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Zheng XX, Ma YQ, Cui YQ, Dong SS, Chang FX, Zhu DL, Huang G. Multiparameter spectral CT-based radiomics in predicting the expression of programmed death ligand 1 in non-small-cell lung cancer. Clin Radiol 2024; 79:e511-e523. [PMID: 38307814 DOI: 10.1016/j.crad.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 02/04/2024]
Abstract
AIM To explore the value of radiomics for predicting the expression of programmed death ligand 1 (PD-L1) in non-small-cell lung cancer (NSCLC) based on multiparameter spectral computed tomography (CT) images. MATERIALS AND METHODS A total of 220 patients with NSCLC were enrolled retrospectively and divided into the training (n=176) and testing (n=44) cohorts. The radiomics features were extracted from the conventional CT images, mono-energy 40 keV images, iodine density (ID) maps, Z-effective maps, and electron density maps. The logistic regression (LR) and support vector machine (SVM) algorithms were employed to build models based on radiomics signatures. The prediction abilities were qualified by the area under the curve (AUC) obtained from the receiver operating characteristic (ROC) curve. Internal validation was performed on the independent testing dataset. RESULTS The combined model for PD-L1 ≥1%, which consisted of the radiomics score (rad-score; p<0.0001), white blood cell (WBC; p=0.027) counts, and air bronchogram (p=0.003), reached the highest performance with the AUCs of 0.873 and 0.917 in the training and testing dataset, respectively, which was better than the radiomics model with the AUCs of 0.842 and 0.886. The combined model for PD-L1 ≥50%, which consisted of rad-score (p<0.0001) and WBC counts (p=0.027), achieved the highest performance in the training and testing dataset with AUCs of 0.932 and 0.903, respectively, which was better than the radiomics model with AUCs of 0.920 and 0.892, respectively. CONCLUSION The radiomics model based on the multiparameter images of spectral CT can predict the expression level of PD-L1 in NSCLC. The combined model can obtain higher prediction efficiency and serves as a promising method for immunotherapy selection.
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Affiliation(s)
- X X Zheng
- Imaging Center Department, Gansu Provincial Maternity and Child-care Hospital, Lanzhou, China
| | - Y Q Ma
- Department of Radiology, Gansu Province Hospital, Lanzhou, China
| | - Y Q Cui
- Department of Radiology, Gansu Province Hospital, Lanzhou, China
| | - S S Dong
- Clinical Science, Philips Healthcare, Shanghai, China
| | - F X Chang
- Imaging Center Department, Gansu Provincial Maternity and Child-care Hospital, Lanzhou, China
| | - D L Zhu
- Imaging Center Department, Gansu Provincial Maternity and Child-care Hospital, Lanzhou, China
| | - G Huang
- Department of Radiology, Gansu Province Hospital, Lanzhou, China.
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Dong SS, Huang XL, Chen YJ. [A case of Zellweger syndrome caused by PEX13 gene variation]. Zhonghua Er Ke Za Zhi 2024; 62:376-378. [PMID: 38527511 DOI: 10.3760/cma.j.cn112140-20231219-00441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Affiliation(s)
- S S Dong
- Child Rehabilitation Center, Jiangmen Maternal and Child Health Hospital, Jiangmen 529000, China
| | - X L Huang
- Child Rehabilitation Center, Jiangmen Maternal and Child Health Hospital, Jiangmen 529000, China
| | - Y J Chen
- Child Rehabilitation Center, Jiangmen Maternal and Child Health Hospital, Jiangmen 529000, China
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Chen XF, Duan YY, Jia YY, Dong QH, Shi W, Zhang Y, Dong SS, Li M, Liu Z, Chen F, Huang XT, Hao RH, Zhu DL, Jing RH, Guo Y, Yang TL. Integrative high-throughput enhancer surveying and functional verification divulges a YY2-condensed regulatory axis conferring risk for osteoporosis. Cell Genom 2024; 4:100501. [PMID: 38335956 PMCID: PMC10943593 DOI: 10.1016/j.xgen.2024.100501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/23/2023] [Accepted: 01/10/2024] [Indexed: 02/12/2024]
Abstract
The precise roles of chromatin organization at osteoporosis risk loci remain largely elusive. Here, we combined chromatin interaction conformation (Hi-C) profiling and self-transcribing active regulatory region sequencing (STARR-seq) to qualify enhancer activities of prioritized osteoporosis-associated single-nucleotide polymorphisms (SNPs). We identified 319 SNPs with biased allelic enhancer activity effect (baaSNPs) that linked to hundreds of candidate target genes through chromatin interactions across 146 loci. Functional characterizations revealed active epigenetic enrichment for baaSNPs and prevailing osteoporosis-relevant regulatory roles for their chromatin interaction genes. Further motif enrichment and network mapping prioritized several putative, key transcription factors (TFs) controlling osteoporosis binding to baaSNPs. Specifically, we selected one top-ranked TF and deciphered that an intronic baaSNP (rs11202530) could allele-preferentially bind to YY2 to augment PAPSS2 expression through chromatin interactions and promote osteoblast differentiation. Our results underline the roles of TF-mediated enhancer-promoter contacts for osteoporosis, which may help to better understand the intricate molecular regulatory mechanisms underlying osteoporosis risk loci.
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Affiliation(s)
- Xiao-Feng Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Key Laboratory of Biology Multiomics and Diseases in Shaanxi Province Higher Education Institutions, Biomedical Informatics and Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China
| | - Yuan-Yuan Duan
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Key Laboratory of Biology Multiomics and Diseases in Shaanxi Province Higher Education Institutions, Biomedical Informatics and Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China
| | - Ying-Ying Jia
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Key Laboratory of Biology Multiomics and Diseases in Shaanxi Province Higher Education Institutions, Biomedical Informatics and Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China
| | - Qian-Hua Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Key Laboratory of Biology Multiomics and Diseases in Shaanxi Province Higher Education Institutions, Biomedical Informatics and Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China
| | - Wei Shi
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Key Laboratory of Biology Multiomics and Diseases in Shaanxi Province Higher Education Institutions, Biomedical Informatics and Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China
| | - Yan Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Key Laboratory of Biology Multiomics and Diseases in Shaanxi Province Higher Education Institutions, Biomedical Informatics and Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Key Laboratory of Biology Multiomics and Diseases in Shaanxi Province Higher Education Institutions, Biomedical Informatics and Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China
| | - Meng Li
- Department of Orthopedics, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Zhongbo Liu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, Shaanxi, China
| | - Fei Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Key Laboratory of Biology Multiomics and Diseases in Shaanxi Province Higher Education Institutions, Biomedical Informatics and Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China
| | - Xiao-Ting Huang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Key Laboratory of Biology Multiomics and Diseases in Shaanxi Province Higher Education Institutions, Biomedical Informatics and Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China
| | - Ruo-Han Hao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Key Laboratory of Biology Multiomics and Diseases in Shaanxi Province Higher Education Institutions, Biomedical Informatics and Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China
| | - Dong-Li Zhu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Key Laboratory of Biology Multiomics and Diseases in Shaanxi Province Higher Education Institutions, Biomedical Informatics and Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China
| | - Rui-Hua Jing
- Department of Ophthalmology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710000, Shaanxi, China
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Key Laboratory of Biology Multiomics and Diseases in Shaanxi Province Higher Education Institutions, Biomedical Informatics and Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China.
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Key Laboratory of Biology Multiomics and Diseases in Shaanxi Province Higher Education Institutions, Biomedical Informatics and Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China; Department of Orthopedics, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China.
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Yao S, Han JZ, Guo J, Wang X, Qian L, Wu H, Shi W, Zhu RJ, Wang JH, Dong SS, Cui LL, Wang Y, Guo Y, Yang TL. The Causal Relationships Between Gut Microbiota, Brain Volume, and Intelligence: A Two-Step Mendelian Randomization Analysis. Biol Psychiatry 2024:S0006-3223(24)01132-6. [PMID: 38432522 DOI: 10.1016/j.biopsych.2024.02.1012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/05/2024] [Accepted: 02/23/2024] [Indexed: 03/05/2024]
Abstract
BACKGROUND Growing evidence indicates that dynamic changes in gut microbiome can affect intelligence; however, whether these relationships are causal remains elusive. We aimed to disentangle the poorly understood causal relationship between gut microbiota and intelligence. METHODS We performed a 2-sample Mendelian randomization (MR) analysis using genetic variants from the largest available genome-wide association studies of gut microbiota (N = 18,340) and intelligence (N = 269,867). The inverse-variance weighted method was used to conduct the MR analyses complemented by a range of sensitivity analyses to validate the robustness of the results. Considering the close relationship between brain volume and intelligence, we applied 2-step MR to evaluate whether the identified effect was mediated by regulating brain volume (N = 47,316). RESULTS We found a risk effect of the genus Oxalobacter on intelligence (odds ratio = 0.968 change in intelligence per standard deviation increase in taxa; 95% CI, 0.952-0.985; p = 1.88 × 10-4) and a protective effect of the genus Fusicatenibacter on intelligence (odds ratio = 1.053; 95% CI, 1.024-1.082; p = 3.03 × 10-4). The 2-step MR analysis further showed that the effect of genus Fusicatenibacter on intelligence was partially mediated by regulating brain volume, with a mediated proportion of 33.6% (95% CI, 6.8%-60.4%; p = .014). CONCLUSIONS Our results provide causal evidence indicating the role of the microbiome in intelligence. Our findings may help reshape our understanding of the microbiota-gut-brain axis and development of novel intervention approaches for preventing cognitive impairment.
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Affiliation(s)
- Shi Yao
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China; Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China; National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Ji-Zhou Han
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Jing Guo
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xin Wang
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Long Qian
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Hao Wu
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Wei Shi
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Ren-Jie Zhu
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Jia-Hao Wang
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Li-Li Cui
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Yan Wang
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China.
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China; National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China.
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5
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Xie XD, Dong SS, Liu RJ, Shi LL, Zhu T. Mechanism of Efferocytosis in Determining Ischaemic Stroke Resolution-Diving into Microglia/Macrophage Functions and Therapeutic Modality. Mol Neurobiol 2024:10.1007/s12035-024-04060-4. [PMID: 38409642 DOI: 10.1007/s12035-024-04060-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/17/2024] [Indexed: 02/28/2024]
Abstract
After ischaemic cerebral vascular injury, efferocytosis-a process known as the efficient clearance of apoptotic cells (ACs) by various phagocytes in both physiological and pathological states-is crucial for maintaining central nervous system (CNS) homeostasis and regaining prognosis. The mechanisms of efferocytosis in ischaemic stroke and its influence on preventing inflammation progression from secondary injury were still not fully understood, despite the fact that the fundamental process of efferocytosis has been described in a series of phases, including AC recognition, phagocyte engulfment, and subsequent degradation. The genetic reprogramming of macrophages and brain-resident microglia after an ischaemic stroke has been equated by some researchers to that of the peripheral blood and brain. Based on previous studies, some molecules, such as signal transducer and activator of transcription 6 (STAT6), peroxisome proliferator-activated receptor γ (PPARG), CD300A, and sigma non-opioid intracellular receptor 1 (SIGMAR1), were discovered to be largely associated with aspects of apoptotic cell elimination and accompanying neuroinflammation, such as inflammatory cytokine release, phenotype transformation, and suppressing of antigen presentation. Exacerbated stroke outcomes are brought on by defective efferocytosis and improper modulation of pertinent signalling pathways in blood-borne macrophages and brain microglia, which also results in subsequent tissue inflammatory damage. This review focuses on recent researches which contain a number of recently discovered mechanisms, such as studies on the relationship between benign efferocytosis and the regulation of inflammation in ischaemic stroke, the roles of some risk factors in disease progression, and current immune approaches that aim to promote efferocytosis to treat some autoimmune diseases. Understanding these pathways provides insight into novel pathophysiological processes and fresh characteristics, which can be used to build cerebral ischaemia targeting techniques.
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Affiliation(s)
- Xiao-Di Xie
- Department of Pathophysiology, School of Basic Medicine, Institute of Neuroregeneration & Neurorehabilitation, Qingdao University, No. 308 Ningxia Road, Qingdao, China
| | - Shan-Shan Dong
- Department of Pathophysiology, School of Basic Medicine, Institute of Neuroregeneration & Neurorehabilitation, Qingdao University, No. 308 Ningxia Road, Qingdao, China
- Department of Rehabilitation Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Ru-Juan Liu
- Department of Pathophysiology, School of Basic Medicine, Institute of Neuroregeneration & Neurorehabilitation, Qingdao University, No. 308 Ningxia Road, Qingdao, China
- Department of Rehabilitation Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Liu-Liu Shi
- Department of Pathophysiology, School of Basic Medicine, Institute of Neuroregeneration & Neurorehabilitation, Qingdao University, No. 308 Ningxia Road, Qingdao, China
- Department of Neurosurgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Ting Zhu
- Department of Pathophysiology, School of Basic Medicine, Institute of Neuroregeneration & Neurorehabilitation, Qingdao University, No. 308 Ningxia Road, Qingdao, China.
