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Roza M, Eriksson ANM, Svanholm S, Berg C, Karlsson O. Male-transmitted transgenerational effects of the herbicide linuron on DNA methylation profiles in Xenopus tropicalis brain and testis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 923:170949. [PMID: 38365020 DOI: 10.1016/j.scitotenv.2024.170949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 01/30/2024] [Accepted: 02/11/2024] [Indexed: 02/18/2024]
Abstract
The herbicide linuron can cause endocrine disrupting effects in Xenopus tropicalis frogs, including offspring that were never exposed to the contaminant. The mechanisms by which these effects are transmitted across generations need to be further investigated. Here, we examined transgenerational alterations of brain and testis DNA methylation profiles paternally inherited from grandfathers developmentally exposed to an environmentally relevant concentration of linuron. Reduced representation bisulfite sequencing (RRBS) revealed numerous differentially methylated regions (DMRs) in brain (3060 DMRs) and testis (2551 DMRs) of the adult male F2 generation. Key genes in the brain involved in somatotropic (igfbp4) and thyrotropic signaling (dio1 and tg) were differentially methylated and correlated with phenotypical alterations in body size, weight, hind limb length and plasma glucose levels, indicating that these methylation changes could be potential mediators of the transgenerational effects of linuron. Testis DMRs were found in genes essential for spermatogenesis, meiosis and germ cell development (piwil1, spo11 and tdrd9) and their methylation levels were correlated with the number of germ cells nests per seminiferous tubule, an endpoint of disrupted spermatogenesis. DMRs were also identified in several genes central for the machinery that regulates the epigenetic landscape including DNA methylation (dnmt3a and mbd2) and histone acetylation (hdac8, ep300, elp3, kat5 and kat14), which may at least partly drive the linuron-induced transgenerational effects. The results from this genome-wide DNA methylation profiling contribute to better understanding of potential transgenerational epigenetic inheritance mechanisms in amphibians.
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Affiliation(s)
- Mauricio Roza
- Science for Life Laboratory, Department of Environmental Science, Stockholm University, Stockholm, Sweden
| | | | - Sofie Svanholm
- Department of Environmental Toxicology, Uppsala University, Uppsala, Sweden
| | - Cecilia Berg
- Department of Environmental Toxicology, Uppsala University, Uppsala, Sweden
| | - Oskar Karlsson
- Science for Life Laboratory, Department of Environmental Science, Stockholm University, Stockholm, Sweden.
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Zhu Z, Ju J, Zhang M, Yang H, Wei W, Zhang Y. Bisphenol A disturbs hepatic apolipoprotein A1 expression and cholesterol metabolism in rare minnow Gobiocypris rarus. Comp Biochem Physiol C Toxicol Pharmacol 2022; 252:109239. [PMID: 34748970 DOI: 10.1016/j.cbpc.2021.109239] [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: 08/18/2021] [Revised: 10/07/2021] [Accepted: 10/31/2021] [Indexed: 11/03/2022]
Abstract
Bisphenol A (BPA) is a well-known plasticizer, which is widely distributed in the aquatic environment. Lots of studies showed that BPA could lead to lipid metabolism disorder in fish, but few studies studied the mechanism from the perspective of lipid transport. Apolipoprotein A1 (ApoA1) is the main component of high-density lipoprotein (HDL), and plays important roles in reverse cholesterol transport (RCT). In this study, we investigated the effect and molecular mechanism of BPA on ApoA1 and its effect on cholesterol in adult male rare minnow. Results showed that BPA could disturb hepatic ApoA1 expression through regulating Esrrg recruitment and DNA methylation in its promoter region, and ultimately up-regulated ApoA1 protein levels. The increased hepatic ApoA1 improved HDL-C levels, enhanced RCT, and disrupted cholesterol levels. The present study reveals the effect and mechanism of BPA on fish cholesterol metabolism from the perspective of cholesterol transport.
