros Blackburn
- Department of Neurosurgery (P.M.R.L., J.-Y.R., S.-C.P., S.D., M.A.A.-S., G.R.C., K.U.F., N.J.P., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Artificial Intelligence and Robotics Laboratory (S.-C.P.), Myongji Hospital, Goyang, Korea; Department of Neurosurgery (B.A.G.), University of Pittsburgh, PA; Department of Neurosurgery (L.D.D., E.E.Z.), Sutter Health, Danville, CA; Department of Neurosurgery (A.S.B.), Albany Medical Center, NY; Department of Neurosurgery (D.L.B.), Emory University, Atlanta, GA; Department of Neurosurgery (H.H.B., B.G.W.), University of Texas Southwestern, Dallas, TX; Department of Neurosurgery (S.B., P.R.C., A.L.D.), University of Texas Health Science Center, Houston; Department of Neurosurgery (E.F.C.), University of California San Francisco, CA; Department of Neurosurgery (G.P.C., A.C.W.), University of California Los Angeles; Department of Neurosurgery (C.A.D.), Lahey Hospital and Medical Center, Burlington, MA; Department of Neurosurgery (M.N.), Helsinki University and Helsinki University Hospital, Finland; Department of Neurosurgery (S.G.O.), University of Colorado, Denver; Department of Neurosurgery (X.S.), Affiliated Fuxing Hospital, Capital Medical University, Beijing, China; Department of Neurosurgery (E.P.V.-G.), Ochsner Medical Center, New Orleans, LA; and Channing Division of Network Medicine (S.T.W., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Edward F Chang
- Department of Neurosurgery (P.M.R.L., J.-Y.R., S.-C.P., S.D., M.A.A.-S., G.R.C., K.U.F., N.J.P., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Artificial Intelligence and Robotics Laboratory (S.-C.P.), Myongji Hospital, Goyang, Korea; Department of Neurosurgery (B.A.G.), University of Pittsburgh, PA; Department of Neurosurgery (L.D.D., E.E.Z.), Sutter Health, Danville, CA; Department of Neurosurgery (A.S.B.), Albany Medical Center, NY; Department of Neurosurgery (D.L.B.), Emory University, Atlanta, GA; Department of Neurosurgery (H.H.B., B.G.W.), University of Texas Southwestern, Dallas, TX; Department of Neurosurgery (S.B., P.R.C., A.L.D.), University of Texas Health Science Center, Houston; Department of Neurosurgery (E.F.C.), University of California San Francisco, CA; Department of Neurosurgery (G.P.C., A.C.W.), University of California Los Angeles; Department of Neurosurgery (C.A.D.), Lahey Hospital and Medical Center, Burlington, MA; Department of Neurosurgery (M.N.), Helsinki University and Helsinki University Hospital, Finland; Department of Neurosurgery (S.G.O.), University of Colorado, Denver; Department of Neurosurgery (X.S.), Affiliated Fuxing Hospital, Capital Medical University, Beijing, China; Department of Neurosurgery (E.P.V.-G.), Ochsner Medical Center, New Orleans, LA; and Channing Division of Network Medicine (S.T.W., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - P Roc Chen
- Department of Neurosurgery (P.M.R.L., J.-Y.R., S.-C.P., S.D., M.A.A.-S., G.R.C., K.U.F., N.J.P., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Artificial Intelligence and Robotics Laboratory (S.-C.P.), Myongji Hospital, Goyang, Korea; Department of Neurosurgery (B.A.G.), University of Pittsburgh, PA; Department of Neurosurgery (L.D.D., E.E.Z.), Sutter Health, Danville, CA; Department of Neurosurgery (A.S.B.), Albany Medical Center, NY; Department of Neurosurgery (D.L.B.), Emory University, Atlanta, GA; Department of Neurosurgery (H.H.B., B.G.W.), University of Texas Southwestern, Dallas, TX; Department of Neurosurgery (S.B., P.R.C., A.L.D.), University of Texas Health Science Center, Houston; Department of Neurosurgery (E.F.C.), University of California San Francisco, CA; Department of Neurosurgery (G.P.C., A.C.W.), University of California Los Angeles; Department of Neurosurgery (C.A.D.), Lahey Hospital and Medical Center, Burlington, MA; Department of Neurosurgery (M.N.), Helsinki University and Helsinki University Hospital, Finland; Department of Neurosurgery (S.G.O.), University of Colorado, Denver; Department of Neurosurgery (X.S.), Affiliated Fuxing Hospital, Capital Medical University, Beijing, China; Department of Neurosurgery (E.P.V.-G.), Ochsner Medical Center, New Orleans, LA; and Channing Division of Network Medicine (S.T.W., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Geoffrey P Colby
- Department of Neurosurgery (P.M.R.L., J.-Y.R., S.-C.P., S.D., M.A.A.-S., G.R.C., K.U.F., N.J.P., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Artificial Intelligence and Robotics Laboratory (S.-C.P.), Myongji Hospital, Goyang, Korea; Department of Neurosurgery (B.A.G.), University of Pittsburgh, PA; Department of Neurosurgery (L.D.D., E.E.Z.), Sutter Health, Danville, CA; Department of Neurosurgery (A.S.B.), Albany Medical Center, NY; Department of Neurosurgery (D.L.B.), Emory University, Atlanta, GA; Department of Neurosurgery (H.H.B., B.G.W.), University of Texas Southwestern, Dallas, TX; Department of Neurosurgery (S.B., P.R.C., A.L.D.), University of Texas Health Science Center, Houston; Department of Neurosurgery (E.F.C.), University of California San Francisco, CA; Department of Neurosurgery (G.P.C., A.C.W.), University of California Los Angeles; Department of Neurosurgery (C.A.D.), Lahey Hospital and Medical Center, Burlington, MA; Department of Neurosurgery (M.N.), Helsinki University and Helsinki University Hospital, Finland; Department of Neurosurgery (S.G.O.), University of Colorado, Denver; Department of Neurosurgery (X.S.), Affiliated Fuxing Hospital, Capital Medical University, Beijing, China; Department of Neurosurgery (E.P.V.-G.), Ochsner Medical Center, New Orleans, LA; and Channing Division of Network Medicine (S.T.W., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Garth Rees Cosgrove
- Department of Neurosurgery (P.M.R.L., J.-Y.R., S.-C.P., S.D., M.A.A.-S., G.R.C., K.U.F., N.J.P., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Artificial Intelligence and Robotics Laboratory (S.-C.P.), Myongji Hospital, Goyang, Korea; Department of Neurosurgery (B.A.G.), University of Pittsburgh, PA; Department of Neurosurgery (L.D.D., E.E.Z.), Sutter Health, Danville, CA; Department of Neurosurgery (A.S.B.), Albany Medical Center, NY; Department of Neurosurgery (D.L.B.), Emory University, Atlanta, GA; Department of Neurosurgery (H.H.B., B.G.W.), University of Texas Southwestern, Dallas, TX; Department of Neurosurgery (S.B., P.R.C., A.L.D.), University of Texas Health Science Center, Houston; Department of Neurosurgery (E.F.C.), University of California San Francisco, CA; Department of Neurosurgery (G.P.C., A.C.W.), University of California Los Angeles; Department of Neurosurgery (C.A.D.), Lahey Hospital and Medical Center, Burlington, MA; Department of Neurosurgery (M.N.), Helsinki University and Helsinki University Hospital, Finland; Department of Neurosurgery (S.G.O.), University of Colorado, Denver; Department of Neurosurgery (X.S.), Affiliated Fuxing Hospital, Capital Medical University, Beijing, China; Department of Neurosurgery (E.P.V.-G.), Ochsner Medical Center, New Orleans, LA; and Channing Division of Network Medicine (S.T.W., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Carlos A David
- Department of Neurosurgery (P.M.R.L., J.-Y.R., S.-C.P., S.D., M.A.A.-S., G.R.C., K.U.F., N.J.P., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Artificial Intelligence and Robotics Laboratory (S.-C.P.), Myongji Hospital, Goyang, Korea; Department of Neurosurgery (B.A.G.), University of Pittsburgh, PA; Department of Neurosurgery (L.D.D., E.E.Z.), Sutter Health, Danville, CA; Department of Neurosurgery (A.S.B.), Albany Medical Center, NY; Department of Neurosurgery (D.L.B.), Emory University, Atlanta, GA; Department of Neurosurgery (H.H.B., B.G.W.), University of Texas Southwestern, Dallas, TX; Department of Neurosurgery (S.B., P.R.C., A.L.D.), University of Texas Health Science Center, Houston; Department of Neurosurgery (E.F.C.), University of California San Francisco, CA; Department of Neurosurgery (G.P.C., A.C.W.), University of California Los Angeles; Department of Neurosurgery (C.A.D.), Lahey Hospital and Medical Center, Burlington, MA; Department of Neurosurgery (M.N.), Helsinki University and Helsinki University Hospital, Finland; Department of Neurosurgery (S.G.O.), University of Colorado, Denver; Department of Neurosurgery (X.S.), Affiliated Fuxing Hospital, Capital Medical University, Beijing, China; Department of Neurosurgery (E.P.V.-G.), Ochsner Medical Center, New Orleans, LA; and Channing Division of Network Medicine (S.T.W., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Arthur L Day
- Department of Neurosurgery (P.M.R.L., J.-Y.R., S.-C.P., S.D., M.A.A.-S., G.R.C., K.U.F., N.J.P., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Artificial Intelligence and Robotics Laboratory (S.-C.P.), Myongji Hospital, Goyang, Korea; Department of Neurosurgery (B.A.G.), University of Pittsburgh, PA; Department of Neurosurgery (L.D.D., E.E.Z.), Sutter Health, Danville, CA; Department of Neurosurgery (A.S.B.), Albany Medical Center, NY; Department of Neurosurgery (D.L.B.), Emory University, Atlanta, GA; Department of Neurosurgery (H.H.B., B.G.W.), University of Texas Southwestern, Dallas, TX; Department of Neurosurgery (S.B., P.R.C., A.L.D.), University of Texas Health Science Center, Houston; Department of Neurosurgery (E.F.C.), University of California San Francisco, CA; Department of Neurosurgery (G.P.C., A.C.W.), University of California Los Angeles; Department of Neurosurgery (C.A.D.), Lahey Hospital and Medical Center, Burlington, MA; Department of Neurosurgery (M.N.), Helsinki University and Helsinki University Hospital, Finland; Department of Neurosurgery (S.G.O.), University of Colorado, Denver; Department of Neurosurgery (X.S.), Affiliated Fuxing Hospital, Capital Medical University, Beijing, China; Department of Neurosurgery (E.P.V.-G.), Ochsner Medical Center, New Orleans, LA; and Channing Division of Network Medicine (S.T.W., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Kai U Frerichs
- Department of Neurosurgery (P.M.R.L., J.-Y.R., S.-C.P., S.D., M.A.A.-S., G.R.C., K.U.F., N.J.P., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Artificial Intelligence and Robotics Laboratory (S.-C.P.), Myongji Hospital, Goyang, Korea; Department of Neurosurgery (B.A.G.), University of Pittsburgh, PA; Department of Neurosurgery (L.D.D., E.E.Z.), Sutter Health, Danville, CA; Department of Neurosurgery (A.S.B.), Albany Medical Center, NY; Department of Neurosurgery (D.L.B.), Emory University, Atlanta, GA; Department of Neurosurgery (H.H.B., B.G.W.), University of Texas Southwestern, Dallas, TX; Department of Neurosurgery (S.B., P.R.C., A.L.D.), University of Texas Health Science Center, Houston; Department of Neurosurgery (E.F.C.), University of California San Francisco, CA; Department of Neurosurgery (G.P.C., A.C.W.), University of California Los Angeles; Department of Neurosurgery (C.A.D.), Lahey Hospital and Medical Center, Burlington, MA; Department of Neurosurgery (M.N.), Helsinki University and Helsinki University Hospital, Finland; Department of Neurosurgery (S.G.O.), University of Colorado, Denver; Department of Neurosurgery (X.S.), Affiliated Fuxing Hospital, Capital Medical University, Beijing, China; Department of Neurosurgery (E.P.V.-G.), Ochsner Medical Center, New Orleans, LA; and Channing Division of Network Medicine (S.T.W., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Mika Niemela
- Department of Neurosurgery (P.M.R.L., J.-Y.R., S.-C.P., S.D., M.A.A.-S., G.R.C., K.U.F., N.J.P., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Artificial Intelligence and Robotics Laboratory (S.-C.P.), Myongji Hospital, Goyang, Korea; Department of Neurosurgery (B.A.G.), University of Pittsburgh, PA; Department of Neurosurgery (L.D.D., E.E.Z.), Sutter Health, Danville, CA; Department of Neurosurgery (A.S.B.), Albany Medical Center, NY; Department of Neurosurgery (D.L.B.), Emory University, Atlanta, GA; Department of Neurosurgery (H.H.B., B.G.W.), University of Texas Southwestern, Dallas, TX; Department of Neurosurgery (S.B., P.R.C., A.L.D.), University of Texas Health Science Center, Houston; Department of Neurosurgery (E.F.C.), University of California San Francisco, CA; Department of Neurosurgery (G.P.C., A.C.W.), University of California Los Angeles; Department of Neurosurgery (C.A.D.), Lahey Hospital and Medical Center, Burlington, MA; Department of Neurosurgery (M.N.), Helsinki University and Helsinki University Hospital, Finland; Department of Neurosurgery (S.G.O.), University of Colorado, Denver; Department of Neurosurgery (X.S.), Affiliated Fuxing Hospital, Capital Medical University, Beijing, China; Department of Neurosurgery (E.P.V.-G.), Ochsner Medical Center, New Orleans, LA; and Channing Division of Network Medicine (S.T.W., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Steven G Ojemann
- Department of Neurosurgery (P.M.R.L., J.-Y.R., S.-C.P., S.D., M.A.A.-S., G.R.C., K.U.F., N.J.P., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Artificial Intelligence and Robotics Laboratory (S.-C.P.), Myongji Hospital, Goyang, Korea; Department of Neurosurgery (B.A.G.), University of Pittsburgh, PA; Department of Neurosurgery (L.D.D., E.E.Z.), Sutter Health, Danville, CA; Department of Neurosurgery (A.S.B.), Albany Medical Center, NY; Department of Neurosurgery (D.L.B.), Emory University, Atlanta, GA; Department of Neurosurgery (H.H.B., B.G.W.), University of Texas Southwestern, Dallas, TX; Department of Neurosurgery (S.B., P.R.C., A.L.D.), University of Texas Health Science Center, Houston; Department of Neurosurgery (E.F.C.), University of California San Francisco, CA; Department of Neurosurgery (G.P.C., A.C.W.), University of California Los Angeles; Department of Neurosurgery (C.A.D.), Lahey Hospital and Medical Center, Burlington, MA; Department of Neurosurgery (M.N.), Helsinki University and Helsinki University Hospital, Finland; Department of Neurosurgery (S.G.O.), University of Colorado, Denver; Department of Neurosurgery (X.S.), Affiliated Fuxing Hospital, Capital Medical University, Beijing, China; Department of Neurosurgery (E.P.V.-G.), Ochsner Medical Center, New Orleans, LA; and Channing Division of Network Medicine (S.T.W., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Nirav J Patel
