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Liang Y, Qu X, Shah NM, Wang T. Towards targeting transposable elements for cancer therapy. Nat Rev Cancer 2024; 24:123-140. [PMID: 38228901 DOI: 10.1038/s41568-023-00653-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/04/2023] [Indexed: 01/18/2024]
Abstract
Transposable elements (TEs) represent almost half of the human genome. Historically deemed 'junk DNA', recent technological advancements have stimulated a wave of research into the functional impact of TEs on gene-regulatory networks in evolution and development, as well as in diseases including cancer. The genetic and epigenetic evolution of cancer involves the exploitation of TEs, whereby TEs contribute directly to cancer-specific gene activities. This Review provides a perspective on the role of TEs in cancer as being a 'double-edged sword', both promoting cancer evolution and representing a vulnerability that could be exploited in cancer therapy. We discuss how TEs affect transcriptome regulation and other cellular processes in cancer. We highlight the potential of TEs as therapeutic targets for cancer. We also summarize technical hurdles in the characterization of TEs with genomic assays. Last, we outline open questions and exciting future research avenues.
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Affiliation(s)
- Yonghao Liang
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Xuan Qu
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Nakul M Shah
- Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA.
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO, USA.
- McDonnell Genome Institute, Washington University School of Medicine, Saint Louis, MO, USA.
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2
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Zhang Z, Zhu XQ, Yang F, Lai NN, Zhu L, Cole K, Hu BY, Li TE, Zhu Y, Zhang LM, Wang S, Zheng Y, Mao H, Zhao Y, Bruns C, Vago R, Tu B, Wong JWH, Fu DL, Qin LX, Dong QZ. Single-cell mapping reveals several immune subsets associated with liver metastasis of pancreatic ductal adenocarcinoma. MED 2023; 4:728-743.e7. [PMID: 37633269 DOI: 10.1016/j.medj.2023.07.010] [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: 10/15/2022] [Revised: 05/08/2023] [Accepted: 07/26/2023] [Indexed: 08/28/2023]
Abstract
BACKGROUND Identifying a metastasis-correlated immune cell composition within the tumor microenvironment (TME) of pancreatic ductal adenocarcinoma (PDAC) will help to develop promising and innovative therapeutic strategies. However, the dynamics of immune cell lineages in the TME of advanced PDAC remains elusive. METHODS Twenty-six samples from 11 patients (including 11 primary tumor tissues, 10 blood, and 5 lymph nodes) with different stages were used to develop a multiscale immune profile. High-dimensional single-cell analysis with mass cytometry was performed to search for metastasis-correlated immune changes in the microenvironment. The findings were further validated by published single-cell RNA sequencing (scRNA-seq) data and multiplex fluorescent immunohistochemistry. FINDINGS High-dimensional single-cell profiling revealed that the three immune-relevant sites formed a distinct immune atlas. Interestingly, the PDAC microenvironment with the potential for metastatic spread to the liver was characterized by a decreased proportion of CD103+PD-1+CD39+ T cells with cytotoxic and exhausted functional status and an increased proportion of CD73+ macrophages. Analysis of scRNA-seq data of PDAC further confirmed the identified subsets and revealed strong potential interactions via various ligand-receptor pairs between the identified T subsets and the macrophages. Moreover, stratified patients with different immune compositions correlated with clinical outcomes of PDAC. CONCLUSIONS Our study uncovered metastasis-correlated immune changes, suggesting that ecosystem-based patient classification in PDAC will facilitate the identification of candidates likely to benefit from immunotherapy. FUNDING This work was supported by the National Key Research and Development Program of China, the Shanghai International Science and Technology Collaboration Program, the Shanghai Sailing Program, and the Key Laboratory of diagnosis and treatment of severe hepato-pancreatic diseases of Zhejiang Province.