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6
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Jiang F, Hu SY, Tian W, Wang NN, Yang N, Dong SS, Song HM, Zhang DJ, Gao HW, Wang C, Wu H, He CY, Zhu DL, Chen XF, Guo Y, Yang Z, Yang TL. A landscape of gene expression regulation for synovium in arthritis. Nat Commun 2024; 15:1409. [PMID: 38360850 PMCID: PMC10869817 DOI: 10.1038/s41467-024-45652-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 01/29/2024] [Indexed: 02/17/2024] Open
Abstract
The synovium is an important component of any synovial joint and is the major target tissue of inflammatory arthritis. However, the multi-omics landscape of synovium required for functional inference is absent from large-scale resources. Here we integrate genomics with transcriptomics and chromatin accessibility features of human synovium in up to 245 arthritic patients, to characterize the landscape of genetic regulation on gene expression and the regulatory mechanisms mediating arthritic diseases predisposition. We identify 4765 independent primary and 616 secondary cis-expression quantitative trait loci (cis-eQTLs) in the synovium and find that the eQTLs with multiple independent signals have stronger effects and heritability than single independent eQTLs. Integration of genome-wide association studies (GWASs) and eQTLs identifies 84 arthritis related genes, revealing 38 novel genes which have not been reported by previous studies using eQTL data from the GTEx project or immune cells. We further develop a method called eQTac to identify variants that could affect gene expression by affecting chromatin accessibility and identify 1517 regions with potential regulatory function of chromatin accessibility. Altogether, our study provides a comprehensive synovium multi-omics resource for arthritic diseases and gains new insights into the regulation of gene expression.
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Affiliation(s)
- Feng Jiang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Shou-Ye Hu
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, P.R. China
| | - Wen Tian
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Nai-Ning Wang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Ning Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Hui-Miao Song
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Da-Jin Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Hui-Wu Gao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Chen Wang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Hao Wu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Chang-Yi He
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Dong-Li Zhu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Xiao-Feng Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Zhi Yang
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, P.R. China.
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China.
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7
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Duan YY, Chen XF, Zhu RJ, Jia YY, Huang XT, Zhang M, Yang N, Dong SS, Zeng M, Feng Z, Zhu DL, Wu H, Jiang F, Shi W, Hu WX, Ke X, Chen H, Liu Y, Jing RH, Guo Y, Li M, Yang TL. High-throughput functional dissection of noncoding SNPs with biased allelic enhancer activity for insulin resistance-relevant phenotypes. Am J Hum Genet 2023; 110:1266-1288. [PMID: 37506691 PMCID: PMC10432149 DOI: 10.1016/j.ajhg.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023] Open
Abstract
Most of the single-nucleotide polymorphisms (SNPs) associated with insulin resistance (IR)-relevant phenotypes by genome-wide association studies (GWASs) are located in noncoding regions, complicating their functional interpretation. Here, we utilized an adapted STARR-seq to evaluate the regulatory activities of 5,987 noncoding SNPs associated with IR-relevant phenotypes. We identified 876 SNPs with biased allelic enhancer activity effects (baaSNPs) across 133 loci in three IR-relevant cell lines (HepG2, preadipocyte, and A673), which showed pervasive cell specificity and significant enrichment for cell-specific open chromatin regions or enhancer-indicative markers (H3K4me1, H3K27ac). Further functional characterization suggested several transcription factors (TFs) with preferential allelic binding to baaSNPs. We also incorporated multi-omics data to prioritize 102 candidate regulatory target genes for baaSNPs and revealed prevalent long-range regulatory effects and cell-specific IR-relevant biological functional enrichment on them. Specifically, we experimentally verified the distal regulatory mechanism at IRS1 locus, in which rs952227-A reinforces IRS1 expression by long-range chromatin interaction and preferential binding to the transcription factor HOXC6 to augment the enhancer activity. Finally, based on our STARR-seq screening data, we predicted the enhancer activity of 227,343 noncoding SNPs associated with IR-relevant phenotypes (fasting insulin adjusted for BMI, HDL cholesterol, and triglycerides) from the largest available GWAS summary statistics. We further provided an open resource (http://www.bigc.online/fnSNP-IR) for better understanding genetic regulatory mechanisms of IR-relevant phenotypes.
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Affiliation(s)
- Yuan-Yuan Duan
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Xiao-Feng Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Ren-Jie Zhu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Ying-Ying Jia
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Xiao-Ting Huang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Meng Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Ning Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Mengqi Zeng
- Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Zhihui Feng
- Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Dong-Li Zhu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Hao Wu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Feng Jiang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Wei Shi
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Wei-Xin Hu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Xin Ke
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Hao Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, School of Medicine, Indiana University, Indianapolis, IN 46202, USA
| | - Rui-Hua Jing
- Department of Ophthalmology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710000, China
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Meng Li
- Department of Orthopedics, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China.
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China; Department of Orthopedics, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China.
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8
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Yu K, Chen XF, Guo J, Wang S, Huang XT, Guo Y, Dong SS, Yang TL. Assessment of bidirectional relationships between brain imaging-derived phenotypes and stroke: a Mendelian randomization study. BMC Med 2023; 21:271. [PMID: 37491271 PMCID: PMC10369749 DOI: 10.1186/s12916-023-02982-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/17/2023] [Indexed: 07/27/2023] Open
Abstract
BACKGROUND Stroke is a major cause of mortality and long-term disability worldwide. Whether the associations between brain imaging-derived phenotypes (IDPs) and stroke are causal is uncertain. METHODS We performed two-sample bidirectional Mendelian randomization (MR) analyses to explore the causal associations between IDPs and stroke. Summary data of 587 brain IDPs (up to 33,224 individuals) from the UK Biobank and five stroke types (sample size range from 301,663 to 446,696, case number range from 5,386 to 40,585) from the MEGASTROKE consortium were used. RESULTS Forward MR indicated 14 IDPs belong to projection fibers or association fibers were associated with stroke. For example, higher genetically determined mean diffusivity (MD) in the right external capsule was causally associated with an increased risk of small vessel stroke (IVW OR = 2.76, 95% CI 2.07 to 3.68, P = 5.87 × 10-12). Reverse MR indicated that genetically determined higher risk of any ischemic stroke was associated with increased isotropic or free water volume fraction (ISOVF) in body of corpus callosum (IVW β = 0.23, 95% CI 0.14 to 0.33, P = 3.22 × 10-7). This IDP is a commissural fiber and it is not included in the IDPs identified by forward MR. CONCLUSIONS We identified 14 IDPs with statistically significant evidence of causal effects on stroke or stroke subtypes. We also identified potential causal effects of stroke on one IDP of commissural fiber. These findings might guide further work toward identifying preventative strategies at the brain imaging levels.
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Affiliation(s)
- Ke Yu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Xiao-Feng Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Jing Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Sen Wang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Xiao-Ting Huang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China.
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China.
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9
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Dong SS, Zhou XP, Peng T, Liu Y. Mitochondrial RNA editing sites affect the phylogenetic reconstruction of gymnosperms. Plant Divers 2023; 45:485-489. [PMID: 37601539 PMCID: PMC10435907 DOI: 10.1016/j.pld.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 08/22/2023]
Abstract
•RNA editing sites may contain homoplasious signals that cause artifactual inferences in phylogenetic analyses.•Excluding RNA editing sites from gymnosperm mitochondrial genes restored the sister relationship of gnetophytes and Pinaceae.•Phylogenetic analysis based on mitochondrial genomic data should carefully evaluate the impact of RNA editing sites.
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Affiliation(s)
- Shan-Shan Dong
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen 518004, Guangdong, China
| | - Xu-Ping Zhou
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen 518004, Guangdong, China
- School of Life Sciences, Guizhou Normal University, Guiyang 550001, Guizhou, China
| | - Tao Peng
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen 518004, Guangdong, China
- School of Life Sciences, Guizhou Normal University, Guiyang 550001, Guizhou, China
| | - Yang Liu
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen 518004, Guangdong, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, Guangdong, China
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10
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Wang NN, Zhang Y, Jiang F, Zhu DL, Di CX, Hu SY, Chen XF, Zhi LQ, Rong Y, Ke X, Duan YY, Dong SS, Yang TL, Yang Z, Guo Y. Enhancer variants on chromosome 2p14 regulating SPRED2 and ACTR2 act as a signal amplifier to protect against rheumatoid arthritis. Am J Hum Genet 2023; 110:625-637. [PMID: 36924774 PMCID: PMC10119143 DOI: 10.1016/j.ajhg.2023.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 02/24/2023] [Indexed: 03/17/2023] Open
Abstract
Genome-wide association studies (GWASs) have repeatedly reported multiple non-coding single-nucleotide polymorphisms (SNPs) at 2p14 associated with rheumatoid arthritis (RA), but their functional roles in the pathological mechanisms of RA remain to be explored. In this study, we integrated a series of bioinformatics and functional experiments and identified three intronic RA SNPs (rs1876518, rs268131, and rs2576923) within active enhancers that can regulate the expression of SPRED2 directly. At the same time, SPRED2 and ACTR2 influence each other as a positive feedback signal amplifier to strengthen the protective role in RA by inhibiting the migration and invasion of rheumatoid fibroblast-like synoviocytes (FLSs). In particular, the transcription factor CEBPB preferentially binds to the rs1876518-T allele to increase the expression of SPRED2 in FLSs. Our findings decipher the molecular mechanisms behind the GWAS signals at 2p14 for RA and emphasize SPRED2 as a potential candidate gene for RA, providing a potential target and direction for precise treatment of RA.
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Affiliation(s)
- Nai-Ning Wang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Yan Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Feng Jiang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Dong-Li Zhu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Chen-Xi Di
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Shou-Ye Hu
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Xiao-Feng Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Li-Qiang Zhi
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Yu Rong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Xin Ke
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Yuan-Yuan Duan
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, 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, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Zhi Yang
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, P.R. China.
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China.
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11
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Wu H, Ke X, Huang W, Shi W, Yao S, Duan YY, Tian W, Dong SS, Xue HZ, Guo Y. Multitissue Integrative Analysis Identifies Susceptibility Genes for Atopic Dermatitis. J Invest Dermatol 2023; 143:602-611.e14. [PMID: 36155055 DOI: 10.1016/j.jid.2022.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 09/02/2022] [Accepted: 09/02/2022] [Indexed: 12/25/2022]
Abstract
Atopic dermatitis (AD) is a chronic relapsing inflammatory skin disease with multiple environmental and genetic factors involved in its etiology. Although lots of genetic loci associated with AD have been reported by GWASs, only a small part of phenotypic variations can be explained. To identify additional susceptibility genes on AD, we conducted a large-scale transcriptome-wide association study using a joint-tissue imputation approach in ∼840,000 European individuals combined with six precomputed gene expression weights of four AD-relevant tissues, including skin fibroblast, lymphocyte, and whole blood. The Mendelian randomization causal inference analysis was performed to estimate the causal effect of transcriptome-wide association study‒identified genes. We identified 51 genes significantly associated with AD after Bonferroni corrections, and 19 genes showed putatively causal associations such as an established gene FLG (P = 3.98 × 10‒10) and seven genes that have not been implicated in previous transcriptome-wide association studies, such as AQP3 (P = 4.43 × 10‒7) and PDCD1 (P = 7.66 × 10‒7). Among them, four genes (AQP3, PDCD1, ADCY3, and DOLPP1) were further supported in differential expression analyses or the Mouse Genome Informatics database. Overall, our study identified susceptibility genes associated with AD, providing, to our knowledge, previously unreported clues in revealing the genetic mechanisms in AD.
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Affiliation(s)
- Hao Wu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Xin Ke
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Wei Huang
- Department of Trauma Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Wei Shi
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Shi Yao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Yuan-Yuan Duan
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Wen Tian
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Han-Zhong Xue
- Department of Trauma Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China; Department of Trauma Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, China.
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12
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Hao RH, Guo Y, Wang C, Chen F, Di CX, Dong SS, Cao QL, Guo J, Rong Y, Yao S, Zhu DL, Chen YX, Chen H, Yang TL. Lineage-specific rearrangement of chromatin loops and epigenomic features during adipocytes and osteoblasts commitment. Cell Death Differ 2022; 29:2503-2518. [PMID: 35906483 PMCID: PMC9751090 DOI: 10.1038/s41418-022-01035-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 06/09/2022] [Accepted: 06/13/2022] [Indexed: 01/31/2023] Open
Abstract
Human mesenchymal stem cells (hMSCs) can be differentiated into adipocytes and osteoblasts. The processes are driven by the rewiring of chromatin architectures and transcriptomic/epigenomic changes. Here, we induced hMSCs to adipogenic and osteogenic differentiation, and performed 2 kb resolution Hi-C experiments for chromatin loops detection. We also generated matched RNA-seq, ChIP-seq and ATAC-seq data for integrative analysis. After comprehensively comparing adipogenesis and osteogenesis, we quantitatively identified lineage-specific loops and screened out lineage-specific enhancers and open chromatin. We reveal that lineage-specific loops can activate gene expression and facilitate cell commitment through combining enhancers and accessible chromatin in a lineage-specific manner. We finally proposed loop-mediated regulatory networks and identified the controlling factors for adipocytes and osteoblasts determination. Functional experiments validated the lineage-specific regulation networks towards IRS2 and RUNX2 that are associated with adipogenesis and osteogenesis, respectively. These results are expected to help better understand the chromatin conformation determinants of hMSCs fate commitment.
