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Xu Y, Huang F, Guo W, Feng K, Zhu L, Zeng Z, Huang T, Cai YD. Characterization of chromatin accessibility patterns in different mouse cell types using machine learning methods at single-cell resolution. Front Genet 2023; 14:1145647. [PMID: 36936430 PMCID: PMC10014730 DOI: 10.3389/fgene.2023.1145647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
Chromatin accessibility is a generic property of the eukaryotic genome, which refers to the degree of physical compaction of chromatin. Recent studies have shown that chromatin accessibility is cell type dependent, indicating chromatin heterogeneity across cell lines and tissues. The identification of markers used to distinguish cell types at the chromosome level is important to understand cell function and classify cell types. In the present study, we investigated transcriptionally active chromosome segments identified by sci-ATAC-seq at single-cell resolution, including 69,015 cells belonging to 77 different cell types. Each cell was represented by existence status on 20,783 genes that were obtained from 436,206 active chromosome segments. The gene features were deeply analyzed by Boruta, resulting in 3897 genes, which were ranked in a list by Monte Carlo feature selection. Such list was further analyzed by incremental feature selection (IFS) method, yielding essential genes, classification rules and an efficient random forest (RF) classifier. To improve the performance of the optimal RF classifier, its features were further processed by autoencoder, light gradient boosting machine and IFS method. The final RF classifier with MCC of 0.838 was constructed. Some marker genes such as H2-Dmb2, which are specifically expressed in antigen-presenting cells (e.g., dendritic cells or macrophages), and Tenm2, which are specifically expressed in T cells, were identified in this study. Our analysis revealed numerous potential epigenetic modification patterns that are unique to particular cell types, thereby advancing knowledge of the critical functions of chromatin accessibility in cell processes.
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Affiliation(s)
- Yaochen Xu
- Department of Mathematics, School of Sciences, Shanghai University, Shanghai, China
| | - FeiMing Huang
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine (SJTUSM) and Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, China
| | - KaiYan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou, China
| | - Lin Zhu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Zhenbing Zeng
- Department of Mathematics, School of Sciences, Shanghai University, Shanghai, China
- *Correspondence: Zhenbing Zeng, ; Tao Huang, ; Yu-Dong Cai,
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Zhenbing Zeng, ; Tao Huang, ; Yu-Dong Cai,
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
- *Correspondence: Zhenbing Zeng, ; Tao Huang, ; Yu-Dong Cai,
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2
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Yan P, Li Z, Xian S, Wang S, Fu Q, Zhu J, Yue X, Zhang X, Chen S, Zhang W, Lu J, Yin H, Huang R, Huang Z. Construction of the prognostic enhancer RNA regulatory network in osteosarcoma. Transl Oncol 2022; 25:101499. [PMID: 36001923 PMCID: PMC9421318 DOI: 10.1016/j.tranon.2022.101499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/08/2022] [Accepted: 07/26/2022] [Indexed: 11/30/2022] Open
Abstract
Our enhancer RNAs-based prognostic model showed good predictive ability in osteosarcoma. CCAAT enhancer binding protein alpha (CEBPA) may regulate CD8A molecule (CD8A). CD8A activation may promote CD3E molecule (CD3E) expression and activate allograft rejection in CD8+ T cells. Above signal axis provided new insights in the mechanism of osteosarcoma tumorigenesis.
Background Osteosarcoma (OS) is a common malignant tumor in osteoarticular system, the 5-year overall survival of which is poor. Enhancer RNAs (eRNAs) have been implicated in the tumorigenesis of various cancer types, whereas their roles in OS tumorigenesis remains largely unclear. Methods Differentially expressed eRNAs (DEEs), transcription factors (DETFs), target genes (DETGs) were identified using limma (Linear Models for Microarray Analysis) package. Prognosis-related DEEs were accessed by univariate Cox regression analysis. A multivariate model was constructed to evaluate the prognosis of OS samples. Prognosis-related DEEs, DETFs, DETGs, immune cells, and hallmark gene sets were co-analyzed to construct an regulatory network. Specific inhibitors were also filtered by connectivity Map analysis. External validation and scRNA-seq analysis were performed to verify our key findings. Results 3,981 DETGs, 468 DEEs, 51 DETFs, and 27 differentially expressed hallmark gene sets were identified. A total of Multivariate risk predicting model based on 18 prognosis-related DEEs showed a high accuracy (area under curve (AUC) = 0.896). GW-8510 was the candidate inhibitor targeting prognosis-related DEEs (mean = 0.670, p < 0.001). Based on the OS tumorigenesis-related regulation network, we identified that CCAAT enhancer binding protein alpha (CEBPA, DETF) may regulate CD8A molecule (CD8A, DEE), thereby promoting the transcription of CD3E molecule (CD3E, DETG), which may affect allograft rejection based on CD8+ T cells. Conclusion We constructed an eRNA-based prognostic model for predicting the OS patients’ prognosis and explored the potential regulation network for OS tumorigenesis by an integrated bioinformatics analysis, providing promising therapeutic targets for OS patients.