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Affiliation(s)
- Ze Zhang
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiao-Qiang Zhu
- State Key Laboratory for Oncogenes and Related Genes, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong, China
| | - Feng Yang
- Department of Pancreatic Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Nan-Nan Lai
- Key Laboratory of Whole-period Monitoring and Precise Intervention of Digestive Cancer, Minhang Hospital, Fudan University, Shanghai, China
| | - Le Zhu
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Kathryn Cole
- Division of Oncology and Hematology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Bei-Yuan Hu
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Tian-En Li
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Ying Zhu
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Lu-Min Zhang
- Key Laboratory of Whole-period Monitoring and Precise Intervention of Digestive Cancer, Minhang Hospital, Fudan University, Shanghai, China
| | - Shun Wang
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Yan Zheng
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Huarong Mao
- Key Laboratory of Whole-period Monitoring and Precise Intervention of Digestive Cancer, Minhang Hospital, Fudan University, Shanghai, China
| | - Yue Zhao
- General, Visceral and Cancer Surgery, University Hospital of Cologne, Cologne, Germany
| | - Christiane Bruns
- General, Visceral and Cancer Surgery, University Hospital of Cologne, Cologne, Germany
| | - Razi Vago
- Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Bo Tu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Jason W H Wong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong, China.
| | - De-Liang Fu
- Department of Pancreatic Surgery, Huashan Hospital, Fudan University, Shanghai, China.
| | - Lun-Xiu Qin
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China.
| | - Qiong-Zhu Dong
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China; Key Laboratory of Whole-period Monitoring and Precise Intervention of Digestive Cancer, Minhang Hospital, Fudan University, Shanghai, China.
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3
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Keighley LM, Lynch-Sutherland CF, Almomani SN, Eccles MR, Macaulay EC. Unveiling the hidden players: The crucial role of transposable elements in the placenta and their potential contribution to pre-eclampsia. Placenta 2023; 141:57-64. [PMID: 37301654 DOI: 10.1016/j.placenta.2023.05.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 05/21/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023]
Abstract
The human placenta is a vital connection between maternal and fetal tissues, allowing for the exchange of molecules and modulation of immune interactions during pregnancy. Interestingly, some of the placenta's unique functions can be attributed to transposable elements (TEs), which are DNA sequences that have mobilised into the genome. Co-option throughout mammalian evolution has led to the generation of TE-derived regulators and TE-derived genes, some of which are expressed in the placenta but silenced in somatic tissues. TE genes encompass both TE-derived genes with a repeat element in the coding region and TE-derived regulatory regions such as alternative promoters and enhancers. Placental-specific TE genes are known to contribute to the placenta's unique functions, and interestingly, they are also expressed in some cancers and share similar functions. There is evidence to support that aberrant activity of TE genes may contribute to placental pathologies, cancer and autoimmunity. In this review, we highlight the crucial roles of TE genes in placental function, and how their dysregulation may lead to pre-eclampsia, a common and dangerous placental condition. We provide a summary of the functional TE genes in the placenta to offer insight into their significance in normal and abnormal human development. Ultimately, this review highlights an opportunity for future research to investigate the potential dysregulation of TE genes in the development of placental pathologies such as pre-eclampsia. Further understanding of TE genes and their role in the placenta could lead to significant improvements in maternal and fetal health.
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Affiliation(s)
- Laura M Keighley
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, 9054, New Zealand
| | - Chiemi F Lynch-Sutherland
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland, New Zealand
| | - Suzan N Almomani
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland, New Zealand
| | - Michael R Eccles
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland, New Zealand
| | - Erin C Macaulay
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, 9054, New Zealand.
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4
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Du J, Kageyama SI, Yamashita R, Tanaka K, Okumura M, Motegi A, Hojo H, Nakamura M, Hirata H, Sunakawa H, Kotani D, Yano T, Kojima T, Hamaya Y, Kojima M, Nakamura Y, Suzuki A, Suzuki Y, Tsuchihara K, Akimoto T. Transposable elements potentiate radiotherapy-induced cellular immune reactions via RIG-I-mediated virus-sensing pathways. Commun Biol 2023; 6:818. [PMID: 37543704 PMCID: PMC10404237 DOI: 10.1038/s42003-023-05080-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 06/28/2023] [Indexed: 08/07/2023] Open
Abstract
Radiotherapy (RT) plus immunotherapy is a promising modality; however, the therapeutic effects are insufficient, and the molecular mechanism requires clarification to further develop combination therapies. Here, we found that the RNA virus sensor pathway dominantly regulates the cellular immune response in NSCLC and ESCC cell lines. Notably, transposable elements (TEs), especially long terminal repeats (LTRs), functioned as key ligands for the RNA virus sensor RIG-I, and the mTOR-LTR-RIG-I axis induced the cellular immune response and dendritic cell and macrophage infiltration after irradiation. Moreover, RIG-I-dependent immune activation was observed in ESCC patient tissue. scRNA sequencing and spatial transcriptome analysis revealed that radiotherapy induced the expression of LTRs, and the RNA virus sensor pathway in immune and cancer cells; this pathway was also found to mediate tumour conversion to an immunological hot state. Here, we report the upstream and ligand of the RNA virus sensor pathway functions in irradiated cancer tissues.