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Affiliation(s)
- Ruo-Han Hao
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Yan Guo
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Chen Wang
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Fei Chen
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Chen-Xi Di
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Shan-Shan Dong
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Qi-Long Cao
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
- Research and Development Department, Qingdao Haier Biotech Co. Ltd, Qingdao, Shandong, 266109, P. R. China
| | - Jing Guo
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Yu Rong
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Shi Yao
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
- National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, P. R. China
| | - Dong-Li Zhu
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Yi-Xiao Chen
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
- National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, P. R. China
| | - Hao Chen
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Tie-Lin Yang
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China.
- National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, P. R. China.
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13
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Zhu DL, Chen XF, Zhou XR, Hu SY, Tuo XM, Hao RH, Dong SS, Jiang F, Rong Y, Yang TL, Yang Z, Guo Y. An Osteoporosis Susceptibility Allele at 11p15 Regulates SOX6 Expression by Modulating TCF4 Chromatin Binding. J Bone Miner Res 2022; 37:1147-1155. [PMID: 35373860 DOI: 10.1002/jbmr.4554] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 11/07/2022]
Abstract
Osteoporosis is an age-related complex disease clinically diagnosed with bone mineral density (BMD). Although several genomewide association studies (GWASs) have discovered multiple noncoding genetic variants at 11p15 influencing osteoporosis risk, the functional mechanisms of these variants remain unknown. Through integrating bioinformatics and functional experiments, a potential functional single-nucleotide polymorphism (SNP; rs1440702) located in an enhancer element was identified and the A allele of rs1440702 acted as an allelic specificities enhancer to increase its distal target gene SOX6 (~600 Kb upstream) expression, which plays a key role in bone formation. We also validated this long-range regulation via conducting chromosome conformation capture (3C) assay. Furthermore, we demonstrated that SNP rs1440702 with a risk allele (rs1440702-A) could increase the activity of the enhancer element by altering the binding affinity of the transcription factor TCF4, resulting in the upregulation expression of SOX6 gene. Collectively, our integrated analyses revealed how the noncoding genetic variants (rs1440702) affect osteoporosis predisposition via long-range gene regulatory mechanisms and identified its target gene SOX6 for downstream biomarker and drug development. © 2022 American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Dong-Li Zhu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China
| | - Xiao-Feng Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China
| | - Xiao-Rong Zhou
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China
| | - Shou-Ye Hu
- Honghui Hospital, Xi'an Jiaotong University, Xi'an, PR China
| | - Xiao-Mei Tuo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China
| | - Ruo-Han Hao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China
| | - Feng Jiang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China
| | - Yu Rong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China
| | - Zhi Yang
- Honghui Hospital, Xi'an Jiaotong University, Xi'an, PR China
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China.,Honghui Hospital, Xi'an Jiaotong University, Xi'an, PR China
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14
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Hu WX, Rong Y, Guo Y, Jiang F, Tian W, Chen H, Dong SS, Yang TL. ExsgRNA: reduce off-target efficiency by on-target mismatched sgRNA. Brief Bioinform 2022; 23:6587171. [PMID: 35580855 DOI: 10.1093/bib/bbac183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/08/2022] [Accepted: 04/23/2022] [Indexed: 11/13/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 gene editing technology has been widely used to facilitate efficient genome editing. Current popular sgRNA design tools only consider the sgRNA perfectly matched to the target site and provide the results without any on-target mismatch. We suppose taking on-target gRNA-DNA mismatches into consideration might provide better sgRNA with similar binding activity and reduced off-target sites. Here, we trained a seq2seq-attention model with feedback-loop architecture, to automatically generate sgRNAs with on-target mismatches. Dual-luciferase reporter experiment showed that multiple sgRNAs with three mismatches could achieve the 80% of the relative activity of the perfect matched sgRNA. Meanwhile, it could reduce the number of off-target sites using sgRNAs with on-target mismatches. Finally, we provided a freely accessible web server sgRNA design tool named ExsgRNA. Users could submit their target sequence to this server and get optimal sgRNAs with less off-targets and similar on-target activity compared with the perfect-matched sgRNA.
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Affiliation(s)
- Wei-Xin Hu
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China
| | - Yu Rong
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China
| | - Yan Guo
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China
| | - Feng Jiang
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China
| | - Wen Tian
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China
| | - Hao Chen
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China
| | - Shan-Shan Dong
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China.,Research Institute of Xi'an Jiaotong University, Zhejiang, China
| | - Tie-Lin Yang
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China
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15
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Ke X, Wu H, Chen YX, Guo Y, Yao S, Guo MR, Duan YY, Wang NN, Shi W, Wang C, Dong SS, Kang H, Dai Z, Yang TL. Individualized pathway activity algorithm identifies oncogenic pathways in pan-cancer analysis. EBioMedicine 2022; 79:104014. [PMID: 35487057 PMCID: PMC9117264 DOI: 10.1016/j.ebiom.2022.104014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 02/07/2023] Open
Abstract
Background Accumulative evidences have shown that dysregulation of biological pathways contributed to the initiation and progression of malignant tumours. Several methods for pathway activity measurement have been proposed, but they are restricted to making comparisons between groups or sensitive to experimental batch effects. Methods We introduced a novel method for individualized pathway activity measurement (IPAM) that is based on the ranking of gene expression levels in individual sample. Taking advantage of IPAM, we calculated the pathway activity of 318 pathways from KEGG database in the 10528 tumour/normal samples of 33 cancer types from TCGA to identify characteristic dysregulated pathways among different cancer types. Findings IPAM precisely quantified the level of activity of each pathway in pan-cancer analysis and exhibited better performance in cancer classification and prognosis prediction over five widely used tools. The average ROC-AUC of cancer diagnostic model using tumour-educated platelets (TEPs) reached 92.84%, suggesting the potential of our algorithm in early diagnosis of cancer. We identified several pathways significantly deregulated and associated with patient survival in a large fraction of cancer types, such as tyrosine metabolism, fatty acid degradation, cell cycle, p53 signalling pathway and DNA replication. We also confirmed the dominant role of metabolic pathways in cancer pathway dysregulation and identified the driving factors of specific pathway dysregulation, such as PPARA for branched-chain amino acid metabolism and NR1I2, NR1I3 for fatty acid metabolism. Interpretation Our study will provide novel clues for understanding the pathological mechanisms of cancer, ultimately paving the way for personalized medicine of cancer. Funding A full list of funding can be found in the Acknowledgements section.
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Affiliation(s)
- Xin Ke
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics and Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, PR China
| | - Hao Wu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics and Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, PR China
| | - Yi-Xiao Chen
- National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, PR China
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics and Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, PR China
| | - Shi Yao
- National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, PR China
| | - Ming-Rui Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics and Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, PR China
| | - Yuan-Yuan Duan
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics and Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, PR China
| | - Nai-Ning Wang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics and Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, PR China
| | - Wei Shi
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics and Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, PR China
| | - Chen Wang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics and Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, PR China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics and Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, PR China
| | - Huafeng Kang
- Department of Oncology, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, PR China
| | - Zhijun Dai
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, PR China
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics and Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, PR China; National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, PR China.
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16
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Liu CC, Dong SS, Chen JB, Wang C, Ning P, Guo Y, Yang TL. MetaDecoder: a novel method for clustering metagenomic contigs. Microbiome 2022; 10:46. [PMID: 35272700 PMCID: PMC8908641 DOI: 10.1186/s40168-022-01237-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Clustering the metagenomic contigs into potential genomes is a key step to investigate the functional roles of microbial populations. Existing algorithms have achieved considerable success with simulated or real sequencing datasets. However, accurately classifying contigs from complex metagenomes is still a challenge. RESULTS We introduced a novel clustering algorithm, MetaDecoder, which can classify metagenomic contigs based on the frequencies of k-mers and coverages. MetaDecoder was built as a two-layer model with the first layer being a GPU-based modified Dirichlet process Gaussian mixture model (DPGMM), which controls the weight of each DPGMM cluster to avoid over-segmentation by dynamically dissolving contigs in small clusters and reassigning them to the remaining clusters. The second layer comprises a semi-supervised k-mer frequency probabilistic model and a modified Gaussian mixture model for modeling the coverage based on single copy marker genes. Benchmarks on simulated and real-world datasets demonstrated that MetaDecoder can be served as a promising approach for effectively clustering metagenomic contigs. CONCLUSIONS In conclusion, we developed the GPU-based MetaDecoder for effectively clustering metagenomic contigs and reconstructing microbial communities from microbial data. Applying MetaDecoder on both simulated and real-world datasets demonstrated that it could generate more complete clusters with lower contamination. Using MetaDecoder, we identified novel high-quality genomes and expanded the existing catalog of bacterial genomes. Video Abstract.
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Affiliation(s)
- Cong-Cong Liu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049 P. R. China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049 P. R. China
| | - Jia-Bin Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049 P. R. China
| | - Chen Wang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049 P. R. China
| | - Pan Ning
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049 P. R. China
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049 P. R. China
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049 P. R. China
- National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi 710004 P. R. China
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17
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Qiao N, Li XX, Chen Y, Xin XY, Yang C, Dong SS, Wang YZ, Li XJ, Hua YP, Wang WM. Three Ln2 compounds (Gd2, Tb2 and Dy2) with a Ln2O2 center showing magnetic refrigeration property and single-molecular magnet behavior. Polyhedron 2022. [DOI: 10.1016/j.poly.2022.115675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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18
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Ke X, Tian X, Yao S, Wu H, Duan YY, Wang NN, Shi W, Yang TL, Dong SS, Huang D, Guo Y. Transcriptome-wide association study identifies multiple genes and pathways associated with thyroid function. Hum Mol Genet 2021; 31:1871-1883. [PMID: 34962261 DOI: 10.1093/hmg/ddab371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/03/2021] [Accepted: 12/20/2021] [Indexed: 11/12/2022] Open
Abstract
Thyroid dysfunction is a common endocrine disease measured by thyroid-stimulating hormone (TSH) level. Although more than 70 genetic loci associated with TSH have been reported through genome-wide association studies (GWASs), the variants can only explain a small fraction of the thyroid function heritability. To identify novel candidate genes for thyroid function, we conducted the first large-scale transcriptome-wide association study (TWAS) for thyroid function using GWAS-summary data for TSH levels in up to 119 715 individuals combined with pre-computed gene expression weights of six panels from four tissue types. The candidate genes identified by TWAS were further validated by TWAS replication and gene expression profiles. We identified 74 conditionally independent genes significantly associated with thyroid function, such as PDE8B (P = 1.67 × 10-282), PDE10A (P = 7.61 × 10-119), NR3C2 (P = 1.50 × 10-92), and CAPZB (P = 3.13 × 10-79). After TWAS replication using UKBB datasets, 26 genes were replicated for significant associations with thyroid-relevant diseases/traits. Among them, 16 gene were causal for their associations to thyroid-relevant diseases/traits and further validated in differential expression analyses, including two novel genes (MFSD6 and RBM47) that did not implicate in previous GWASs. Enrichment analyses detected several pathways associated with thyroid function, such as the cAMP signaling pathway (P = 7.27 × 10-4), hemostasis (P = 3.74 × 10-4), and platelet activation, signaling, and aggregation (P = 9.98 × 10-4). Our study identified multiple candidate genes and pathways associated with thyroid function, providing novel clues for revealing the genetic mechanisms of thyroid function and disease.
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Affiliation(s)
- Xin Ke
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China, 710049
| | - Xin Tian
- Department of Orthopaedics, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Shi Yao
- National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China, 710004
| | - Hao Wu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China, 710049
| | - Yuan-Yuan Duan
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China, 710049
| | - Nai-Ning Wang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China, 710049
| | - Wei Shi
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China, 710049
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China, 710049.,National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China, 710004
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China, 710049.,Research Institute of Xi'an Jiaotong University, Hangzhou, Zhejiang, P. R. China
| | - Dageng Huang
- Department of Orthopaedics, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China, 710049.,Department of Orthopaedics, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
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Yang-Zhou CH, Cao JX, Dong SS, Chen SH, Michael RN. Phosphorus Co-Existing in Water: A New Mechanism to Boost Boron Removal by Calcined Oyster Shell Powder. Molecules 2021; 27:54. [PMID: 35011286 PMCID: PMC8746779 DOI: 10.3390/molecules27010054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/13/2021] [Accepted: 12/20/2021] [Indexed: 11/20/2022] Open
Abstract
The removal of boron (B) from water by co-precipitation with hydroxyapatite (HAP) has been extensively studied due to its low cost, ease of use and high efficiency. However, there is no explicit mechanism to express how resolved B was trapped by HAP. Thus, in this work, the process of removing B from water was studied using a low-cost calcium (Ca) precipitation agent derived from used waste oyster shells. The results showed that the removal rate of B in the simulated wastewater by calcined oyster shell (COS) in the presence of phosphorus (P) is up to more than 90%, as opposed to virtually no removal without phosphate. For B removal, the treated water needs to be an alkaline solution with a high pH above 12, where B is removed as [CaB(OH)4]+ but is not molecular. Finally, the synergistic mechanism of co-precipitation between HAP and dissolved B, occlusion co-precipitation, was explained in detail. The proposed method discovered the relationship between Ca, P and B, and was aimed at removing B without secondary pollution through co-precipitation.