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Affiliation(s)
- Penghui Yan
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Zhenyu Li
- Tongji University School of Medicine, Shanghai 200092, China
| | - Shuyuan Xian
- Tongji University School of Medicine, Shanghai 200092, China
| | - Siqiao Wang
- Tongji University School of Medicine, Shanghai 200092, China; Division of Spine, Department of Orthopedics, Tongji Hospital Affiliated to Tongji University School of Medicine, Shanghai 200065, China
| | - Qing Fu
- Tongji University School of Medicine, Shanghai 200092, China
| | - Jiwen Zhu
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Xi Yue
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Xinkun Zhang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Department of Orthopedics, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Shaofeng Chen
- Department of Orthopedics, The First Affiliated Hospital of Naval Medical University, Shanghai 200433, China
| | - Wei Zhang
- Department of Burn Surgery, The First Affiliated Hospital of Naval Medical University, Shanghai 200433, China
| | - Jianyu Lu
- Department of Burn Surgery, The First Affiliated Hospital of Naval Medical University, Shanghai 200433, China
| | - Huabin Yin
- Department of Orthopedics, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200065, China.
| | - Runzhi Huang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Tongji University School of Medicine, Shanghai 200092, China; Department of Burn Surgery, The First Affiliated Hospital of Naval Medical University, Shanghai 200433, China.
| | - Zongqiang Huang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
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3
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Aziz S, Rasheed F, Zahra R, König S. Gastric Cancer Pre-Stage Detection and Early Diagnosis of Gastritis Using Serum Protein Signatures. Molecules 2022; 27:molecules27092857. [PMID: 35566209 PMCID: PMC9099457 DOI: 10.3390/molecules27092857] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/22/2022] [Accepted: 04/27/2022] [Indexed: 02/04/2023] Open
Abstract
Background: A gastric cancer (GC) diagnosis relies on histopathology. Endoscopy rates are increasing. Helicobacter pylori infection is a major GC risk factor. In an effort to elucidate abundant blood biomarkers, and potentially reduce the number of diagnostic surgical interventions, we investigated sera and biopsies from a cohort of 219 H. pylori positive and negative patients diagnosed with GC, gastritis, and ulcers. This allowed the comparative investigation of the different gastroduodenal diseases, and the exclusion of protein changes resulting from bacterial infection or inflammation of the gastric mucosa when searching for GC-dependent proteins. Methods: High-definition mass spectrometry-based expression analysis of tryptically digested proteins was performed, followed by multivariate statistical and network analyses for the different disease groups, with respect to H. pylori infection status. Significantly regulated proteins differing more than two-fold between groups were shortlisted, and their role in gastritis and GC discussed. Results: We present data of comparative protein analyses of biopsies and sera from patients suffering from mild to advanced gastritis, ulcers, and early to advanced GC, in conjunction with a wealth of metadata, clinical information, histopathological evaluation, and H. pylori infection status. We used samples from pre-malignant stages to extract prospective serum markers for early-stage GC, and present a 29-protein marker panel containing, amongst others, integrin β-6 and glutathione peroxidase. Furthermore, ten serum markers specific for advanced GC, independent of H. pylori infection, are provided. They include CRP, protein S100A9, and kallistatin. The majority of these proteins were previously discussed in the context of cancer or GC. In addition, we detected hypoalbuminemia and increased fibrinogen serum levels in gastritis. Conclusion: Two protein panels were suggested for the development of multiplex tests for GC serum diagnostics. For most of the elements contained in these panels, individual commercial tests are available. Thus, we envision the design of multi-protein assays, incorporating several to all of the panel members, in order to gain a level of specificity that cannot be achieved by testing a single protein alone. As their development and validation will take time, gastritis diagnosis based on the fibrinogen to albumin serum ratio may be a quick way forward. Its determination at the primary/secondary care level for early diagnosis could significantly reduce the number of referrals to endoscopy. Preventive measures are in high demand. The protein marker panels presented in this work will contribute to improved GC diagnostics, once they have been transferred from a research result to a practical tool.
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Affiliation(s)
- Shahid Aziz
- BreathMAT Lab, Pakistan Institute of Nuclear Science and Technology (PINSTEC), Islamabad 44000, Pakistan; (S.A.); (F.R.)