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Affiliation(s)
- Zhu Zhu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Jian Ju
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Meng Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Hui Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Wenzhi Wei
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yingying Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
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3
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Zhang Y, Zhang M, Zhu Z, Yang H, Wei W, Li B. Bisphenol A regulates apolipoprotein A1 expression through estrogen receptors and DNA methlylation and leads to cholesterol disorder in rare minnow testis. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021; 241:105999. [PMID: 34678657 DOI: 10.1016/j.aquatox.2021.105999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/02/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
Bisphenol A (BPA) is a well-known plasticizer that widely distributed in the aquatic environment. BPA has many adverse effects on reproduction. However, few studies have investigated the mechanism of BPA affecting reproduction from the perspective of lipid metabolism. Apolipoprotein A1 (ApoA1) is the major component of high-density lipoprotein (HDL), and plays critical roles in reverse cholesterol transport (RCT). In this study, in order to investigate the effect and molecular mechanism of BPA on testicular ApoA1 and the role of ApoA1 in BPA induced abnormal spermatogenesis, adult male rare minnow Gobiocypris rarus were exposed to 15 μg/L of BPA for 1, 3 and 5 weeks. Results showed that BPA could significantly affect testicular ApoA1 mRNA and protein levels, testicular cholesterol levels, plasmatic sex hormone levels and the integrity of sperm head membrane. The main mechanism of BPA regulating ApoA1 expression is to alter Esr recruitment and CpG sites DNA methylation in ApoA1 promoter. The induced ApoA1 up-regulated high density lipoprotein cholesterol levels and enhanced RCT, and finally decreased the testicular free cholesterol levels. This is likely a key mechanism by which BPA induces sex hormone disorder and sperm head membrane damage. The present study reveals the mechanism by which BPA interferes with spermatogenesis from the perspective of cholesterol transport.
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Affiliation(s)
- Yingying Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Meng Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Zhu Zhu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Hui Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Wenzhi Wei
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Bichun Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
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Zhou Z, Zhu Y, Zhang Z, Jiang T, Ling Z, Yang B, Li W. Comparative Analysis of Promoters and Enhancers in the Pituitary Glands of the Bama Xiang and Large White Pigs. Front Genet 2021; 12:697994. [PMID: 34367256 PMCID: PMC8343535 DOI: 10.3389/fgene.2021.697994] [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: 04/20/2021] [Accepted: 06/29/2021] [Indexed: 12/14/2022] Open
Abstract
The epigenetic regulation of gene expression is implicated in complex diseases in humans and various phenotypes in other species. There has been little exploration of regulatory elements in the pig. Here, we performed chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) to profile histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 27 acetylation (H3K27ac) in the pituitary gland of adult Bama Xiang and Large White pigs, which have divergent evolutionary histories and large phenotypic differences. We identified a total of 65,044 non-redundant regulatory regions, including 23,680 H3K4me3 peaks and 61,791 H3K27ac peaks (12,318 proximal and 49,473 distal), augmenting the catalog of pituitary regulatory elements in pigs. We found 793 H3K4me3 and 3,602 H3K27ac peaks that show differential activity between the two breeds, overlapping with genes involved in the Notch signaling pathway, response to growth hormone (GH), thyroid hormone signaling pathway, and immune system, and enriched for binding motifs of transcription factors (TFs), including JunB, ATF3, FRA1, and BATF. We further identified 2,025 non-redundant super enhancers from H3K27ac ChIP-seq data, among which 302 were shared in all samples of cover genes enriched for biological processes related to pituitary function. This study generated a valuable dataset of H3K4me3 and H3K27ac regions in porcine pituitary glands and revealed H3K4me3 and H3K27ac peaks with differential activity between Bama Xiang and Large White pigs.
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Affiliation(s)
- Zhimin Zhou
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yaling Zhu
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China.,Laboratory Animal Research Center, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Zhen Zhang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Tao Jiang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Ziqi Ling
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Bin Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Wanbo Li
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China.,Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China
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Abstract
Age-associated changes in gene expression in skeletal muscle of healthy individuals reflect accumulation of damage and compensatory adaptations to preserve tissue integrity. To characterize these changes, RNA was extracted and sequenced from muscle biopsies collected from 53 healthy individuals (22-83 years old) of the GESTALT study of the National Institute on Aging-NIH. Expression levels of 57,205 protein-coding and non-coding RNAs were studied as a function of aging by linear and negative binomial regression models. From both models, 1134 RNAs changed significantly with age. The most differentially abundant mRNAs encoded proteins implicated in several age-related processes, including cellular senescence, insulin signaling, and myogenesis. Specific mRNA isoforms that changed significantly with age in skeletal muscle were enriched for proteins involved in oxidative phosphorylation and adipogenesis. Our study establishes a detailed framework of the global transcriptome and mRNA isoforms that govern muscle damage and homeostasis with age.