- Department of Neurosurgery (P.M.R.L., J.-Y.R., S.-C.P., S.D., M.A.A.-S., G.R.C., K.U.F., N.J.P., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Artificial Intelligence and Robotics Laboratory (S.-C.P.), Myongji Hospital, Goyang, Korea; Department of Neurosurgery (B.A.G.), University of Pittsburgh, PA; Department of Neurosurgery (L.D.D., E.E.Z.), Sutter Health, Danville, CA; Department of Neurosurgery (A.S.B.), Albany Medical Center, NY; Department of Neurosurgery (D.L.B.), Emory University, Atlanta, GA; Department of Neurosurgery (H.H.B., B.G.W.), University of Texas Southwestern, Dallas, TX; Department of Neurosurgery (S.B., P.R.C., A.L.D.), University of Texas Health Science Center, Houston; Department of Neurosurgery (E.F.C.), University of California San Francisco, CA; Department of Neurosurgery (G.P.C., A.C.W.), University of California Los Angeles; Department of Neurosurgery (C.A.D.), Lahey Hospital and Medical Center, Burlington, MA; Department of Neurosurgery (M.N.), Helsinki University and Helsinki University Hospital, Finland; Department of Neurosurgery (S.G.O.), University of Colorado, Denver; Department of Neurosurgery (X.S.), Affiliated Fuxing Hospital, Capital Medical University, Beijing, China; Department of Neurosurgery (E.P.V.-G.), Ochsner Medical Center, New Orleans, LA; and Channing Division of Network Medicine (S.T.W., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Xiangen Shi
- Department of Neurosurgery (P.M.R.L., J.-Y.R., S.-C.P., S.D., M.A.A.-S., G.R.C., K.U.F., N.J.P., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Artificial Intelligence and Robotics Laboratory (S.-C.P.), Myongji Hospital, Goyang, Korea; Department of Neurosurgery (B.A.G.), University of Pittsburgh, PA; Department of Neurosurgery (L.D.D., E.E.Z.), Sutter Health, Danville, CA; Department of Neurosurgery (A.S.B.), Albany Medical Center, NY; Department of Neurosurgery (D.L.B.), Emory University, Atlanta, GA; Department of Neurosurgery (H.H.B., B.G.W.), University of Texas Southwestern, Dallas, TX; Department of Neurosurgery (S.B., P.R.C., A.L.D.), University of Texas Health Science Center, Houston; Department of Neurosurgery (E.F.C.), University of California San Francisco, CA; Department of Neurosurgery (G.P.C., A.C.W.), University of California Los Angeles; Department of Neurosurgery (C.A.D.), Lahey Hospital and Medical Center, Burlington, MA; Department of Neurosurgery (M.N.), Helsinki University and Helsinki University Hospital, Finland; Department of Neurosurgery (S.G.O.), University of Colorado, Denver; Department of Neurosurgery (X.S.), Affiliated Fuxing Hospital, Capital Medical University, Beijing, China; Department of Neurosurgery (E.P.V.-G.), Ochsner Medical Center, New Orleans, LA; and Channing Division of Network Medicine (S.T.W., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Edison P Valle-Giler
- Department of Neurosurgery (P.M.R.L., J.-Y.R., S.-C.P., S.D., M.A.A.-S., G.R.C., K.U.F., N.J.P., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Artificial Intelligence and Robotics Laboratory (S.-C.P.), Myongji Hospital, Goyang, Korea; Department of Neurosurgery (B.A.G.), University of Pittsburgh, PA; Department of Neurosurgery (L.D.D., E.E.Z.), Sutter Health, Danville, CA; Department of Neurosurgery (A.S.B.), Albany Medical Center, NY; Department of Neurosurgery (D.L.B.), Emory University, Atlanta, GA; Department of Neurosurgery (H.H.B., B.G.W.), University of Texas Southwestern, Dallas, TX; Department of Neurosurgery (S.B., P.R.C., A.L.D.), University of Texas Health Science Center, Houston; Department of Neurosurgery (E.F.C.), University of California San Francisco, CA; Department of Neurosurgery (G.P.C., A.C.W.), University of California Los Angeles; Department of Neurosurgery (C.A.D.), Lahey Hospital and Medical Center, Burlington, MA; Department of Neurosurgery (M.N.), Helsinki University and Helsinki University Hospital, Finland; Department of Neurosurgery (S.G.O.), University of Colorado, Denver; Department of Neurosurgery (X.S.), Affiliated Fuxing Hospital, Capital Medical University, Beijing, China; Department of Neurosurgery (E.P.V.-G.), Ochsner Medical Center, New Orleans, LA; and Channing Division of Network Medicine (S.T.W., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Anthony C Wang
- Department of Neurosurgery (P.M.R.L., J.-Y.R., S.-C.P., S.D., M.A.A.-S., G.R.C., K.U.F., N.J.P., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Artificial Intelligence and Robotics Laboratory (S.-C.P.), Myongji Hospital, Goyang, Korea; Department of Neurosurgery (B.A.G.), University of Pittsburgh, PA; Department of Neurosurgery (L.D.D., E.E.Z.), Sutter Health, Danville, CA; Department of Neurosurgery (A.S.B.), Albany Medical Center, NY; Department of Neurosurgery (D.L.B.), Emory University, Atlanta, GA; Department of Neurosurgery (H.H.B., B.G.W.), University of Texas Southwestern, Dallas, TX; Department of Neurosurgery (S.B., P.R.C., A.L.D.), University of Texas Health Science Center, Houston; Department of Neurosurgery (E.F.C.), University of California San Francisco, CA; Department of Neurosurgery (G.P.C., A.C.W.), University of California Los Angeles; Department of Neurosurgery (C.A.D.), Lahey Hospital and Medical Center, Burlington, MA; Department of Neurosurgery (M.N.), Helsinki University and Helsinki University Hospital, Finland; Department of Neurosurgery (S.G.O.), University of Colorado, Denver; Department of Neurosurgery (X.S.), Affiliated Fuxing Hospital, Capital Medical University, Beijing, China; Department of Neurosurgery (E.P.V.-G.), Ochsner Medical Center, New Orleans, LA; and Channing Division of Network Medicine (S.T.W., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Babu G Welch
- Department of Neurosurgery (P.M.R.L., J.-Y.R., S.-C.P., S.D., M.A.A.-S., G.R.C., K.U.F., N.J.P., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Artificial Intelligence and Robotics Laboratory (S.-C.P.), Myongji Hospital, Goyang, Korea; Department of Neurosurgery (B.A.G.), University of Pittsburgh, PA; Department of Neurosurgery (L.D.D., E.E.Z.), Sutter Health, Danville, CA; Department of Neurosurgery (A.S.B.), Albany Medical Center, NY; Department of Neurosurgery (D.L.B.), Emory University, Atlanta, GA; Department of Neurosurgery (H.H.B., B.G.W.), University of Texas Southwestern, Dallas, TX; Department of Neurosurgery (S.B., P.R.C., A.L.D.), University of Texas Health Science Center, Houston; Department of Neurosurgery (E.F.C.), University of California San Francisco, CA; Department of Neurosurgery (G.P.C., A.C.W.), University of California Los Angeles; Department of Neurosurgery (C.A.D.), Lahey Hospital and Medical Center, Burlington, MA; Department of Neurosurgery (M.N.), Helsinki University and Helsinki University Hospital, Finland; Department of Neurosurgery (S.G.O.), University of Colorado, Denver; Department of Neurosurgery (X.S.), Affiliated Fuxing Hospital, Capital Medical University, Beijing, China; Department of Neurosurgery (E.P.V.-G.), Ochsner Medical Center, New Orleans, LA; and Channing Division of Network Medicine (S.T.W., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Edie E Zusman
- Department of Neurosurgery (P.M.R.L., J.-Y.R., S.-C.P., S.D., M.A.A.-S., G.R.C., K.U.F., N.J.P., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Artificial Intelligence and Robotics Laboratory (S.-C.P.), Myongji Hospital, Goyang, Korea; Department of Neurosurgery (B.A.G.), University of Pittsburgh, PA; Department of Neurosurgery (L.D.D., E.E.Z.), Sutter Health, Danville, CA; Department of Neurosurgery (A.S.B.), Albany Medical Center, NY; Department of Neurosurgery (D.L.B.), Emory University, Atlanta, GA; Department of Neurosurgery (H.H.B., B.G.W.), University of Texas Southwestern, Dallas, TX; Department of Neurosurgery (S.B., P.R.C., A.L.D.), University of Texas Health Science Center, Houston; Department of Neurosurgery (E.F.C.), University of California San Francisco, CA; Department of Neurosurgery (G.P.C., A.C.W.), University of California Los Angeles; Department of Neurosurgery (C.A.D.), Lahey Hospital and Medical Center, Burlington, MA; Department of Neurosurgery (M.N.), Helsinki University and Helsinki University Hospital, Finland; Department of Neurosurgery (S.G.O.), University of Colorado, Denver; Department of Neurosurgery (X.S.), Affiliated Fuxing Hospital, Capital Medical University, Beijing, China; Department of Neurosurgery (E.P.V.-G.), Ochsner Medical Center, New Orleans, LA; and Channing Division of Network Medicine (S.T.W., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Scott T Weiss
- Department of Neurosurgery (P.M.R.L., J.-Y.R., S.-C.P., S.D., M.A.A.-S., G.R.C., K.U.F., N.J.P., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Artificial Intelligence and Robotics Laboratory (S.-C.P.), Myongji Hospital, Goyang, Korea; Department of Neurosurgery (B.A.G.), University of Pittsburgh, PA; Department of Neurosurgery (L.D.D., E.E.Z.), Sutter Health, Danville, CA; Department of Neurosurgery (A.S.B.), Albany Medical Center, NY; Department of Neurosurgery (D.L.B.), Emory University, Atlanta, GA; Department of Neurosurgery (H.H.B., B.G.W.), University of Texas Southwestern, Dallas, TX; Department of Neurosurgery (S.B., P.R.C., A.L.D.), University of Texas Health Science Center, Houston; Department of Neurosurgery (E.F.C.), University of California San Francisco, CA; Department of Neurosurgery (G.P.C., A.C.W.), University of California Los Angeles; Department of Neurosurgery (C.A.D.), Lahey Hospital and Medical Center, Burlington, MA; Department of Neurosurgery (M.N.), Helsinki University and Helsinki University Hospital, Finland; Department of Neurosurgery (S.G.O.), University of Colorado, Denver; Department of Neurosurgery (X.S.), Affiliated Fuxing Hospital, Capital Medical University, Beijing, China; Department of Neurosurgery (E.P.V.-G.), Ochsner Medical Center, New Orleans, LA; and Channing Division of Network Medicine (S.T.W., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Rose Du
- Department of Neurosurgery (P.M.R.L., J.-Y.R., S.-C.P., S.D., M.A.A.-S., G.R.C., K.U.F., N.J.P., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Artificial Intelligence and Robotics Laboratory (S.-C.P.), Myongji Hospital, Goyang, Korea; Department of Neurosurgery (B.A.G.), University of Pittsburgh, PA; Department of Neurosurgery (L.D.D., E.E.Z.), Sutter Health, Danville, CA; Department of Neurosurgery (A.S.B.), Albany Medical Center, NY; Department of Neurosurgery (D.L.B.), Emory University, Atlanta, GA; Department of Neurosurgery (H.H.B., B.G.W.), University of Texas Southwestern, Dallas, TX; Department of Neurosurgery (S.B., P.R.C., A.L.D.), University of Texas Health Science Center, Houston; Department of Neurosurgery (E.F.C.), University of California San Francisco, CA; Department of Neurosurgery (G.P.C., A.C.W.), University of California Los Angeles; Department of Neurosurgery (C.A.D.), Lahey Hospital and Medical Center, Burlington, MA; Department of Neurosurgery (M.N.), Helsinki University and Helsinki University Hospital, Finland; Department of Neurosurgery (S.G.O.), University of Colorado, Denver; Department of Neurosurgery (X.S.), Affiliated Fuxing Hospital, Capital Medical University, Beijing, China; Department of Neurosurgery (E.P.V.-G.), Ochsner Medical Center, New Orleans, LA; and Channing Division of Network Medicine (S.T.W., R.D.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
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19
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Zhong Z, Wang Y, Wang M, Yang F, Thomas QA, Xue Y, Zhang Y, Liu W, Jami-Alahmadi Y, Xu L, Feng S, Marquardt S, Wohlschlegel JA, Ausin I, Jacobsen SE. Histone chaperone ASF1 mediates H3.3-H4 deposition in Arabidopsis. Nat Commun 2022; 13:6970. [PMID: 36379930 PMCID: PMC9666630 DOI: 10.1038/s41467-022-34648-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 11/01/2022] [Indexed: 11/16/2022] Open
Abstract
Histone chaperones and chromatin remodelers control nucleosome dynamics, which are essential for transcription, replication, and DNA repair. The histone chaperone Anti-Silencing Factor 1 (ASF1) plays a central role in facilitating CAF-1-mediated replication-dependent H3.1 deposition and HIRA-mediated replication-independent H3.3 deposition in yeast and metazoans. Whether ASF1 function is evolutionarily conserved in plants is unknown. Here, we show that Arabidopsis ASF1 proteins display a preference for the HIRA complex. Simultaneous mutation of both Arabidopsis ASF1 genes caused a decrease in chromatin density and ectopic H3.1 occupancy at loci typically enriched with H3.3. Genetic, transcriptomic, and proteomic data indicate that ASF1 proteins strongly prefers the HIRA complex over CAF-1. asf1 mutants also displayed an increase in spurious Pol II transcriptional initiation and showed defects in the maintenance of gene body CG DNA methylation and in the distribution of histone modifications. Furthermore, ectopic targeting of ASF1 caused excessive histone deposition, less accessible chromatin, and gene silencing. These findings reveal the importance of ASF1-mediated histone deposition for proper epigenetic regulation of the genome.
