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Yang Z, Liu X, Xu H, Teschendorff AE, Xu L, Li J, Fu M, Liu J, Zhou H, Wang Y, Zhang L, He Y, Lv K, Yang H. Integrative analysis of genomic and epigenomic regulation reveals miRNA mediated tumor heterogeneity and immune evasion in lower grade glioma. Commun Biol 2024; 7:824. [PMID: 38971948 PMCID: PMC11227553 DOI: 10.1038/s42003-024-06488-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 06/21/2024] [Indexed: 07/08/2024] Open
Abstract
The expression dysregulation of microRNAs (miRNA) has been widely reported during cancer development, however, the underling mechanism remains largely unanswered. In the present work, we performed a systematic integrative study for genome-wide DNA methylation, copy number variation and miRNA expression data to identify mechanisms underlying miRNA dysregulation in lower grade glioma. We identify 719 miRNAs whose expression was associated with alterations of copy number variation or promoter methylation. Integrative multi-omics analysis revealed four subtypes with differing prognoses. These glioma subtypes exhibited distinct immune-related characteristics as well as clinical and genetic features. By construction of a miRNA regulatory network, we identified candidate miRNAs associated with immune evasion and response to immunotherapy. Finally, eight prognosis related miRNAs were validated to promote cell migration, invasion and proliferation through in vitro experiments. Our study reveals the crosstalk among DNA methylation, copy number variation and miRNA expression for immune regulation in glioma, and could have important implications for patient stratification and development of biomarkers for immunotherapy approaches.
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Affiliation(s)
- Zhen Yang
- Center for Medical Research and Innovation of Pudong Hospital, and Intelligent Medicine Institute, Shanghai Medical College, Fudan University, 131 Dongan Road, Shanghai, 200032, China.
| | - Xiaocen Liu
- Department of Nuclear Medicine, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, 241001, Anhui, China
- Anhui Province Key Laboratory of Non-Coding RNA Basic and Clinical Transformation, Wuhu, 241001, Anhui, China
- Key Laboratory of Non-Coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu, 241001, Anhui, China
| | - Hao Xu
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, 200040, China
- Neurosurgical Institute of Fudan University, Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, 200040, China
| | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Lingjie Xu
- Emergency Department, West China Hospital, West China School of Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Jingyi Li
- Department of Medical Cosmetology, Beijing Tiantan Hospital, Capital Medical University, 100070, Beijing, China
| | - Minjie Fu
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, 200040, China
- Neurosurgical Institute of Fudan University, Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, 200040, China
| | - Jun Liu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, 241001, Anhui, China
| | - Hanyu Zhou
- Anhui Province Key Laboratory of Non-Coding RNA Basic and Clinical Transformation, Wuhu, 241001, Anhui, China
- Key Laboratory of Non-Coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu, 241001, Anhui, China
- Central Laboratory, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, 241001, Anhui, China
| | - Yingying Wang
- Department of Nuclear Medicine, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, 241001, Anhui, China
| | - Licheng Zhang
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, 200040, China
- Neurosurgical Institute of Fudan University, Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, 200040, China
| | - Yungang He
- Shanghai Fifth People's Hospital, and Intelligent Medicine Institute, Shanghai Medical College, Fudan University, 131 Dongan Road, Shanghai, 200032, China
| | - Kun Lv
- Anhui Province Key Laboratory of Non-Coding RNA Basic and Clinical Transformation, Wuhu, 241001, Anhui, China.
- Key Laboratory of Non-Coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu, 241001, Anhui, China.
- Central Laboratory, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, 241001, Anhui, China.
| | - Hui Yang
- Anhui Province Key Laboratory of Non-Coding RNA Basic and Clinical Transformation, Wuhu, 241001, Anhui, China.
- Key Laboratory of Non-Coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu, 241001, Anhui, China.
- Central Laboratory, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, 241001, Anhui, China.
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Xu D, Zhang C, Bi X, Xu J, Guo S, Li P, Shen Y, Cai J, Zhang N, Tian G, Zhang H, Wang H, Li Q, Jiang H, Wang B, Li X, Li Y, Li K. Mapping enhancer and chromatin accessibility landscapes charts the regulatory network of Alzheimer's disease. Comput Biol Med 2024; 168:107802. [PMID: 38056211 DOI: 10.1016/j.compbiomed.2023.107802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/20/2023] [Accepted: 11/29/2023] [Indexed: 12/08/2023]
Abstract
BACKGROUND Enhancers are regulatory elements that target and modulate gene expression and play a role in human health and disease. However, the roles of enhancer regulatory circuit abnormalities driven by epigenetic alterations in Alzheimer's disease (AD) are unclear. METHODS In this study, a multiomic integrative analysis was performed to map enhancer and chromatin accessibility landscapes and identify regulatory network abnormalities in AD. We identified differentially methylated enhancers and constructed regulatory networks across brain regions using AD brain tissue samples. Through the integration of snATAC-seq and snRNA-seq datasets, we mapped enhancers with DNA methylation alterations (DMA) and chromatin accessibility landscapes. Core regulatory triplets that contributed to AD neuropathology in specific cell types were further prioritized. RESULTS We revealed widespread DNA methylation alterations (DMA) in the enhancers of AD patients across different brain regions. In addition, the genome-wide transcription factor (TF) binding profiles showed that enhancers with DMA are pervasively regulated by TFs. The TF-enhancer-gene regulatory network analysis identified core regulatory triplets that are associated with brain and immune cell proportions and play important roles in AD pathogenesis. Enhancer regulatory circuits with DMA exhibited distinct chromatin accessibility patterns, which were further characterized at single-cell resolutions. CONCLUSIONS Our study comprehensively investigated DNA methylation-mediated regulatory circuit abnormalities and provided novel insights into the potential pathogenesis of AD.