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan;
- IZKF Core Unit Proteomics, University of Münster, 48149 Münster, Germany
| | - Faisal Rasheed
- BreathMAT Lab, Pakistan Institute of Nuclear Science and Technology (PINSTEC), Islamabad 44000, Pakistan; (S.A.); (F.R.)
| | - Rabaab Zahra
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan;
| | - Simone König
- IZKF Core Unit Proteomics, University of Münster, 48149 Münster, Germany
- Correspondence:
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Genome-wide association study reveals genetic variants associated with HIV-1C infection in a Botswana study population. Proc Natl Acad Sci U S A 2021; 118:2107830118. [PMID: 34782459 DOI: 10.1073/pnas.2107830118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2021] [Indexed: 11/18/2022] Open
Abstract
Although there have been many studies of gene variant association with different stages of HIV/AIDS progression in United States and European cohorts, few gene-association studies have assessed genic determinants in sub-Saharan African populations, which have the highest density of HIV infections worldwide. We carried out genome-wide association studies on 766 study participants at risk for HIV-1 subtype C (HIV-1C) infection in Botswana. Three gene associations (AP3B1, PTPRA, and NEO1) were shown to have significant association with HIV-1C acquisition. Each gene association was replicated within Botswana or in the United States-African American or United States-European American AIDS cohorts or in both. Each associated gene has a prior reported influence on HIV/AIDS pathogenesis. Thirteen previously discovered AIDS restriction genes were further replicated in the Botswana cohorts, extending our confidence in these prior AIDS restriction gene reports. This work presents an early step toward the identification of genetic variants associated with and affecting HIV acquisition or AIDS progression in the understudied HIV-1C afflicted Botswana population.
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5
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Blumenthal MJ, Cornejo Castro EM, Whitby D, Katz AA, Schäfer G. Evidence for altered host genetic factors in KSHV infection and KSHV-related disease development. Rev Med Virol 2020; 31:e2160. [PMID: 33043529 PMCID: PMC8047912 DOI: 10.1002/rmv.2160] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/06/2020] [Accepted: 08/08/2020] [Indexed: 01/09/2023]
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiological agent of Kaposi's sarcoma (KS), the most common AIDS-related malignancy. It also causes other rare, but certainly underreported, KSHV-associated pathologies, namely primary effusion lymphoma, multicentric Castleman disease and KSHV inflammatory cytokine syndrome. Epidemiology and pathogenicity studies point to the potential for host genetic predisposition to KSHV infection and/or the subsequent development of KSHV-associated pathologies partly explaining the peculiar geographic and population-specific incidence of KSHV and associated pathologies and discrepancies in KSHV exposure and infection and KSHV infection and disease development. This review consolidates the current knowledge of host genetic factors involved in the KSHV-driven pathogenesis. Studies reviewed here indicate a plausible connection between KSHV susceptibility and host genetic factors that affect either viral access to host cells via entry mechanisms or host innate immunity to viral infection. Subsequent to infection, KSHV-associated pathogenesis, reviewed here primarily in the context of KS, is likely influenced by an orchestrated concert of innate immune system interactions, downstream inflammatory pathways and oncogenic mechanisms. The association studies reviewed here point to interesting candidate genes that may prove important in achieving a more nuanced understanding of the pathogenesis and therapeutic targeting of KSHV and associated diseases. Recent studies on host genetic factors suggest numerous candidate genes strongly associated with KSHV infection or subsequent disease development, particularly innate immune system mediators. Taken together, these contribute toward our understanding of the geographic prevalence and population susceptibility to KSHV and KSHV-associated diseases.
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Affiliation(s)
- Melissa J Blumenthal
- International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa.,Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa.,Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Elena Maria Cornejo Castro
- Viral Oncology Section, AIDS and Cancer Virus Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Denise Whitby
- Viral Oncology Section, AIDS and Cancer Virus Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Arieh A Katz
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa.,Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Georgia Schäfer
- International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa.,Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa.,Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
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6
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Zeng X, Tsui JCC, Shi M, Peng J, Cao CY, Kan LLY, Lau CPY, Liang Y, Wang L, Liu L, Chen Z, Tsui SKW. Genome-Wide Characterization of Host Transcriptional and Epigenetic Alterations During HIV Infection of T Lymphocytes. Front Immunol 2020; 11:2131. [PMID: 33013899 PMCID: PMC7511662 DOI: 10.3389/fimmu.2020.02131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 08/06/2020] [Indexed: 12/12/2022] Open
Abstract
Background and methods: Host genomic alterations are closely related to dysfunction of CD4+ T lymphocytes in the HIV–host interplay. However, the roles of aberrant DNA methylation and gene expression in the response to HIV infection are not fully understood. We investigated the genome-wide DNA methylation and transcriptomic profiles in two HIV-infected T lymphocyte cell lines using high-throughput sequencing. Results: Based on DNA methylation data, we identified 3,060 hypomethylated differentially methylated regions (DMRs) and 2,659 hypermethylated DMRs in HIV-infected cells. Transcription-factor-binding motifs were significantly associated with methylation alterations, suggesting that DNA methylation modulates gene expression by affecting the binding to transcription factors during HIV infection. In support of this hypothesis, genes with promoters overlapping with DMRs were enriched in the biological function related to transcription factor activities. Furthermore, the analysis of gene expression data identified 1,633 upregulated genes and 2,142 downregulated genes on average in HIV-infected cells. These differentially expressed genes (DEGs) were significantly enriched in apoptosis-related pathways. Our results suggest alternative splicing as an additional mechanism that may contribute to T-cell apoptosis during HIV infection. We also demonstrated a genome-scale correlation between DNA methylation and gene expression in HIV-infected cells. We identified 831 genes with alterations in both DNA methylation and gene expression, which were enriched in apoptosis. Our results were validated using various experimental methods. In addition, consistent with our in silico results, a luciferase assay showed that the activity of the PDX1 and SMAD3 promoters was significantly decreased in the presence of HIV proteins, indicating the potential of these genes as genetic markers of HIV infection. Conclusions: Our results suggest important roles for DNA methylation and gene expression regulation in T-cell apoptosis during HIV infection. We propose a list of novel genes related to these processes for further investigation. This study also provides a comprehensive characterization of changes occurring at the transcriptional and epigenetic levels in T cells in response to HIV infection.