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Affiliation(s)
- Zhenhui Zhong
- grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 USA
| | - Yafei Wang
- grid.144022.10000 0004 1760 4150State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences and Institute of Future Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Ming Wang
- grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 USA
| | - Fan Yang
- grid.144022.10000 0004 1760 4150State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences and Institute of Future Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Quentin Angelo Thomas
- grid.5254.60000 0001 0674 042XCopenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Yan Xue
- grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 USA
| | - Yaxin Zhang
- grid.256111.00000 0004 1760 2876Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Wanlu Liu
- grid.512487.dZhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining, 314400 Zhejiang China
| | - Yasaman Jami-Alahmadi
- grid.19006.3e0000 0000 9632 6718Department of Biological Chemistry, University of California, Los Angeles, CA 90095 USA
| | - Linhao Xu
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Stadt Seeland, 06466 Germany
| | - Suhua Feng
- grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California, Los Angeles, CA 90095 USA
| | - Sebastian Marquardt
- grid.5254.60000 0001 0674 042XCopenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - James A. Wohlschlegel
- grid.19006.3e0000 0000 9632 6718Department of Biological Chemistry, University of California, Los Angeles, CA 90095 USA
| | - Israel Ausin
- grid.144022.10000 0004 1760 4150State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences and Institute of Future Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Steven E. Jacobsen
- grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095 USA
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20
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Huang D, Feng X, Yang H, Wang J, Zhang W, Fan X, Dong X, Chen K, Yu Y, Ma X, Yi X, Li M. QTLbase2: an enhanced catalog of human quantitative trait loci on extensive molecular phenotypes. Nucleic Acids Res 2022; 51:D1122-D1128. [PMID: 36330927 PMCID: PMC9825467 DOI: 10.1093/nar/gkac1020] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/17/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
Deciphering the fine-scale molecular mechanisms that shape the genetic effects at disease-associated loci from genome-wide association studies (GWAS) remains challenging. The key avenue is to identify the essential molecular phenotypes that mediate the causal variant and disease under particular biological conditions. Therefore, integrating GWAS signals with context-specific quantitative trait loci (QTLs) (such as different tissue/cell types, disease states, and perturbations) from extensive molecular phenotypes would present important strategies for full understanding of disease genetics. Via persistent curation and systematic data processing of large-scale human molecular trait QTLs (xQTLs), we updated our previous QTLbase database (now QTLbase2, http://mulinlab.org/qtlbase) to comprehensively analyze and visualize context-specific QTLs across 22 molecular phenotypes and over 95 tissue/cell types. Overall, the resource features the following major updates and novel functions: (i) 960 more genome-wide QTL summary statistics from 146 independent studies; (ii) new data for 10 previously uncompiled QTL types; (iii) variant query scope expanded to fit 195 QTL datasets based on whole-genome sequencing; (iv) supports filtering and comparison of QTLs for different biological conditions, such as stimulation types and disease states; (v) a new linkage disequilibrium viewer to facilitate variant prioritization across tissue/cell types and QTL types.
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Affiliation(s)
| | | | - Hongxi Yang
- Department of Pharmacology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Jianhua Wang
- Department of Pharmacology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Wenwen Zhang
- Department of Pharmacology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xutong Fan
- Department of Pharmacology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xiaobao Dong
- Department of Bioinformatics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Kexin Chen
- Department of Bioinformatics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Ying Yu
- Department of Pharmacology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xin Ma
- Correspondence may also be addressed to Xin Ma.
| | - Xianfu Yi
- Correspondence may also be addressed to Xianfu Yi.
| | - Mulin Jun Li
- To whom correspondence should be addressed. Tel: +86 22 83336668; Fax: +86 22 83336668;
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21
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Qi X, Jia Y, Pan C, Li C, Wen Y, Hao J, Liu L, Cheng B, Cheng S, Yao Y, Zhang F. Index of multiple deprivation contributed to common psychiatric disorders: A systematic review and comprehensive analysis. Neurosci Biobehav Rev 2022; 140:104806. [PMID: 35926729 DOI: 10.1016/j.neubiorev.2022.104806] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 04/08/2022] [Accepted: 07/31/2022] [Indexed: 10/16/2022]
Abstract
BACKGROUND Limited studies have been conducted to explore the interaction effects of social environmental and genetic factors on the risks of common psychiatric disorders. METHODS 56,613-106,695 individuals were collected from the UK Biobank cohort. Logistic or liner regression models were first used to evaluate the associations of index of multiple deprivation (IMD) with bipolar disorder (BD), depression and anxiety in UK Biobank cohort. Then, for the significant IMD associated with BD, depression and anxiety, genome-wide gene-environment interaction study (GWEIS) was performed by PLINK 2.0. RESULT Totally, the higher levels of IMD were significantly associated with higher risks of BD, depression and anxiety. For BD, GWEIS identified multiple significant SNPs interacting with IMD, such as rs75182167 for income and rs111841503 for education. For depression and anxiety, GWEIS found significant SNPs interacting with income and education, such as rs147013419 for income and rs142366753 for education. CONCLUSION Social environmental deprivations contributed to the risks of psychiatric disorders. Besides, we reported multiple candidate genetic loci interacting with IMD, providing novel insights into the biological mechanism.
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Affiliation(s)
- Xin Qi
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yumeng Jia
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Chuyu Pan
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Chune Li
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yan Wen
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Jingcan Hao
- Cancer Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Li Liu
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Bolun Cheng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Shiqiang Cheng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yao Yao
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China.
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22
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Wang L, You X, Ruan D, Shao R, Dai HQ, Shen W, Xu GL, Liu W, Zou W. TET enzymes regulate skeletal development through increasing chromatin accessibility of RUNX2 target genes. Nat Commun 2022; 13:4709. [PMID: 35953487 PMCID: PMC9372040 DOI: 10.1038/s41467-022-32138-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/13/2022] [Indexed: 12/03/2022] Open
Abstract
The Ten-eleven translocation (TET) family of dioxygenases mediate cytosine demethylation by catalyzing the oxidation of 5-methylcytosine (5mC). TET-mediated DNA demethylation controls the proper differentiation of embryonic stem cells and TET members display functional redundancy during early gastrulation. However, it is unclear if TET proteins have functional significance in mammalian skeletal development. Here, we report that Tet genes deficiency in mesoderm mesenchymal stem cells results in severe defects of bone development. The existence of any single Tet gene allele can support early bone formation, suggesting a functional redundancy of TET proteins. Integrative analyses of RNA-seq, Whole Genome Bisulfite Sequencing (WGBS), 5hmC-Seal and Assay for Transposase-Accessible Chromatin (ATAC-seq) demonstrate that TET-mediated demethylation increases the chromatin accessibility of target genes by RUNX2 and facilities RUNX2-regulated transcription. In addition, TET proteins interact with RUNX2 through their catalytic domain to regulate cytosine methylation around RUNX2 binding region. The catalytic domain is indispensable for TET enzymes to regulate RUNX2 transcription activity on its target genes and to regulate bone development. These results demonstrate that TET enzymes function to regulate RUNX2 activity and maintain skeletal homeostasis. Here the authors investigate the role of the TET family of DNA demethylases in mammalian skeletal development. They find that loss of TETs leads to hypermethylation that results in decreased chromatin accessibility of RUNX2 target genes, repressing osteoblast differentiation and leading to skeletal defects in mouse such as short limbs.
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Affiliation(s)
- Lijun Wang
- Institute of Microsurgery on Extremities, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Xiuling You
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Dengfeng Ruan
- Department of Orthopedic Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, 310009, China.,Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining, 314400, China
| | - Rui Shao
- Institute of Microsurgery on Extremities, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Hai-Qiang Dai
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Weiliang Shen
- Department of Orthopedic Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, 310009, China
| | - Guo-Liang Xu
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Wanlu Liu
- Department of Orthopedic Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, 310009, China. .,Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining, 314400, China.
| | - Weiguo Zou
- Institute of Microsurgery on Extremities, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China. .,State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China.
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23
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Liu N, Sadlon T, Wong YY, Pederson S, Breen J, Barry SC. 3DFAACTS-SNP: using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of type 1 diabetes (T1D) risk. Epigenetics Chromatin 2022; 15:24. [PMID: 35773720 PMCID: PMC9244893 DOI: 10.1186/s13072-022-00456-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 06/06/2022] [Indexed: 11/26/2022] Open
Abstract
Background Genome-wide association studies (GWAS) have enabled the discovery of single nucleotide polymorphisms (SNPs) that are significantly associated with many autoimmune diseases including type 1 diabetes (T1D). However, many of the identified variants lie in non-coding regions, limiting the identification of mechanisms that contribute to autoimmune disease progression. To address this problem, we developed a variant filtering workflow called 3DFAACTS-SNP to link genetic variants to target genes in a cell-specific manner. Here, we use 3DFAACTS-SNP to identify candidate SNPs and target genes associated with the loss of immune tolerance in regulatory T cells (Treg) in T1D. Results Using 3DFAACTS-SNP, we identified from a list of 1228 previously fine-mapped variants, 36 SNPs with plausible Treg-specific mechanisms of action. The integration of cell type-specific chromosome conformation capture data in 3DFAACTS-SNP identified 266 regulatory regions and 47 candidate target genes that interact with these variant-containing regions in Treg cells. We further demonstrated the utility of the workflow by applying it to three other SNP autoimmune datasets, identifying 16 Treg-centric candidate variants and 60 interacting genes. Finally, we demonstrate the broad utility of 3DFAACTS-SNP for functional annotation of all known common (> 10% allele frequency) variants from the Genome Aggregation Database (gnomAD). We identified 9376 candidate variants and 4968 candidate target genes, generating a list of potential sites for future T1D or other autoimmune disease research. Conclusions We demonstrate that it is possible to further prioritise variants that contribute to T1D based on regulatory function, and illustrate the power of using cell type-specific multi-omics datasets to determine disease mechanisms. Our workflow can be customised to any cell type for which the individual datasets for functional annotation have been generated, giving broad applicability and utility. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-022-00456-5.