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Affiliation(s)
- Chi-Hao Yang-Zhou
- Key Laboratory of Jiangxi Province for Persistent Pollutants Control and Resources Recycle, Nanchang Hangkong University, Nanchang 330063, China; (C.-H.Y.-Z.); (J.-X.C.); (S.-S.D.)
| | - Jia-Xin Cao
- Key Laboratory of Jiangxi Province for Persistent Pollutants Control and Resources Recycle, Nanchang Hangkong University, Nanchang 330063, China; (C.-H.Y.-Z.); (J.-X.C.); (S.-S.D.)
| | - Shan-Shan Dong
- Key Laboratory of Jiangxi Province for Persistent Pollutants Control and Resources Recycle, Nanchang Hangkong University, Nanchang 330063, China; (C.-H.Y.-Z.); (J.-X.C.); (S.-S.D.)
| | - Su-Hua Chen
- Key Laboratory of Jiangxi Province for Persistent Pollutants Control and Resources Recycle, Nanchang Hangkong University, Nanchang 330063, China; (C.-H.Y.-Z.); (J.-X.C.); (S.-S.D.)
| | - Ruby N. Michael
- School of Engineering and Built Environment, Griffith University, Nathan, QLD 4111, Australia;
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20
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Zhang K, Dong SS, Guo Y, Tang SH, Wu H, Yao S, Wang PF, Zhang K, Xue HZ, Huang W, Ding J, Yang TL. Causal Associations Between Blood Lipids and COVID-19 Risk: A Two-Sample Mendelian Randomization Study. Arterioscler Thromb Vasc Biol 2021; 41:2802-2810. [PMID: 34496635 PMCID: PMC8545250 DOI: 10.1161/atvbaha.121.316324] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Supplemental Digital Content is available in the text. Objective: Coronavirus disease 2019 (COVID-19) is a global pandemic caused by the severe acute respiratory syndrome coronavirus 2. It has been reported that dyslipidemia is correlated with COVID-19, and blood lipids levels, including total cholesterol, HDL-C (high-density lipoprotein cholesterol), and LDL-C (low-density lipoprotein cholesterol) levels, were significantly associated with disease severity. However, the causalities of blood lipids on COVID-19 are not clear. Approach and Results: We performed 2-sample Mendelian randomization (MR) analyses to explore the causal effects of blood lipids on COVID-19 susceptibility and severity. Using the outcome data from the UK Biobank (1221 cases and 4117 controls), we observed potential positive causal effects of dyslipidemia (odds ratio [OR], 1.27 [95% CI, 1.08–1.49], P=3.18×10−3), total cholesterol (OR, 1.19 [95% CI, 1.07–1.32], P=8.54×10−4), and ApoB (apolipoprotein B; OR, 1.18 [95% CI, 1.07–1.29], P=1.01×10−3) on COVID-19 susceptibility after Bonferroni correction. In addition, the effects of total cholesterol (OR, 1.01 [95% CI, 1.00–1.02], P=2.29×10−2) and ApoB (OR, 1.01 [95% CI, 1.00–1.02], P=2.22×10−2) on COVID-19 susceptibility were also identified using outcome data from the host genetics initiative (14 134 cases and 1 284 876 controls). Conclusions: In conclusion, we found that higher total cholesterol and ApoB levels might increase the risk of COVID-19 infection.
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Affiliation(s)
- Kun Zhang
- Department of Trauma Surgery, Honghui Hospital, College of Medicine (K.Z., Y.G., P.-F.W., K.Z., H.-Z.X., W.H., T.-L.Y.), Xi'an Jiaotong University, Shaanxi, PR China.,Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology (K.Z., S.-S.D., Y.G., S.-H.T., H.W., S.Y., J.D., T.-L.Y.), Xi'an Jiaotong University, Shaanxi, PR China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology (K.Z., S.-S.D., Y.G., S.-H.T., H.W., S.Y., J.D., T.-L.Y.), Xi'an Jiaotong University, Shaanxi, PR China
| | - Yan Guo
- Department of Trauma Surgery, Honghui Hospital, College of Medicine (K.Z., Y.G., P.-F.W., K.Z., H.-Z.X., W.H., T.-L.Y.), Xi'an Jiaotong University, Shaanxi, PR China.,Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology (K.Z., S.-S.D., Y.G., S.-H.T., H.W., S.Y., J.D., T.-L.Y.), Xi'an Jiaotong University, Shaanxi, PR China
| | - Shi-Hao Tang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology (K.Z., S.-S.D., Y.G., S.-H.T., H.W., S.Y., J.D., T.-L.Y.), Xi'an Jiaotong University, Shaanxi, PR China
| | - Hao Wu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology (K.Z., S.-S.D., Y.G., S.-H.T., H.W., S.Y., J.D., T.-L.Y.), Xi'an Jiaotong University, Shaanxi, PR China
| | - Shi Yao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology (K.Z., S.-S.D., Y.G., S.-H.T., H.W., S.Y., J.D., T.-L.Y.), Xi'an Jiaotong University, Shaanxi, PR China
| | - Peng-Fei Wang
- Department of Trauma Surgery, Honghui Hospital, College of Medicine (K.Z., Y.G., P.-F.W., K.Z., H.-Z.X., W.H., T.-L.Y.), Xi'an Jiaotong University, Shaanxi, PR China
| | - Kun Zhang
- Department of Trauma Surgery, Honghui Hospital, College of Medicine (K.Z., Y.G., P.-F.W., K.Z., H.-Z.X., W.H., T.-L.Y.), Xi'an Jiaotong University, Shaanxi, PR China
| | - Han-Zhong Xue
- Department of Trauma Surgery, Honghui Hospital, College of Medicine (K.Z., Y.G., P.-F.W., K.Z., H.-Z.X., W.H., T.-L.Y.), Xi'an Jiaotong University, Shaanxi, PR China
| | - Wei Huang
- Department of Trauma Surgery, Honghui Hospital, College of Medicine (K.Z., Y.G., P.-F.W., K.Z., H.-Z.X., W.H., T.-L.Y.), Xi'an Jiaotong University, Shaanxi, PR China
| | - Jian Ding
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology (K.Z., S.-S.D., Y.G., S.-H.T., H.W., S.Y., J.D., T.-L.Y.), Xi'an Jiaotong University, Shaanxi, PR China
| | - Tie-Lin Yang
- Department of Trauma Surgery, Honghui Hospital, College of Medicine (K.Z., Y.G., P.-F.W., K.Z., H.-Z.X., W.H., T.-L.Y.), Xi'an Jiaotong University, Shaanxi, PR China.,Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology (K.Z., S.-S.D., Y.G., S.-H.T., H.W., S.Y., J.D., T.-L.Y.), Xi'an Jiaotong University, Shaanxi, PR China
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Chen JB, Dong SS, Yao S, Duan YY, Hu WX, Chen H, Wang NN, Chen XF, Hao RH, Thynn HN, Guo MR, Zhang YJ, Rong Y, Chen YX, Zhou FL, Guo Y, Yang TL. Modeling circRNA expression pattern with integrated sequence and epigenetic features demonstrates the potential involvement of H3K79me2 in circRNA expression. Bioinformatics 2021; 37:3386. [PMID: 34430971 DOI: 10.1093/bioinformatics/btab510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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22
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Dong SS, Zhu DL, Zhou XR, Rong Y, Zeng M, Chen JB, Jiang F, Tuo XM, Feng Z, Yang TL, Guo Y. An Intronic Risk SNP rs12454712 for Central Obesity Acts As an Allele-Specific Enhancer To Regulate BCL2 Expression. Diabetes 2021; 70:1679-1688. [PMID: 34035043 DOI: 10.2337/db20-1151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 05/10/2021] [Indexed: 11/13/2022]
Abstract
Genome-wide association studies (GWAS) have reproducibly associated the single nucleotide polymorphism (SNP) rs12454712 with waist-to-hip ratio adjusted for BMI (WHRadjBMI), but the functional role underlying this intronic variant is unknown. Integrative genomic and epigenomic analyses supported rs12454712 as a functional independent variant. We further demonstrated that rs12454712 acted as an allele-specific enhancer regulating expression of its located gene BCL2 by using dual-luciferase reporter assays and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9. Specifically, the rs12454712-C allele can bind transcription factor ZNF329, which efficiently elevates the enhancer activity and increases BCL2 expression. Knocking down Bcl2 in 3T3-L1 cells led to the downregulation of adipogenic differentiation marker genes and increased cell apoptosis. A significant negative correlation between BCL2 expression in subcutaneous adipose tissues and obesity was observed. Our findings illustrate the molecular mechanisms behind the intronic SNP rs12454712 for central obesity, which would be a potential and promising target for developing appropriate therapies.
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Affiliation(s)
- Shan-Shan Dong
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Research Institute of Xi'an Jiaotong University, Hangzhou, Zhejiang, China
| | - Dong-Li Zhu
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xiao-Rong Zhou
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Yu Rong
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Mengqi Zeng
- Center for Mitochondrial Biology and Medicine, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Jia-Bin Chen
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Feng Jiang
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xiao-Mei Tuo
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Zhihui Feng
- Center for Mitochondrial Biology and Medicine, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Tie-Lin Yang
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Yan Guo
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
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Rong Y, Dong SS, Hu WX, Guo Y, Chen YX, Chen JB, Zhu DL, Chen H, Yang TL. DDRS: Detection of drug response SNPs specifically in patients receiving drug treatment. Comput Struct Biotechnol J 2021; 19:3650-3657. [PMID: 34257842 PMCID: PMC8254081 DOI: 10.1016/j.csbj.2021.06.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 06/16/2021] [Accepted: 06/16/2021] [Indexed: 12/15/2022] Open
Abstract
Detecting SNPs associated with drug efficacy or toxicity is helpful to facilitate personalized medicine. Previous studies usually find SNPs associated with clinical outcome only in patients received a specific treatment. However, without information from patients without drug treatment, it is possible that the detected SNPs are associated with patients' clinical outcome even without drug treatment. Here we aimed to detect drug response SNPs based on data from patients with and without drug treatment through combing the cox proportional-hazards model and pairwise Kaplan-Meier survival analysis. A pipeline named Detection of Drug Response SNPs (DDRS) was built and applied to TCGA breast cancer data including 363 patients with doxorubicin treatment and 321 patients without any drug treatment. We identified 548 doxorubicin associated SNPs. Drug response score derived from these SNPs were associated with drug-resistant level (indicated by IC50) of breast cancer cell lines. Enrichment analyses showed that these SNPs were enriched in active epigenetic regulation markers (e.g., H3K27ac). Compared with random genes, the cis-eQTL genes of these SNPs had a shorter protein-protein interaction distance to doxorubicin associated genes. In addition, linear discriminant analysis showed that the eQTL gene expression levels could be used to predict clinical outcome for patients with doxorubicin treatment (AUC = 0.738). Specifically, we identified rs2817101 as a drug response SNP for doxorubicin treatment. Higher expression level of its cis-eQTL gene GSTA1 is associated with poorer survival. This approach can also be applied to identify new drug associated SNPs in other cancers.
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Affiliation(s)
- Yu Rong
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China
| | - Shan-Shan Dong
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China
| | - Wei-Xin Hu
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China
| | - Yan Guo
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China
| | - Yi-Xiao Chen
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China
| | - Jia-Bin Chen
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China
| | - Dong-Li Zhu
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China
| | - Hao Chen
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China
| | - Tie-Lin Yang
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China.,National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, PR China
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24
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Yao S, Wu H, Ding JM, Wang ZX, Ullah T, Dong SS, Chen H, Guo Y. Transcriptome-wide association study identifies multiple genes associated with childhood body mass index. Int J Obes (Lond) 2021; 45:1105-1113. [PMID: 33627773 DOI: 10.1038/s41366-021-00780-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 01/14/2021] [Accepted: 02/01/2021] [Indexed: 01/31/2023]
Abstract
BACKGROUND Childhood obesity is one of the most common and costly nutritional problems with high heritability. The genetic mechanism of childhood obesity remains unclear. Here, we conducted a transcriptome-wide association study (TWAS) to identify novel genes for childhood obesity. METHODS By integrating the GWAS summary of childhood body mass index (BMI), we conducted TWAS analyses with pre-computed gene expression weights in 39 obesity priority tissues. The GWAS summary statistics of childhood BMI were derived from the early growth genetics consortium with 35,668 children from 20 studies. RESULTS We identified 15 candidate genes for childhood BMI after Bonferroni corrections. The most significant gene, ADCY3, was identified in 13 tissues, including adipose, brain, and blood. Interestingly, eight genes were only identified in the specific tissue, such as FAIM2 in the brain (P = 2.04 × 10-7) and fat mass and obesity-associated gene (FTO) in the muscle (P = 1.93 × 10-8). Compared with the TWAS results of adult BMI, we found that one gene TUBA1B with predominant influence only on childhood BMI in the muscle (P = 1.12 × 10-7). We evaluated the candidate genes by querying public databases and identified 12 genes functionally related to obesity phenotypes, including nine differentially expressed genes during the differentiation of human preadipocyte cells. The remaining genes (FAM150B, KNOP1, and LMBR1L) were regarded as novel candidate genes for childhood BMI. CONCLUSIONS Our study identified multiple candidate genes for childhood BMI, providing novel clues for understanding the genetic mechanism of childhood obesity.
