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Wu B, Koehler AN, Westcott PMK. New opportunities to overcome T cell dysfunction: the role of transcription factors and how to target them. Trends Biochem Sci 2024:S0968-0004(24)00189-0. [PMID: 39277450 DOI: 10.1016/j.tibs.2024.08.002] [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: 12/20/2023] [Revised: 08/12/2024] [Accepted: 08/14/2024] [Indexed: 09/17/2024]
Abstract
Immune checkpoint blockade (ICB) therapies, which block inhibitory receptors on T cells, can be efficacious in reinvigorating dysfunctional T cell responses. However, most cancers do not respond to these therapies and even in those that respond, tumors can acquire resistance. New strategies are needed to rescue and recruit T cell responses across patient populations and disease states. In this review, we define mechanisms of T cell dysfunction, focusing on key transcription factor (TF) networks. We discuss the complex and sometimes contradictory roles of core TFs in both T cell function and dysfunction. Finally, we review strategies to target TFs using small molecule modulators, which represent a challenging but highly promising opportunity to tune the T cell response toward sustained immunity.
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Affiliation(s)
- Bocheng Wu
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Angela N Koehler
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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2
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Bao K, Gu X, Song Y, Zhou Y, Chen Y, Yu X, Yuan W, Shi L, Zheng J, Hong M. TCF-1 and TOX regulate the memory formation of intestinal group 2 innate lymphoid cells in asthma. Nat Commun 2024; 15:7850. [PMID: 39245681 PMCID: PMC11381517 DOI: 10.1038/s41467-024-52252-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 08/31/2024] [Indexed: 09/10/2024] Open
Abstract
Immune memory has been expanded to group 2 innate lymphoid cells (ILC2s), but the cellular and molecular bases remain incompletely understood. Based on house dust mite (HDM)-induced mice asthma models and human samples, we applied flow cytometry, parabiosis, in vivo imaging and adoptive transplantation to confirm the persistence, migration and function of CD45+lineage-CD90.2+NK1.1-NKp46-ST2-KLRG1+IL-17RB+ memory-like ILC2s (ml-ILC2s). Regulated by CCR9/CCL25 and S1P signaling, ml-ILC2s reside in the lamina propria of small intestines (siLP) in asthma remission, and subsequently move to airway upon re-encountering antigens or alarmins. Furthermore, ml-ILC2s possess properties of longevity, potential of rapid proliferation and producing IL-13, and display transcriptional characteristics with up-regulation of Tox and Tcf-7. ml-ILC2s transplantation restore the asthmatic changes abrogated by Tox and Tcf7 knockdown. Our data identify siLP ml-ILC2s as a memory-like subset, which promotes asthma relapse. Targeting TCF-1 and TOX might be promising for preventing asthma recurrence.
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Affiliation(s)
- Kaifan Bao
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
- Department of Immunology, School of Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
| | - Xiaoqun Gu
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yajun Song
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yijing Zhou
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yanyan Chen
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Xi Yu
- Nanjing Haikerui Pharmaceutical Technology Co., LTD, Nanjing, 210023, China
| | - Weiyuan Yuan
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Liyun Shi
- Department of Immunology, School of Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Jie Zheng
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
- Department of Pharmacology, School of Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
| | - Min Hong
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
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3
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Kang K, Lin X, Chen P, Liu H, Liu F, Xiong W, Li G, Yi M, Li X, Wang H, Xiang B. T cell exhaustion in human cancers. Biochim Biophys Acta Rev Cancer 2024; 1879:189162. [PMID: 39089484 DOI: 10.1016/j.bbcan.2024.189162] [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: 01/30/2024] [Revised: 07/23/2024] [Accepted: 07/24/2024] [Indexed: 08/04/2024]
Abstract
T cell exhaustion refers to a progressive state in which T cells become functionally impaired due to sustained antigenic stimulation, which is characterized by increased expression of immune inhibitory receptors, but weakened effector functions, reduced self-renewal capacity, altered epigenetics, transcriptional programme and metabolism. T cell exhaustion is one of the major causes leading to immune escape of cancer, creating an environment that supports tumor development and metastatic spread. In addition, T cell exhaustion plays a pivotal role to the efficacy of current immunotherapies for cancer. This review aims to provide a comprehensive view of roles of T cell exhaustion in cancer development and progression. We summerized the regulatory mechanisms that involved in T cell exhaustion, including transcription factors, epigenetic and metabolic reprogramming events, and various microenvironmental factors such as cytokines, microorganisms, and tumor autocrine substances. The paper also discussed the challenges posed by T cell exhaustion to cancer immunotherapies, including immune checkpoint blockade (ICB) therapies and chimeric antigen receptor T cell (CAR-T) therapy, highlightsing the obstacles encountered in ICB therapies and CAR-T therapies due to T cell exhaustion. Finally, the article provides an overview of current therapeutic options aimed to reversing or alleviating T cell exhaustion in ICB and CAR-T therapies. These therapeutic approaches seek to overcome T cell exhaustion and enhance the effectiveness of immunotherapies in treating tumors.
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Affiliation(s)
- Kuan Kang
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China; The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha 410008, Hunan, China; The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha 410078, Hunan, China
| | - Xin Lin
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China; The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha 410008, Hunan, China; The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha 410078, Hunan, China
| | - Pan Chen
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
| | - Huai Liu
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China; Department of Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, China
| | - Feng Liu
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China; Department of Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, China
| | - Wei Xiong
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China; The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha 410008, Hunan, China; The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha 410078, Hunan, China
| | - Guiyuan Li
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China; The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha 410008, Hunan, China; The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha 410078, Hunan, China
| | - Mei Yi
- Department of Dermatology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Xiayu Li
- Hunan Key Laboratory of Nonresolving Infammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha 410013, Hunan, China.
| | - Hui Wang
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China; Department of Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, China.
| | - Bo Xiang
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China; The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha 410008, Hunan, China; The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha 410078, Hunan, China; FuRong Laboratory, Changsha 410078, Hunan, China.
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4
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Das A, Martinez-Ruiz GU, Bouladoux N, Stacy A, Moraly J, Vega-Sendino M, Zhao Y, Lavaert M, Ding Y, Morales-Sanchez A, Harly C, Seedhom MO, Chari R, Awasthi P, Ikeuchi T, Wang Y, Zhu J, Moutsopoulos NM, Chen W, Yewdell JW, Shapiro VS, Ruiz S, Taylor N, Belkaid Y, Bhandoola A. Transcription factor Tox2 is required for metabolic adaptation and tissue residency of ILC3 in the gut. Immunity 2024; 57:1019-1036.e9. [PMID: 38677292 PMCID: PMC11096055 DOI: 10.1016/j.immuni.2024.04.001] [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: 12/06/2023] [Revised: 02/13/2024] [Accepted: 04/03/2024] [Indexed: 04/29/2024]
Abstract
Group 3 innate lymphoid cells (ILC3) are the major subset of gut-resident ILC with essential roles in infections and tissue repair, but how they adapt to the gut environment to maintain tissue residency is unclear. We report that Tox2 is critical for gut ILC3 maintenance and function. Gut ILC3 highly expressed Tox2, and depletion of Tox2 markedly decreased ILC3 in gut but not at central sites, resulting in defective control of Citrobacter rodentium infection. Single-cell transcriptional profiling revealed decreased expression of Hexokinase-2 in Tox2-deficient gut ILC3. Consistent with the requirement for hexokinases in glycolysis, Tox2-/- ILC3 displayed decreased ability to utilize glycolysis for protein translation. Ectopic expression of Hexokinase-2 rescued Tox2-/- gut ILC3 defects. Hypoxia and interleukin (IL)-17A each induced Tox2 expression in ILC3, suggesting a mechanism by which ILC3 adjusts to fluctuating environments by programming glycolytic metabolism. Our results reveal the requirement for Tox2 to support the metabolic adaptation of ILC3 within the gastrointestinal tract.