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Affiliation(s)
- Ning Liu
- South Australian Health and Medical Research Institute, Adelaide, Australia.,Robinson Research Institute, University of Adelaide, Adelaide, Australia.,Bioinformatics Hub, School of Biological Sciences, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, Australia
| | - Timothy Sadlon
- Robinson Research Institute, University of Adelaide, Adelaide, Australia.,Women's and Children's Health Network, Women's and Children's Hospital, Adelaide, Australia
| | - Ying Y Wong
- Robinson Research Institute, University of Adelaide, Adelaide, Australia.,Women's and Children's Health Network, Women's and Children's Hospital, Adelaide, Australia
| | - Stephen Pederson
- Bioinformatics Hub, School of Biological Sciences, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, Australia
| | - James Breen
- South Australian Health and Medical Research Institute, Adelaide, Australia. .,Robinson Research Institute, University of Adelaide, Adelaide, Australia. .,Bioinformatics Hub, School of Biological Sciences, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, Australia. .,Black Ochre Data Labs, Indigenous Genomics, Telethon Kids Institute, Adelaide, Australia. .,John Curtin School of Medical Research, Australian National University, Canberra, Australia.
| | - Simon C Barry
- Robinson Research Institute, University of Adelaide, Adelaide, Australia.,Women's and Children's Health Network, Women's and Children's Hospital, Adelaide, Australia
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24
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Feitosa MF, Wojczynski MK, Anema JA, Daw EW, Wang L, Santanasto AJ, Nygaard M, Province MA. Genetic pleiotropy between pulmonary function and age-related traits: The Long Life Family Study. J Gerontol A Biol Sci Med Sci 2022; 79:glac046. [PMID: 35180297 PMCID: PMC10873520 DOI: 10.1093/gerona/glac046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Pulmonary function (PF) progressively declines with aging. Forced expiratory volume in the first second (FEV1) and forced vital capacity (FVC) are predictors of morbidity of pulmonary and cardiovascular diseases and all-cause mortality. In addition, reduced PF is associated with elevated chronic low-grade systemic inflammation, glucose metabolism, body fatness, and low muscle strength. It may suggest pleiotropic genetic effects between PF with these age-related factors. METHODS We evaluated whether FEV1 and FVC share common pleiotropic genetic effects factors with interleukin-6, high-sensitivity C-reactive protein, body mass index, muscle (grip) strength, plasma glucose, and glycosylated hemoglobin in 3,888 individuals (age range: 26-106). We employed sex-combined and sex-specific correlated meta-analyses to test whether combining genome-wide association p-values from two or more traits enhances the ability to detect variants sharing effects on these correlated traits. RESULTS We identified 32 loci for PF, including 29 novel pleiotropic loci associated with pulmonary function and (i) body fatness (CYP2U1/SGMS2), (ii) glucose metabolism (CBWD1/DOCK8 and MMUT/CENPQ), (iii) inflammatory markers (GLRA3/HPGD, TRIM9, CALN1, CTNNB1/ZNF621, GATA5/SLCO4A1/NTSR1, and NPVF/C7orf31/CYCS), and (iv) muscle strength (MAL2, AC008825.1/LINC02103, AL136418.1). CONCLUSIONS The identified genes/loci for PF and age-related traits suggest their underlying shared genetic effects, which can explain part of their phenotypic correlations. Integration of gene expression and genomic annotation data shows enrichment of our genetic variants in lung, blood, adipose, pancreas, and muscles, among others. Our findings highlight the critical roles of identified gene/locus in systemic inflammation, glucose metabolism, strength performance, PF, and pulmonary disease, which are involved in accelerated biological aging.
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Affiliation(s)
- Mary F Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Mary K Wojczynski
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jason A Anema
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - E Warwick Daw
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Lihua Wang
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Adam J Santanasto
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Marianne Nygaard
- Epidemiology, Biostatistics, and Biodemography, Department of Public Health, University of Southern Denmark, Odense C, Denmark
| | - Michael A Province
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
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25
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Xiang X, Tao Y, DiRusso J, Hsu FM, Zhang J, Xue Z, Pontis J, Trono D, Liu W, Clark AT. Human reproduction is regulated by retrotransposons derived from ancient Hominidae-specific viral infections. Nat Commun 2022; 13:463. [PMID: 35075135 PMCID: PMC8786967 DOI: 10.1038/s41467-022-28105-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 12/16/2021] [Indexed: 12/26/2022] Open
Abstract
Germ cells are essential to pass DNA from one generation to the next. In human reproduction, germ cell development begins with the specification of primordial germ cells (PGCs) and a failure to specify PGCs leads to human infertility. Recent studies have revealed that the transcription factor network required for PGC specification has diverged in mammals, and this has a significant impact on our understanding of human reproduction. Here, we reveal that the Hominidae-specific Transposable Elements (TEs) LTR5Hs, may serve as TEENhancers (TE Embedded eNhancers) to facilitate PGC specification. LTR5Hs TEENhancers become transcriptionally active during PGC specification both in vivo and in vitro with epigenetic reprogramming leading to increased chromatin accessibility, localized DNA demethylation, enrichment of H3K27ac, and occupation of key hPGC transcription factors. Inactivation of LTR5Hs TEENhancers with KRAB mediated CRISPRi has a significant impact on germ cell specification. In summary, our data reveals the essential role of Hominidae-specific LTR5Hs TEENhancers in human germ cell development. The transcription factor network required for primordial germ cell (PGC) specification is known to diverge in mammals. Here the authors show that hominidae-specific transposable element (TE) LTR5Hs becomes transcriptionally active during PGC specification, and LTR5Hs inactivation abrogates human PGC specification
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Affiliation(s)
- Xinyu Xiang
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Rd., Haining, 314400, China
| | - Yu Tao
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jonathan DiRusso
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Fei-Man Hsu
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jinchun Zhang
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Rd., Haining, 314400, China
| | - Ziwei Xue
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Rd., Haining, 314400, China
| | - Julien Pontis
- School of Life Sciences, Ecole Polytechnique Fe ́de ́rale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fe ́de ́rale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Wanlu Liu
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Rd., Haining, 314400, China. .,Department of Orthopedic Surgery of the Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310029, China. .,Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China. .,Alibaba-Zhejiang University Joint Research Center of Future DigitalHealthcare, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Amander T Clark
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA. .,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA. .,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, 90095, USA. .,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
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26
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Wu J, Chen Y, Wang P, Caselli RJ, Thompson PM, Wang J, Wang Y. Integrating Transcriptomics, Genomics, and Imaging in Alzheimer's Disease: A Federated Model. FRONTIERS IN RADIOLOGY 2022; 1:777030. [PMID: 37492173 PMCID: PMC10365097 DOI: 10.3389/fradi.2021.777030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/21/2021] [Indexed: 07/27/2023]
Abstract
Alzheimer's disease (AD) affects more than 1 in 9 people age 65 and older and becomes an urgent public health concern as the global population ages. In clinical practice, structural magnetic resonance imaging (sMRI) is the most accessible and widely used diagnostic imaging modality. Additionally, genome-wide association studies (GWAS) and transcriptomics-the study of gene expression-also play an important role in understanding AD etiology and progression. Sophisticated imaging genetics systems have been developed to discover genetic factors that consistently affect brain function and structure. However, most studies to date focused on the relationships between brain sMRI and GWAS or brain sMRI and transcriptomics. To our knowledge, few methods have been developed to discover and infer multimodal relationships among sMRI, GWAS, and transcriptomics. To address this, we propose a novel federated model, Genotype-Expression-Imaging Data Integration (GEIDI), to identify genetic and transcriptomic influences on brain sMRI measures. The relationships between brain imaging measures and gene expression are allowed to depend on a person's genotype at the single-nucleotide polymorphism (SNP) level, making the inferences adaptive and personalized. We performed extensive experiments on publicly available Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset. Experimental results demonstrated our proposed method outperformed state-of-the-art expression quantitative trait loci (eQTL) methods for detecting genetic and transcriptomic factors related to AD and has stable performance when data are integrated from multiple sites. Our GEIDI approach may offer novel insights into the relationship among image biomarkers, genotypes, and gene expression and help discover novel genetic targets for potential AD drug treatments.
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Affiliation(s)
- Jianfeng Wu
- School of Computing and Augmented Intelligence, Arizona State University, Tempe, AZ, United States
| | - Yanxi Chen
- School of Computing and Augmented Intelligence, Arizona State University, Tempe, AZ, United States
| | - Panwen Wang
- Department of Health Sciences Research and Center for Individualized Medicine, Mayo Clinic Arizona, Scottsdale, AZ, United States
| | - Richard J. Caselli
- Department of Neurology, Mayo Clinic Arizona, Scottsdale, AZ, United States
| | - Paul M. Thompson
- Imaging Genetics Center, Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Junwen Wang
- Department of Health Sciences Research and Center for Individualized Medicine, Mayo Clinic Arizona, Scottsdale, AZ, United States
| | - Yalin Wang
- School of Computing and Augmented Intelligence, Arizona State University, Tempe, AZ, United States
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27
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Huang G, Wang Y, Qin L, Huang B, Yu X. Association and functional analysis of angiotensin-converting enzyme 2 genetic variants with the pathogenesis of pre-eclampsia. Front Endocrinol (Lausanne) 2022; 13:926512. [PMID: 36419766 PMCID: PMC9676981 DOI: 10.3389/fendo.2022.926512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 10/07/2022] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVE The aim of this study was to investigate the relationship between potential functional single-nucleotide polymorphisms (SNPs) of the angiotensin-converting enzyme 2 (ACE2) gene and the pathogenesis of pre-eclampsia (PE) in Guangxi, China. MATERIALS AND METHODS A case-control study was conducted involving 327 PE cases and 591 age-matched, normal, singleton pregnant women. Potential functional ACE2 gene variants (rs2106809 A>G, rs6632677 G>C, and rs2074192 C>T) were selected and genotyped using kompetitive allele-specific PCR. The strength of the associations between the studied genetic variants and the risk of PE were evaluated using odds ratios (ORs) and corresponding 95% confidence intervals (CIs). RESULT After adjusting for age and body mass index (BMI), unconditional logistic regression analysis showed that rs2106809 A>G was significantly associated with PE risk (AG vs. AA, OR = 1.43, 95% CI = 1.03-1.99, p = 0.034; AG/GG vs. AA, OR = 1.45, 95% CI = 1.06-1.99, p = 0.019), especially with severe PE (AG vs. AA, adjusted OR = 1.70, 95% CI = 1.10-2.61; AG/GG vs. AA, adjusted OR = 1.71, 95% CI = 1.14-2.57). Further stratified analysis showed that rs2106809 was even more pronounced in subjects in the pre-pregnancy BMI (pre-BMI) >23 kg/m2 (adjusted OR = 2.14, 95% CI = 1.32-3.45) and triglyceride (TG) >2.84 mmol/L subgroups (adjusted OR = 1.81, 95% CI = 1.09-3.01) under the dominant genetic model. We also found that rs2106809 interacted with pre-BMI (p interaction = 0.040), thereby affecting an individual's genetic susceptibility to PE. Multiple dimension reduction analysis demonstrated that rs2106809 made the best one-locus model, and the three-locus model was the best interaction model for predicting PE risk. Functional analysis suggested that rs2106809 A>G causes a change in the reliability of classifications of two putative splice sites in the ACE2 gene, potentially regulating the expression of functional genes (PIR, ACE2, and CLTRN) in multiple tissues and cell lines (p< 0.05). CONCLUSION The ACE2 gene rs2106809 A>G variant is significantly associated with the risk of PE via individual locus effects and/or complex gene-gene and gene-environment interactions. Regulating the expression of functional genes such as PIR, ACE2, and CLTRN may be the molecular mechanism by which rs2106809 increases an individual's susceptibility to PE.