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Affiliation(s)
- Xi Zeng
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, China.,School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Joseph Chi-Ching Tsui
- Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Hong Kong, China
| | - Mai Shi
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jie Peng
- Acquired Immunodeficiency Syndrome (AIDS) Institute, The University of Hong Kong, Hong Kong, China
| | - Cyanne Ye Cao
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Lea Ling-Yu Kan
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Carol Po-Ying Lau
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yonghao Liang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Lingyi Wang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Li Liu
- Acquired Immunodeficiency Syndrome (AIDS) Institute, The University of Hong Kong, Hong Kong, China
| | - Zhiwei Chen
- Acquired Immunodeficiency Syndrome (AIDS) Institute, The University of Hong Kong, Hong Kong, China
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China.,Centre for Microbial Genomics and Proteomics, The Chinese University of Hong Kong, Hong Kong, China
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7
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Guan X, Guan Z, Song C. Expression profile analysis identifies key genes as prognostic markers for metastasis of osteosarcoma. Cancer Cell Int 2020; 20:104. [PMID: 32256213 PMCID: PMC7106759 DOI: 10.1186/s12935-020-01179-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 03/17/2020] [Indexed: 12/16/2022] Open
Abstract
Background OS is the most common malignant tumor of bone which was featured with osteoid or immature bone produced by the malignant cells, and biomarkers are urgently needed to identify patients with this aggressive disease. Methods We downloaded gene expression profiles from GEO and TARGET datasets for OS, respectively, and performed WGCNA to identify the key module. Whereafter, functional annotation and GSEA demonstrated the relationships between target genes and OS. Results In this study, we discovered four key genes-ALOX5AP, HLA-DMB, HLA-DRA and SPINT2 as new prognostic markers and confirmed their relationship with OS metastasis in the validation set. Conclusions In conclusion, ALOX5AP, HLA-DMB, HLA-DRA and SPINT2 were identified by bioinformatics analysis as possible prognostic markers for OS metastasis.
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Affiliation(s)
- Xiaoqing Guan
- 1Center for Cancer Bioinformatics, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Zhiyuan Guan
- 2Department of Orthopaedics, Peking University Third Hospital, Beijing, China.,Beijing Key Laboratory of Spinal Diseases, 49 North Garden Rd Haidian District, Beijing, China
| | - Chunli Song
- 2Department of Orthopaedics, Peking University Third Hospital, Beijing, China.,Beijing Key Laboratory of Spinal Diseases, 49 North Garden Rd Haidian District, Beijing, China
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8
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Cornejo Castro EM, Morrison BJ, Marshall VA, Labo N, Miley WJ, Clements N, Nelson G, Ndom P, Stolka K, Hemingway-Foday JJ, Abassora M, Gao X, Smith JS, Carrington M, Whitby D. Relationship between human leukocyte antigen alleles and risk of Kaposi's sarcoma in Cameroon. Genes Immun 2019; 20:684-689. [PMID: 31105266 DOI: 10.1038/s41435-019-0077-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/24/2019] [Accepted: 04/28/2019] [Indexed: 01/29/2023]
Abstract
Several studies published to date report associations between human leukocyte antigen (HLA) alleles and different types of Kaposi's Sarcoma (KS). However, there is little concordance between the HLA alleles identified and the populations studied. To test whether HLA alleles associate with KS in a Cameroonian case-control study, we performed high-resolution HLA typing in KSHV seropositive individuals. Among HIV-positive individuals, carriers of HLA-B*14:01 were at a significantly higher risk of AIDS-KS (p = 0.033). For HIV-negative patients, a gene-wise comparison of allele frequencies identified the HLA-B (p = 0.008) and -DQA1 (p = 0.002) loci as possible risk factors for endemic KS. Our study provides additional understanding of genetic determinants of KS and their implications in disease pathogenesis. Further validation of these findings is needed to define the functional relevance of these associations.