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Affiliation(s)
- Arundhoti Das
- Laboratory of Genome Integrity, Center for Cancer Research, NCI, NIH, Bethesda, MD, USA
| | - Gustavo Ulises Martinez-Ruiz
- Laboratory of Genome Integrity, Center for Cancer Research, NCI, NIH, Bethesda, MD, USA; Faculty of Medicine, Research Division, National Autonomous University of Mexico, Mexico City, Mexico; Children's Hospital of Mexico Federico Gomez, Mexico City, Mexico
| | - Nicolas Bouladoux
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, NIAID, NIH, Bethesda, MD, USA
| | - Apollo Stacy
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, NIAID, NIH, Bethesda, MD, USA; Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Josquin Moraly
- Pediatric Oncology Branch, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Maria Vega-Sendino
- Laboratory of Genome Integrity, Center for Cancer Research, NCI, NIH, Bethesda, MD, USA
| | - Yongge Zhao
- Laboratory of Genome Integrity, Center for Cancer Research, NCI, NIH, Bethesda, MD, USA
| | - Marieke Lavaert
- Laboratory of Genome Integrity, Center for Cancer Research, NCI, NIH, Bethesda, MD, USA
| | - Yi Ding
- Laboratory of Genome Integrity, Center for Cancer Research, NCI, NIH, Bethesda, MD, USA
| | - Abigail Morales-Sanchez
- Laboratory of Genome Integrity, Center for Cancer Research, NCI, NIH, Bethesda, MD, USA; Children's Hospital of Mexico Federico Gomez, Mexico City, Mexico
| | - Christelle Harly
- Université de Nantes, CNRS, Inserm, CRCINA, Nantes, France; LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France
| | - Mina O Seedhom
- Laboratory of Viral Diseases, NIAID, NIH, Bethesda, MD, USA
| | - Raj Chari
- Genome Modification Core, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Parirokh Awasthi
- Mouse Modeling Core, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Tomoko Ikeuchi
- Oral Immunity and Infection Section, NIDCR, NIH, Bethesda, MD, USA
| | - Yueqiang Wang
- Shenzhen Typhoon HealthCare, Shenzhen, Guangdong, China
| | - Jinfang Zhu
- Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | | | - WanJun Chen
- Mucosal Immunology Section, NIDCR, NIH, Bethesda, MD, USA
| | | | | | - Sergio Ruiz
- Laboratory of Genome Integrity, Center for Cancer Research, NCI, NIH, Bethesda, MD, USA
| | - Naomi Taylor
- Pediatric Oncology Branch, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, NIAID, NIH, Bethesda, MD, USA
| | - Avinash Bhandoola
- Laboratory of Genome Integrity, Center for Cancer Research, NCI, NIH, Bethesda, MD, USA.
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Han X, Zhang G, Wu X, Xu S, Liu J, Wang K, Liu T, Wu P. Microfluidics-enabled fluorinated assembly of EGCG-ligands-siTOX nanoparticles for synergetic tumor cells and exhausted t cells regulation in cancer immunotherapy. J Nanobiotechnology 2024; 22:90. [PMID: 38439048 PMCID: PMC10910710 DOI: 10.1186/s12951-024-02328-4] [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: 11/10/2023] [Accepted: 02/01/2024] [Indexed: 03/06/2024] Open
Abstract
Immune checkpoint inhibitor (ICI)-derived evolution offers a versatile means of developing novel immunotherapies that targets programmed death-ligand 1 (PD-L1)/programmed death-1 (PD-1) axis. However, one major challenge is T cell exhaustion, which contributes to low response rates in "cold" tumors. Herein, we introduce a fluorinated assembly system of LFNPs/siTOX complexes consisting of fluorinated EGCG (FEGCG), fluorinated aminolauric acid (LA), and fluorinated polyethylene glycol (PEG) to efficiently deliver small interfering RNA anti-TOX (thymus high mobility group box protein, TOX) for synergistic tumor cells and exhausted T cells regulation. Using a microfluidic approach, a library of LFNPs/siTOX complexes were prepared by altering the placement of the hydrophobe (LA), the surface PEGylation density, and the siTOX ratio. Among the different formulations tested, the lead formulation, LFNPs3-3/siTOX complexes, demonstrated enhanced siRNA complexation, sensitive drug release, improved stability and delivery efficacy, and acceptable biosafety. Upon administration by the intravenous injection, this formulation was able to evoke a robust immune response by inhibiting PD-L1 expression and mitigating T cell exhaustion. Overall, this study provides valuable insights into the fluorinated assembly and concomitant optimization of the EGCG-based delivery system. Furthermore, it offers a promising strategy for cancer immunotherapy, highlighting its potential in improving response rates in ''cold'' tumors.
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Affiliation(s)
- Xiaowei Han
- Department of Radiology, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China
- Department of Hepatobiliary Surgery, Innovative Institute of Tumor Immunity and Medicine (ITIM), Anhui Province Key Laboratory of Tumor Immune Microenvironment and Immunotherapy, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui, China
| | - Guozheng Zhang
- Department of Radiology, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China
| | - Xiaozhen Wu
- School of Pharmacy, Nantong University, Nantong, 226001, China
| | - Shufeng Xu
- Department of Radiology, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China
| | - Jiahuan Liu
- Department of Radiology, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China
| | - Kaikai Wang
- School of Pharmacy, Nantong University, Nantong, 226001, China
| | - Tianqing Liu
- NICM Health Research Institute, Western Sydney University, Sydney, NSW, 2145, Australia.
| | - Pengkai Wu
- Department of Hepatobiliary Surgery, Innovative Institute of Tumor Immunity and Medicine (ITIM), Anhui Province Key Laboratory of Tumor Immune Microenvironment and Immunotherapy, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui, China.
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Chamoto K, Yaguchi T, Tajima M, Honjo T. Insights from a 30-year journey: function, regulation and therapeutic modulation of PD1. Nat Rev Immunol 2023; 23:682-695. [PMID: 37185300 DOI: 10.1038/s41577-023-00867-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2023] [Indexed: 05/17/2023]
Abstract
PD1 was originally discovered in 1992 as a molecule associated with activation-induced cell death in T cells. Over the past 30 years, it was found that PD1 has a critical role in avoiding overactivation-induced cell death and autoimmunity, whereas its inhibition unleashes anticancer immunity. Here, we outline the journey from the discovery of PD1 to its role as a breakthrough target in cancer immunotherapy. We describe its regulation and function and examine how a mechanistic understanding of PD1 signalling suggests a central function in setting the T cell activation threshold, thereby controlling T cell proliferation, differentiation, exhaustion and metabolic status. This threshold theory, in combination with new insights into T cell metabolism and a better understanding of immune cell modulation by the microbiota, can provide guidance for the development of efficient combination therapies. Moreover, we discuss the mechanisms underlying immune-related adverse events after PD1-targeted therapy and their possible treatment.
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Affiliation(s)
- Kenji Chamoto
- Division of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomonori Yaguchi
- Division of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masaki Tajima
- Division of Integrated High-Order Regulatory Systems, Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tasuku Honjo
- Division of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto University, Kyoto, Japan.
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Wang T, Zhao R, Zhi J, Liu Z, Wu A, Yang Z, Wang W, Ni T, Jing L, Yu M. Tox4 regulates transcriptional elongation and reinitiation during murine T cell development. Commun Biol 2023; 6:613. [PMID: 37286708 DOI: 10.1038/s42003-023-04992-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 05/30/2023] [Indexed: 06/09/2023] Open
Abstract
HMG protein Tox4 is a regulator of PP1 phosphatases with unknown function in development. Here we show that Tox4 conditional knockout in mice reduces thymic cellularity, partially blocks T cell development, and decreases ratio of CD8 to CD4 through decreasing proliferation and increasing apoptosis of CD8 cells. In addition, single-cell RNA-seq discovered that Tox4 loss also impairs proliferation of the fast-proliferating double positive (DP) blast population within DP cells in part due to downregulation of genes critical for proliferation, notably Cdk1. Moreover, genes with high and low expression level are more dependent on Tox4 than genes with medium expression level. Mechanistically, Tox4 may facilitate transcriptional reinitiation and restrict elongation in a dephosphorylation-dependent manner, a mechanism that is conserved between mouse and human. These results provide insights into the role of TOX4 in development and establish it as an evolutionarily conserved regulator of transcriptional elongation and reinitiation.