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Affiliation(s)
- Shi Yao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Hao Wu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Jing-Miao Ding
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Zhuo-Xin Wang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Tahir Ullah
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Hao Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China.
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China.
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25
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Yao S, Wu H, Liu TT, Wang JH, Ding JM, Guo J, Rong Y, Ke X, Hao RH, Dong SS, Yang TL, Guo Y. Epigenetic Element-Based Transcriptome-Wide Association Study Identifies Novel Genes for Bipolar Disorder. Schizophr Bull 2021; 47:1642-1652. [PMID: 33772305 PMCID: PMC8530404 DOI: 10.1093/schbul/sbab023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Since the bipolar disorder (BD) signals identified by genome-wide association study (GWAS) often reside in the non-coding regions, understanding the biological relevance of these genetic loci has proven to be complicated. Transcriptome-wide association studies (TWAS) providing a powerful approach to identify novel disease risk genes and uncover possible causal genes at loci identified previously by GWAS. However, these methods did not consider the importance of epigenetic regulation in gene expression. Here, we developed a novel epigenetic element-based transcriptome-wide association study (ETWAS) that tested the effects of genetic variants on gene expression levels with the epigenetic features as prior and further mediated the association between predicted expression and BD. We conducted an ETWAS consisting of 20 352 cases and 31 358 controls and identified 44 transcriptome-wide significant hits. We found 14 conditionally independent genes, and 10 genes that did not previously implicate with BD were regarded as novel candidate genes, such as ASB16 in the cerebellar hemisphere (P = 9.29 × 10-8). We demonstrated that several genome-wide significant signals from the BD GWAS driven by genetically regulated expression, and NEK4 explained 90.1% of the GWAS signal. Additionally, ETWAS identified genes could explain heritability beyond that explained by GWAS-associated SNPs (P = 5.60 × 10-66). By querying the SNPs in the final models of identified genes in phenome databases, we identified several phenotypes previously associated with BD, such as schizophrenia and depression. In conclusion, ETWAS is a powerful method, and we identified several novel candidate genes associated with BD.
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Affiliation(s)
- Shi Yao
- National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi 710004, P. R. China,Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, P. R. China
| | - Hao Wu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, P. R. China
| | - Tong-Tong Liu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, P. R. China
| | - Jia-Hao Wang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, P. R. China
| | - Jing-Miao Ding
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, P. R. China
| | - Jing Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, P. R. China
| | - Yu Rong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, P. R. China
| | - Xin Ke
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, P. R. China
| | - Ruo-Han Hao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, P. R. China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, P. R. China
| | - Tie-Lin Yang
- National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi 710004, P. R. China,Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, P. R. China
| | - Yan Guo
- National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi 710004, P. R. China,Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, P. R. China,To whom correspondence should be addressed; tel: +86-29-62818386, fax: +86-29-62818386, e-mail:
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26
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Dong SS, Zhang K, Guo Y, Ding JM, Rong Y, Feng JC, Yao S, Hao RH, Jiang F, Chen JB, Wu H, Chen XF, Yang TL. Phenome-wide investigation of the causal associations between childhood BMI and adult trait outcomes: a two-sample Mendelian randomization study. Genome Med 2021; 13:48. [PMID: 33771188 PMCID: PMC8004431 DOI: 10.1186/s13073-021-00865-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 03/11/2021] [Indexed: 12/28/2022] Open
Abstract
Background Childhood obesity is reported to be associated with the risk of many diseases in adulthood. However, observational studies cannot fully account for confounding factors. We aimed to systematically assess the causal associations between childhood body mass index (BMI) and various adult traits/diseases using two-sample Mendelian randomization (MR). Methods After data filtering, 263 adult traits genetically correlated with childhood BMI (P < 0.05) were subjected to MR analyses. Inverse-variance weighted, MR-Egger, weighted median, and weighted mode methods were used to estimate the causal effects. Multivariable MR analysis was performed to test whether the effects of childhood BMI on adult traits are independent from adult BMI. Results We identified potential causal effects of childhood obesity on 60 adult traits (27 disease-related traits, 27 lifestyle factors, and 6 other traits). Higher childhood BMI was associated with a reduced overall health rating (β = − 0.10, 95% CI − 0.13 to − 0.07, P = 6.26 × 10−11). Specifically, higher childhood BMI was associated with increased odds of coronary artery disease (OR = 1.09, 95% CI 1.06 to 1.11, P = 4.28 × 10−11), essential hypertension (OR = 1.12, 95% CI 1.08 to 1.16, P = 1.27 × 10−11), type 2 diabetes (OR = 1.36, 95% CI 1.30 to 1.43, P = 1.57 × 10−34), and arthrosis (OR = 1.09, 95% CI 1.06 to 1.12, P = 8.80 × 10−9). However, after accounting for adult BMI, the detrimental effects of childhood BMI on disease-related traits were no longer present (P > 0.05). For dietary habits, different from conventional understanding, we found that higher childhood BMI was associated with low calorie density food intake. However, this association might be specific to the UK Biobank population. Conclusions In summary, we provided a phenome-wide view of the effects of childhood BMI on adult traits. Multivariable MR analysis suggested that the associations between childhood BMI and increased risks of diseases in adulthood are likely attributed to individuals remaining obese in later life. Therefore, ensuring that childhood obesity does not persist into later life might be useful for reducing the detrimental effects of childhood obesity on adult diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00865-3.
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Affiliation(s)
- Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Kun Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Jing-Miao Ding
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Yu Rong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Jun-Cheng Feng
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Shi Yao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Ruo-Han Hao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Feng Jiang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Jia-Bin Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Hao Wu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Xiao-Feng Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China. .,National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, 710004, China.
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27
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Yi D, Ding XB, Dong SS, Shao C, Zhao LJ. Clinical characteristics of adult-type annular pancreas: A case report. World J Clin Cases 2020; 8:5722-5728. [PMID: 33344566 PMCID: PMC7716324 DOI: 10.12998/wjcc.v8.i22.5722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 08/24/2020] [Accepted: 10/20/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Annular pancreas (AP) is a rare congenital abnormal rotation of the pancreas. AP rarely occurs in adults. Pancreatic tumors and ampullary tumors are related to AP, so the discovery and treatment of AP are essential.
CASE SUMMARY This study investigated the clinical manifestations, imaging features, complications, and treatment of six patients diagnosed with AP at the Department of Hepatobiliary and Pancreatic Surgery, First Hospital of Jilin University from January 2010 to June 2020. There were four males and two females, with an average age of 56.00 ± 9.86 years old. In this study, abdominal pain and jaundice were the main clinical manifestations. Imaging can show the “crocodile jaw sign” or “double bubble sign”.
CONCLUSION For patients with duodenal or biliary obstruction, physicians should give priority to AP when imaging examinations suggest that the duodenum is wrapped with tissue similar to the density of the pancreas. Symptomatic patients should actively undergo surgical treatment.
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Affiliation(s)
- Dan Yi
- Department of Hepatobiliary and Pancreatic Surgery, First Hospital of Jilin University, Changchun 130021, Jilin Province, China
| | - Xiao-Bo Ding
- Department of Radiology, First Hospital of Jilin University, Changchun 130021, Jilin Province, China
| | - Shan-Shan Dong
- Department of Hepatobiliary and Pancreatic Surgery, First Hospital of Jilin University, Changchun 130021, Jilin Province, China
| | - Chen Shao
- Department of Pathology, Beijing You’an Hospital, Beijing 100069, China
| | - Li-Jing Zhao
- Department of Rehabilitation, School of Nursing, Jilin University, Changchun 130021, Jilin Province, China
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28
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Chen YX, Rong Y, Jiang F, Chen JB, Duan YY, Dong SS, Zhu DL, Chen H, Yang TL, Dai Z, Guo Y. An integrative multi-omics network-based approach identifies key regulators for breast cancer. Comput Struct Biotechnol J 2020; 18:2826-2835. [PMID: 33133424 PMCID: PMC7585874 DOI: 10.1016/j.csbj.2020.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 09/13/2020] [Accepted: 10/01/2020] [Indexed: 02/06/2023] Open
Abstract
Although genome-wide association studies (GWASs) have successfully identified thousands of risk variants for human complex diseases, understanding the biological function and molecular mechanisms of the associated SNPs involved in complex diseases is challenging. Here we developed a framework named integrative multi-omics network-based approach (IMNA), aiming to identify potential key genes in regulatory networks by integrating molecular interactions across multiple biological scales, including GWAS signals, gene expression-based signatures, chromatin interactions and protein interactions from the network topology. We applied this approach to breast cancer, and prioritized key genes involved in regulatory networks. We also developed an abnormal gene expression score (AGES) signature based on the gene expression deviation of the top 20 rank-ordered genes in breast cancer. The AGES values are associated with genetic variants, tumor properties and patient survival outcomes. Among the top 20 genes, RNASEH2A was identified as a new candidate gene for breast cancer. Thus, our integrative network-based approach provides a genetic-driven framework to unveil tissue-specific interactions from multiple biological scales and reveal potential key regulatory genes for breast cancer. This approach can also be applied in other complex diseases such as ovarian cancer to unravel underlying mechanisms and help for developing therapeutic targets.
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Affiliation(s)
- Yi-Xiao Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China
| | - Yu Rong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China
| | - Feng Jiang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China
| | - Jia-Bin Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China
| | - Yuan-Yuan Duan
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China
| | - Dong-Li Zhu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China.,Research Institute of Xi'an Jiaotong University, Zhejiang Province 311215, PR China
| | - Hao Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China.,Research Institute of Xi'an Jiaotong University, Zhejiang Province 311215, PR China
| | - Zhijun Dai
- Department of Breast Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, PR China
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China
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Dong SS, He WM, Ji JJ, Zhang C, Guo Y, Yang TL. LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on variant call format files. Brief Bioinform 2020; 22:5939575. [PMID: 33126247 DOI: 10.1093/bib/bbaa227] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/04/2020] [Accepted: 08/21/2020] [Indexed: 11/14/2022] Open
Abstract
The triangular correlation heatmap aiming to visualize the linkage disequilibrium (LD) pattern and haplotype block structure of SNPs is ubiquitous component of population-based genetic studies. However, current tools suffered from the problem of time and memory consuming. Here, we developed LDBlockShow, an open source software, for visualizing LD and haplotype blocks from variant call format files. It is time and memory saving. In a test dataset with 100 SNPs from 60 000 subjects, it was at least 10.60 times faster and used only 0.03-13.33% of physical memory as compared with other tools. In addition, it could generate figures that simultaneously display additional statistical context (e.g. association P-values) and genomic region annotations. It can also compress the SVG files with a large number of SNPs and support subgroup analysis. This fast and convenient tool will facilitate the visualization of LD and haplotype blocks for geneticists.
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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
| | - Wei-Ming He
- Senior Bioinformatics Engineer in BGI Genomics
| | | | - Chi Zhang
- Senior Bioinformatics Engineer in BGI Genomics
| | - Yan Guo
- 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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30
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Chen JB, Dong SS, Yao S, Duan YY, Hu WX, Chen H, Wang NN, Chen XF, Hao RH, Thynn HN, Guo MR, Zhang YJ, Rong Y, Chen YX, Zhou FL, Guo Y, Yang TL. Modeling circRNA expression pattern with integrated sequence and epigenetic features demonstrates the potential involvement of H3K79me2 in circRNA expression. Bioinformatics 2020; 36:4739-4748. [PMID: 32539144 DOI: 10.1093/bioinformatics/btaa567] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 05/07/2020] [Accepted: 06/08/2020] [Indexed: 01/22/2023] Open
Abstract
MOTIVATION CircRNAs are an abundant class of non-coding RNAs with widespread, cell-/tissue-specific patterns. Previous work suggested that epigenetic features might be related to circRNA expression. However, the contribution of epigenetic changes to circRNA expression has not been investigated systematically. Here, we built a machine learning framework named CIRCScan, to predict circRNA expression in various cell lines based on the sequence and epigenetic features. RESULTS The predicted accuracy of the expression status models was high with area under the curve of receiver operating characteristic (ROC) values of 0.89-0.92 and the false-positive rates of 0.17-0.25. Predicted expressed circRNAs were further validated by RNA-seq data. The performance of expression-level prediction models was also good with normalized root-mean-square errors of 0.28-0.30 and Pearson's correlation coefficient r over 0.4 in all cell lines, along with Spearman's correlation coefficient ρ of 0.33-0.46. Noteworthy, H3K79me2 was highly ranked in modeling both circRNA expression status and levels across different cells. Further analysis in additional nine cell lines demonstrated a significant enrichment of H3K79me2 in circRNA flanking intron regions, supporting the potential involvement of H3K79me2 in circRNA expression regulation. AVAILABILITY AND IMPLEMENTATION The CIRCScan assembler is freely available online for academic use at https://github.com/johnlcd/CIRCScan. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jia-Bin Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Shi Yao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Yuan-Yuan Duan
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Wei-Xin Hu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Hao Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Nai-Ning Wang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Xiao-Feng Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Ruo-Han Hao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Hlaing Nwe Thynn
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Ming-Rui Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Yu-Jie Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Yu Rong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Yi-Xiao Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Fu-Ling Zhou
- Department of Hematopathology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Zhongnan Hospital of Wuhan University, Wuhan 430071, 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: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [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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Zhang C, Dong SS, Xu JY, He WM, Yang TL. PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. Bioinformatics 2020; 35:1786-1788. [PMID: 30321304 DOI: 10.1093/bioinformatics/bty875] [Citation(s) in RCA: 578] [Impact Index Per Article: 144.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/20/2018] [Accepted: 10/12/2018] [Indexed: 01/02/2023] Open
Abstract
MOTIVATION Linkage disequilibrium (LD) decay is of great interest in population genetic studies. However, no tool is available now to do LD decay analysis from variant call format (VCF) files directly. In addition, generation of pair-wise LD measurements for whole genome SNPs usually resulting in large storage wasting files. RESULTS We developed PopLDdecay, an open source software, for LD decay analysis from VCF files. It is fast and is able to handle large number of variants from sequencing data. It is also storage saving by avoiding exporting pair-wise results of LD measurements. Subgroup analyses are also supported. AVAILABILITY AND IMPLEMENTATION PopLDdecay is freely available at https://github.com/BGI-shenzhen/PopLDdecay.