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Affiliation(s)
- Elena M Cornejo Castro
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, MD, USA
| | - Brian J Morrison
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, MD, USA
| | - Vickie A Marshall
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, MD, USA
| | - Nazzarena Labo
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, MD, USA
| | - Wendell J Miley
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, MD, USA
| | - Nathan Clements
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, MD, USA
| | - George Nelson
- CCR Collaborative Bioinformatics Resource (CCBR), Center for Cancer Research, NCI, Bethesda, MD, USA.,Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | - Kristen Stolka
- RTI International, Research Triangle Park, Triangle Park, NC, USA
| | | | | | - Xiaojiang Gao
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Denise Whitby
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, MD, USA.
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9
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Bibert S, Wójtowicz A, Taffé P, Tarr PE, Bernasconi E, Furrer H, Günthard HF, Hoffmann M, Kaiser L, Osthoff M, Fellay J, Cavassini M, Bochud PY. Interferon lambda 3/4 polymorphisms are associated with AIDS-related Kaposi's sarcoma. AIDS 2018; 32:2759-2765. [PMID: 30234607 DOI: 10.1097/qad.0000000000002004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND Kaposi's sarcoma, the most common AIDS-related cancer, represents a major public concern in resource-limited countries. Single nucleotide polymorphisms within the Interferon lambda 3/4 region (IFNL3/4) determine the expression, function of IFNL4, and influence the clinical course of an increasing number of viral infections. OBJECTIVES To analyze whether IFNL3/4 variants are associated with susceptibility to AIDS-related Kaposi's sarcoma among MSM enrolled in the Swiss HIV Cohort Study (SHCS). METHODS The risk of developing Kaposi's sarcoma according to the carriage of IFNL3/4 SNPs rs8099917 and rs12980275 and their haplotypic combinations was assessed by using cumulative incidence curves and Cox regression models, accounting for relevant covariables. RESULTS Kaposi's sarcoma was diagnosed in 221 of 2558 MSM Caucasian SHCS participants. Both rs12980275 and rs8099917 were associated with an increased risk of Kaposi's sarcoma (cumulative incidence 15 versus 10%, P = 0.01 and 16 versus 10%, P = 0.009, respectively). Diplotypes predicted to produce the active P70 form (cumulative incidence 16 versus 10%, P = 0.01) but not the less active S70 (cumulative incidence 11 versus 10%, P = 0.7) form of IFNL4 were associated with an increased risk of Kaposi's sarcoma, compared with those predicted not to produce IFNL4. The associations remained significant in a multivariate Cox regression model after adjustment for age at infection, combination antiretroviral therapy, median CD4+ T-cell count nadir and CD4+ slopes (hazard ratio 1.42, 95% confidence interval 1.06-1.89, P = 0.02 for IFLN P70 versus no IFNL4). CONCLUSION This study reports for the first time an association between IFNL3/4 polymorphisms and susceptibility to AIDS-related Kaposi's sarcoma.
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Affiliation(s)
| | | | - Patrick Taffé
- Institute for Social and Preventive Medicine, University (IUMSP), Lausanne University Hospital, Lausanne
| | - Philip E Tarr
- Department of Medicine, Kantonspital Baselland, University of Basel, Bruderholz
| | - Enos Bernasconi
- Division of Infectious diseases, Regional hospital of Lugano, Lugano
| | - Hansjakob Furrer
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich
- Institute of Medical Virology, University of Zurich, Zurich
| | - Matthias Hoffmann
- Division of Infectious Diseases and Hospital Epidemiology, Department of Internal Medicine, Cantonal Hospital St. Gallen, St. Gallen
| | - Laurent Kaiser
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospital of Geneva and Medical School, University of Geneva, Geneva
| | - Michael Osthoff
- Division of Infectious Diseases and Hospital Epidemiology and Department of Internal Medicine, University Hospital Basel, Basel
| | - Jacques Fellay
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne
- Precision Medicine unit, Lausanne University Hospital, Lausanne, Switzerland
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10
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Blumenthal MJ, Schutz C, Meintjes G, Mohamed Z, Mendelson M, Ambler JM, Whitby D, Mackelprang RD, Carse S, Katz AA, Schäfer G. EPHA2 sequence variants are associated with susceptibility to Kaposi's sarcoma-associated herpesvirus infection and Kaposi's sarcoma prevalence in HIV-infected patients. Cancer Epidemiol 2018; 56:133-139. [PMID: 30176543 PMCID: PMC6206435 DOI: 10.1016/j.canep.2018.08.