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Affiliation(s)
- Talang Wang
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ruoyu Zhao
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200052, China
| | - Junhong Zhi
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ziling Liu
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Aiwei Wu
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zimei Yang
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Weixu Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438, China
| | - Ting Ni
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438, China
| | - Lili Jing
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ming Yu
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200052, China.
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8
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Zhou J, Toh SHM, Tan TK, Balan K, Lim JQ, Tan TZ, Xiong S, Jia Y, Ng SB, Peng Y, Jeyasekharan AD, Fan S, Lim ST, Ong CAJ, Ong CK, Sanda T, Chng WJ. Super-enhancer-driven TOX2 mediates oncogenesis in Natural Killer/T Cell Lymphoma. Mol Cancer 2023; 22:69. [PMID: 37032358 PMCID: PMC10084643 DOI: 10.1186/s12943-023-01767-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 03/24/2023] [Indexed: 04/11/2023] Open
Abstract
BACKGROUND Extranodal natural killer/T-cell lymphoma (NKTL) is an aggressive type of non-Hodgkin lymphoma with dismal outcome. A better understanding of disease biology and key oncogenic process is necessary for the development of targeted therapy. Super-enhancers (SEs) have been shown to drive pivotal oncogenes in various malignancies. However, the landscape of SEs and SE-associated oncogenes remain elusive in NKTL. METHODS We used Nano-ChIP-seq of the active enhancer marker histone H3 lysine 27 acetylation (H3K27ac) to profile unique SEs NKTL primary tumor samples. Integrative analysis of RNA-seq and survival data further pinned down high value, novel SE oncogenes. We utilized shRNA knockdown, CRISPR-dCas9, luciferase reporter assay, ChIP-PCR to investigate the regulation of transcription factor (TF) on SE oncogenes. Multi-color immunofluorescence (mIF) staining was performed on an independent cohort of clinical samples. Various function experiments were performed to evaluate the effects of TOX2 on the malignancy of NKTL in vitro and in vivo. RESULTS SE landscape was substantially different in NKTL samples in comparison with normal tonsils. Several SEs at key transcriptional factor (TF) genes, including TOX2, TBX21(T-bet), EOMES, RUNX2, and ID2, were identified. We confirmed that TOX2 was aberrantly overexpressed in NKTL relative to normal NK cells and high expression of TOX2 was associated with worse survival. Modulation of TOX2 expression by shRNA, CRISPR-dCas9 interference of SE function impacted on cell proliferation, survival and colony formation ability of NKTL cells. Mechanistically, we found that RUNX3 regulates TOX2 transcription by binding to the active elements of its SE. Silencing TOX2 also impaired tumor formation of NKTL cells in vivo. Metastasis-associated phosphatase PRL-3 has been identified and validated as a key downstream effector of TOX2-mediated oncogenesis. CONCLUSIONS Our integrative SE profiling strategy revealed the landscape of SEs, novel targets and insights into molecular pathogenesis of NKTL. The RUNX3-TOX2-SE-TOX2-PRL-3 regulatory pathway may represent a hallmark of NKTL biology. Targeting TOX2 could be a valuable therapeutic intervene for NKTL patients and warrants further study in clinic.
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Affiliation(s)
- Jianbiao Zhou
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- NUS Centre for Cancer Research (N2CR), 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Sabrina Hui-Min Toh
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Tze King Tan
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Kalpnaa Balan
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Jing Quan Lim
- Division of Cellular and Molecular Research, Lymphoma Genomic Translational Research Laboratory, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610, Singapore
- Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Tuan Zea Tan
- Genomics and Data Analytics Core (GeDaC), Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
| | - Sinan Xiong
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Yunlu Jia
- Department of Medical Oncology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Siok-Bian Ng
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119074, Singapore
| | - Yanfen Peng
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Anand D Jeyasekharan
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- NUS Centre for Cancer Research (N2CR), 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Shuangyi Fan
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119074, Singapore
| | - Soon Thye Lim
- Director's office, National Cancer Centre, Singapore, 168583, Singapore
- Office of Education, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Chin-Ann Johnny Ong
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre, Singapore, 168583, Singapore
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Singapore, 168583, Singapore
- Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre, Singapore, 168583, Singapore
- SingHealth Duke-NUS Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore, 169857, Singapore
- SingHealth Duke-NUS Surgery Academic Clinical Program, Duke-NUS Medical School, Singapore, 169857, Singapore
- Institute of Molecular and Cell Biology, A*STAR Research Entities, Singapore, 138673, Singapore
| | - Choon Kiat Ong
- Division of Cellular and Molecular Research, Lymphoma Genomic Translational Research Laboratory, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610, Singapore.
- Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore.
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
| | - Wee-Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore.
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
- NUS Centre for Cancer Research (N2CR), 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore.
- Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), National University Health System (NUHS), 1E, Kent Ridge Road, Singapore, 119228, Singapore.
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9
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Ford BR, Poholek AC. Regulation and Immunotherapeutic Targeting of the Epigenome in Exhausted CD8 T Cell Responses. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:869-879. [PMID: 36947818 PMCID: PMC10037537 DOI: 10.4049/jimmunol.2200681] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 01/04/2023] [Indexed: 03/24/2023]
Abstract
Exhaustion is a state of CD8 T cell differentiation that occurs in settings of chronic Ag such as tumors, chronic viral infection, and autoimmunity. Cellular differentiation is driven by a series of environmental signals that promote epigenetic landscapes that set transcriptomes needed for function. For CD8 T cells, the epigenome that underlies exhaustion is distinct from effector and memory cell differentiation, suggesting that signals early on set in motion a process where the epigenome is modified to promote a trajectory toward a dysfunctional state. Although we know many signals that promote exhaustion, putting this in the context of the epigenetic changes that occur during differentiation has been less clear. In this review, we aim to summarize the epigenetic changes associated with exhaustion in the context of signals that promote it, highlighting immunotherapeutic studies that support these observations or areas for future therapeutic opportunities.
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Affiliation(s)
- B Rhodes Ford
- Division of Pediatric Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA; and Department of Immunology, University of Pittsburgh, Pittsburgh, PA
| | - Amanda C Poholek
- Division of Pediatric Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA; and Department of Immunology, University of Pittsburgh, Pittsburgh, PA
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10
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Niu H, Wang H. TOX regulates T lymphocytes differentiation and its function in tumor. Front Immunol 2023; 14:990419. [PMID: 36969216 PMCID: PMC10035881 DOI: 10.3389/fimmu.2023.990419] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 02/27/2023] [Indexed: 03/11/2023] Open
Abstract
Thymocyte selection-associated high mobility group box protein (TOX) is expressed differently at all T lymphocytes development stages. Owing to more advanced scientific and technological means, including single-cell sequencing technology, heterogeneity of T lymphocytes and TOX has gradually been revealed. Further exploration of such heterogeneity will help us comprehend the developmental stage and functional characteristics of T lymphocytes in greater detail. Emerging evidence supports its regulation not only in exhausting, but also in activating T lymphocytes, thereby verifying TOX heterogeneity. TOX can be used not only as a latent intervention target for tumor diseases and chronic infections, and a therapeutic strategy for autoimmune diseases, but also as a critical factor predicting the drug response and overall survival of patients with malignant tumors.