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Huang W, Wu K, Wu R, Chen Z, Zhai W, Zheng J. Bioinformatic gene analysis for possible biomarkers and therapeutic targets of hypertension-related renal cell carcinoma. Transl Androl Urol 2020; 9:2675-2687. [PMID: 33457239 PMCID: PMC7807377 DOI: 10.21037/tau-20-817] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Renal cell carcinoma (RCC) is one of the most prevalent malignant tumors of the urinary system. Hypertension can cause hypertensive nephropathy (HN). Meanwhile, Hypertension is considered to be related to kidney cancer. We analyzed co-expressed genes to find out the relationship between hypertension and RCC and show possible biomarkers and novel therapeutic targets of hypertension-related RCC. METHODS We identified the differentially expressed genes (DEGs) of HN and RCC through analyzing Gene Expression Omnibus (GEO) datasets GSE99339, GSE99325, GSE53757 and GSE15641 by means of bioinformatics analysis, respectively. Then we evaluated these genes with protein-protein interaction (PPI) networks, Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and CTD database. Subsequently, we verified co-expressed DEGs with Gene Expression Profiling Interactive Analysis (GEPIA) database. Finally, corresponding predicted miRNAs of co-expressed DEGs were identified and verified via mirDIP database and Starbase, respectively. RESULTS We identified 9 co-expressed DEGs, including BCAT1, CORO1A, CRIP1, ESRRG, FN1, LYZ, PYCARD, SAP30, and PTRF. CRIP1 and ESRRG and their corresponding predicted miRNAs, especially hsa-miR-221-5p, hsa-miR-205-5p, hsa-miR-152-3p and hsa-miR-137 may be notably related to hypertension-related RCC. CONCLUSIONS CRIP1 and ESRRG genes have great potential to become novel biomarkers and therapeutic targets concerning hypertension-related RCC.
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Affiliation(s)
- Wenjie Huang
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ke Wu
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ruoyu Wu
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhiguo Chen
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Zhai
- Department of Urology, Renji Hospital, School of Medicine in Shanghai Jiao Tong University, Shanghai, China
| | - Junhua Zheng
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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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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Bharadwaj U, Kasembeli MM, Robinson P, Tweardy DJ. Targeting Janus Kinases and Signal Transducer and Activator of Transcription 3 to Treat Inflammation, Fibrosis, and Cancer: Rationale, Progress, and Caution. Pharmacol Rev 2020; 72:486-526. [PMID: 32198236 PMCID: PMC7300325 DOI: 10.1124/pr.119.018440] [Citation(s) in RCA: 165] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Before it was molecularly cloned in 1994, acute-phase response factor or signal transducer and activator of transcription (STAT)3 was the focus of intense research into understanding the mammalian response to injury, particularly the acute-phase response. Although known to be essential for liver production of acute-phase reactant proteins, many of which augment innate immune responses, molecular cloning of acute-phase response factor or STAT3 and the research this enabled helped establish the central function of Janus kinase (JAK) family members in cytokine signaling and identified a multitude of cytokines and peptide hormones, beyond interleukin-6 and its family members, that activate JAKs and STAT3, as well as numerous new programs that their activation drives. Many, like the acute-phase response, are adaptive, whereas several are maladaptive and lead to chronic inflammation and adverse consequences, such as cachexia, fibrosis, organ dysfunction, and cancer. Molecular cloning of STAT3 also enabled the identification of other noncanonical roles for STAT3 in normal physiology, including its contribution to the function of the electron transport chain and oxidative phosphorylation, its basal and stress-related adaptive functions in mitochondria, its function as a scaffold in inflammation-enhanced platelet activation, and its contributions to endothelial permeability and calcium efflux from endoplasmic reticulum. In this review, we will summarize the molecular and cellular biology of JAK/STAT3 signaling and its functions under basal and stress conditions, which are adaptive, and then review maladaptive JAK/STAT3 signaling in animals and humans that lead to disease, as well as recent attempts to modulate them to treat these diseases. In addition, we will discuss how consideration of the noncanonical and stress-related functions of STAT3 cannot be ignored in efforts to target the canonical functions of STAT3, if the goal is to develop drugs that are not only effective but safe. SIGNIFICANCE STATEMENT: Key biological functions of Janus kinase (JAK)/signal transducer and activator of transcription (STAT)3 signaling can be delineated into two broad categories: those essential for normal cell and organ development and those activated in response to stress that are adaptive. Persistent or dysregulated JAK/STAT3 signaling, however, is maladaptive and contributes to many diseases, including diseases characterized by chronic inflammation and fibrosis, and cancer. A comprehensive understanding of JAK/STAT3 signaling in normal development, and in adaptive and maladaptive responses to stress, is essential for the continued development of safe and effective therapies that target this signaling pathway.