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/20/2018] [Accepted: 08/21/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND To determine if variations exist in the KSHV host receptor EPHA2's coding region that affect KSHV infectivity and/or KS prevalence among South African HIV-infected patients. METHODS A retrospective candidate gene association study was performed on 150 patients which were randomly selected from a total of 756 HIV-infected patients and grouped according to their KS status and KSHV serodiagnosis; namely group 1: KS+/KSHV+; group 2: KS-/KSHV+; group 3: KS-/KSHV-. Peripheral blood DNA was used to extract DNA and PCR amplify and sequence the entire EPHA2 coding region, which was compared to the NCBI reference through multiple alignment. RESULTS 100% (95% CI 92.9-100%) of the KS positive patients, and 31.6% (95% CI 28.3-35.1%) of the KS negative patients were found to be KSHV seropositive. Aggregate variation across the entire EPHA2 coding region identified an association with KS (OR = 6.6 (95% CI 2.8, 15.9), p = 2.2 × 10-5). This was primarily driven by variation in the functionally important protein tyrosine kinase domain (Pkinase-Tyr; OR = 4.9 (95% CI 1.9, 12.4), p = 0.001) and the sterile-α-motif (SAM; OR = 13.8 (95% CI 1.7, 111.6), p = 0.014). Mutation analysis revealed two novel, non-synonymous heterozygous variants (c.2254 T > C: OR undefined, adj. p = 0.02; and c.2990 G > T: OR undefined, adj. p = 0.04) in Pkinase-Tyr and SAM, respectively, to be statistically associated with KS; and a novel heterozygous transition (c.2727C > T: OR = 6.4 (95% CI 1.4, 28.4), adj. p = 0.03) in Pkinase-Tyr to be statistically associated with KSHV. CONCLUSIONS Variations in the KSHV entry receptor gene EPHA2 affected susceptibility to KSHV infection and KS development in a South African HIV-infected patient cohort.
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Affiliation(s)
- Melissa J Blumenthal
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, University of Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
| | - Charlotte Schutz
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa; Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, South Africa
| | - Graeme Meintjes
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa; Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, South Africa
| | - Zainab Mohamed
- Division of Radiation Oncology, Department of Radiation Medicine, University of Cape Town, South Africa
| | - Marc Mendelson
- Division of Infectious Diseases & HIV Medicine, Department of Medicine, University of Cape Town, South Africa
| | - Jon M Ambler
- Computational Biology Group, Department of Integrative Biomedical Sciences, University of Cape Town, South Africa
| | - Denise Whitby
- Viral Oncology Section, AIDS and Cancer Virus Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, NIH, USA
| | | | - Sinead Carse
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, University of Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
| | - Arieh A Katz
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, University of Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
| | - Georgia Schäfer
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, University of Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa.
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11
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Yao Y, Liu M, Zang F, Yue M, Xia X, Feng Y, Fan H, Zhang Y, Huang P, Yu R. Association between human leucocyte antigen-DO polymorphisms and interferon/ribavirin treatment response in hepatitis C virus type 1 infection in Chinese population: a prospective study. BMJ Open 2018; 8:e019406. [PMID: PMID: 29654010 PMCID: PMC5898346 DOI: 10.1136/bmjopen-2017-019406] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE The human leucocyte antigen-DO (HLA-DO) gene located in the HLA non-classical class-II region may play a role in treatment response to hepatitis C virus (HCV). This study was conducted to explore the role of single nucleotide polymorphisms (SNPs) in HLA-DO in responding to HCV therapy. SETTING All patients were recruited between January 2011 and September 2016 from the Jurong People's Hospital, Jiangsu Province, China. PARTICIPANTS A total of 346 chronic hepatitis C (CHC) patients who finished the 48-week pegylated interferon-alpha and ribavirin (PEG IFN-α/RBV) treatment were enrolled in this study. All patients were former remunerated blood donors. The inclusion criteria for patients were as follows: (1) treatment-naive and treated with PEG IFN-α/RBV, (2) HCV RNA was present in serum for over 6 months before treatment, (3) negative for hepatitis B (HBV) or HIV infection and (4) lacked any other hepatic diseases.All participants in this study were Chinese Han population and infected with HCV genotype 1b and treated with subcutaneous PEG IFN-α at a dose of 180 µg once a week with the addition of 800-1000 mg/d RBV according to weight orally for 48 weeks. RESULTS The SNPs HLA-DOA rs1044429 and HLA-DOB rs2284191 and rs2856997 of 18 SNPs were correlated with HCV treatment response in the Chinese Han population. The dominant model indicated that patients carrying favourable genotypes at rs1044429 AA and rs2284191 AA were more likely to achieve sustained virological response (SVR) (OR 1.99, 95% CI 1.25 to 3.19; OR 2.71, 95% CI 1.58 to 4.63, respectively), while patients carrying unfavourable genotypes at rs2856997 GG were less likely to achieve SVR (OR 0.48, 95% CI 0.29 to 0.78). CONCLUSION Genetic variations at rs1044429, rs2284191 and rs2856997 were independent predictors of HCV treatment response in the Chinese Han population.