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11
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Application of ATAC-seq in tumor-specific T cell exhaustion. Cancer Gene Ther 2023; 30:1-10. [PMID: 35794339 PMCID: PMC9842510 DOI: 10.1038/s41417-022-00495-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/06/2022] [Accepted: 06/08/2022] [Indexed: 01/21/2023]
Abstract
Researches show that chronic viral infection and persistent antigen and/or inflammatory signal exposure in cancer causes the functional status of T cells to be altered, mainly by major changes in the epigenetic and metabolic environment, which then leads to T cell exhaustion. The discovery of the immune checkpoint pathway is an important milestone in understanding and reversing T cell exhaustion. Antibodies targeting these pathways have shown superior ability to reverse T cell exhaustion. However, there are still some limitations in immune checkpoint blocking therapy, such as the short-term nature of therapeutic effects and high individual heterogeneity. Assay for transposase-accessible chromatin with sequencing(ATAC-seq) is a method used to analyze the accessibility of whole-genome chromatin. It uses hyperactive Tn5 transposase to assess chromatin accessibility. Recently, a growing number of studies have reported that ATAC-seq can be used to characterize the dynamic changes of epigenetics in the process of T cell exhaustion. It has been determined that immune checkpoint blocking can only temporarily restore the function of exhausted T cells because of an irreversible change in the epigenetics of exhausted T cells. In this study, we review the latest developments, which provide a clearer molecular understanding of T cell exhaustion, reveal potential new therapeutic targets for persistent viral infection and cancer, and provide new insights for designing effective immunotherapy for treating cancer and chronic infection.
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12
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Li S, Yang S, Hong Y. Higher thymocyte selection-associated high mobility group box (TOX) expression predicts poor prognosis in patients with ovarian cancer. BMC Cancer 2022; 22:1216. [PMID: 36434543 PMCID: PMC9701062 DOI: 10.1186/s12885-022-10336-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/18/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Ovarian cancer is one of the most lethal gynecologic malignancies with a dismal prognosis that poses a serious threat to human health, highlighting the need for more knowledge about what is required for identifying some biomarkers for early diagnosis, prediction of prognosis and disease monitoring. TOX, a critical transcription factor related to the development of malignancies that contributing to lymphocytes not just T cells, had been proved prognostic value in some spectrum of cancers. Here, we aimed to study the prognostic role of TOX in ovarian cancer. RESULTS We found that TOX was not only expressed in CD8 T cells but also tumor cells. TOX expression score was higher in ovarian cancer tissues and correlated with survival status. Survival analysis revealed that ovarian cancer patients with high TOX expression score generally shorter overall survival and disease-free survival times. Univariate and Multivariate Cox demonstrated that TOX expression score could be used as an independent prognostic factor for patients with ovarian cancer. CONCLUSION TOX expression in ovarian cancer could be a promising tool for predict overall survival of ovarian cancer patients.
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Affiliation(s)
- Sai Li
- grid.13402.340000 0004 1759 700XDepartment of gynecologic oncology, Women’s Hospital, Zhejiang University school of medicine, Hangzhou, China
| | - Sifu Yang
- grid.506977.a0000 0004 1757 7957Cancer Center, Department of Medical Oncology, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang China
| | - Yupeng Hong
- grid.506977.a0000 0004 1757 7957Cancer Center, Department of Medical Oncology, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang China
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13
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Ford BR, Vignali PDA, Rittenhouse NL, Scharping NE, Peralta R, Lontos K, Frisch AT, Delgoffe GM, Poholek AC. Tumor microenvironmental signals reshape chromatin landscapes to limit the functional potential of exhausted T cells. Sci Immunol 2022; 7:eabj9123. [PMID: 35930654 PMCID: PMC9851604 DOI: 10.1126/sciimmunol.abj9123] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Response rates to immunotherapy in solid tumors remain low due in part to the elevated prevalence of terminally exhausted T cells, a hypofunctional differentiation state induced through persistent antigen and stress signaling. However, the mechanisms promoting progression to terminal exhaustion in the tumor remain undefined. Using the low-input chromatin immunoprecipitation sequencing method CUT&RUN, we profiled the histone modification landscape of tumor-infiltrating CD8+ T cells throughout differentiation. We found that terminally exhausted T cells had unexpected chromatin features that limit their transcriptional potential. Terminally exhausted T cells had a substantial fraction of active chromatin, including active enhancers enriched for bZIP/AP-1 transcription factor motifs that lacked correlated gene expression, which was restored by immunotherapeutic costimulatory signaling. Reduced transcriptional potential was also driven by an increase in histone bivalency, which we linked directly to hypoxia exposure. Enforced expression of the hypoxia-insensitive histone demethylase Kdm6b was sufficient to overcome hypoxia, increase function, and promote antitumor immunity. Our study reveals the specific epigenetic changes mediated by histone modifications during T cell differentiation that support exhaustion in cancer, highlighting that their altered function is driven by improper costimulatory signals and environmental factors. These data suggest that even terminally exhausted T cells may remain competent for transcription in settings of increased costimulatory signaling and reduced hypoxia.
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Affiliation(s)
- B. Rhodes Ford
- Division of Pediatric Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Paolo D. A. Vignali
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Natalie L. Rittenhouse
- Division of Pediatric Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Nicole E. Scharping
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Ronal Peralta
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Konstantinos Lontos
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Department of Oncology, University of Pittsburgh Medical Center, Pittsburgh, PA 15260, USA
| | - Andrew T. Frisch
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Greg M. Delgoffe
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Corresponding author. (G.M.D.); (A.C.P.)
| | - Amanda C. Poholek
- Division of Pediatric Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Corresponding author. (G.M.D.); (A.C.P.)
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14
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Han J, Wan M, Ma Z, He P. The TOX subfamily: all-round players in the immune system. Clin Exp Immunol 2022; 208:268-280. [PMID: 35485425 PMCID: PMC9226143 DOI: 10.1093/cei/uxac037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 03/29/2022] [Accepted: 04/26/2022] [Indexed: 12/14/2022] Open
Abstract
The thymocyte selection-related HMG box protein (TOX) subfamily comprises evolutionarily conserved DNA-binding proteins, and is expressed in certain immune cell subsets and plays key roles in the development of CD4+ T cells, innate lymphoid cells (ILCs), T follicular helper (Tfh) cells, and in CD8+ T-cell exhaustion. Although its roles in CD4+ T and natural killer (NK) cells have been extensively studied, recent findings have demonstrated previously unknown roles for TOX in the development of ILCs, Tfh cells, as well as CD8+ T-cell exhaustion; however, the molecular mechanism underlying TOX regulation of these immune cells remains to be elucidated. In this review, we discuss recent studies on the influence of TOX on the development of various immune cells and CD8+ T-cell exhaustion and the roles of specific TOX family members in the immune system. Moreover, this review suggests candidate regulatory targets for cell therapy and immunotherapies.
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Affiliation(s)
- Jiawen Han
- Central Laboratory, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Minjie Wan
- Central Laboratory, The First Hospital of Jilin University, Changchun, Jilin, China.,Department of Hepatology, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Zhanchuan Ma
- Central Laboratory, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Ping He
- Department of Gastroenterology, The First Hospital of Jilin University, Changchun, Jilin, China
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15
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Philip M, Schietinger A. CD8 + T cell differentiation and dysfunction in cancer. Nat Rev Immunol 2022; 22:209-223. [PMID: 34253904 PMCID: PMC9792152 DOI: 10.1038/s41577-021-00574-3] [Citation(s) in RCA: 403] [Impact Index Per Article: 201.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/02/2021] [Indexed: 02/07/2023]
Abstract
CD8+ T cells specific for cancer cells are detected within tumours. However, despite their presence, tumours progress. The clinical success of immune checkpoint blockade and adoptive T cell therapy demonstrates the potential of CD8+ T cells to mediate antitumour responses; however, most patients with cancer fail to achieve long-term responses to immunotherapy. Here we review CD8+ T cell differentiation to dysfunctional states during tumorigenesis. We highlight similarities and differences between T cell dysfunction and other hyporesponsive T cell states and discuss the spatio-temporal factors contributing to T cell state heterogeneity in tumours. An important challenge is predicting which patients will respond to immunotherapeutic interventions and understanding which T cell subsets mediate the clinical response. We explore our current understanding of what determines T cell responsiveness and resistance to immunotherapy and point out the outstanding research questions.