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Affiliation(s)
- Gongchen Huang
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, School of Public Health, Guilin Medical University, Guilin, China
| | - Yukun Wang
- Scientific Experiment Center, Guilin Medical University, Guilin, China
| | - Linyuan Qin
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, School of Public Health, Guilin Medical University, Guilin, China
| | - Bo Huang
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, School of Public Health, Guilin Medical University, Guilin, China
| | - Xiangyuan Yu
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, School of Public Health, Guilin Medical University, Guilin, China
- Institute of Preventive Medicine, School of Public Health, Guilin Medical University, Guilin, China
- *Correspondence: Xiangyuan Yu, ;
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28
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Huang G, Liang Q, Wang Y, Qin L, Yang H, Lin L, Yu X. Association of ACE2 gene functional variants with gestational diabetes mellitus risk in a southern Chinese population. Front Endocrinol (Lausanne) 2022; 13:1052906. [PMID: 36531495 PMCID: PMC9752565 DOI: 10.3389/fendo.2022.1052906] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 10/31/2022] [Indexed: 12/03/2022] Open
Abstract
OBJECTIVE To explore the relationship between angiotensin-converting enzyme 2 (ACE2) genetic variants and gestational diabetes mellitus (GDM) in a southern Chinese population. METHODS Potential functional variants (rs2106809, rs6632677, and rs2074192) of ACE2 were selected and genotyped in 566 GDM patients and 710 normal pregnaõncies in Guilin, China. The odds ratio (OR) and its corresponding 95% confidence interval (CI) were used to evaluate the association between genetic variant and GDM risk, and then the false positive report probability, multifactor dimensional reduction (MDR), and bioinformatics tools were used to confirm the significant association in the study. RESULTS After adjusting for age and prepregnancy body mass index, logistic regression analysis showed that ACE2 rs6632677 was significantly associated with a decreased risk of GDM (CC vs. GG: adjusted OR = 0.09, 95% CI: 0.01 - 0.71, P = .023; GC/CC vs. GG: adjusted OR = 0.68, 95% CI = 0.46 - 0.99, P = .048; and CC vs. GG/GC: adjusted OR = 0.09, 95% CI = 0.01 - 0.72, P = .024), whereas rs2074192 was associated with increased GDM risk (TT vs. CC/CT: adjusted OR = 1.38, 95% CI = 1.08 - 1.75, P = .009). Furthermore, we found that rs6632677 interacted with SBP (P interaction = .043) and FPG (P interaction = .021) and rs2074192 interacted with HDL-c (P interaction = .029) and LDL-c (P interaction = .035) to influence the GDM risk of the individual. In the MDR analysis, the rs6632677 was the best one-locus model, and the three-loci model was the best interaction model to predict GDM risk. In addition, functional analysis confirmed that rs2074192 may regulate the splicing process of ACE2 gene. CONCLUSION ACE2 gene variants are significantly associated with the risk of GDM via gene-gene and gene-environment combinations. The rs2074192 C > T affects the splicing of the ACE2 gene, which may be a potential mechanism leading to the changed susceptibility of an individual female during pregnancy to GDM.
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Affiliation(s)
- Gongchen Huang
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, School of Public Health, Guilin Medical University, Guilin, China
| | - Qiulian Liang
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, School of Public Health, Guilin Medical University, Guilin, China
| | - Yukun Wang
- Scientific Experiment Center, Guilin Medical University, Guilin, China
| | - Linyuan Qin
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, School of Public Health, Guilin Medical University, Guilin, China
| | - Haili Yang
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, School of Public Health, Guilin Medical University, Guilin, China
| | - Lin Lin
- Laboratory of Gynecologic Oncology, Department of Gynecology, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- *Correspondence: Lin Lin, ; Xiangyuan Yu,
| | - Xiangyuan Yu
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, School of Public Health, Guilin Medical University, Guilin, China
- *Correspondence: Lin Lin, ; Xiangyuan Yu,
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29
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Dai H, Chu X, Liang Q, Wang M, Li L, Zhou Y, Zheng Z, Wang W, Wang Z, Li H, Wang J, Zheng H, Zhao Y, Liu L, Yao H, Luo M, Wang Q, Kang S, Li Y, Wang K, Song F, Zhang R, Wu X, Cheng X, Zhang W, Wei Q, Li MJ, Chen K. Genome-wide association and functional interrogation identified a variant at 3p26.1 modulating ovarian cancer survival among Chinese women. Cell Discov 2021; 7:121. [PMID: 34930913 PMCID: PMC8688503 DOI: 10.1038/s41421-021-00342-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 09/23/2021] [Indexed: 12/03/2022] Open
Abstract
Ovarian cancer survival varies considerably among patients, to which germline variation may also contribute in addition to mutational signatures. To identify genetic markers modulating ovarian cancer outcome, we performed a genome-wide association study in 2130 Chinese ovarian cancer patients and found a hitherto unrecognized locus at 3p26.1 to be associated with the overall survival (Pcombined = 8.90 × 10−10). Subsequent statistical fine-mapping, functional annotation, and eQTL mapping prioritized a likely casual SNP rs9311399 in the non-coding regulatory region. Mechanistically, rs9311399 altered its enhancer activity through an allele-specific transcription factor binding and a long-range interaction with the promoter of a lncRNA BHLHE40-AS1. Deletion of the rs9311399-associated enhancer resulted in expression changes in several oncogenic signaling pathway genes and a decrease in tumor growth. Thus, we have identified a novel genetic locus that is associated with ovarian cancer survival possibly through a long-range gene regulation of oncogenic pathways.
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Affiliation(s)
- Hongji Dai
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xinlei Chu
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Qian Liang
- Department of Pharmacology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Mengyun Wang
- Cancer Institute, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lian Li
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Yao Zhou
- Department of Pharmacology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zhanye Zheng
- Department of Pharmacology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Wei Wang
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Zhao Wang
- Department of Pharmacology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Haixin Li
- Cancer Biobank, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Jianhua Wang
- Department of Pharmacology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Hong Zheng
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Yanrui Zhao
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Luyang Liu
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Hongcheng Yao
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Menghan Luo
- Department of Pharmacology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Qiong Wang
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Shan Kang
- Department of Obstetrics and Gynaecology, Hebei Medical University, Fourth Hospital, Shijiazhuang, China
| | - Yan Li
- Department of Molecular Biology, Hebei Medical University, Fourth Hospital, Shijiazhuang, China
| | - Ke Wang
- Department of Gynecologic Oncology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Fengju Song
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Ruoxin Zhang
- Cancer Institute, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaohua Wu
- Cancer Institute, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xi Cheng
- Cancer Institute, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wei Zhang
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, NC, USA.,Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Qingyi Wei
- Cancer Institute, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China. .,Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA. .,Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, USA.
| | - Mulin Jun Li
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China. .,Department of Pharmacology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China.
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30
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Yi X, Zheng Z, Xu H, Zhou Y, Huang D, Wang J, Feng X, Zhao K, Fan X, Zhang S, Dong X, Wang Z, Shen Y, Cheng H, Shi L, Li MJ. Interrogating cell type-specific cooperation of transcriptional regulators in 3D chromatin. iScience 2021; 24:103468. [PMID: 34888502 PMCID: PMC8634045 DOI: 10.1016/j.isci.2021.103468] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/23/2021] [Accepted: 11/12/2021] [Indexed: 12/14/2022] Open
Abstract
Context-specific activities of transcription regulators (TRs) in the nucleus modulate spatiotemporal gene expression precisely. Using the largest ChIP-seq data and chromatin loops in the human K562 cell line, we initially interrogated TR cooperation in 3D chromatin via a graphical model and revealed many known and novel TRs manipulating context-specific pathways. To explore TR cooperation across broad tissue/cell types, we systematically leveraged large-scale open chromatin profiles, computational footprinting, and high-resolution chromatin interactions to investigate tissue/cell type-specific TR cooperation. We first delineated a landscape of TR cooperation across 40 human tissue/cell types. Network modularity analyses uncovered the commonality and specificity of TR cooperation in different conditions. We also demonstrated that TR cooperation information can better interpret the disease-causal variants identified by genome-wide association studies and recapitulate cell states during neural development. Our study characterizes shared and unique patterns of TR cooperation associated with the cell type specificity of gene regulation in 3D chromatin. Computational inference of transcriptional regulator (TR) cooperation in 3D chromatin A landscape of 3D TR cooperation across 40 human tissue/cell types TR cooperation can better interpret the disease-causal variants identified by GWAS Cooperation of certain TRs shapes context-specific gene regulation in cell development
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Affiliation(s)
- Xianfu Yi
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin 300070, China.,Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
| | - Zhanye Zheng
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Hang Xu
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
| | - Yao Zhou
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Dandan Huang
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Jianhua Wang
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Xiangling Feng
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Ke Zhao
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Xutong Fan
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Shijie Zhang
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Xiaobao Dong
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China.,Department of Genetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Zhao Wang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Yujun Shen
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Hui Cheng
- State Key Laboratory of Experimental Hematology, Chinese Academy of Medical Sciences, Tianjin 300070, China
| | - Lei Shi
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Mulin Jun Li
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China.,Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
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31
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Kononov S, Mal G, Azarova I, Klyosova E, Bykanova M, Churnosov M, Polonikov A. Pharmacogenetic loci for rosuvastatin are associated with intima-media thickness change and coronary artery disease risk. Pharmacogenomics 2021; 23:15-34. [PMID: 34905955 DOI: 10.2217/pgs-2021-0097] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: Polymorphisms at LPA, LDLR, APOE, APOC1, MYLIP and ABCG2 are attractive targets for assessment of their impact on lipid-lowering therapy with rosuvastatin. The present study investigated whether polymorphisms at these genes are associated with the risk of coronary artery disease (CAD) development, and reduction of atherogenic lipids and carotid intima-media thickness (CIMT) in CAD patients, taking rosuvastatin. Materials & methods: 190 CAD patients and 1697 subjects were enrolled in pharmacogenetic and genetic association study, respectively. SNP genotyping was done using the MassARRAY-4 system. Results: MYLIP rs6924995, rs3757354, APOC1 rs445925, LDLR rs6511720, APOE rs7412, ABCG2 rs2199936, rs1481012 variants were significantly associated with CAD susceptibility (p = 0.016, 0.0003, <0.0001, <0.0001, 0.013, 0.016, 0.0035, respectively), as well as with CIMT regression (except ABCG2 variants; p = 0.05, 0.039, 0.039, 0.016, 0.0065), and changes in plasma lipids during rosuvastatin therapy. Conclusion: The studied polymorphisms possess pleiotropic effects on plasma lipids and CIMT, CAD susceptibility, and determine lipid-lowering response to rosuvastatin.
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Affiliation(s)
- Stanislav Kononov
- Department of Internal Medicine N 2, Kursk State Medical University, 14 Pirogova St., Kursk 305035, Russian Federation
| | - Galina Mal
- Department of Pharmacology, Kursk State Medical University, 3 Karl Marx St., Kursk 305041, Russian Federation
| | - Iuliia Azarova
- Department of Biological Chemistry, Kursk State Medical University, 3 Karl Marx St., Kursk 305041, Russian Federation.,Laboratory of Biochemical Genetics & Metabolomics, Research Institute for Genetic & Molecular Epidemiology, Kursk State Medical University, 18 Yamskaya St., Kursk 305041,, Russian Federation
| | - Elena Klyosova
- Laboratory of Biochemical Genetics & Metabolomics, Research Institute for Genetic & Molecular Epidemiology, Kursk State Medical University, 18 Yamskaya St., Kursk 305041,, Russian Federation.,Department of Biology, Medical Genetics & Ecology, Kursk State Medical University, 3 Karl Marx St., Kursk 305041, Russian Federation
| | - Marina Bykanova
- Department of Biology, Medical Genetics & Ecology, Kursk State Medical University, 3 Karl Marx St., Kursk 305041, Russian Federation.,Laboratory of Genomic Research, Research Institute for Genetic & Molecular Epidemiology, Kursk State Medical University, 18 Yamskaya St., Kursk 305041, Russian Federation
| | - Mikhail Churnosov
- Department of Medical Biological Disciplines, Belgorod State University, 85 Pobeda St., Belgorod 308015, Russian Federation
| | - Alexey Polonikov
- Department of Biology, Medical Genetics & Ecology, Kursk State Medical University, 3 Karl Marx St., Kursk 305041, Russian Federation.,Laboratory of Statistical Genetics & Bioinformatics, Research Institute for Genetic & Molecular Epidemiology, Kursk State Medical University, 18 Yamskaya St., Kursk 305041, Russian Federation
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32
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Cerruti E, Gisbert C, Drost HG, Valentino D, Portis E, Barchi L, Prohens J, Lanteri S, Comino C, Catoni M. Grafting vigour is associated with DNA de-methylation in eggplant. HORTICULTURE RESEARCH 2021; 8:241. [PMID: 34719687 PMCID: PMC8558322 DOI: 10.1038/s41438-021-00660-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 07/20/2021] [Accepted: 07/30/2021] [Indexed: 05/08/2023]
Abstract
In horticulture, grafting is a popular technique used to combine positive traits from two different plants. This is achieved by joining the plant top part (scion) onto a rootstock which contains the stem and roots. Rootstocks can provide resistance to stress and increase plant production, but despite their wide use, the biological mechanisms driving rootstock-induced alterations of the scion phenotype remain largely unknown. Given that epigenetics plays a relevant role during distance signalling in plants, we studied the genome-wide DNA methylation changes induced in eggplant (Solanum melongena) scion using two interspecific rootstocks to increase vigour. We found that vigour was associated with a change in scion gene expression and a genome-wide hypomethylation in the CHH context. Interestingly, this hypomethylation correlated with the downregulation of younger and potentially more active long terminal repeat retrotransposable elements (LTR-TEs), suggesting that graft-induced epigenetic modifications are associated with both physiological and molecular phenotypes in grafted plants. Our results indicate that the enhanced vigour induced by heterografting in eggplant is associated with epigenetic modifications, as also observed in some heterotic hybrids.