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Affiliation(s)
- Uddalak Bharadwaj
- Department of Infectious Diseases, Infection Control & Employee Health, Division of Internal Medicine (U.B., M.M.K., P.R., D.J.T.), and Department of Molecular and Cellular Oncology (D.J.T.), University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Moses M Kasembeli
- Department of Infectious Diseases, Infection Control & Employee Health, Division of Internal Medicine (U.B., M.M.K., P.R., D.J.T.), and Department of Molecular and Cellular Oncology (D.J.T.), University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Prema Robinson
- Department of Infectious Diseases, Infection Control & Employee Health, Division of Internal Medicine (U.B., M.M.K., P.R., D.J.T.), and Department of Molecular and Cellular Oncology (D.J.T.), University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - David J Tweardy
- Department of Infectious Diseases, Infection Control & Employee Health, Division of Internal Medicine (U.B., M.M.K., P.R., D.J.T.), and Department of Molecular and Cellular Oncology (D.J.T.), University of Texas, MD Anderson Cancer Center, Houston, Texas
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Yang J, Gong Y, Jiang Q, Liu L, Li S, Zhou Q, Huang F, Liu Z. Circular RNA Expression Profiles in Nasopharyngeal Carcinoma by Sequence Analysis. Front Oncol 2020; 10:601. [PMID: 32426279 PMCID: PMC7204547 DOI: 10.3389/fonc.2020.00601] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 04/01/2020] [Indexed: 12/31/2022] Open
Abstract
Circular RNAs (circRNAs), as a burgeoning sort of non-coding RNAs (ncRNAs), can regulate the expression of parental genes as miRNA sponges. This study was designed to explore the circRNA expression profile of nasopharyngeal carcinoma (NPC). High-throughput sequencing was performed to identify the circRNA expression profile of NPC patients compared with healthy controls. A total of 93 upregulated circRNAs and 77 downregulated circRNAs were identified. The expression levels of the top three upregulated and three downregulated circRNAs annotated by circBase were validated by quantitative real-time PCR (qRT-PCR). GO and KEGG analyses showed that these differentially expressed circRNAs were potentially implicated in NPC pathogenesis. CircRNA-miRNA-target gene network analysis revealed a potential mechanism that hsa_circ_0002375 (circKITLG) may be involved in NPC through sponging up miR-3198 and interfering with its downstream targets. Silencing of circKITLG inhibited NPC cell proliferation, migration, and invasion in vitro. This study provides a leading and fundamental circRNA expression profile of NPC.