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Affiliation(s)
- Mary Philip
- Vanderbilt Center for Immunobiology, Vanderbilt-Ingram Cancer Center, Department of Medicine/Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, TN, USA.,;
| | - Andrea Schietinger
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,;
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16
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Immune Regulatory Processes of the Tumor Microenvironment under Malignant Conditions. Int J Mol Sci 2021; 22:ijms222413311. [PMID: 34948104 PMCID: PMC8706102 DOI: 10.3390/ijms222413311] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/03/2021] [Accepted: 12/05/2021] [Indexed: 02/07/2023] Open
Abstract
The tumor microenvironment (TME) is a critical regulator of tumor growth, progression, and metastasis. Since immune cells represent a large fraction of the TME, they play a key role in mediating pro- and anti-tumor immune responses. Immune escape, which suppresses anti-tumor immunity, enables tumor cells to maintain their proliferation and growth. Numerous mechanisms, which have been intensively studied in recent years, are involved in this process and based on these findings, novel immunotherapies have been successfully developed. Here, we review the composition of the TME and the mechanisms by which immune evasive processes are regulated. In detail, we describe membrane-bound and soluble factors, their regulation, and their impact on immune cell activation in the TME. Furthermore, we give an overview of the tumor/antigen presentation and how it is influenced under malignant conditions. Finally, we summarize novel TME-targeting agents, which are already in clinical trials for different tumor entities.
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17
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Al-Khaykanee AM, Abdel-Rahman AAH, Essa A, Gadallah ANAA, Ali BH, Al-Aqar AA, Badr EAE, Shehab-Eldeen S. Genetic polymorphism of fibroblast growth factor receptor 2 and trinucleotide repeat-containing 9 influence the susceptibility to HCV-induced hepatocellular carcinoma. Clin Res Hepatol Gastroenterol 2021; 45:101636. [PMID: 33740609 DOI: 10.1016/j.clinre.2021.101636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/23/2020] [Accepted: 01/16/2021] [Indexed: 02/04/2023]
Abstract
BACKGROUND Fibroblast growth factor receptor 2 (FGFR2) and trinucleotide repeat-containing 9 (TRNC9) gene polymorphisms have been associated with some cancers. We aimed to assess the association of FGFR2 rs2981582 and TRNC9 rs12443621 polymorphisms with hepatocellular cancer risk. METHODS One hundred patients with HCV-induced HCC, 100 patients with chronic HCV infection, and 100 controls were genotyped for FGFR2 rs2981582 and TNRC9 rs12443621 using allele-specific Real-Time PCR analysis. RESULTS FGFR2 rs2981582 genotype TT was associated with increased risk of HCC when compared to controls (OR = 3.09, 95% CI = 1.24-7.68). However, it was significantly associated with a lower risk of HCC when using HCV patients as controls (OR = 0.21, 95% CI = 0.09-0.5), and T-allele of FGFR2 appears to be a protective allele against HCC in HCV patients (OR = 0.42, 95% CI = 0.21-0.85). While AG and GG genotypes of TNRC9 rs12443621 were linked with significantly increased risk of HCC (OR = 3.91, 95% CI = 2.02-7.6 and OR = 9.26, 95% CI = 3.21-26.7 respectively) and HCV patients carrying G allele were at increased risk of HCC by 2.7-fold. A significant high frequency of small tumor size and early-stage of HCC were observed in patients carrying FGFR2 rs2981582 genotype CT and TT (P = 0.029 and <0.001 respectively), while, TNRC9 rs12443621 genotype AG and GG were associated large tumor size and late-stage of HCC (P < 0.001 and 0.015 respectively). CONCLUSIONS SNPs in rs2981582 for FGFR2 and rs12443621 for TNRC9 gene were associated with HCC susceptibility, suggesting their implication in hepatocarcinogenesis in chronically HCV-infected patients.
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Affiliation(s)
| | | | - Abdallah Essa
- Tropical Medicine Department, Faculty of Medicine, Menoufia University, Egypt
| | | | - Bushra Hameed Ali
- Chemistry Department, College of Education for Pure Science, Ibn Al-Haitham, University of Baghdad, Iraq
| | | | - Eman A E Badr
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Menoufia University, Egypt
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18
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Liang C, Zhao Y, Chen C, Huang S, Deng T, Zeng X, Tan J, Zha X, Chen S, Li Y. Higher TOX Genes Expression Is Associated With Poor Overall Survival for Patients With Acute Myeloid Leukemia. Front Oncol 2021; 11:740642. [PMID: 34692519 PMCID: PMC8532529 DOI: 10.3389/fonc.2021.740642] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/20/2021] [Indexed: 12/11/2022] Open
Abstract
Thymocyte selection-associated HMG box (TOX) is a transcription factor that belongs to the high mobility group box (HMG-box) superfamily, which includes four subfamily members: TOX, TOX2, TOX3, and TOX4. TOX is related to the formation of multiple malignancies and contributes to CD8+ T cell exhaustion in solid tumors. However, little is known about the role of TOX genes in hematological malignancies. In this study, we explored the prognostic value of TOX genes from 40 patients with de novo acute myeloid leukemia (AML) by quantitative real-time PCR (qRT-PCR) in a training cohort and validated the results using transcriptome data from 167 de novo AML patients from the Cancer Genome Atlas (TCGA) database. In the training cohort, higher expression of TOX and TOX4 was detected in the AML samples, whereas lower TOX3 expression was found. Moreover, both the training and validation results indicated that higher TOX2, TOX3, and TOX4 expression of AML patients (3-year OS: 0% vs. 37%, P = 0.036; 3-year OS: 4% vs. 61%, P < 0.001; 3-year OS: 0% vs. 32%, P = 0.010) and the AML patients with highly co-expressed TOX, TOX2, TOX4 genes (3-year OS: 0% vs. 25% vs. 75%, P = 0.001) were associated with poor overall survival (OS). Interestingly, TOX2 was positively correlated with CTLA-4, PD-1, TIGIT, and PDL-2 (rs = 0.43, P = 0.006; rs = 0.43, P = 0.006; rs = 0.56, P < 0.001; rs = 0.54, P < 0.001). In conclusion, higher expression of TOX genes was associated with poor OS for AML patients, which was related to the up-regulation of immune checkpoint genes. These data might provide novel predictors for AML outcome and direction for further investigation of the possibility of using TOX genes in novel targeted therapies for AML.
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Affiliation(s)
- Chaofeng Liang
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China
| | - Yujie Zhao
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China
| | - Cunte Chen
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China
| | - Shuxin Huang
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China
| | - Tairan Deng
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China
| | - Xiangbo Zeng
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China
| | - Jiaxiong Tan
- Department of Hematology, First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Xianfeng Zha
- Department of Clinical Laboratory, First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Shaohua Chen
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China
| | - Yangqiu Li
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China
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19
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Nguyen Thi Ngoc Thanh, Tram PB, Tuyet NHH, Uyen NHP, Tien LTM, Anh DN, Van LTT, Luan HH, Hue NT. Association of Polymorphisms in Genes Involved in DNA Repair and Cell Cycle Arrest with Breast Cancer in a Vietnamese Case-Control Cohort. CYTOL GENET+ 2021. [DOI: 10.3103/s0095452721040101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Epigenetic Regulation of Cancer Immune Cells. Semin Cancer Biol 2021; 83:377-383. [PMID: 34182142 DOI: 10.1016/j.semcancer.2021.06.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 05/06/2021] [Accepted: 06/23/2021] [Indexed: 12/17/2022]
Abstract
The epigenetic regulation of immune response involves reversible and heritable changes that do not alter the DNA sequence. Though there have been extensive studies accomplished relating to epigenetic changes in cancer cells, recent focus has been shifted on epigenetic-mediated changes in the immune cells including T cells, Macrophages, Natural Killer cells and anti-tumor immune responses. This review compiles the most relevant and recent literature related to the role of epigenetic mechanisms including DNA methylation and histone modifications in immune cells of wide range of cancers. We also include recent research with respect to role of the most relevant transcription factors that epigenetically control the anti-tumor immune response. Finally, a statement of future direction that promises to look forward for strategies to improve immunotherapy in cancer.