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Affiliation(s)
- Junyan Du
- Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Shun-Ichiro Kageyama
- Division of Radiation Oncology and Particle Therapy, National Cancer Center Hospital East, Chiba, Japan.
- Department of Radiation Oncology, National Cancer Center Hospital East, Chiba, Japan.
| | - Riu Yamashita
- Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Kosuke Tanaka
- Division of Cancer Immunology, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Masayuki Okumura
- Division of Radiation Oncology and Particle Therapy, National Cancer Center Hospital East, Chiba, Japan
| | - Atsushi Motegi
- Division of Radiation Oncology and Particle Therapy, National Cancer Center Hospital East, Chiba, Japan
| | - Hidehiro Hojo
- Division of Radiation Oncology and Particle Therapy, National Cancer Center Hospital East, Chiba, Japan
| | - Masaki Nakamura
- Division of Radiation Oncology and Particle Therapy, National Cancer Center Hospital East, Chiba, Japan
| | - Hidenari Hirata
- Division of Radiation Oncology and Particle Therapy, National Cancer Center Hospital East, Chiba, Japan
| | - Hironori Sunakawa
- Department of Gastroenterology and Endoscopy, National Cancer Center Hospital East, Chiba, Japan
| | - Daisuke Kotani
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Tomonori Yano
- Department of Gastroenterology and Endoscopy, National Cancer Center Hospital East, Chiba, Japan
| | - Takashi Kojima
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Yamato Hamaya
- Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Motohiro Kojima
- Division of Pathology, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Yuka Nakamura
- Division of Pathology, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Ayako Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Katsuya Tsuchihara
- Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Tetsuo Akimoto
- Division of Radiation Oncology and Particle Therapy, National Cancer Center Hospital East, Chiba, Japan
- Department of Radiation Oncology, National Cancer Center Hospital East, Chiba, Japan
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Chang YS, Hsu MH, Chung CC, Chen HD, Tu SJ, Lee YT, Yen JC, Liu TC, Chang JG. Comprehensive Analysis and Drug Modulation of Human Endogenous Retrovirus in Hepatocellular Carcinomas. Cancers (Basel) 2023; 15:3664. [PMID: 37509325 PMCID: PMC10377948 DOI: 10.3390/cancers15143664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/12/2023] [Accepted: 07/16/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND Human endogenous retroviruses (HERVs) play an important role in the development of cancer and many diseases. Here, we comprehensively explored the impact of HERVs on hepatocellular carcinomas (HCCs). METHODS We employed Telescope to identify HERVs and quantify their expression in the total RNA sequencing data obtained from 254 HCC samples, comprising 254 tumor tissues and 34 matched normal tissues. RESULTS In total, 3357 locus-specific activations of HERVs were differentially expressed, and 180 were correlated with patient survival. Using these 180 HERVs for classification, we found four subgroups with survival correlation. Higher expression levels of the 180 HERVs were correlated with poorer survival, while age, AFP, some mutations, and copy and structural variants differed among subgroups. The differential expression of host genes in high expression of these 180 HERVs primarily involved the activation of pathways related to immunity and infection, lipid and atherosclerosis, MAPK and NF-kB signaling, and cytokine-cytokine receptor interactions. Conversely, there was a suppression of pathways associated with RNA processing, including nucleocytoplasmic transport, surveillance and ribosome biogenesis, and transcriptional misregulation in cancer pathways. Almost all genes involved in HERV activation restriction, KRAB zinc finger proteins, RNA nucleocytoplasmic transport, stemness, HLA and antigen processing and presentation, and immune checkpoints were overexpressed in cancerous tissues, and many over-expressed HERV-related nearby genes were correlated with high HERV activation and poor survival. Twenty-three immune and stromal cells showed higher expression in non-cancerous than cancerous tissues, and seven were correlated with HERV activation. Small-molecule modulation of alternative splicing (AS) altered the expression of survival-related HERVs and their activation-related genes, as well as nearby genes. CONCLUSION Comprehensive and integrated approaches for evaluating HERV expression and their correlation with specific pathways have the potential to provide new companion diagnostics and therapeutic strategies for HCC.