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Affiliation(s)
- Chi Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China.,BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | | | - Wei-Ming He
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China.,BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
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Li M, Yao S, Duan YY, Zhang YJ, Guo Y, Niu HM, Dong SS, Qiu YS, Yang TL. Transcription Factor Enrichment Analysis in Enhancers Identifies EZH2 as a Susceptibility Gene for Osteoporosis. J Clin Endocrinol Metab 2020; 105:5675148. [PMID: 31833556 DOI: 10.1210/clinem/dgz270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 12/11/2019] [Indexed: 02/13/2023]
Abstract
PURPOSE Genome-wide association studies (GWASs) have identified hundreds of single nucleotide polymorphisms (SNPs) associated with osteoporosis. Most of these SNPs are noncoding variants and could be mapped to enhancers. Transcription factors (TFs) play important roles in gene regulation via enhancers harboring these SNPs; thus, we aimed to identify common regulatory TFs binding to enhancers associated with osteoporosis. METHODS We first annotated all the osteoporosis-related SNPs identified by GWASs to enhancers and conducted TF enrichment analyses to identify common TFs binding to osteoporosis-associated enhancers. We further conducted genetic association analyses between the identified TFs and bone mineral density (BMD) in a Han Chinese population. RESULTS After functional annotation, a total of 5081 osteoporosis-related SNPs were mapped to enhancers. TF enrichment analyses identified 2 significant TFs after multiple testing adjustments, which are EZH2 (Padj = .028) and NRSF (Padj = .038). We also found 1 SNP, rs111851041, in EZH2 was significantly associated with BMD both at the hip and spine after multiple testing adjustments (hip BMD: P = 4.32 × 10-4; spine BMD: P = 2.72 × 10-3). The expression of EZH2 decreased significantly from 12 to 48 hours of osteogenic differentiation. And functional validation showed that EZH2 was associated with osteoporosis-related phenotypes in knockout mice. CONCLUSIONS By conducting TF enrichment analyses, we identified EZH2 as a common TF binding to osteoporosis-associated enhancers, and EZH2 was also associated with BMD in a Chinese population. EZH2 is functionally related to bone phenotypes. The identified gene could provide new insight into osteoporosis pathophysiology and highlight opportunities for future clinical and pharmacological research on osteoporosis.
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Affiliation(s)
- Meng Li
- Department of Orthopedics, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, P.R. China
| | - Shi Yao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Yuan-Yuan Duan
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Yu-Jie Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, 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, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Hui-Min Niu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Yu-Sheng Qiu
- Department of Orthopedics, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, P.R. China
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
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Zhang J, Fu XX, Li RQ, Zhao X, Liu Y, Li MH, Zwaenepoel A, Ma H, Goffinet B, Guan YL, Xue JY, Liao YY, Wang QF, Wang QH, Wang JY, Zhang GQ, Wang ZW, Jia Y, Wang MZ, Dong SS, Yang JF, Jiao YN, Guo YL, Kong HZ, Lu AM, Yang HM, Zhang SZ, Van de Peer Y, Liu ZJ, Chen ZD. The hornwort genome and early land plant evolution. Nat Plants 2020; 6:107-118. [PMID: 32042158 PMCID: PMC7027989 DOI: 10.1038/s41477-019-0588-4] [Citation(s) in RCA: 145] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 12/20/2019] [Indexed: 05/10/2023]
Abstract
Hornworts, liverworts and mosses are three early diverging clades of land plants, and together comprise the bryophytes. Here, we report the draft genome sequence of the hornwort Anthoceros angustus. Phylogenomic inferences confirm the monophyly of bryophytes, with hornworts sister to liverworts and mosses. The simple morphology of hornworts correlates with low genetic redundancy in plant body plan, while the basic transcriptional regulation toolkit for plant development has already been established in this early land plant lineage. Although the Anthoceros genome is small and characterized by minimal redundancy, expansions are observed in gene families related to RNA editing, UV protection and desiccation tolerance. The genome of A. angustus bears the signatures of horizontally transferred genes from bacteria and fungi, in particular of genes operating in stress-response and metabolic pathways. Our study provides insight into the unique features of hornworts and their molecular adaptations to live on land.
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Affiliation(s)
- Jian Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xin-Xing Fu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rui-Qi Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiang Zhao
- PubBio-Tech Services Corporation, Wuhan, China
| | - Yang Liu
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
| | - Ming-He Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Arthur Zwaenepoel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Hong Ma
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Bernard Goffinet
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Yan-Long Guan
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jia-Yu Xue
- Center for Plant Diversity and Systematics, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yi-Ying Liao
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Qing-Feng Wang
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Qing-Hua Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jie-Yu Wang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Guo-Qiang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | | | - Yu Jia
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Mei-Zhi Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Shan-Shan Dong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Jian-Fen Yang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Yuan-Nian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Hong-Zhi Kong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - An-Ming Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | | | - Shou-Zhou Zhang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China.
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, Pretoria, South Africa.
- College of Horticulture, Nanjing Agricultural University, Nanjing, China.
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China.
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Zhi-Duan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.
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Yang TL, Shen H, Liu A, Dong SS, Zhang L, Deng FY, Zhao Q, Deng HW. A road map for understanding molecular and genetic determinants of osteoporosis. Nat Rev Endocrinol 2020; 16:91-103. [PMID: 31792439 PMCID: PMC6980376 DOI: 10.1038/s41574-019-0282-7] [Citation(s) in RCA: 176] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/18/2019] [Indexed: 12/16/2022]
Abstract
Osteoporosis is a highly prevalent disorder characterized by low bone mineral density and an increased risk of fracture, termed osteoporotic fracture. Notably, bone mineral density, osteoporosis and osteoporotic fracture are highly heritable; however, determining the genetic architecture, and especially the underlying genomic and molecular mechanisms, of osteoporosis in vivo in humans is still challenging. In addition to susceptibility loci identified in genome-wide association studies, advances in various omics technologies, including genomics, transcriptomics, epigenomics, proteomics and metabolomics, have all been applied to dissect the pathogenesis of osteoporosis. However, each technology individually cannot capture the entire view of the disease pathology and thus fails to comprehensively identify the underlying pathological molecular mechanisms, especially the regulatory and signalling mechanisms. A change to the status quo calls for integrative multi-omics and inter-omics analyses with approaches in 'systems genetics and genomics'. In this Review, we highlight findings from genome-wide association studies and studies using various omics technologies individually to identify mechanisms of osteoporosis. Furthermore, we summarize current studies of data integration to understand, diagnose and inform the treatment of osteoporosis. The integration of multiple technologies will provide a road map to illuminate the complex pathogenesis of osteoporosis, especially from molecular functional aspects, in vivo in humans.
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Affiliation(s)
- 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, China
| | - Hui Shen
- Center of Bioinformatics and Genomics, Department of Global Biostatistics and Data Science, Tulane University, New Orleans, LA, USA
| | - Anqi Liu
- Center of Bioinformatics and Genomics, Department of Global Biostatistics and Data Science, Tulane University, New Orleans, LA, USA
| | - 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, China
| | - Lei Zhang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Jiangsu, China
| | - Fei-Yan Deng
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Jiangsu, China
| | - Qi Zhao
- Department of Preventive Medicine, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Hong-Wen Deng
- Center of Bioinformatics and Genomics, Department of Global Biostatistics and Data Science, Tulane University, New Orleans, LA, USA.
- School of Basic Medical Science, Central South University, Changsha, China.
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Yao S, Dong SS, Ding JM, Rong Y, Zhang YJ, Chen H, Chen JB, Chen YX, Yan H, Dai Z, Guo Y. Sex-specific SNP-SNP interaction analyses within topologically associated domains reveals ANGPT1 as a novel tumor suppressor gene for lung cancer. Genes Chromosomes Cancer 2020; 59:13-22. [PMID: 31385379 DOI: 10.1002/gcc.22793] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 07/16/2019] [Accepted: 07/22/2019] [Indexed: 01/24/2023] Open
Abstract
Genetic interaction has been recognized to be an important cause of the missing heritability. The topologically associating domain (TAD) is a self-interacting genomic region, and the DNA sequences within a TAD physically interact with each other more frequently. Sex differences influence cancer susceptibility at the genetic level. Here, we performed both regular and sex-specific genetic interaction analyses within TAD to identify susceptibility genes for lung cancer in 5204 lung cancer patients and 7389 controls. We found that one SNP pair, rs4262299-rs1654701, was associated with lung cancer in women after multiple testing corrections (combined P = 8.52 × 10-9 ). Single-SNP analyses did not detect significant association signals for these two SNPs. Both identified SNPs are located in the intron region of ANGPT1. We further found that 5% of nonsmall cell lung cancer patients have an alteration in ANGPT1, indicated the potential role of ANGPT1 in the neoplastic progression in lung cancer. The expression of ANGPT1 was significantly down-regulated in patients in lung squamous cell carcinoma and lung adenocarcinoma. We checked the interaction effect on the ANGPT1 expression and lung cancer and found that the minor allele "G" of rs1654701 increased ANGPT1 gene expression and decreased lung cancer risk with the increased dosage of "A" of rs4262299, which consistent with the tumor suppressor function of ANGPT1. Survival analyses found that the high expression of ANGPT1 was individually associated with a higher survival probability in lung cancer patients. In summary, our results suggest that ANGPT1 may be a novel tumor suppressor gene for lung cancer.
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Affiliation(s)
- Shi Yao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - 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, Shaanxi, P. R. China
| | - Jing-Miao Ding
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Yu Rong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Yu-Jie Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Hao Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Jia-Bin Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Yi-Xiao Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Han Yan
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Zhijun Dai
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, 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, Shaanxi, P. R. China
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Thynn HN, Chen XF, Hu WX, Duan YY, Zhu DL, Chen H, Wang NN, Chen HH, Rong Y, Lu BJ, Yang M, Jiang F, Dong SS, Guo Y, Yang TL. An Allele-Specific Functional SNP Associated with Two Systemic Autoimmune Diseases Modulates IRF5 Expression by Long-Range Chromatin Loop Formation. J Invest Dermatol 2019; 140:348-360.e11. [PMID: 31421124 DOI: 10.1016/j.jid.2019.06.147] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 06/02/2019] [Accepted: 06/18/2019] [Indexed: 02/07/2023]
Abstract
Both systemic lupus erythematosus (SLE) and systemic sclerosis (SSc) are autoimmune diseases sharing similar genetic backgrounds. Genome-wide association studies have constantly disclosed numerous genetic variants conferring to both disease risks at 7q32.1, but the functional mechanisms underlying them are still largely unknown. Through a series of bioinformatics and functional analyses, we prioritized a potential independent functional single-nucleotide polymorphism (rs13239597) within TNPO3 promoter region, residing in a putative enhancer element and validated that IRF5 is the distal target gene (∼118 kb) of rs13239597, which is a key regulator involved in pathogenic autoantibody dysregulation, increasing risk of both SLE and SSc. We experimentally validated the long-range chromatin interactions between rs13239597 and IRF5 using chromosome conformation capture assay. We further demonstrated that rs13239597-A acted as an allele-specific enhancer regulating IRF5 expression, independently of TNPO3 by using dual-luciferase reporter assays and CRISPR-Cas9. Particularly, the transcription factor EVI1 could preferentially bind to rs13239597-A allele and increase the enhancer activity to regulate IRF5 expression. Taken together, our results uncovered a mechanistic insight of a noncoding functional variant acting as an allele-specific distal enhancer to directly modulate IRF5 expression, which might obligate in understanding of complex genetic architectures of SLE and SSc pathogenesis.