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Affiliation(s)
- Elisa Cerruti
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Carmina Gisbert
- Institute for Conservation & Improvement of Valencian Agrodiversity (COMAV), Universitat Politècnica de València, Valencia, Spain
| | - Hajk-Georg Drost
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Computational Biology Group, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Danila Valentino
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Ezio Portis
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Lorenzo Barchi
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Jaime Prohens
- Institute for Conservation & Improvement of Valencian Agrodiversity (COMAV), Universitat Politècnica de València, Valencia, Spain
| | - Sergio Lanteri
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Cinzia Comino
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy.
| | - Marco Catoni
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK.
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom.
- Institute for Sustainable Plant Protection, National Research Council of Italy, Torino, Italy.
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33
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Wei S, Tao J, Xu J, Chen X, Wang Z, Zhang N, Zuo L, Jia Z, Chen H, Sun H, Yan Y, Zhang M, Lv H, Kong F, Duan L, Ma Y, Liao M, Xu L, Feng R, Liu G, Project TEWAS, Jiang Y. Ten Years of EWAS. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2100727. [PMID: 34382344 PMCID: PMC8529436 DOI: 10.1002/advs.202100727] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/11/2021] [Indexed: 06/13/2023]
Abstract
Epigenome-wide association study (EWAS) has been applied to analyze DNA methylation variation in complex diseases for a decade, and epigenome as a research target has gradually become a hot topic of current studies. The DNA methylation microarrays, next-generation, and third-generation sequencing technologies have prepared a high-quality platform for EWAS. Here, the progress of EWAS research is reviewed, its contributions to clinical applications, and mainly describe the achievements of four typical diseases. Finally, the challenges encountered by EWAS and make bold predictions for its future development are presented.
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Affiliation(s)
- Siyu Wei
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Junxian Tao
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Jing Xu
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Xingyu Chen
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Zhaoyang Wang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Nan Zhang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Lijiao Zuo
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Zhe Jia
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Haiyan Chen
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Hongmei Sun
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Yubo Yan
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Mingming Zhang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Hongchao Lv
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Fanwu Kong
- The EWAS ProjectHarbinChina
- Department of NephrologyThe Second Affiliated HospitalHarbin Medical UniversityHarbin150001China
| | - Lian Duan
- The EWAS ProjectHarbinChina
- The First Affiliated Hospital of Wenzhou Medical UniversityWenzhou325000China
| | - Ye Ma
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Mingzhi Liao
- The EWAS ProjectHarbinChina
- College of Life SciencesNorthwest A&F UniversityYanglingShanxi712100China
| | - Liangde Xu
- The EWAS ProjectHarbinChina
- School of Biomedical EngineeringWenzhou Medical UniversityWenzhou325035China
| | - Rennan Feng
- The EWAS ProjectHarbinChina
- Department of Nutrition and Food HygienePublic Health CollegeHarbin Medical UniversityHarbin150081China
| | - Guiyou Liu
- The EWAS ProjectHarbinChina
- Beijing Institute for Brain DisordersCapital Medical UniversityBeijing100069China
| | | | - Yongshuai Jiang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
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34
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Huang D, Zhou Y, Yi X, Fan X, Wang J, Yao H, Sham PC, Hao J, Chen K, Li MJ. VannoPortal: multiscale functional annotation of human genetic variants for interrogating molecular mechanism of traits and diseases. Nucleic Acids Res 2021; 50:D1408-D1416. [PMID: 34570217 PMCID: PMC8728305 DOI: 10.1093/nar/gkab853] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/05/2021] [Accepted: 09/14/2021] [Indexed: 12/16/2022] Open
Abstract
Interpreting the molecular mechanism of genomic variations and their causal relationship with diseases/traits are important and challenging problems in the human genetic study. To provide comprehensive and context-specific variant annotations for biologists and clinicians, here, by systematically integrating over 4TB genomic/epigenomic profiles and frequently-used annotation databases from various biological domains, we develop a variant annotation database, called VannoPortal. In general, the database has following major features: (i) systematically integrates 40 genome-wide variant annotations and prediction scores regarding allele frequency, linkage disequilibrium, evolutionary signature, disease/trait association, tissue/cell type-specific epigenome, base-wise functional prediction, allelic imbalance and pathogenicity; (ii) equips with our recent novel index system and parallel random-sweep searching algorithms for efficient management of backend databases and information extraction; (iii) greatly expands context-dependent variant annotation to incorporate large-scale epigenomic maps and regulatory profiles (such as EpiMap) across over 33 tissue/cell types; (iv) compiles many genome-scale base-wise prediction scores for regulatory/pathogenic variant classification beyond protein-coding region; (v) enables fast retrieval and direct comparison of functional evidence among linked variants using highly interactive web panel in addition to plain table; (vi) introduces many visualization functions for more efficient identification and interpretation of functional variants in single web page. VannoPortal is freely available at http://mulinlab.org/vportal.
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Affiliation(s)
- Dandan Huang
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Yao Zhou
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Xianfu Yi
- School of Biomedical Engineering, Tianjin Medical University, Tianjin 300070, China
| | - Xutong Fan
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Jianhua Wang
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Hongcheng Yao
- Centre for PanorOmic Sciences-Genomics and Bioinformatics Cores, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China
| | - Pak Chung Sham
- Centre for PanorOmic Sciences-Genomics and Bioinformatics Cores, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China
| | - Jihui Hao
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
| | - Mulin Jun Li
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China.,Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
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35
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Yang G, Singh S, McDonough CW, Lamba JK, Hamadeh I, Holliday LS, Wang D, Katz J, Lakatos PA, Balla B, Kosa JP, Pelliccioni GA, Price DK, Van Driest SL, Figg WD, Langaee T, Moreb JS, Gong Y. Genome-wide Association Study Identified Chromosome 8 Locus Associated with Medication-Related Osteonecrosis of the Jaw. Clin Pharmacol Ther 2021; 110:1558-1569. [PMID: 34390503 PMCID: PMC8630710 DOI: 10.1002/cpt.2397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/30/2021] [Indexed: 12/12/2022]
Abstract
Medication‐related osteonecrosis of the jaw (MRONJ) is a rare but serious drug‐related adverse event. To identify pharmacogenomic markers of MRONJ associated with bisphosphonate therapy, we conducted a genomewide association study (GWAS) meta‐analysis followed by functional analysis of 5,008 individuals of European ancestry treated with bisphosphonates, which includes the largest number of MRONJ cases to date (444 cases and 4,564 controls). Discovery GWAS was performed in randomly selected 70% of the patients with cancer and replication GWAS was performed in the remaining 30% of the patients with cancer treated with intravenous bisphosphonates followed by meta‐analysis of all 3,639 patients with cancer. GWAS was also performed in 1,369 patients with osteoporosis treated with oral bisphosphonates. The lead single‐nucleotide polymorphism (SNP), rs2736308 on chromosome 8, was associated with an increased risk of MRONJ with an odds ratio (OR) of 2.71 and 95% confidence interval (CI) of 1.90–3.86 (P = 3.57*10−8) in the meta‐analysis of patients with cancer. This SNP was validated in the MRONJ GWAS in patients with osteoporosis (OR: 2.82, 95% CI: 1.55–4.09, P = 6.84*10−4). The meta‐analysis combining patients with cancer and patients with osteoporosis yielded the same lead SNP rs2736308 on chromosome 8 as the top SNP (OR: 2.74, 95% CI: 2.09–3.39, P = 9.65*10−11). This locus is associated with regulation of the BLK, CTSB, and FDFT1 genes, which had been associated with bone mineral density. FDFT1 encodes a membrane‐associated enzyme, which is implicated in the bisphosphonate pathway. This study provides insights into the potential mechanism of MRONJ.
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Affiliation(s)
- Guang Yang
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Sonal Singh
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Caitrin W McDonough
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Jatinder K Lamba
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA.,UF Health Cancer Center, Gainesville, Florida, USA
| | - Issam Hamadeh
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA.,Cancer Pharmacology Department, Levine Cancer Institute, Charlotte, North Carolina, USA
| | - L Shannon Holliday
- Department of Orthodontics, College of Dentistry, University of Florida, Gainesville, Florida, USA
| | - Danxin Wang
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Joseph Katz
- Department of Oral Medicine, College of Dentistry, University of Florida, Gainesville, Florida, USA
| | - Peter A Lakatos
- Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
| | - Bernadett Balla
- Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
| | - Janos P Kosa
- Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
| | - Gian Andrea Pelliccioni
- Department of Biomedical and Neuromotor Sciences - Section of Dentistry, Alma Mater Studiorum-Università di Bologna, Bologna, Italy
| | - Douglas K Price
- Genitourinary Malignancies Branch National Cancer Institute, Bethesda, Maryland, USA
| | - Sara L Van Driest
- Departments of Pediatrics and Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - William D Figg
- Genitourinary Malignancies Branch National Cancer Institute, Bethesda, Maryland, USA
| | - Taimour Langaee
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Jan S Moreb
- Hematology, Transplantation and Cellular Therapy Department, Novant Health Cancer Institute, Winston-Salem, North Carolina, USA
| | - Yan Gong
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA.,UF Health Cancer Center, Gainesville, Florida, USA
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36
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Liu C, Yan S, Chen H, Wu Z, Li L, Cheng L, Li H, Li Y. Association of GTF2I, NFKB1, and TYK2 Regional Polymorphisms With Systemic Sclerosis in a Chinese Han Population. Front Immunol 2021; 12:640083. [PMID: 34248934 PMCID: PMC8261294 DOI: 10.3389/fimmu.2021.640083] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 06/07/2021] [Indexed: 12/03/2022] Open
Abstract
Objectives Systemic sclerosis (SSc) is an uncommon autoimmune disease that varies with ethnicity. Single nucleotide polymorphisms (SNPs) in the GTFSI, NFKB1, and TYK2 genes have been reported to be associated with SSc in other populations and in individuals with various autoimmune diseases. This study aimed to investigate the association between these SNPs and susceptibility to SSc in a Chinese Han population. Method A case-control study was performed in 343 patients with SSc and 694 ethnically matched healthy controls. SNPs in GTF2I, NFKB1, and TYK2 were genotyped using a Sequenom MassArray iPLEX system. Association analyses were performed using PLINK v1.90 software. Result Our study demonstrated that the GTF2I rs117026326 T allele and the GTF2I rs73366469 C allele were strongly associated with patients with SSc (P = 6.97E-10 and P = 1.33E-08, respectively). Patients carrying the GTF2I rs117026326 TT genotype and the GTF2I rs73366469 CC genotype had a strongly increased risk of SSc (P = 6.25E-09 and P = 1.67E-08, respectively), and those carrying the NFKB1 rs1599961 AA genotype had a suggestively significantly increased risk of SSc (P = 0.014). Moreover, rs117026326 and rs73366469 were associated with SSc in different genetic models (additive model, dominant model, and recessive model) (P < 0.05) whereas rs1599961 was associated with SSc in the dominant genetic model but not in the addictive and recessive models (P = 0.0026). TYK2 rs2304256 was not significantly associated with SSc in this study. Conclusion GTF2I rs117026326 and rs73366469 SNPs were strongly associated with SSc in this Chinese Han population. NFKB1 rs1599961 showed a suggestive association with SSc, and no significant association was found between TYK2 rs2304256 and SSc in this Chinese Han population.
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Affiliation(s)
- Chenxi Liu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Songxin Yan
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Haizhen Chen
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.,Department of Clinical Laboratory, The First Hospital of Jilin University, Jilin, China
| | - Ziyan Wu
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Liubing Li
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Linlin Cheng
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Haolong Li
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yongzhe Li
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
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Sobczyk MK, Richardson TG, Zuber V, Min JL, Gaunt TR, Paternoster L. Triangulating molecular evidence to prioritize candidate causal genes at established atopic dermatitis loci. J Invest Dermatol 2021; 141:2620-2629. [PMID: 33901562 PMCID: PMC8592116 DOI: 10.1016/j.jid.2021.03.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/12/2021] [Accepted: 03/25/2021] [Indexed: 01/16/2023]
Abstract
Genome-wide association studies for atopic dermatitis (AD) have identified 25 reproducible loci. We attempt to prioritize candidate causal genes at these loci using extensive molecular resources compiled into a bioinformatics pipeline. We identified a list of 103 molecular resources for AD aetiology, including expression, protein and DNA methylation QTL datasets in skin or immune-relevant tissues which were tested for overlap with GWAS signals. This was combined with functional annotation using regulatory variant prediction, and features such as promoter-enhancer interactions, expression studies and variant fine-mapping. For each gene at each locus, we condensed the evidence into a prioritization score. Across the investigated loci, we detected significant enrichment of genes with adaptive immune regulatory function and epidermal barrier formation among the top prioritized genes. At 8 loci, we were able to prioritize a single candidate gene (IL6R, ADO, PRR5L, IL7R, ETS1, INPP5D, MDM1, TRAF3). In addition, at 6 of the 25 loci, our analysis prioritizes less familiar candidates (SLC22A5, IL2RA, MDM1, DEXI, ADO, STMN3). Our analysis provides support for previously implicated genes at several AD GWAS loci, as well as evidence for plausible additional candidates at others, which may represent potential targets for drug discovery.