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Affiliation(s)
- Ya-Sian Chang
- Center for Precision Medicine, China Medical University Hospital, Taichung 40447, Taiwan
- Epigenome Research Center, China Medical University Hospital, Taichung 40447, Taiwan
- Department of Laboratory Medicine, China Medical University Hospital, Taichung 40447, Taiwan
- School of Medicine, China Medical University, Taichung 40402, Taiwan
| | - Ming-Hon Hsu
- Center for Precision Medicine, China Medical University Hospital, Taichung 40447, Taiwan
- Epigenome Research Center, China Medical University Hospital, Taichung 40447, Taiwan
- Department of Laboratory Medicine, China Medical University Hospital, Taichung 40447, Taiwan
| | - Chin-Chun Chung
- Center for Precision Medicine, China Medical University Hospital, Taichung 40447, Taiwan
- Epigenome Research Center, China Medical University Hospital, Taichung 40447, Taiwan
| | - Hong-Da Chen
- Center for Precision Medicine, China Medical University Hospital, Taichung 40447, Taiwan
- Epigenome Research Center, China Medical University Hospital, Taichung 40447, Taiwan
- Department of Laboratory Medicine, China Medical University Hospital, Taichung 40447, Taiwan
| | - Siang-Jyun Tu
- Center for Precision Medicine, China Medical University Hospital, Taichung 40447, Taiwan
- Epigenome Research Center, China Medical University Hospital, Taichung 40447, Taiwan
- Department of Laboratory Medicine, China Medical University Hospital, Taichung 40447, Taiwan
| | - Ya-Ting Lee
- Center for Precision Medicine, China Medical University Hospital, Taichung 40447, Taiwan
- Epigenome Research Center, China Medical University Hospital, Taichung 40447, Taiwan
| | - Ju-Chen Yen
- Center for Precision Medicine, China Medical University Hospital, Taichung 40447, Taiwan
- Epigenome Research Center, China Medical University Hospital, Taichung 40447, Taiwan
| | - Ta-Chih Liu
- Department of Hematology-Oncology, Chang Bing Show Chwan Memorial Hospital, Changhua 50544, Taiwan
| | - Jan-Gowth Chang
- Center for Precision Medicine, China Medical University Hospital, Taichung 40447, Taiwan
- Epigenome Research Center, China Medical University Hospital, Taichung 40447, Taiwan
- Department of Laboratory Medicine, China Medical University Hospital, Taichung 40447, Taiwan
- School of Medicine, China Medical University, Taichung 40402, Taiwan
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6
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Zhong F, Lin Y, Zhao L, Yang C, Ye Y, Shen Z. Reshaping the tumour immune microenvironment in solid tumours via tumour cell and immune cell DNA methylation: from mechanisms to therapeutics. Br J Cancer 2023:10.1038/s41416-023-02292-0. [PMID: 37117649 DOI: 10.1038/s41416-023-02292-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 04/30/2023] Open
Abstract
In recent years, the tumour microenvironment (TME) of solid tumours has attracted more and more attention from researchers, especially those non-tumour components such as immune cells. Infiltration of various immune cells causes tumour immune microenvironment (TIME) heterogeneity, and results in different therapeutic effects. Accumulating evidence showed that DNA methylation plays a crucial role in remodelling TIME and is associated with the response towards immune checkpoint inhibitors (ICIs). During carcinogenesis, DNA methylation profoundly changes, specifically, there is a global loss of DNA methylation and increased DNA methylation at the promoters of suppressor genes. Immune cell differentiation is disturbed, and exclusion of immune cells from the TME occurs at least in part due to DNA methylation reprogramming. Therefore, pharmaceutical interventions targeting DNA methylation are promising. DNA methyltransferase inhibitors (DNMTis) enhance antitumor immunity by inducing transcription of transposable elements and consequent viral mimicry. DNMTis upregulate the expression of tumour antigens, mediate immune cells recruitment and reactivate exhausted immune cells. In preclinical studies, DNMTis have shown synergistic effect when combined with immunotherapies, suggesting new strategies to treat refractory solid tumours.