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Affiliation(s)
- Jing Yang
- Department of Gastroenterology, The First Affiliated Hospital of University of South China, Hengyang, China
| | - Yongqian Gong
- Department of Otorhinolaryngology, The First Affiliated Hospital of University of South China, Hengyang, China
| | - Qingshan Jiang
- Department of Otorhinolaryngology, The First Affiliated Hospital of University of South China, Hengyang, China
| | - Lijun Liu
- Department of Otorhinolaryngology, The First Affiliated Hospital of University of South China, Hengyang, China
| | - Shuyan Li
- Department of Otorhinolaryngology, The First Affiliated Hospital of University of South China, Hengyang, China
| | - Quanjun Zhou
- Department of Otorhinolaryngology, The First Affiliated Hospital of University of South China, Hengyang, China
| | - Fang Huang
- Department of Otorhinolaryngology, The First Affiliated Hospital of University of South China, Hengyang, China
| | - Zhifeng Liu
- Department of Otorhinolaryngology, The First Affiliated Hospital of University of South China, Hengyang, China
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Dong SS, Guo Y, Yang TL. Addressing the Missing Heritability Problem With the Help of Regulatory Features. Evol Bioinform Online 2019; 15:1176934319860861. [PMID: 31320792 PMCID: PMC6610400 DOI: 10.1177/1176934319860861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 06/10/2019] [Indexed: 12/02/2022] Open
Abstract
Genome-wide association studies (GWASs) have successfully identified thousands of
susceptibility loci for human complex diseases. However, missing heritability is still a
challenging problem. Considering most GWAS loci are located in regulatory elements, we
recently developed a pipeline named functional disease-associated single-nucleotide
polymorphisms (SNPs) prediction (FDSP), to predict novel susceptibility loci for complex
diseases based on the interpretation of regulatory features and published GWAS results
with machine learning. When applied to type 2 diabetes and hypertension, the predicted
susceptibility loci by FDSP were proved to be capable of explaining additional
heritability. In addition, potential target genes of the predicted positive SNPs were
significantly enriched in disease-related pathways. Our results suggested that taking
regulatory features into consideration might be a useful way to address the missing
heritability problem. We hope FDSP could offer help for the identification of novel
susceptibility loci for complex diseases.
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Affiliation(s)
- Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P. R. China
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Hu W, Lv J, Han M, Yang Z, Li T, Jiang S, Yang Y. STAT3: The art of multi-tasking of metabolic and immune functions in obesity. Prog Lipid Res 2018; 70:17-28. [DOI: 10.1016/j.plipres.2018.04.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/04/2018] [Accepted: 04/06/2018] [Indexed: 02/07/2023]
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Sugden LA, Atkinson EG, Fischer AP, Rong S, Henn BM, Ramachandran S. Localization of adaptive variants in human genomes using averaged one-dependence estimation. Nat Commun 2018; 9:703. [PMID: 29459739 PMCID: PMC5818606 DOI: 10.1038/s41467-018-03100-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 01/19/2018] [Indexed: 12/19/2022] Open
Abstract
Statistical methods for identifying adaptive mutations from population genetic data face several obstacles: assessing the significance of genomic outliers, integrating correlated measures of selection into one analytic framework, and distinguishing adaptive variants from hitchhiking neutral variants. Here, we introduce SWIF(r), a probabilistic method that detects selective sweeps by learning the distributions of multiple selection statistics under different evolutionary scenarios and calculating the posterior probability of a sweep at each genomic site. SWIF(r) is trained using simulations from a user-specified demographic model and explicitly models the joint distributions of selection statistics, thereby increasing its power to both identify regions undergoing sweeps and localize adaptive mutations. Using array and exome data from 45 ‡Khomani San hunter-gatherers of southern Africa, we identify an enrichment of adaptive signals in genes associated with metabolism and obesity. SWIF(r) provides a transparent probabilistic framework for localizing beneficial mutations that is extensible to a variety of evolutionary scenarios.
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Affiliation(s)
- Lauren Alpert Sugden
- Center for Computational Molecular Biology, Brown University, Providence, RI, 02912, USA.
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, 02912, USA.
| | - Elizabeth G Atkinson
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Annie P Fischer
- Division of Applied Mathematics, Brown University, Providence, RI, 02912, USA
| | - Stephen Rong
- Center for Computational Molecular Biology, Brown University, Providence, RI, 02912, USA
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02912, USA
| | - Brenna M Henn
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Sohini Ramachandran
- Center for Computational Molecular Biology, Brown University, Providence, RI, 02912, USA.
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, 02912, USA.
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13
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Dong SS, Guo Y, Yao S, Chen YX, He MN, Zhang YJ, Chen XF, Chen JB, Yang TL. Integrating regulatory features data for prediction of functional disease-associated SNPs. Brief Bioinform 2017; 20:26-32. [DOI: 10.1093/bib/bbx094] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Indexed: 12/21/2022] Open
Affiliation(s)
- Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University
| | - Shi Yao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University
| | - Yi-Xiao Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University
| | - Mo-Nan He
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University
| | - Yu-Jie Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University
| | - Xiao-Feng Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University
| | - Jia-Bin Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University
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