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Affiliation(s)
- Dahua Xu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital, Hainan Medical University, Haikou 571199, China
| | - Chunrui Zhang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100020, China
| | - Xiaoman Bi
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital, Hainan Medical University, Haikou 571199, China
| | - Jiankai Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Shengnan Guo
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital, Hainan Medical University, Haikou 571199, China
| | - Peihu Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital, Hainan Medical University, Haikou 571199, China
| | - Yutong Shen
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital, Hainan Medical University, Haikou 571199, China
| | - Jiale Cai
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital, Hainan Medical University, Haikou 571199, China
| | - Nihui Zhang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital, Hainan Medical University, Haikou 571199, China
| | - Guanghui Tian
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital, Hainan Medical University, Haikou 571199, China
| | - Haifei Zhang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital, Hainan Medical University, Haikou 571199, China
| | - Hong Wang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital, Hainan Medical University, Haikou 571199, China
| | - Qifu Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital, Hainan Medical University, Haikou 571199, China
| | - Hongyan Jiang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital, Hainan Medical University, Haikou 571199, China
| | - Bo Wang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital, Hainan Medical University, Haikou 571199, China.
| | - Xia Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital, Hainan Medical University, Haikou 571199, China.
| | - Yongsheng Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital, Hainan Medical University, Haikou 571199, China.
| | - Kongning Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital, Hainan Medical University, Haikou 571199, China.
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Xu J, Jiang T, Guo J, Pan T, Li Y. Landscape and perturbation of enhancer-driven core transcription regulatory circuits in cancer. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 32:872-874. [PMID: 37273782 PMCID: PMC10238570 DOI: 10.1016/j.omtn.2023.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Affiliation(s)
- Juan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Tiantongfei Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Jiyu Guo
- School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin 150081, China
| | - Tao Pan
- College of Biomedical Information and Engineering, Hainan Medical University, Haikou 571199, China
| | - Yongsheng Li
- School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin 150081, China
- College of Biomedical Information and Engineering, Hainan Medical University, Haikou 571199, China
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Wang Y, Liu F, Wu J, Zhang MQ, Chai JL, Cao C. G protein inhibitory α subunit 2 is a molecular oncotarget of human glioma. Int J Biol Sci 2023; 19:865-879. [PMID: 36778118 PMCID: PMC9909998 DOI: 10.7150/ijbs.79355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 12/27/2022] [Indexed: 01/11/2023] Open
Abstract
Identification of novel therapeutic oncotargets for human glioma is extremely important. Here we tested expression, potential functions and underlying mechanisms of G protein inhibitory α subunit 2 (Gαi2) in glioma. Bioinformatics analyses revealed that Gαi2 expression is significantly elevated in human glioma, correlating with poor patients' survival, higher tumor grade and wild-type IDH status. Moreover, increased Gαi2 expression was also in local glioma tissues and different glioma cells. In primary and immortalized (A172) glioma cells, Gαi2 shRNA or knockout (KO, by Cas9-sgRNA) potently suppressed viability, proliferation, and mobility, and induced apoptosis. Ectopic Gαi2 overexpression, using a lentiviral construct, further augmented malignant behaviors in glioma cells. p65 phosphorylation, NFκB activity and expression of NFκB pathway genes were decreased in Gαi2-depleted primary glioma cells, but increased following Gαi2 overexpression. There was an increased binding between Gαi2 promoter and Sp1 (specificity protein 1) transcription factor in glioma tissues and different glioma cells. In primary glioma cells Gαi2 expression was significantly reduced following Sp1 silencing, KO or inhibition. In vivo studies revealed that Gαi2 shRNA-expressing AAV intratumoral injection hindered growth of subcutaneous glioma xenografts in nude mice. Moreover, Gαi2 KO inhibited intracranial glioma xenograft in nude mice. Gαi2 depletion, NFκB inhibition and apoptosis induction were observed in subcutaneous and intracranial glioma xenografts with Gαi2 depletion. Together, overexpressed Gαi2 is important for glioma cell growth possibly by promoting NFκB cascade activation.