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Affiliation(s)
- Maria K Sobczyk
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
| | - Tom G Richardson
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
| | - Verena Zuber
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK; MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Josine L Min
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
| | - Lavinia Paternoster
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK.
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Dharshini SAP, Jemimah S, Taguchi YH, Gromiha MM. Exploring Common Therapeutic Targets for Neurodegenerative Disorders Using Transcriptome Study. Front Genet 2021; 12:639160. [PMID: 33815473 PMCID: PMC8017312 DOI: 10.3389/fgene.2021.639160] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
Alzheimer's disease (AD) and Parkinson's disease (PD) are well-known neuronal degenerative disorders that share common pathological events. Approved medications alleviate symptoms but do not address the root cause of the disease. Energy dysfunction in the neuronal population leads to various pathological events and ultimately results in neuronal death. Identifying common therapeutic targets for these disorders may help in the drug discovery process. The Brodmann area 9 (BA9) region is affected in both the disease conditions and plays an essential role in cognitive, motor, and memory-related functions. Analyzing transcriptome data of BA9 provides deep insights related to common pathological pathways involved in AD and PD. In this work, we map the preprocessed BA9 fastq files generated by RNA-seq for disease and control samples with reference hg38 genomic assembly and identify common variants and differentially expressed genes (DEG). These variants are predominantly located in the 3' UTR (non-promoter) region, affecting the conserved transcription factor (TF) binding motifs involved in the methylation and acetylation process. We have constructed BA9-specific functional interaction networks, which show the relationship between TFs and DEGs. Based on expression signature analysis, we propose that MAPK1, VEGFR1/FLT1, and FGFR1 are promising drug targets to restore blood-brain barrier functionality by reducing neuroinflammation and may save neurons.
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Affiliation(s)
- S Akila Parvathy Dharshini
- Protein Bioinformatics Lab, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India
| | - Sherlyn Jemimah
- Protein Bioinformatics Lab, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India
| | - Y H Taguchi
- Department of Physics, Chuo University, Hachioji, Japan
| | - M Michael Gromiha
- Protein Bioinformatics Lab, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India
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39
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Hu X, Estecio MR, Chen R, Reuben A, Wang L, Fujimoto J, Carrot-Zhang J, McGranahan N, Ying L, Fukuoka J, Chow CW, Pham HHN, Godoy MCB, Carter BW, Behrens C, Zhang J, Antonoff MB, Sepesi B, Lu Y, Pass HI, Kadara H, Scheet P, Vaporciyan AA, Heymach JV, Wistuba II, Lee JJ, Futreal PA, Su D, Issa JPJ, Zhang J. Evolution of DNA methylome from precancerous lesions to invasive lung adenocarcinomas. Nat Commun 2021; 12:687. [PMID: 33514726 PMCID: PMC7846738 DOI: 10.1038/s41467-021-20907-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 12/17/2020] [Indexed: 12/17/2022] Open
Abstract
The evolution of DNA methylome and methylation intra-tumor heterogeneity (ITH) during early carcinogenesis of lung adenocarcinoma has not been systematically studied. We perform reduced representation bisulfite sequencing of invasive lung adenocarcinoma and its precursors, atypical adenomatous hyperplasia, adenocarcinoma in situ and minimally invasive adenocarcinoma. We observe gradual increase of methylation aberrations and significantly higher level of methylation ITH in later-stage lesions. The phylogenetic patterns inferred from methylation aberrations resemble those based on somatic mutations suggesting parallel methylation and genetic evolution. De-convolution reveal higher ratio of T regulatory cells (Tregs) versus CD8 + T cells in later-stage diseases, implying progressive immunosuppression with neoplastic progression. Furthermore, increased global hypomethylation is associated with higher mutation burden, copy number variation burden and AI burden as well as higher Treg/CD8 ratio, highlighting the potential impact of methylation on chromosomal instability, mutagenesis and tumor immune microenvironment during early carcinogenesis of lung adenocarcinomas.
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Affiliation(s)
- Xin Hu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Marcos R Estecio
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Center of Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Runzhe Chen
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Alexandre Reuben
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Junya Fujimoto
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jian Carrot-Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Nicholas McGranahan
- Cancer Research United Kingdom-University College London Lung Cancer Centre of Excellence, London, SW73RP, UK
| | - Lisha Ying
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, 310022, Hangzhou, China
- Zhejiang Cancer Research Institute, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), 310022, Hangzhou, China
| | - Junya Fukuoka
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 8528523, Japan
| | - Chi-Wan Chow
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Hoa H N Pham
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 8528523, Japan
| | - Myrna C B Godoy
- Department of Thoracic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Brett W Carter
- Department of Thoracic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Carmen Behrens
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Mara B Antonoff
- Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Boris Sepesi
- Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Center of Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Harvey I Pass
- Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, NY, 10016, USA
| | - Humam Kadara
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Paul Scheet
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ara A Vaporciyan
- Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - John V Heymach
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ignacio I Wistuba
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - J Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - Dan Su
- Department of Pathology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), 310022, Hangzhou, China.
| | | | - Jianjun Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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40
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Implications of venous thromboembolism GWAS reported genetic makeup in the clinical outcome of ovarian cancer patients. THE PHARMACOGENOMICS JOURNAL 2020; 21:222-232. [PMID: 33161412 DOI: 10.1038/s41397-020-00201-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 10/16/2020] [Accepted: 10/23/2020] [Indexed: 12/24/2022]
Abstract
Ovarian cancer (OC) represents the most lethal gynaecological neoplasia. Conversely, venous thromboembolism (VTE) and OC are intricately connected, with many haemostatic components favouring OC progression. In light of this bilateral relationship, genome-wide association studies (GWAS) have reported several single-nucleotide polymorphisms (SNPs) associated with VTE risk that could be used as predictors of OC clinical outcome for better therapeutic management strategies. Thus, the present study aimed to analyse the impact of VTE GWAS-identified SNPs on the clinical outcome of 336 epithelial ovarian cancer (EOC) patients. Polymorphism genotyping was performed using the TaqMan® Allelic Discrimination methodology. Carriers with the ZFPM2 rs4734879 G allele presented a significantly higher 5-year OS, 10-year OS and disease-free survival (DFS) compared to AA genotype patients with FIGO I/II stages (P = 0.009, P = 0.001 and P = 0.003, respectively). Regarding SLC19A2 rs2038024 polymorphism, carriers with the CC genotype presented a significantly lower 5-year OS, 10-year OS and DFS compared to A allele carriers in the same FIGO subgroup (P < 0.001, P = 0.004 and P = 0.005, respectively). As for CNTN6 rs6764623 polymorphism, carriers with the CC genotype presented a significantly lower 5-year OS compared to A allele carriers with FIGO I/II stages (P = 0.015). As for OTUD7A rs7164569, F11 rs4253417 and PROCR rs10747514, no significant impact on EOC patients' survival was observed. However, future studies are required to validate these results and uncover the biological mechanisms underlying our results.
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41
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Liu X, Xu W, Leng F, Hao C, Kolora SRR, Li W. Prioritizing long range interactions in noncoding regions using GWAS and deletions perturbed TADs. Comput Struct Biotechnol J 2020; 18:2945-2952. [PMID: 33209206 PMCID: PMC7642798 DOI: 10.1016/j.csbj.2020.10.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 10/08/2020] [Accepted: 10/12/2020] [Indexed: 01/22/2023] Open
Abstract
Genome-wide association studies (GWAS) have contributed significantly to predisposing the disease etiology by associating single nucleotide polymorphisms (SNPs) with complex diseases. However, most GWAS-SNPs are in the noncoding regions that may affect distal genes via long range enhancer-promoter interactions. Thus, the common practice on GWAS discoveries cannot fully reveal the molecular mechanisms underpinning complex diseases. It is known that perturbations of topological associated domains (TADs) lead to long range interactions which underlie disease etiology. To identify the probable long range interactions in noncoding regions via GWAS and TADs perturbed by deletions, we integrated datasets from GWAS-SNPs, enhancers, TADs, and deletions. After ranking and clustering, we prioritized 201,132 high confident pairs of GWAS-SNPs and target genes. In this study, we performed a systematic inference on noncoding regions via GWAS-SNPs and deletion-perturbed TADs to boost GWAS discovery power. The high confident pairs of GWAS-SNPs and target genes (SE-Gs) provide the promising candidates to understand the molecular mechanisms underlying complex diseases with emphasis on the three-dimensional genome.
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Affiliation(s)
- Xuanshi Liu
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China.,MOE Key Laboratory of Major Diseases in Children, Beijing, China.,Genetics and Birth Defects Control Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Wenjian Xu
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China.,MOE Key Laboratory of Major Diseases in Children, Beijing, China.,Genetics and Birth Defects Control Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Fei Leng
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China.,MOE Key Laboratory of Major Diseases in Children, Beijing, China.,Genetics and Birth Defects Control Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Chanjuan Hao
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China.,MOE Key Laboratory of Major Diseases in Children, Beijing, China.,Genetics and Birth Defects Control Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Sree Rohit Raj Kolora
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Wei Li
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China.,MOE Key Laboratory of Major Diseases in Children, Beijing, China.,Genetics and Birth Defects Control Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
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42
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Huang D, Yi X, Zhou Y, Yao H, Xu H, Wang J, Zhang S, Nong W, Wang P, Shi L, Xuan C, Li M, Wang J, Li W, Kwan HS, Sham PC, Wang K, Li MJ. Ultrafast and scalable variant annotation and prioritization with big functional genomics data. Genome Res 2020; 30:1789-1801. [PMID: 33060171 PMCID: PMC7706736 DOI: 10.1101/gr.267997.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 09/22/2020] [Indexed: 02/06/2023]
Abstract
The advances of large-scale genomics studies have enabled compilation of cell type–specific, genome-wide DNA functional elements at high resolution. With the growing volume of functional annotation data and sequencing variants, existing variant annotation algorithms lack the efficiency and scalability to process big genomic data, particularly when annotating whole-genome sequencing variants against a huge database with billions of genomic features. Here, we develop VarNote to rapidly annotate genome-scale variants in large and complex functional annotation resources. Equipped with a novel index system and a parallel random-sweep searching algorithm, VarNote shows substantial performance improvements (two to three orders of magnitude) over existing algorithms at different scales. It supports both region-based and allele-specific annotations and introduces advanced functions for the flexible extraction of annotations. By integrating massive base-wise and context-dependent annotations in the VarNote framework, we introduce three efficient and accurate pipelines to prioritize the causal regulatory variants for common diseases, Mendelian disorders, and cancers.
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Affiliation(s)
- Dandan Huang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Xianfu Yi
- School of Biomedical Engineering, Tianjin Medical University, Tianjin 300070, China
| | - Yao Zhou
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Hongcheng Yao
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China
| | - Hang Xu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China.,School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China
| | - Jianhua Wang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Shijie Zhang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Wenyan Nong
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Panwen Wang
- Department of Health Sciences Research and Center for Individualized Medicine, Mayo Clinic, Scottsdale, Arizona 85259, USA
| | - Lei Shi
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Chenghao Xuan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Miaoxin Li
- Center for Genome Research, Center for Precision Medicine, Zhongshan School of Medicine, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Junwen Wang
- Department of Health Sciences Research and Center for Individualized Medicine, Mayo Clinic, Scottsdale, Arizona 85259, USA
| | - Weidong Li
- Department of Genetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Hoi Shan Kwan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Pak Chung Sham
- Centre of Genomics Sciences, Departments of Psychiatry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Mulin Jun Li
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China.,Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
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43
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Chen XF, Guo MR, Duan YY, Jiang F, Wu H, Dong SS, Zhou XR, Thynn HN, Liu CC, Zhang L, Guo Y, Yang TL. Multiomics dissection of molecular regulatory mechanisms underlying autoimmune-associated noncoding SNPs. JCI Insight 2020; 5:136477. [PMID: 32879140 PMCID: PMC7526455 DOI: 10.1172/jci.insight.136477] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 07/16/2020] [Indexed: 12/16/2022] Open
Abstract
More than 90% of autoimmune-associated variants are located in noncoding regions, leading to challenges in deciphering the underlying causal roles of functional variants and genes and biological mechanisms. Therefore, to reduce the gap between traditional genetic findings and mechanistic understanding of disease etiologies and clinical drug development, it is important to translate systematically the regulatory mechanisms underlying noncoding variants. Here, we prioritized functional noncoding SNPs with regulatory gene targets associated with 19 autoimmune diseases by incorporating hundreds of immune cell-specific multiomics data. The prioritized SNPs are associated with transcription factor (TF) binding, histone modification, or chromatin accessibility, indicating their allele-specific regulatory roles. Their target genes are significantly enriched in immunologically related pathways and other known immunologically related functions. We found that 90.1% of target genes are regulated by distal SNPs involving several TFs (e.g., the DNA-binding protein CCCTC-binding factor [CTCF]), suggesting the importance of long-range chromatin interaction in autoimmune diseases. Moreover, we predicted potential drug targets for autoimmune diseases, including 2 genes (NFKB1 and SH2B3) with known drug indications on other diseases, highlighting their potential drug repurposing opportunities. Taken together, these findings may provide useful information for future experimental follow-up and drug applications on autoimmune diseases.