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Affiliation(s)
- Hlaing Nwe Thynn
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Xiao-Feng Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Wei-Xin Hu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Yuan-Yuan Duan
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Dong-Li Zhu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Hao Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Nai-Ning Wang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Huan-Huan Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Yu Rong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Bing-Jie Lu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Man Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Feng Jiang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - 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, Shaanxi 710049, 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, Shaanxi 710049, 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, Shaanxi 710049, 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Niu HM, Yang P, Chen HH, Hao RH, Dong SS, Yao S, Chen XF, Yan H, Zhang YJ, Chen YX, Jiang F, Yang TL, Guo Y. Comprehensive functional annotation of susceptibility SNPs prioritized 10 genes for schizophrenia. Transl Psychiatry 2019; 9:56. [PMID: 30705251 PMCID: PMC6355777 DOI: 10.1038/s41398-019-0398-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 12/27/2018] [Accepted: 01/10/2019] [Indexed: 12/18/2022] Open
Abstract
Nearly 95% of susceptibility SNPs identified by genome-wide association studies (GWASs) are located in non-coding regions, which causes a lot of difficulty in deciphering their biological functions on disease pathogenesis. Here, we aimed to conduct a comprehensive functional annotation for all the schizophrenia susceptibility loci obtained from GWASs. Considering varieties of epigenomic regulatory elements, we annotated all 22,688 acquired susceptibility SNPs according to their genomic positions to obtain functional SNPs. The comprehensive annotation indicated that these functional SNPs are broadly involved in diverse biological processes. Histone modification enrichment showed that H3K27ac, H3K36me3, H3K4me1, and H3K4me3 were related to the development of schizophrenia. Transcription factors (TFs) prediction, methylation quantitative trait loci (meQTL) analyses, expression quantitative trait loci (eQTL) analyses, and proteomic quantitative trait loci analyses (pQTL) identified 447 target protein-coding genes. Subsequently, differential expression analyses between schizophrenia cases and controls, nervous system phenotypes from mouse models, and protein-protein interaction with known schizophrenia-related pathways and genes were carried out with our target genes. We finaly prioritized 10 target genes for schizophrenia (CACNA1C, CLU, CSNK2B, GABBR1, GRIN2A, MAPK3, NOTCH4, SRR, TNF, and SYNGAP1). Our results may serve as an encyclopedia of schizophrenia susceptibility SNPs and offer holistic guides for post-GWAS functional experiments.
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Affiliation(s)
- Hui-Min Niu
- 0000 0001 0599 1243grid.43169.39Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, 710049 Xi’an, China
| | - Ping Yang
- grid.489086.bDepartment of Psychiatry, Hunan Brain Hospital, Changsha, Hunan Province China
| | - Huan-Huan Chen
- 0000 0001 0599 1243grid.43169.39Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, 710049 Xi’an, China
| | - Ruo-Han Hao
- 0000 0001 0599 1243grid.43169.39Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, 710049 Xi’an, China
| | - Shan-Shan Dong
- 0000 0001 0599 1243grid.43169.39Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, 710049 Xi’an, China
| | - Shi Yao
- 0000 0001 0599 1243grid.43169.39Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, 710049 Xi’an, China
| | - Xiao-Feng Chen
- 0000 0001 0599 1243grid.43169.39Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, 710049 Xi’an, China
| | - Han Yan
- 0000 0001 0599 1243grid.43169.39Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, 710049 Xi’an, China
| | - Yu-Jie Zhang
- 0000 0001 0599 1243grid.43169.39Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, 710049 Xi’an, China
| | - Yi-Xiao Chen
- 0000 0001 0599 1243grid.43169.39Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, 710049 Xi’an, China
| | - Feng Jiang
- 0000 0001 0599 1243grid.43169.39Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, 710049 Xi’an, China
| | - Tie-Lin Yang
- 0000 0001 0599 1243grid.43169.39Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, 710049 Xi’an, China
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, 710049, Xi'an, China.
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Chen YX, Guo Y, Dong SS, Chen XF, Chen JB, Zhang YJ, Yao S, Thynn HN, Zhi L, Yang TL. Runs of homozygosity associate with decreased risks of lung cancer in never-smoking East Asian females. J Cancer 2018; 9:3858-3866. [PMID: 30410588 PMCID: PMC6218761 DOI: 10.7150/jca.22855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 02/24/2018] [Indexed: 12/14/2022] Open
Abstract
Although genome-wide association studies (GWASs) have identified some risk single-nucleotide polymorphisms in East Asian never-smoking females, the unexplained missing heritability is still required to be investigated. Runs of homozygosity (ROHs) are thought to be a type of genetic variation acting on human complex traits and diseases. We detected ROHs in 8,881 East Asian never-smoking women. The summed ROHs were used to fit a logistic regression model which noteworthily revealed a significant association between ROHs and the decreased risk of lung cancer (P < 0.05). We identified 4 common ROHs regions located at 2p22.1, which were significantly associated with decreased risk of lung cancer (P = 2.00 × 10-4 - 1.35 × 10-4). Functional annotation was conducted to investigate the regulatory function of ROHs. The common ROHs were overlapped with potential regulatory elements, such as active epigenome elements and chromatin states in lung-derived cell lines. SOS1 and ARHGEF33 were significantly up-regulated as the putative target genes of the identified ROHs in lung cancer samples according to the analysis of differently expressed genes. Our results suggest that ROHs could act as recessive contributing factors and regulatory elements to influence the risk of lung cancer in never-smoking East Asian females.
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Affiliation(s)
- Yi-Xiao Chen
- Department of Joint Surgery, Honghui Hospital; The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Xi'an Jiaotong University, Xi'an, P. R. China.,Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710049, 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, Shaanxi Province, 710049, P. R. China
| | - 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, Shaanxi Province, 710049, P. R. China
| | - Xiao-Feng Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710049, P. R. China
| | - Jia-Bin Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710049, P. R. China
| | - Yu-Jie Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710049, P. R. China
| | - Shi Yao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710049, P. R. China
| | - Hlaing Nwe Thynn
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710049, P. R. China
| | - Liqiang Zhi
- Department of Joint Surgery, Honghui Hospital; The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Tie-Lin Yang
- Department of Joint Surgery, Honghui Hospital; The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Xi'an Jiaotong University, Xi'an, P. R. China.,Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710049, P. R. China
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Yao ZX, Yang JF, Liu Y, Dong SS, Wu H, Zhang SZ. The complete chloroplast genome of Magnolia sinostellata (Magnoliaceae), a rare and endangered species of China. Mitochondrial DNA B Resour 2018; 3:742-743. [PMID: 33474307 PMCID: PMC7800173 DOI: 10.1080/23802359.2018.1481794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 05/09/2018] [Indexed: 11/02/2022] Open
Abstract
Magnolia sinostellata Chiu & Chen is a rare and endangered species endemic to subtropical China. Here we assembled and annotated the complete chloroplast (cp) genome of M. sinostellata. The chloroplast genome of M. sinostellata is 160,076 bp in length and encodes 79 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosomal RNA (rRNA) genes. The maximum-likelihood (ML) phylogenetic analysis result reveals that M. sinostellata is most closely related to M. biondii.
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Affiliation(s)
- Zhang-Xiu Yao
- College of Life Sciences, South China Agricultural University, Guangzhou, China
- Fairy Lake Botanical Garden Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Jian-Fen Yang
- Fairy Lake Botanical Garden Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Yang Liu
- Fairy Lake Botanical Garden Shenzhen & Chinese Academy of Sciences, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
| | - Shan-Shan Dong
- Fairy Lake Botanical Garden Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Hong Wu
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Shou-Zhou Zhang
- Fairy Lake Botanical Garden Shenzhen & Chinese Academy of Sciences, Shenzhen, China
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Zhu DL, Chen XF, Hu WX, Dong SS, Lu BJ, Rong Y, Chen YX, Chen H, Thynn HN, Wang NN, Guo Y, Yang TL. Multiple Functional Variants at 13q14 Risk Locus for Osteoporosis Regulate RANKL Expression Through Long-Range Super-Enhancer. J Bone Miner Res 2018. [PMID: 29528523 DOI: 10.1002/jbmr.3419] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
RANKL is a key regulator involved in bone metabolism, and a drug target for osteoporosis. The clinical diagnosis and assessment of osteoporosis are mainly based on bone mineral density (BMD). Previous powerful genomewide association studies (GWASs) have identified multiple intergenic single-nucleotide polymorphisms (SNPs) located over 100 kb upstream of RANKL and 65 kb downstream of AKAP11 at 13q14.11 for osteoporosis. Whether these SNPs exert their roles on osteoporosis through RANKL is unknown. In this study, we conducted integrative analyses combining expression quantitative trait locus (eQTL), genomic chromatin interaction (high-throughput chromosome conformation capture [Hi-C]), epigenetic annotation, and a series of functional assays. The eQTL analysis identified six potential functional SNPs (rs9533090, rs9594738, r8001611, rs9533094, rs9533095, and rs9594759) exclusively correlated with RANKL gene expression (p < 0.001) at 13q14.11. Co-localization analyses suggested that eQTL signal for RANKL and BMD-GWAS signal shared the same causal variants. Hi-C analysis and functional annotation further validated that the first five osteoporosis SNPs are located in a super-enhancer region to regulate the expression of RANKL via long-range chromosomal interaction. Particularly, dual-luciferase assay showed that the region harboring rs9533090 in the super-enhancer has the strongest enhancer activity, and rs9533090 is an allele-specific regulatory SNP. Furthermore, deletion of the region harboring rs9533090 using CRISPR/Cas9 genome editing significantly reduced RANKL expression in both mRNA level and protein level. Finally, we found that the rs9533090-C robustly recruits transcription factor NFIC, which efficiently elevates the enhancer activity and increases the RANKL expression. In summary, we provided a feasible method to identify regulatory noncoding SNPs to distally regulate their target gene underlying the pathogenesis of osteoporosis by using bioinformatics data analyses and experimental validation. Our findings would be a potential and promising therapeutic target for precision medicine in osteoporosis. © 2018 American Society for Bone and Mineral Research.
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Affiliation(s)
- Dong-Li Zhu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Shaanxi, Xi'an, People's Republic of China
| | - Xiao-Feng Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Shaanxi, Xi'an, People's Republic of China
| | - Wei-Xin Hu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Shaanxi, Xi'an, People's Republic of China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Shaanxi, Xi'an, People's Republic of China
| | - Bing-Jie Lu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Shaanxi, Xi'an, People's Republic of China
| | - Yu Rong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Shaanxi, Xi'an, People's Republic of China
| | - Yi-Xiao Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Shaanxi, Xi'an, People's Republic of China
| | - Hao Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Shaanxi, Xi'an, People's Republic of China
| | - Hlaing Nwe Thynn
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Shaanxi, Xi'an, People's Republic of China
| | - Nai-Ning Wang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Shaanxi, Xi'an, People's Republic of China
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Shaanxi, Xi'an, People's Republic of China
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Shaanxi, Xi'an, People's Republic of China
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Chen XF, Zhu DL, Yang M, Hu WX, Duan YY, Lu BJ, Rong Y, Dong SS, Hao RH, Chen JB, Chen YX, Yao S, Thynn HN, Guo Y, Yang TL. An Osteoporosis Risk SNP at 1p36.12 Acts as an Allele-Specific Enhancer to Modulate LINC00339 Expression via Long-Range Loop Formation. Am J Hum Genet 2018; 102:776-793. [PMID: 29706346 PMCID: PMC5986728 DOI: 10.1016/j.ajhg.2018.03.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 02/28/2018] [Indexed: 01/10/2023] Open
Abstract
Genome-wide association studies (GWASs) have reproducibly associated variants within intergenic regions of 1p36.12 locus with osteoporosis, but the functional roles underlying these noncoding variants are unknown. Through an integrative functional genomic and epigenomic analyses, we prioritized rs6426749 as a potential causal SNP for osteoporosis at 1p36.12. Dual-luciferase assay and CRISPR/Cas9 experiments demonstrate that rs6426749 acts as a distal allele-specific enhancer regulating expression of a lncRNA (LINC00339) (∼360 kb) via long-range chromatin loop formation and that this loop is mediated by CTCF occupied near rs6426749 and LINC00339 promoter region. Specifically, rs6426749-G allele can bind transcription factor TFAP2A, which efficiently elevates the enhancer activity and increases LINC00339 expression. Downregulation of LINC00339 significantly increases the expression of CDC42 in osteoblast cells, which is a pivotal regulator involved in bone metabolism. Our study provides mechanistic insight into how a noncoding SNP affects osteoporosis by long-range interaction, a finding that could indicate promising therapeutic targets for osteoporosis.
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Affiliation(s)
- Xiao-Feng Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P. R. China
| | - Dong-Li Zhu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P. R. China
| | - Man Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P. R. China
| | - Wei-Xin Hu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P. R. China
| | - Yuan-Yuan Duan
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P. R. China
| | - Bing-Jie Lu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P. R. China
| | - Yu Rong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P. R. China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P. R. China
| | - Ruo-Han Hao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P. R. China
| | - Jia-Bin Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P. R. China
| | - Yi-Xiao Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P. R. China
| | - Shi Yao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P. R. China
| | - Hlaing Nwe Thynn
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P. R. China
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P. R. China.
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P. R. China.