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21
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Markopoulou K, Chase BA, Premkumar AP, Schoneburg B, Kartha N, Wei J, Yu H, Epshteyn A, Garduno L, Pham A, Vazquez R, Frigerio R, Maraganore D. Variable Effects of PD-Risk Associated SNPs and Variants in Parkinsonism-Associated Genes on Disease Phenotype in a Community-Based Cohort. Front Neurol 2021; 12:662278. [PMID: 33935957 PMCID: PMC8079937 DOI: 10.3389/fneur.2021.662278] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 03/18/2021] [Indexed: 11/13/2022] Open
Abstract
Genetic risk factors for Parkinson's disease (PD) risk and progression have been identified from genome-wide association studies (GWAS), as well as studies of familial forms of PD, implicating common variants at more than 90 loci and pathogenic or likely pathogenic variants at 16 loci. With the goal of understanding whether genetic variants at these PD-risk loci/genes differentially contribute to individual clinical phenotypic characteristics of PD, we used structured clinical documentation tools within the electronic medical record in an effort to provide a standardized and detailed clinical phenotypic characterization at the point of care in a cohort of 856 PD patients. We analyzed common SNPs identified in previous GWAS studies, as well as low-frequency and rare variants at parkinsonism-associated genes in the MDSgene database for their association with individual clinical characteristics and test scores at baseline assessment in our community-based PD patient cohort: age at onset, disease duration, Unified Parkinson's Disease Rating Scale I-VI, cognitive status, initial and baseline motor and non-motor symptoms, complications of levodopa therapy, comorbidities and family history of neurological disease with one or more than one affected family members. We find that in most cases an individual common PD-risk SNP identified in GWAS is associated with only a single clinical feature or test score, while gene-level tests assessing low-frequency and rare variants reveal genes associated in either a unique or partially overlapping manner with the different clinical features and test scores. Protein-protein interaction network analysis of the identified genes reveals that while some of these genes are members of already identified protein networks others are not. These findings indicate that genetic risk factors for PD differentially affect the phenotypic presentation and that genes associated with PD risk are also differentially associated with individual disease phenotypic characteristics at baseline. These findings raise the intriguing possibility that different SNPs/gene effects impact discrete phenotypic characteristics. Furthermore, they support the hypothesis that different gene and protein-protein interaction networks that underlie PD risk, the PD phenotype, and the neurodegenerative process leading to the disease phenotype, and point to the significance of the genetic background on disease phenotype.
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Affiliation(s)
- Katerina Markopoulou
- Department of Neurology, NorthShore University HealthSystem, Evanston, IL, United States
| | - Bruce A. Chase
- Health Information Technology, NorthShore University HealthSystem, Evanston, IL, United States
| | - Ashvini P. Premkumar
- Department of Neurology, NorthShore University HealthSystem, Evanston, IL, United States
| | - Bernadette Schoneburg
- Department of Neurology, NorthShore University HealthSystem, Evanston, IL, United States
| | - Ninith Kartha
- Department of Neurology, NorthShore University HealthSystem, Evanston, IL, United States
| | - Jun Wei
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL, United States
| | - Hongjie Yu
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL, United States
| | - Alexander Epshteyn
- Health Information Technology, NorthShore University HealthSystem, Evanston, IL, United States
| | - Lisette Garduno
- Department of Neurology, NorthShore University HealthSystem, Evanston, IL, United States
| | - Anna Pham
- Department of Neurology, NorthShore University HealthSystem, Evanston, IL, United States
| | - Rosa Vazquez
- Department of Neurology, NorthShore University HealthSystem, Evanston, IL, United States
| | - Roberta Frigerio
- Department of Neurology, NorthShore University HealthSystem, Evanston, IL, United States
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22
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Liang C, Huang S, Zhao Y, Chen S, Li Y. TOX as a potential target for immunotherapy in lymphocytic malignancies. Biomark Res 2021; 9:20. [PMID: 33743809 PMCID: PMC7981945 DOI: 10.1186/s40364-021-00275-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/10/2021] [Indexed: 02/07/2023] Open
Abstract
TOX (thymocyte selection-associated HMG BOX) is a member of a family of transcriptional factors that contain the highly conserved high mobility group box (HMG-box) region. Increasing studies have shown that TOX is involved in maintaining tumors and promoting T cell exhaustion. In this review, we summarized the biological functions of TOX and its contribution as related to lymphocytic malignancies. We also discussed the potential role of TOX as an immune biomarker and target in immunotherapy for hematological malignancies.
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Affiliation(s)
- Chaofeng Liang
- Key Laboratory for Regenerative Medicine of Ministry of Education; Institute of Hematology, School of Medicine, Jinan University, Guangzhou, 510632, China.,Department of Anatomy and Molecular Embryology, Institute of Anatomy, Ruhr-University Bochum, 44801, Bochum, Germany
| | - Shuxin Huang
- Key Laboratory for Regenerative Medicine of Ministry of Education; Institute of Hematology, School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Yujie Zhao
- Key Laboratory for Regenerative Medicine of Ministry of Education; Institute of Hematology, School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Shaohua Chen
- Key Laboratory for Regenerative Medicine of Ministry of Education; Institute of Hematology, School of Medicine, Jinan University, Guangzhou, 510632, China.
| | - Yangqiu Li
- Key Laboratory for Regenerative Medicine of Ministry of Education; Institute of Hematology, School of Medicine, Jinan University, Guangzhou, 510632, China.
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23
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HIV-1 Latency and Viral Reservoirs: Existing Reversal Approaches and Potential Technologies, Targets, and Pathways Involved in HIV Latency Studies. Cells 2021; 10:cells10020475. [PMID: 33672138 PMCID: PMC7926981 DOI: 10.3390/cells10020475] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/14/2021] [Accepted: 02/20/2021] [Indexed: 02/07/2023] Open
Abstract
Eradication of latent human immunodeficiency virus (HIV) infection is a global health challenge. Reactivation of HIV latency and killing of virus-infected cells, the so-called "kick and kill" or "shock and kill" approaches, are a popular strategy for HIV cure. While antiretroviral therapy (ART) halts HIV replication by targeting multiple steps in the HIV life cycle, including viral entry, integration, replication, and production, it cannot get rid of the occult provirus incorporated into the host-cell genome. These latent proviruses are replication-competent and can rebound in cases of ART interruption or cessation. In general, a very small population of cells harbor provirus, serve as reservoirs in ART-controlled HIV subjects, and are capable of expressing little to no HIV RNA or proteins. Beyond the canonical resting memory CD4+ T cells, HIV reservoirs also exist within tissue macrophages, myeloid cells, brain microglial cells, gut epithelial cells, and hematopoietic stem cells (HSCs). Despite a lack of active viral production, latently HIV-infected subjects continue to exhibit aberrant cellular signaling and metabolic dysfunction, leading to minor to major cellular and systemic complications or comorbidities. These include genomic DNA damage; telomere attrition; mitochondrial dysfunction; premature aging; and lymphocytic, cardiac, renal, hepatic, or pulmonary dysfunctions. Therefore, the arcane machineries involved in HIV latency and its reversal warrant further studies to identify the cryptic mechanisms of HIV reservoir formation and clearance. In this review, we discuss several molecules and signaling pathways, some of which have dual roles in maintaining or reversing HIV latency and reservoirs, and describe some evolving strategies and possible approaches to eliminate viral reservoirs and, ultimately, cure/eradicate HIV infection.