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44
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Lau A, So HC. Turning genome-wide association study findings into opportunities for drug repositioning. Comput Struct Biotechnol J 2020; 18:1639-1650. [PMID: 32670504 PMCID: PMC7334463 DOI: 10.1016/j.csbj.2020.06.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 06/05/2020] [Accepted: 06/05/2020] [Indexed: 02/02/2023] Open
Abstract
Drug development is a very costly and lengthy process, while repositioned or repurposed drugs could be brought into clinical practice within a shorter time-frame and at a much reduced cost. Numerous computational approaches to drug repositioning have been developed, but methods utilizing genome-wide association studies (GWASs) data are less explored. The past decade has observed a massive growth in the amount of data from GWAS; the rich information contained in GWAS has great potential to guide drug repositioning or discovery. While multiple tools are available for finding the most relevant genes from GWAS hits, searching for top susceptibility genes is only one way to guide repositioning, which has its own limitations. Here we provide a comprehensive review of different computational approaches that employ GWAS data to guide drug repositioning. These methods include selecting top candidate genes from GWAS as drug targets, deducing drug candidates based on drug-drug and disease-disease similarities, searching for reversed expression profiles between drugs and diseases, pathway-based methods as well as approaches based on analysis of biological networks. Each method is illustrated with examples, and their respective strengths and limitations are discussed. We also discussed several areas for future research.
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Affiliation(s)
- Alexandria Lau
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hon-Cheong So
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research of Common Diseases, Kunming Zoology Institute of Zoology and The Chinese University of Hong Kong, Hong Kong SAR, China
- Department of Psychiatry, The Chinese University of Hong Kong, Hong Kong SAR, China
- Margaret K.L. Cheung Research Centre for Management of Parkinsonism, The Chinese University of Hong Kong, Hong Kong SAR, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Brain and Mind Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
- Hong Kong Branch of the Chinese Academy of Sciences Center for Excellence in Animal Evolution and Genetics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Corresponding author at: School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
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45
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Zou H, Wu LX, Tan L, Shang FF, Zhou HH. Significance of Single-Nucleotide Variants in Long Intergenic Non-protein Coding RNAs. Front Cell Dev Biol 2020; 8:347. [PMID: 32523949 PMCID: PMC7261909 DOI: 10.3389/fcell.2020.00347] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/20/2020] [Indexed: 12/15/2022] Open
Abstract
Single-nucleotide variants (SNVs) are the most common genetic variants and universally present in the human genome. Genome-wide association studies (GWASs) have identified a great number of disease or trait-associated variants, many of which are located in non-coding regions. Long intergenic non-protein coding RNAs (lincRNAs) are the major subtype of long non-coding RNAs; lincRNAs play crucial roles in various disorders and cellular models via multiple mechanisms. With rapid growth in the number of the identified lincRNAs and genetic variants, there is great demand for an investigation of SNVs in lincRNAs. Hence, in this article, we mainly summarize the significant role of SNVs within human lincRNA regions. Some pivotal variants may serve as risk factors for the development of various disorders, especially cancer. They may also act as important regulatory signatures involved in the modulation of lincRNAs in a tissue- or disorder-specific manner. An increasing number of researches indicate that lincRNA variants would potentially provide additional options for genetic testing and disease risk assessment in the personalized medicine era.
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Affiliation(s)
- Hecun Zou
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Lan-Xiang Wu
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Lihong Tan
- Chongqing Medical and Pharmaceutical College, Chongqing, China.,Xiangya Hospital, Central South University, Changsha, China
| | - Fei-Fei Shang
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Hong-Hao Zhou
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China.,Xiangya Hospital, Central South University, Changsha, China
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46
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Li X, Shi L, Wang Y, Zhong J, Zhao X, Teng H, Shi X, Yang H, Ruan S, Li M, Sun ZS, Zhan Q, Mao F. OncoBase: a platform for decoding regulatory somatic mutations in human cancers. Nucleic Acids Res 2020; 47:D1044-D1055. [PMID: 30445567 PMCID: PMC6323961 DOI: 10.1093/nar/gky1139] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/11/2018] [Indexed: 12/16/2022] Open
Abstract
Whole-exome and whole-genome sequencing have revealed millions of somatic mutations associated with different human cancers, and the vast majority of them are located outside of coding sequences, making it challenging to directly interpret their functional effects. With the rapid advances in high-throughput sequencing technologies, genome-scale long-range chromatin interactions were detected, and distal target genes of regulatory elements were determined using three-dimensional (3D) chromatin looping. Herein, we present OncoBase (http://www.oncobase.biols.ac.cn/), an integrated database for annotating 81 385 242 somatic mutations in 68 cancer types from more than 120 cancer projects by exploring their roles in distal interactions between target genes and regulatory elements. OncoBase integrates local chromatin signatures, 3D chromatin interactions in different cell types and reconstruction of enhancer-target networks using state-of-the-art algorithms. It employs informative visualization tools to display the integrated local and 3D chromatin signatures and effects of somatic mutations on regulatory elements. Enhancer-promoter interactions estimated from chromatin interactions are integrated into a network diffusion system that quantitatively prioritizes somatic mutations and target genes from a large pool. Thus, OncoBase is a useful resource for the functional annotation of regulatory noncoding regions and systematically benchmarking the regulatory effects of embedded noncoding somatic mutations in human carcinogenesis.
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Affiliation(s)
- Xianfeng Li
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China.,Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Leisheng Shi
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Wang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Jianing Zhong
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000,China
| | - Xiaolu Zhao
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Huajing Teng
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaohui Shi
- Sino-Danish college, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haonan Yang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shasha Ruan
- Department of Clinical Oncology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430072, China
| | - MingKun Li
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhong Sheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Qimin Zhan
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Fengbiao Mao
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
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47
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Zhang S, He Y, Liu H, Zhai H, Huang D, Yi X, Dong X, Wang Z, Zhao K, Zhou Y, Wang J, Yao H, Xu H, Yang Z, Sham PC, Chen K, Li MJ. regBase: whole genome base-wise aggregation and functional prediction for human non-coding regulatory variants. Nucleic Acids Res 2020; 47:e134. [PMID: 31511901 PMCID: PMC6868349 DOI: 10.1093/nar/gkz774] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 08/29/2019] [Indexed: 12/19/2022] Open
Abstract
Predicting the functional or pathogenic regulatory variants in the human non-coding genome facilitates the interpretation of disease causation. While numerous prediction methods are available, their performance is inconsistent or restricted to specific tasks, which raises the demand of developing comprehensive integration for those methods. Here, we compile whole genome base-wise aggregations, regBase, that incorporate largest prediction scores. Building on different assumptions of causality, we train three composite models to score functional, pathogenic and cancer driver non-coding regulatory variants respectively. We demonstrate the superior and stable performance of our models using independent benchmarks and show great success to fine-map causal regulatory variants on specific locus or at base-wise resolution. We believe that regBase database together with three composite models will be useful in different areas of human genetic studies, such as annotation-based casual variant fine-mapping, pathogenic variant discovery as well as cancer driver mutation identification. regBase is freely available at https://github.com/mulinlab/regBase.
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Affiliation(s)
- Shijie Zhang
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Key Laboratory of Inflammation Biology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Yukun He
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Key Laboratory of Inflammation Biology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Huanhuan Liu
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Key Laboratory of Inflammation Biology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Haoyu Zhai
- Department of Computer Science, University of Illinois Urbana-Champaign, IL, USA
| | - Dandan Huang
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Key Laboratory of Inflammation Biology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xianfu Yi
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
| | - Xiaobao Dong
- Department of Genetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zhao Wang
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Key Laboratory of Inflammation Biology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Ke Zhao
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Key Laboratory of Inflammation Biology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Yao Zhou
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Key Laboratory of Inflammation Biology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Jianhua Wang
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Key Laboratory of Inflammation Biology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Hongcheng Yao
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Hang Xu
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Zhenglu Yang
- College of Computer Science, Nankai University, Tianjin, China
| | - Pak Chung Sham
- Centre of Genomics Sciences, State Key Laboratory of Brain and Cognitive Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Mulin Jun Li
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Key Laboratory of Inflammation Biology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China.,Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
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48
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Xu H, Zhang S, Yi X, Plewczynski D, Li MJ. Exploring 3D chromatin contacts in gene regulation: The evolution of approaches for the identification of functional enhancer-promoter interaction. Comput Struct Biotechnol J 2020; 18:558-570. [PMID: 32226593 PMCID: PMC7090358 DOI: 10.1016/j.csbj.2020.02.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 02/21/2020] [Accepted: 02/22/2020] [Indexed: 12/12/2022] Open
Abstract
Mechanisms underlying gene regulation are key to understand how multicellular organisms with various cell types develop from the same genetic blueprint. Dynamic interactions between enhancers and genes are revealed to play central roles in controlling gene transcription, but the determinants to link functional enhancer-promoter pairs remain elusive. A major challenge is the lack of reliable approach to detect and verify functional enhancer-promoter interactions (EPIs). In this review, we summarized the current methods for detecting EPIs and described how developing techniques facilitate the identification of EPI through assessing the merits and drawbacks of these methods. We also reviewed recent state-of-art EPI prediction methods in terms of their rationale, data usage and characterization. Furthermore, we briefly discussed the evolved strategies for validating functional EPIs.
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Affiliation(s)
- Hang Xu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin, China
| | - Shijie Zhang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin, China
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xianfu Yi
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
| | - Dariusz Plewczynski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Koszykowa 75, 00-662 Warsaw, Poland
| | - Mulin Jun Li
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin, China
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
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49
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Zheng Z, Huang D, Wang J, Zhao K, Zhou Y, Guo Z, Zhai S, Xu H, Cui H, Yao H, Wang Z, Yi X, Zhang S, Sham PC, Li MJ. QTLbase: an integrative resource for quantitative trait loci across multiple human molecular phenotypes. Nucleic Acids Res 2020; 48:D983-D991. [PMID: 31598699 PMCID: PMC6943073 DOI: 10.1093/nar/gkz888] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/24/2019] [Accepted: 10/02/2019] [Indexed: 12/20/2022] Open
Abstract
Recent advances in genome sequencing and functional genomic profiling have promoted many large-scale quantitative trait locus (QTL) studies, which connect genotypes with tissue/cell type-specific cellular functions from transcriptional to post-translational level. However, no comprehensive resource can perform QTL lookup across multiple molecular phenotypes and investigate the potential cascade effect of functional variants. We developed a versatile resource, named QTLbase, for interpreting the possible molecular functions of genetic variants, as well as their tissue/cell-type specificity. Overall, QTLbase has five key functions: (i) curating and compiling genome-wide QTL summary statistics for 13 human molecular traits from 233 independent studies; (ii) mapping QTL-relevant tissue/cell types to 78 unified terms according to a standard anatomogram; (iii) normalizing variant and trait information uniformly, yielding >170 million significant QTLs; (iv) providing a rich web client that enables phenome- and tissue-wise visualization; and (v) integrating the most comprehensive genomic features and functional predictions to annotate the potential QTL mechanisms. QTLbase provides a one-stop shop for QTL retrieval and comparison across multiple tissues and multiple layers of molecular complexity, and will greatly help researchers interrogate the biological mechanism of causal variants and guide the direction of functional validation. QTLbase is freely available at http://mulinlab.org/qtlbase.
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Affiliation(s)
- Zhanye Zheng
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Dandan Huang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Jianhua Wang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Ke Zhao
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Yao Zhou
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Zhenyang Guo
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China
| | - Sinan Zhai
- School of Biomedical Engineering, Tianjin Medical University, Tianjin 300070, China
| | - Hang Xu
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Hui Cui
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Hongcheng Yao
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China
| | - Zhao Wang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Xianfu Yi
- School of Biomedical Engineering, Tianjin Medical University, Tianjin 300070, China
| | - Shijie Zhang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Pak Chung Sham
- Centre of Genomics Sciences, State Key Laboratory of Brain and Cognitive Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China
| | - Mulin Jun Li
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
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50
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Method for Bisulfite Sequencing Data Analysis for Whole-Genome Level DNA Methylation Detection in Legumes. Methods Mol Biol 2020; 2107:127-145. [PMID: 31893445 DOI: 10.1007/978-1-0716-0235-5_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Methylation of cytosines in DNA is the most stable type of epigenetic modification that is established and maintained by different enzymes. In plants, DNA methylation is inherited from one generation to another leaving an epigenetic mark as a memory of previous state, which may include encounter with stress or pathogen. Advancement in the next generation sequencing technologies has enabled the profiling of methylation marks. Whole-genome bisulfite sequencing (WGBS) has the potential to unravel the patterns of DNA methylation at single-base resolution. Though the sequencing technologies have evolved drastically, analysis of WGBS data still remains challenging. Here, we provide a methodology for performing WGBS data analysis along with critical steps for identification of methylation marks in plant genomes including legumes.
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