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Affiliation(s)
- Yinan Yao
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Mei Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Feng Zang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ming Yue
- Department of Infectious Diseases, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yue Feng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Haozhi Fan
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yun Zhang
- Institute of Epidemiology and Microbiology, Huadong Research Institute for Medicine and Biotechnics, Nanjing, China
| | - Peng Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
- Key Laboratory of Infectious Diseases, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Rongbin Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
- Key Laboratory of Infectious Diseases, School of Public Health, Nanjing Medical University, Nanjing, China
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Alvaro-Benito M, Morrison E, Wieczorek M, Sticht J, Freund C. Human leukocyte Antigen-DM polymorphisms in autoimmune diseases. Open Biol 2017; 6:rsob.160165. [PMID: 27534821 PMCID: PMC5008016 DOI: 10.1098/rsob.160165] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 07/19/2016] [Indexed: 12/20/2022] Open
Abstract
Classical MHC class II (MHCII) proteins present peptides for CD4+ T-cell surveillance and are by far the most prominent risk factor for a number of autoimmune disorders. To date, many studies have shown that this link between particular MHCII alleles and disease depends on the MHCII's particular ability to bind and present certain peptides in specific physiological contexts. However, less attention has been paid to the non-classical MHCII molecule human leucocyte antigen-DM, which catalyses peptide exchange on classical MHCII proteins acting as a peptide editor. DM function impacts the presentation of both antigenic peptides in the periphery and key self-peptides during T-cell development in the thymus. In this way, DM activity directly influences the response to pathogens, as well as mechanisms of self-tolerance acquisition. While decreased DM editing of particular MHCII proteins has been proposed to be related to autoimmune disorders, no experimental evidence for different DM catalytic properties had been reported until recently. Biochemical and structural investigations, together with new animal models of loss of DM activity, have provided an attractive foundation for identifying different catalytic efficiencies for DM allotypes. Here, we revisit the current knowledge of DM function and discuss how DM function may impart autoimmunity at the organism level.
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Affiliation(s)
- Miguel Alvaro-Benito
- Protein Biochemistry Group, Institute for Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Eliot Morrison
- Protein Biochemistry Group, Institute for Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Marek Wieczorek
- Protein Biochemistry Group, Institute for Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Jana Sticht
- Protein Biochemistry Group, Institute for Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Christian Freund
- Protein Biochemistry Group, Institute for Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
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Polymorphisms of HLA-DM on Treatment Response to Interferon/Ribavirin in Patients with Chronic Hepatitis C Virus Type 1 Infection. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2016; 13:ijerph13101030. [PMID: 27775635 PMCID: PMC5086769 DOI: 10.3390/ijerph13101030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 09/29/2016] [Accepted: 10/13/2016] [Indexed: 12/20/2022]
Abstract
Background: HLA-DM gene, which is related to antigen processing and presentation and located in the non-classical class-II region of human leukocyte antigen (HLA) region, may play a crucial role in chronic hepatitis C virus (HCV) infection treatment outcomes. The study was conducted to evaluate the role of the variant of several single nucleotide polymorphisms (SNPs) in HLA-DM gene in HCV treatment outcomes. Methods: We genotyped four SNPs from the candidate genes (HLA-DMA and DMB) in 336 patients who were treated with pegylated interferon-alpha and ribavirin (PEG IFN-α/RBV). Multivariate analysis of factors predicting sustained virological response (SVR) was conducted. Results: HLA-DMA rs1063478 and DMB rs23544 were independent factors of HCV treatment outcomes in Chinese Han population. Individuals who carried favorable genotypes of rs1063478TT and rs23544GG were more likely to achieve SVR {Dominant model: odds ratio (OR) = 2.05, 95% confidence interval (CI) = 1.24–3.41; OR = 2.04, 95% CI =1.23–3.35, respectively}. Rs23544, rs1063478, baseline glucose, baseline platelet and T4 level were independent predictors of SVR. The area under the receiver operating characteristic (ROC) curve (AUC) was 0.740. Conclusions: The genetic variation of rs1063478 and rs23544 are associated with the treatment outcomes in the Chinese Han population.