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24
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Han HS, Jeong S, Kim H, Kim HD, Kim AR, Kwon M, Park SH, Woo CG, Kim HK, Lee KH, Seo SP, Kang HW, Kim WT, Kim WJ, Yun SJ, Shin EC. TOX-expressing terminally exhausted tumor-infiltrating CD8 + T cells are reinvigorated by co-blockade of PD-1 and TIGIT in bladder cancer. Cancer Lett 2020; 499:137-147. [PMID: 33249194 DOI: 10.1016/j.canlet.2020.11.035] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/28/2020] [Accepted: 11/23/2020] [Indexed: 12/25/2022]
Abstract
Exhausted T cells in the tumor microenvironment are major targets of immunotherapies. However, the exhaustion status of CD8+ tumor-infiltrating lymphocytes (TILs) in bladder cancer has not been comprehensively evaluated. Herein, we examined distinct exhaustion status of CD8+ TILs based on the level of programmed cell death-1 (PD-1) and thymocyte selection-associated high mobility group box protein (TOX) expression in urothelial bladder cancer. We also evaluated the reinvigoration of exhausted CD8+ TILs upon ex vivo treatment with inhibitory checkpoint blockers. TOX-expressing PD-1highCD8+ TILs had the highest expression of immune checkpoint receptors (ICRs), the most terminally exhausted features, and the highest tumor antigen reactivity among PD-1+CD8+ TILs. Bladder cancer patients with a high percentage of PD-1highTOX+CD8+ TILs had more progressed T-cell exhaustion features and higher programmed death-ligand 1 expression in tumor tissues. TIGIT was the most frequent co-expressed ICR on PD-1+CD8+ TILs, and TIGIT blockade enhanced the PD-1 blockade-mediated cytokine production by CD8+ TILs from bladder cancer patients. Our findings provide an improved understanding of the heterogeneous exhaustion status of CD8+ TILs and additional immunotherapy strategies to improve outcomes of bladder cancer patients.
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Affiliation(s)
- Hye Sook Han
- Department of Internal Medicine, Chungbuk National University College of Medicine, Cheongju, Republic of Korea; Department of Internal Medicine, Chungbuk National University Hospital, Cheongju, Republic of Korea
| | - Seongju Jeong
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Hyunglae Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Hyung-Don Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - A Reum Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Minsuk Kwon
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Su-Hyung Park
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Chang Gok Woo
- Department of Pathology, Chungbuk National University Hospital, Cheongju, Republic of Korea
| | - Hee Kyung Kim
- Department of Internal Medicine, Chungbuk National University Hospital, Cheongju, Republic of Korea
| | - Ki Hyeong Lee
- Department of Internal Medicine, Chungbuk National University College of Medicine, Cheongju, Republic of Korea; Department of Internal Medicine, Chungbuk National University Hospital, Cheongju, Republic of Korea
| | - Sung Pil Seo
- Department of Urology, Chungbuk National University Hospital, Cheongju, Republic of Korea
| | - Ho Won Kang
- Department of Urology, Chungbuk National University Hospital, Cheongju, Republic of Korea; Department of Urology, Chungbuk National University College of Medicine, Cheongju, Republic of Korea
| | - Won Tae Kim
- Department of Urology, Chungbuk National University Hospital, Cheongju, Republic of Korea; Department of Urology, Chungbuk National University College of Medicine, Cheongju, Republic of Korea
| | - Wun-Jae Kim
- Department of Urology, Chungbuk National University Hospital, Cheongju, Republic of Korea; Department of Urology, Chungbuk National University College of Medicine, Cheongju, Republic of Korea
| | - Seok Joong Yun
- Department of Urology, Chungbuk National University Hospital, Cheongju, Republic of Korea; Department of Urology, Chungbuk National University College of Medicine, Cheongju, Republic of Korea.
| | - Eui-Cheol Shin
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea.
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25
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Coulcher JF, Roure A, Chowdhury R, Robert M, Lescat L, Bouin A, Carvajal Cadavid J, Nishida H, Darras S. Conservation of peripheral nervous system formation mechanisms in divergent ascidian embryos. eLife 2020; 9:e59157. [PMID: 33191918 PMCID: PMC7710358 DOI: 10.7554/elife.59157] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 11/13/2020] [Indexed: 01/23/2023] Open
Abstract
Ascidians with very similar embryos but highly divergent genomes are thought to have undergone extensive developmental system drift. We compared, in four species (Ciona and Phallusia for Phlebobranchia, Molgula and Halocynthia for Stolidobranchia), gene expression and gene regulation for a network of six transcription factors regulating peripheral nervous system (PNS) formation in Ciona. All genes, but one in Molgula, were expressed in the PNS with some differences correlating with phylogenetic distance. Cross-species transgenesis indicated strong levels of conservation, except in Molgula, in gene regulation despite lack of sequence conservation of the enhancers. Developmental system drift in ascidians is thus higher for gene regulation than for gene expression and is impacted not only by phylogenetic distance, but also in a clade-specific manner and unevenly within a network. Finally, considering that Molgula is divergent in our analyses, this suggests deep conservation of developmental mechanisms in ascidians after 390 My of separate evolution.
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Affiliation(s)
- Joshua F Coulcher
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM)Banyuls-sur-MerFrance
| | - Agnès Roure
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM)Banyuls-sur-MerFrance
| | - Rafath Chowdhury
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM)Banyuls-sur-MerFrance
| | - Méryl Robert
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM)Banyuls-sur-MerFrance
| | - Laury Lescat
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM)Banyuls-sur-MerFrance
| | - Aurélie Bouin
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM)Banyuls-sur-MerFrance
| | - Juliana Carvajal Cadavid
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM)Banyuls-sur-MerFrance
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka UniversityToyonakaJapan
| | - Sébastien Darras
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM)Banyuls-sur-MerFrance
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26
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Role, function and regulation of the thymocyte selection-associated high mobility group box protein in CD8 + T cell exhaustion. Immunol Lett 2020; 229:1-7. [PMID: 33186634 DOI: 10.1016/j.imlet.2020.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 10/25/2020] [Accepted: 11/07/2020] [Indexed: 12/31/2022]
Abstract
Thymocyte selection-associated high mobility group box protein (TOX), a member of the high-motility group box (HMG) protein superfamily, is an evolutionarily conserved DNA-binding protein. It functions as a transcription factor that modulates transcriptional programs by binding to DNA in a structure-dependent manner. It has been well established that TOX is required for the development of CD4+ T cells, natural killer (NK) cells and innate lymphoid cells (ILCs), as well as the autoimmunity mediated by CD8+ T cells. Recently, emerging evidence supports an essential role for TOX in the induction of T cell exhaustion in the setting of tumor or chronic viral infection by mediating transcriptional and epigenetic changes, which are cardinal hallmarks of exhausted T cells. Moreover, TOX plays a key role in the persistence of antigen-specific T cells and in the mitigation of tissue damage caused by immunopathology over the course of tumorigenesis and chronic infection. Additionally, TOX contributes to the high level of programmed cell death protein 1 (PD-1) on the cell surface by participating in the process of endocytic recycling of PD-1. In this review, we summarize the most recent information about the role of TOX in the process of T cell exhaustion, which enriches our understanding of the molecular mechanisms of CD8+ T cell exhaustion upon chronic antigen stimulation and reveals promising therapeutic targets for persisting infection and cancer.