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Affiliation(s)
- Fengyun Zhong
- Department of Gastroenterological Surgery, Peking University People's Hospital, 100044, Beijing, P. R. China
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, 100044, Beijing, P. R. China
| | - Yilin Lin
- Department of Gastroenterological Surgery, Peking University People's Hospital, 100044, Beijing, P. R. China
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, 100044, Beijing, P. R. China
| | - Long Zhao
- Department of Gastroenterological Surgery, Peking University People's Hospital, 100044, Beijing, P. R. China
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, 100044, Beijing, P. R. China
| | - Changjiang Yang
- Department of Gastroenterological Surgery, Peking University People's Hospital, 100044, Beijing, P. R. China
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, 100044, Beijing, P. R. China
| | - Yingjiang Ye
- Department of Gastroenterological Surgery, Peking University People's Hospital, 100044, Beijing, P. R. China
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, 100044, Beijing, P. R. China
| | - Zhanlong Shen
- Department of Gastroenterological Surgery, Peking University People's Hospital, 100044, Beijing, P. R. China.
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, 100044, Beijing, P. R. China.
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Mosaddeghi P, Farahmandnejad M, Zarshenas MM. The role of transposable elements in aging and cancer. Biogerontology 2023:10.1007/s10522-023-10028-z. [PMID: 37017895 DOI: 10.1007/s10522-023-10028-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/06/2023] [Indexed: 04/06/2023]
Abstract
Transposable elements (TEs) constitute a large portion of the human genome. Various mechanisms at the transcription and post-transcription levels developed to suppress TE activity in healthy conditions. However, a growing body of evidence suggests that TE dysregulation is involved in various human diseases, including age-related diseases and cancer. In this review, we explained how sensing TEs by the immune system could induce innate immune responses, chronic inflammation, and following age-related diseases. We also noted that inflammageing and exogenous carcinogens could trigger the upregulation of TEs in precancerous cells. Increased inflammation could enhance epigenetic plasticity and upregulation of early developmental TEs, which rewires the transcriptional networks and gift the survival advantage to the precancerous cells. In addition, upregulated TEs could induce genome instability, activation of oncogenes, or inhibition of tumor suppressors and consequent cancer initiation and progression. So, we suggest that TEs could be considered therapeutic targets in aging and cancer.
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Affiliation(s)
- Pouria Mosaddeghi
- Medicinal Plants Processing Research Center, School of Pharmacy, Shiraz University of Medical Science, Shiraz, Iran
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mitra Farahmandnejad
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
- Quality Control of Drug Products Department, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad M Zarshenas
- Department of Phytopharmaceuticals (Traditional Pharmacy), School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
- Epilepsy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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8
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Transposable Elements and Human Diseases: Mechanisms and Implication in the Response to Environmental Pollutants. Int J Mol Sci 2022; 23:ijms23052551. [PMID: 35269693 PMCID: PMC8910135 DOI: 10.3390/ijms23052551] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 02/06/2023] Open
Abstract
Transposable elements (TEs) are recognized as major players in genome plasticity and evolution. The high abundance of TEs in the human genome, especially the Alu and Long Interspersed Nuclear Element-1 (LINE-1) repeats, makes them responsible for the molecular origin of several diseases. This involves several molecular mechanisms that are presented in this review: insertional mutation, DNA recombination and chromosomal rearrangements, modification of gene expression, as well as alteration of epigenetic regulations. This literature review also presents some of the more recent and/or more classical examples of human diseases in which TEs are involved. Whether through insertion of LINE-1 or Alu elements that cause chromosomal rearrangements, or through epigenetic modifications, TEs are widely implicated in the origin of human cancers. Many other human diseases can have a molecular origin in TE-mediated chromosomal recombination or alteration of gene structure and/or expression. These diseases are very diverse and include hemoglobinopathies, metabolic and neurological diseases, and common diseases. Moreover, TEs can also have an impact on aging. Finally, the exposure of individuals to stresses and environmental contaminants seems to have a non-negligible impact on the epigenetic derepression and mobility of TEs, which can lead to the development of diseases. Thus, improving our knowledge of TEs may lead to new potential diagnostic markers of diseases.