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Dong SS, Yao S, Chen YX, Guo Y, Zhang YJ, Niu HM, Hao RH, Shen H, Tian Q, Deng HW, Yang TL. Detecting epistasis within chromatin regulatory circuitry reveals CAND2 as a novel susceptibility gene for obesity. Int J Obes (Lond) 2018; 43:450-456. [PMID: 29717274 DOI: 10.1038/s41366-018-0069-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/14/2018] [Accepted: 02/13/2018] [Indexed: 01/03/2023]
Abstract
BACKGROUND Genome-wide association studies have identified many susceptibility loci for obesity. However, missing heritability problem is still challenging and ignorance of genetic interactions is believed to be an important cause. Current methods for detecting interactions usually do not consider regulatory elements in non-coding regions. Interaction analyses within chromatin regulatory circuitry may identify new susceptibility loci. METHODS We developed a pipeline named interaction analyses within chromatin regulatory circuitry (IACRC), to identify genetic interactions impacting body mass index (BMI). Potential interacting SNP pairs were obtained based on Hi-C datasets, PreSTIGE (Predicting Specific Tissue Interactions of Genes and Enhancers) algorithm, and super enhancer regions. SNP × SNP analyses were next performed in three GWAS datasets, including 2286 unrelated Caucasians from Kansas City, 3062 healthy Caucasians from the Gene Environment Association Studies initiative, and 3164 Hispanic subjects from the Women's Health Initiative. RESULTS A total of 16,643,227 SNP × SNP analyses were performed. Meta-analyses showed that two SNP pairs, rs6808450-rs9813534 (combined P = 2.39 × 10-9) and rs6808450-rs3773306 (combined P = 2.89 × 10-9) were associated with BMI after multiple testing corrections. Single-SNP analyses did not detect significant association signals for these three SNPs. In obesity relevant cells, rs6808450 is located in intergenic enhancers, while rs9813534 and rs3773306 are located in the region of strong transcription regions of CAND2 and RPL32, respectively. The expression of CAND2 was significantly downregulated after the differentiation of human Simpson-Golabi-Behmel syndrome (SGBS) preadipocyte cells (P = 0.0241). Functional validation in the International Mouse Phenotyping Consortium database showed that CAND2 was associated with increased lean body mass and decreased total body fat amount. CONCLUSIONS Detecting epistasis within chromatin regulatory circuitry identified CAND2 as a novel obesity susceptibility gene. We hope IACRC could facilitate the interaction analyses for complex diseases and offer new insights into solving the missing heritability problem.
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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, 710049, People's Republic of China
| | - Shi Yao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Yi-Xiao Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of 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, 710049, People's Republic of China
| | - Yu-Jie Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Hui-Min Niu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Ruo-Han Hao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Hui Shen
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Qing Tian
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Hong-Wen Deng
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - 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, 710049, People's Republic of China.
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Li JB, Ruan YY, Hu B, Dong SS, Bi TN, Lin A, Yan WH. Importance of the plasma soluble HLA-G levels for prognostic stratification with traditional prognosticators in colorectal cancer. Oncotarget 2018; 8:48854-48862. [PMID: 28415627 PMCID: PMC5564730 DOI: 10.18632/oncotarget.16457] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 03/13/2017] [Indexed: 01/14/2023] Open
Abstract
An increased peripheral soluble HLA-G (sHLA-G) expression has been observed in various malignancies while its prognostic significance was rather limited. In this study, the prognostic value of plasma sHLA-G in 178 colorectal cancer (CRC) patients was investigated. sHLA-G levels were analyzed by specific enzyme-linked immunosorbent assay. Data showed sHLA-G levels were significantly increased in CRC patients compared with normal controls (36.8 U/ml vs 25.4 U/ml, p = 0.009). sHLA-G in the died were obviously higher than that of alive CRC patients (46.8 U/ml vs 27.4 U/ml, p = 0.012). Patients with sHLA-G above median levels (≥ 36.8 U/ml, sHLA-Ghigh) had a significantly shorter survival time than those with sHLA-Glow (< 36.8 U/ml, p < 0.001), and sHLA-G could be an independent prognostic factor for CRC patients. With stratification of clinical parameters in survival by sHLA-Glow and sHLA-Ghigh, sHLA-G exhibited a significant predictive value for CRC patients of the female (p = 0.036), the elder (p = 0.009), advanced tumor burden (T3 + 4, p = 0.038), regional lymph node status (N0, p = 0.041), both metastasis status (M0, p = 0.014) and (M1, p=0.018), and clinical stage (I + II, p = 0.018), respectively. Summary, our data demonstrated for the first time that sHLA-G levels is an independent prognosis factor and improves the prognostic stratification offered by traditional prognosticators in CRC patients.
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Affiliation(s)
- Jing-Bo Li
- Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang, People's Republic of China
| | - Yan-Yun Ruan
- Human Tissue Bank, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang, People's Republic of China
| | - Bin Hu
- Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang, People's Republic of China
| | - Shan-Shan Dong
- Human Tissue Bank, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang, People's Republic of China
| | - Tie-Nan Bi
- Department of Gastrointestinal Surgery, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang, People's Republic of China
| | - Aifen Lin
- Human Tissue Bank, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang, People's Republic of China
| | - Wei-Hua Yan
- Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang, People's Republic of China.,Department of Laboratory Medicine, Xianju People's Hospital, Xianju, Zhejiang, People's Republic of China
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Hao RH, Gao JL, Li M, Huang W, Zhu DL, Thynn HN, Dong SS, Guo Y. Association between fibroblast growth factor 21 and bone mineral density in adults. Endocrine 2018; 59:296-303. [PMID: 29299795 DOI: 10.1007/s12020-017-1507-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 12/19/2017] [Indexed: 10/18/2022]
Abstract
PURPOSE Animal-based studies have reported a decrease in bone mass resulting from high level of fibroblast growth factor 21 (FGF21). However, the correlation between plasma FGF21 levels and bone mineral density (BMD) is paradoxical in previous human-based studies, and the associations between FGF21 gene polymorphisms and BMD haven't been reported yet. Therefore, here, we evaluated plasma FGF21 levels with sufficient study samples, and performed genetic association test to reveal the physiological and genetic role of FGF21 on BMD in adults. METHODS Plasma and genetic samples containing 168 and 569 Han Chinese subjects, respectively, were employed in this study. Fasting plasma FGF21 levels were determined using enzyme-linked immunosorbent assay (ELISA). Regional BMD values were measured by dual energy X-ray absorptiometry (DXA). Five variants of FGF21 gene were successfully genotyped. RESULTS Physiological association suggested that plasma FGF21 levels were inversely correlated with BMD in femoral neck (Neck-BMD: P = 0.039) and Ward's triangle (Ward's-BMD: P = 0.002) of hip region. A FGF21 gene variant, rs490942, was significantly associated with the increase of Ward's-BMD in total (P = 0.027) and female (P = 0.016) cohorts, as well as Neck-BMD in female cohort (P = 7.45 × 10-3). Meanwhile, eQTL results indicated that this SNP was related to the decreased level of FGF21 gene expression. CONCLUSIONS Taking together from both physiological and genetic levels, we suggest that FGF21 is inversely associated with regional BMD. And we haven't observed sex-specific effect in this study.
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Affiliation(s)
- Ruo-Han Hao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Jun-Ling Gao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Meng Li
- Departments of Orthopaedics, the First Affiliated Hospital, School of Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Wei Huang
- Department of Trauma Surgery, Honghui Hospital, College of Medicine, Xi'an Jiaotong University, Xi'an, 710054, China
| | - Dong-Li Zhu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Hlaing Nwe Thynn
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - 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, 710049, 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, 710049, China.
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Liu XY, Dai XH, Zou W, Yu XP, Teng W, Wang Y, Yu WW, Ma HH, Chen QX, Liu P, Guan RQ, Dong SS. Acupuncture through Baihui (DU20) to Qubin (GB7) mitigates neurological impairment after intracerebral hemorrhage. Neural Regen Res 2018; 13:1425-1432. [PMID: 30106055 PMCID: PMC6108213 DOI: 10.4103/1673-5374.235298] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Inflammation plays an important role in nerve defects caused by intracerebral hemorrhage. Repairing brain damage by inhibiting the macrophage-inducible C-type lectin/spleen tyrosine kinase (Mincle/Syk) signaling pathway is a potential new target for treating cerebral hemorrhage. In this study, we aimed to determine whether acupuncture through Baihui (DU20) to Qubin (GB7) is an effective treatment for intracerebral hemorrhage through the Mincle/Syk signaling pathway. An intracerebral hemorrhage rat model was established by autologous blood infusion into the caudate nucleus. Acupuncture through Baihui to Qubin was performed for 30 minutes, once every 12 hours, for a total of three times. Piceatannol (34.62 mg/kg), a Syk inhibitor, was intraperitoneally injected as a control. Modified neurological severity score was used to assess neurological function. Brain water content was measured. Immunohistochemistry and western blot assay were used to detect immunoreactivity and protein expression levels of Mincle, Syk, and CARD9. Real-time polymerase chain reaction was used to determine interleukin-1β mRNA levels. Hematoxylin-eosin staining was performed to observe histopathological changes. Our results showed that acupuncture through Baihui to Qubin remarkably improved neurological function and brain water content, and inhibited immunoreactivity and expression of Mincle, Syk, CARD9, and interkeukin-1β. Moreover, this effect was similar to piceatannol. These findings suggest that acupuncture through Baihui to Qubin can improve neurological impairment after cerebral hemorrhage by inhibiting the Mincle/Syk signaling pathway.
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Affiliation(s)
- Xiao-Ying Liu
- Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang Province, China
| | - Xiao-Hong Dai
- The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang Province, China
| | - Wei Zou
- The First Affiliated Hospital of Heilongjiang University of Chinese Medicine; Clinical Key Laboratory of Integrated Traditional Chinese and Western Medicine of Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang Province, China
| | - Xue-Ping Yu
- The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang Province, China
| | - Wei Teng
- The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang Province, China
| | - Ying Wang
- Department of Pharmacology of Dali University, Dali, Yunnan Province, China
| | - Wei-Wei Yu
- The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang Province, China
| | - Hui-Hui Ma
- The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang Province, China
| | - Qiu-Xin Chen
- The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang Province, China
| | - Peng Liu
- Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang Province, China
| | - Rui-Qiao Guan
- Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang Province, China
| | - Shan-Shan Dong
- Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang Province, China
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Dong SS, Shao WZ, Yang L, Ye HJ, Zhen L. Surface characterization and degradation behavior of polyimide films induced by coupling irradiation treatment. RSC Adv 2018; 8:28152-28160. [PMID: 35542697 PMCID: PMC9084296 DOI: 10.1039/c8ra05744c] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 07/31/2018] [Indexed: 12/13/2022] Open
Abstract
Schematic of irradiation-load-heating coupling treatment and degradation process of polyimide film.
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Affiliation(s)
- Shan-Shan Dong
- School of Materials Science and Engineering
- Harbin Institute of Technology
- Harbin
- China
| | - Wen-Zhu Shao
- School of Materials Science and Engineering
- Harbin Institute of Technology
- Harbin
- China
| | - Li Yang
- School of Materials Science and Engineering
- Harbin Institute of Technology
- Harbin
- China
| | - Hui-Jian Ye
- Institute of Polymer Materials and Engineering
- College of Materials Science and Engineering
- Zhejiang University of Technology
- Hangzhou
- China
| | - Liang Zhen
- School of Materials Science and Engineering
- Harbin Institute of Technology
- Harbin
- China
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Yao S, Guo Y, Dong SS, Hao RH, Chen XF, Chen YX, Chen JB, Tian Q, Deng HW, Yang TL. Regulatory element-based prediction identifies new susceptibility regulatory variants for osteoporosis. Hum Genet 2017. [PMID: 28634715 DOI: 10.1007/s00439-017-1825-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Despite genome-wide association studies (GWASs) have identified many susceptibility genes for osteoporosis, it still leaves a large part of missing heritability to be discovered. Integrating regulatory information and GWASs could offer new insights into the biological link between the susceptibility SNPs and osteoporosis. We generated five machine learning classifiers with osteoporosis-associated variants and regulatory features data. We gained the optimal classifier and predicted genome-wide SNPs to discover susceptibility regulatory variants. We further utilized Genetic Factors for Osteoporosis Consortium (GEFOS) and three in-house GWASs samples to validate the associations for predicted positive SNPs. The random forest classifier performed best among all machine learning methods with the F1 score of 0.8871. Using the optimized model, we predicted 37,584 candidate SNPs for osteoporosis. According to the meta-analysis results, a list of regulatory variants was significantly associated with osteoporosis after multiple testing corrections and contributed to the expression of known osteoporosis-associated protein-coding genes. In summary, combining GWASs and regulatory elements through machine learning could provide additional information for understanding the mechanism of osteoporosis. The regulatory variants we predicted will provide novel targets for etiology research and treatment of osteoporosis.
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Affiliation(s)
- Shi Yao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, People's Republic of 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, Shaanxi, 710049, People's Republic of China
| | - 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, Shaanxi, 710049, People's Republic of China
| | - Ruo-Han Hao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, People's Republic of China
| | - Xiao-Feng Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, People's Republic of China
| | - Yi-Xiao Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, People's Republic of China
| | - Jia-Bin Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, People's Republic of China
| | - Qing Tian
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Hong-Wen Deng
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - 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, Shaanxi, 710049, People's Republic of China.
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