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Affiliation(s)
- Yin Wang
- Institute of Neuroscience, Soochow University, Institute for Excellence in Clinical Medicine of Kunshan First People's Hospital and Soochow University, Suzhou, China.,Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of Neuroscience, Soochow University, Suzhou, China
| | - Fang Liu
- Department of Neurosurgery, The affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Jiang Wu
- Department of Neurosurgery, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Mei-Qing Zhang
- Institute of Neuroscience, Soochow University, Institute for Excellence in Clinical Medicine of Kunshan First People's Hospital and Soochow University, Suzhou, China.,Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of Neuroscience, Soochow University, Suzhou, China
| | - Jin-Long Chai
- Institute of Neuroscience, Soochow University, Institute for Excellence in Clinical Medicine of Kunshan First People's Hospital and Soochow University, Suzhou, China.,Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of Neuroscience, Soochow University, Suzhou, China
| | - Cong Cao
- Institute of Neuroscience, Soochow University, Institute for Excellence in Clinical Medicine of Kunshan First People's Hospital and Soochow University, Suzhou, China.,Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of Neuroscience, Soochow University, Suzhou, China.,The Affiliated Eye Hospital, Nanjing Medical University, Nanjing, China
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5
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Li Y, Zhang Y, Pan T, Zhou P, Zhou W, Gao Y, Zheng S, Xu J. Shedding light on the hidden human proteome expands immunopeptidome in cancer. Brief Bioinform 2022; 23:6533503. [PMID: 35189633 DOI: 10.1093/bib/bbac034] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/07/2022] [Accepted: 01/25/2022] [Indexed: 01/04/2023] Open
Abstract
Unrestrained cellular growth and immune escape of a tumor are associated with the incidental errors of the genome and transcriptome. Advances in next-generation sequencing have identified thousands of genomic and transcriptomic aberrations that generate variant peptides that assemble the hidden proteome, further expanding the immunopeptidome. Emerging next-generation sequencing technologies and a number of computational methods estimated the abundance of immune infiltration from bulk transcriptome have advanced our understanding of tumor microenvironments. Here, we will characterize several major types of tumor-specific antigens arising from single-nucleotide variants, insertions and deletions, gene fusion, alternative splicing, RNA editing and non-coding RNAs. Finally, we summarize the current state-of-the-art computational and experimental approaches or resources and provide an integrative pipeline for the identification of candidate tumor antigens. Together, the systematic investigation of the hidden proteome in cancer will help facilitate the development of effective and durable immunotherapy targets for cancer.
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Affiliation(s)
- Yongsheng Li
- College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou 571199, China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Tao Pan
- College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou 571199, China
| | - Ping Zhou
- Department of Radiotherapy, the First Affiliated Hospital of Hainan Medical University, Hainan, China
| | - Weiwei Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yueying Gao
- College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou 571199, China
| | - Shaojiang Zheng
- Key Laboratory of Emergency and Trauma of Ministry of Education, Tumor Institute of the First Affiliated Hospital, Hainan Medical University, Haikou, 571199, China
| | - Juan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
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Jiang T, Zhou W, Chang Z, Zou H, Bai J, Sun Q, Pan T, Xu J, Li Y, Li X. ImmReg: the regulon atlas of immune-related pathways across cancer types. Nucleic Acids Res 2021; 49:12106-12118. [PMID: 34755873 PMCID: PMC8643631 DOI: 10.1093/nar/gkab1041] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/10/2021] [Accepted: 10/14/2021] [Indexed: 01/05/2023] Open
Abstract
Immune system gene regulation perturbation has been found to be a major cause of the development of various types of cancer. Numbers of mechanisms contribute to gene expression regulation, thus, systematically identification of potential regulons of immune-related pathways is critical to cancer immunotherapy. Here, we comprehensively chart the landscape of transcription factors, microRNAs, RNA binding proteins and long noncoding RNAs regulation in 17 immune-related pathways across 33 cancers. The potential immunology regulons are likely to exhibit higher expressions in immune cells, show expression perturbations in cancer, and are significantly correlated with immune cell infiltrations. We also identify a panel of clinically relevant immunology regulons across cancers. Moreover, the regulon atlas of immune-related pathways helps prioritizing cancer-related genes (i.e. ETV7, miR-146a-5p, ZFP36 and HCP5). We further identified two molecular subtypes of glioma (cold and hot tumour phenotypes), which were characterized by differences in immune cell infiltrations, expression of checkpoints, and prognosis. Finally, we developed a user-friendly resource, ImmReg (http://bio-bigdata.hrbmu.edu.cn/ImmReg/), with multiple modules to visualize, browse, and download immunology regulation. Our study provides a comprehensive landscape of immunology regulons, which will shed light on future development of RNA-based cancer immunotherapies.
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Affiliation(s)
- Tiantongfei Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Weiwei Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Zhenghong Chang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Haozhe Zou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Jing Bai
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Qisen Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Tao Pan
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou 571199, China
| | - Juan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Yongsheng Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou 571199, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou 571199, China
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