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Zhuo X, Chen L, Lai Z, Liu J, Li S, Hu A, Lin Y. Protein phosphatase 1 regulatory subunit 3G (PPP1R3G) correlates with poor prognosis and immune infiltration in lung adenocarcinoma. Bioengineered 2021; 12:8336-8346. [PMID: 34592886 PMCID: PMC8806970 DOI: 10.1080/21655979.2021.1985817] [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] [Indexed: 11/06/2022] Open
Abstract
The protein phosphatase 1 regulatory subunit 3 G (PPP1R3G) participates in many tumor biological processes; however, its effects on lung adenocarcinoma (LUAD) have not been clarified. Therefore, this study aimed to explore the correlation between PPP1R3G and the prognosis and immune invasion of LUAD. We evaluated the relationship between PPP1R3G and LUAD using a wide range of databases and analysis tools, including UALCAN, TIMER, miRDB, The Human Protein Atlas and the MethSurv database. First, we explored the mRNA and protein expression levels of PPP1R3G in LUAD, and results were validated using real-time PCR. Next, we explored the relationship between PPP1R3G expression and clinical features. Finally, Kaplan-Meier curves and Cox regression were employed to investigate the prognostic significance of PPP1R3G in LUAD. In addition, we explored the relationship between the expression of PPP1R3G and immune infiltration using the TIMER database. We analyzed the relationship between PPP1R3G and methylation using MethSurv database. Results showed that PPP1R3G expression in LUAD tissues was higher than that in normal tissues, and high expression was suggestive of a poor prognosis. Moreover, PPP1R3G expression was positively correlated with the immune infiltration of CD4 + T cells, macrophages, neutrophils, and dendritic cells. PPP1R3G copy number variations also demonstrated remarkable associations with the levels of B cells, CD4 + T cells, macrophages, neutrophils, and dendritic cells. Finally, a PPP1R3G-associated regulatory network was constructed. Overall, PPP1R3G might be a poor prognostic biomarker for LUAD and is associated with tumor immune cell infiltration. Abbreviations: LUAD: Lung adenocarcinoma; PPP1R3G: The protein phosphatase 1 regulatory subunit 3G; OS: overall survival; CI: confidence interval; CNV: copy number variance; HR: Hazard Ratio; ROC: receiver operating characteristic curve; AUC: area under the curve; TCGA: The Cancer Genome Atlas
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Affiliation(s)
- Xingli Zhuo
- Department of emergency and critical care medicine, The Affiliated Suzhou Science&Technology Town Hospital of Nanjing Medical University, Suzhou, China
| | - Lan Chen
- Department of Respiratory Medicine, Gannan Medical University, Ganzhou, China
| | - Zongwei Lai
- Department of Respiratory Medicine, Gannan Medical University, Ganzhou, China
| | - Jiansheng Liu
- Department of Respiratory Medicine, Ganzhou People's Hospital, Ganzhou, China
| | - Shengjun Li
- Department of emergency and critical care medicine, The Affiliated Suzhou Science&Technology Town Hospital of Nanjing Medical University, Suzhou, China
| | - Ahu Hu
- Department of emergency and critical care medicine, The Affiliated Suzhou Science&Technology Town Hospital of Nanjing Medical University, Suzhou, China
| | - Yuansheng Lin
- Department of emergency and critical care medicine, The Affiliated Suzhou Science&Technology Town Hospital of Nanjing Medical University, Suzhou, China
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