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Lin H, Sui W, Tan Q, Chen J, Zhang Y, Ou M, Xue W, Li F, Cao C, Sun Y, Dai Y. Integrated analyses of a major histocompatibility complex, methylation and transcribed ultra-conserved regions in systemic lupus erythematosus. Int J Mol Med 2015; 37:139-48. [PMID: 26717903 DOI: 10.3892/ijmm.2015.2416] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 10/05/2015] [Indexed: 11/05/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a multifactorial autoimmune disease which affects different organs and systems that, has a complex genetic inheritance, and is affected by both epigenetic and environmental risk factors. Previous studies on SLE have lacked the statistical power and genetic resolution to fully determine the influence of major histocompatibility complex (MHC) on SLE. In this study, in order to determine this influence, a total of 15 patients with SLE and 15 healthy controls were enrolled. MHC region capture technology, hMeDIP-chip, transcribed ultra-conserved region (T-UCR) microarray and bioinformatics analysis were utilized for both groups. The results revealed methylated CpG enrichment at 6 loci in the MHC segment of SLE. We found 4 single-nucleotide polymorphisms (SNPs) in the CpG promoter of human leukocyte antigen-B (HLA-B) and 2 SNPs in chr6:29521110‑29521833. No significant GO term or KEGG pathway enrichment was noted for an immune-correlated process in the SLE patients for the corresponding CpG-methylated genes. In this study, T-UCR was not discovered in the MHC segment. The analysis of SNPs (rs1050683, rs12697943, rs17881210, rs1065378, rs17184255 and rs16895070) and gene expression in peripheral blood lymphocytes indicated that these SNPs were associated with the occurrence of SLE. Further studies are warranted to examine the roles of these SNPs in the pathogenesis of SLE. Integrative analysis technology provided a view of the molecular signaling pathways in SLE.
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Affiliation(s)
- Hua Lin
- Nephrology Department of 181st Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi 541002, P.R. China
| | - Weiguo Sui
- Nephrology Department of 181st Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi 541002, P.R. China
| | - Qiupei Tan
- Nephrology Department of 181st Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi 541002, P.R. China
| | - Jiejing Chen
- Nephrology Department of 181st Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi 541002, P.R. China
| | - Yue Zhang
- Nephrology Department of 181st Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi 541002, P.R. China
| | - Minglin Ou
- Nephrology Department of 181st Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi 541002, P.R. China
| | - Wen Xue
- Nephrology Department of 181st Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi 541002, P.R. China
| | - Fengyan Li
- Nephrology Department of 181st Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi 541002, P.R. China
| | - Cuihui Cao
- Nephrology Department of 181st Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi 541002, P.R. China
| | - Yufeng Sun
- Nephrology Department of 181st Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi 541002, P.R. China
| | - Yong Dai
- The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong 518020, P.R. China
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Comparative physiogenomic analyses of weight loss in response to 2 modes of bariatric surgery: demonstration with candidate neuropsychiatric and cardiometabolic genes. Surg Obes Relat Dis 2015; 12:369-77. [PMID: 26968501 DOI: 10.1016/j.soard.2015.09.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 09/10/2015] [Accepted: 09/23/2015] [Indexed: 12/22/2022]
Abstract
BACKGROUND Surgical weight loss response is variable, with suboptimal outcomes in some patients. We hypothesized that genetic biomarkers may be related to weight change. METHODS We tested 330 single nucleotide polymorphisms (SNPs) in genes relevant to metabolic regulation in 161 patients whose decrease in body mass index (BMI), 1 year after laparoscopic adjustable gastric banding (LAGB) or Roux-en-Y gastric bypass (RYGB), was small (lowest quartile response) or large (highest quartile response). LAGB patients whose BMI decreased≤4.7 or≥10.2 units comprised groups I (n = 43) and II (n = 40), respectively. RYGB patients whose BMI decreased≤13.6 or≥19.8 units comprised groups III (n = 39) and IV (n = 39), respectively. Within each surgery, SNPs with large differences in reference allele frequency (z score>2, corresponding to values displaced 2 standard deviations [SD] from the mean for all SNPs) in low versus high quartiles, were identified. We compared reference allele frequencies, within surgical procedure, using the χ(2) test (using Bonferroni correction for multiple testing). RESULTS The mean percent excess weight losses (±SD) corresponding to groups I, II, III, and IV were: 16 (±12), 64 (±30), 55 (±16), and 75 (±17), respectively. SNPs with z score>2 were identified in genes involved in LAGB response, lipid metabolic regulation (APOE, rs439401; APOC4, rs2288911), neural processes (DRD3, rs167771; HTR3 B, rs3758987), and xeno- or endobiotic metabolism (CYP3 A4, rs12333983); and for RYGB response, in lipid transport (SCARB1, rs10846744), folate metabolism (MTHFR, rs2066470), regulation of glycolysis in immune cells (HIF1 A, rs1951795), vitamin K cycling (VKORC1, rs2359612), and xeno- or endobiotic metabolism (CYP3 A4, rs2242480). For LAGB response, APOE SNP frequencies were significantly different. CONCLUSIONS With further validation, information derived from patient DNA may be useful to predict surgical weight loss outcomes and guide selection of surgical approach.
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