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27
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Castillo-Higuera T, Alarcón-Granados MC, Marin-Suarez J, Moreno-Ortiz H, Esteban-Pérez CI, Ferrebuz-Cardozo AJ, Forero-Castro M, Camargo-Vill Alba G. A Comprehensive Overview of Common Polymorphic Variants in Genes Related to Polycystic Ovary Syndrome. Reprod Sci 2020; 28:2399-2412. [PMID: 33174186 DOI: 10.1007/s43032-020-00375-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 10/21/2020] [Indexed: 01/07/2023]
Abstract
Polycystic ovary syndrome (PCOS) is one of the most common endocrine-metabolic disorders in women of reproductive age. It is characterized by an increase in the biosynthesis of androgens, anovulation, and infertility. PCOS has been reported as a polygenic entity in which multiple single nucleotide polymorphisms (SNPs) are associated with the clinical features of the pathology. Herein, we describe the common polymorphic variants in genes related to PCOS, their role in its pathogenesis, and etiology. Whole-genome association studies have been focused on women from Asian and European populations. The most common genes associated with PCOS are DENND1A, THADA, FSHR, and LHCGR. However, other genes have been associated with PCOS such as AMH, AMHR2, ADIPOQ, FTO, HNF1A, CYP19, YAP1, HMGA2, RAB5B, SUOX, INSR, and TOX3. Nevertheless, the relationship between the biological functions of these genes and the development of the pathology is unclear. Studies in each gene in different populations do not always comply with a general pattern, so researching these variants is essential for better understanding of this polygenic syndrome. Future population studies should be carried out to evaluate biological processes, incidence rates, allelic and genotypic frequencies, and genetic susceptibility factors that predispose PCOS.
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Affiliation(s)
- Tatiana Castillo-Higuera
- Maestría en Ciencias Biológicas, Universidad Pedagógica y Tecnológica de Colombia, Tunja, 150003, Colombia.,Escuela de Ciencias Biológicas. Grupo de investigación en Ciencias Biomédicas (GICBUPTC), Universidad Pedagógica y Tecnológica de Colombia, Avenida Central del Norte 39-115, Tunja, 150003, Colombia
| | - María Camila Alarcón-Granados
- Escuela de Ciencias Biológicas. Grupo de investigación en Ciencias Biomédicas (GICBUPTC), Universidad Pedagógica y Tecnológica de Colombia, Avenida Central del Norte 39-115, Tunja, 150003, Colombia
| | - Johana Marin-Suarez
- Maestría en Ciencias Biológicas, Universidad Pedagógica y Tecnológica de Colombia, Tunja, 150003, Colombia.,Escuela de Ciencias Biológicas. Grupo de investigación en Ciencias Biomédicas (GICBUPTC), Universidad Pedagógica y Tecnológica de Colombia, Avenida Central del Norte 39-115, Tunja, 150003, Colombia
| | | | | | | | - Maribel Forero-Castro
- Escuela de Ciencias Biológicas. Grupo de investigación en Ciencias Biomédicas (GICBUPTC), Universidad Pedagógica y Tecnológica de Colombia, Avenida Central del Norte 39-115, Tunja, 150003, Colombia.
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28
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Sima C, Iordache P, Poenaru E, Manolescu A, Poenaru C, Jinga V. Genome-wide association study of nephrolithiasis in an Eastern European population. Int Urol Nephrol 2020; 53:309-313. [PMID: 32865774 DOI: 10.1007/s11255-020-02606-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/06/2020] [Indexed: 12/25/2022]
Abstract
PURPOSE Nephrolithiasis is a urological pathology that occurs at high rates and carries a great burden in terms of costs. The probability of recurrence is significant, necessitating improvements in prophylaxis and understanding of the disease mechanism. Despite the high heritability of this disease, only five genome-wide association studies (GWAS) of nephrolithiasis have been published. METHODS We selected 335 unrelated confirmed nephrolithiasis cases from two major sample collection projects (blood and buccal swabs) in Romania. DNA was extracted from whole blood and buccal swabs at deCODE Genetics (Reykjavik, Iceland) and genotyped. RESULTS Single-nucleotide polymorphisms identified from this GWAS implicated biological pathways and gene ontologies involving solute transport, renal physiology, and calcium homeostasis. Three loci especially emerged as candidates with a highly significant association with nephrolithiasis: RS10917682 in Regulator of G protein signaling 5, which has crucial roles in mRNA regulation and has been linked to renal cell carcinoma; RS1118528 in Solute carrier family 25 member 24, which encodes a mitochondrial ATP-Mg/phosphate carrier protein that likely influences a variety of important cellular pathways; and the TOX2-associated locus rs4437026, because TOX2 is upregulated in several tumor types and linked to tumor progression. CONCLUSION This study is the largest kidney stone-related GWAS reported in an Eastern European population and the first GWAS performed in a Romanian population to investigate the genetic risk factors for nephrolithiasis. We identified several loci that warrant further investigation for a better understanding of this highly heritable condition.
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Affiliation(s)
- C Sima
- "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania
- "Prof. Dr. Th. Burghele" Clinical Hospital, Bucharest, Romania
| | - P Iordache
- "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania
- Exigia Medical, Bucharest, Romania
| | - E Poenaru
- "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania.
| | | | | | - V Jinga
- "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania
- "Prof. Dr. Th. Burghele" Clinical Hospital, Bucharest, Romania
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29
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Zhang H, Fan F, Yu Y, Wang Z, Liu F, Dai Z, Zhang L, Liu Z, Cheng Q. Clinical characterization, genetic profiling, and immune infiltration of TOX in diffuse gliomas. J Transl Med 2020; 18:305. [PMID: 32762688 PMCID: PMC7409670 DOI: 10.1186/s12967-020-02460-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 07/26/2020] [Indexed: 01/19/2023] Open
Abstract
Background Immunotherapies targeting glioblastoma (GBM) have led to significant improvements in patient outcomes. TOX is closely associated with the immune environment surrounding tumors, but its role in gliomas is not fully understood. Methods Using data from The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA), we analyzed the transcriptomes of 1691 WHO grade I-IV human glioma samples. The R language was used to perform most of the statistical analyses. Somatic mutations and somatic copy number variation (CNV) were analyzed using GISTIC 2.0. Results TOX was down-regulated in malignant gliomas compared to low grade gliomas, and upregulated in the proneural and IDH mutant subtypes of GBM. TOXlow tumours are associated with the loss of PTEN and amplification of EGFR, while TOXhigh tumours harbor frequent mutations in IDH1 (91%). TOX was highly expressed in leading edge regions of tumours. Gene ontology and pathway analyses demonstrated that TOX was enriched in multiple immune related processes including lymphocyte migration in GBM. Finally, TOX had a negative association with the infiltration of several immune cell types in the tumour microenvironment. Conclusion TOX has the potential to be a new prognostic marker for GBM.
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Affiliation(s)
- Hao Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Fan Fan
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.,Center for Medical Genetics and Hunan Provincial Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yuanqiang Yu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zeyu Wang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Fangkun Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ziyu Dai
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Liyang Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China. .,Department of Medicine, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA. .,Clinical Diagnosis and Therapeutic Center of Glioma, Xiangya Hospital, Central South University, Changsha, 410078, Hunan, People's Republic of China.
| | - Zhixiong Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China. .,Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
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30
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Expression pattern, regulation, and clinical significance of TOX in breast cancer. Cancer Immunol Immunother 2020; 70:349-363. [PMID: 32757053 DOI: 10.1007/s00262-020-02689-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 07/30/2020] [Indexed: 12/11/2022]
Abstract
Thymocyte selection-associated high mobility group box protein (TOX) is a transcription factor implicated in the regulation of T cell exhaustion during chronic infection and cancer. While TOX is being targeted for cancer immunotherapy, limited information is available about its significance in breast cancer and other solid tumors. We performed a comprehensive analysis of TOX gene expression, its epigenetic regulation, protein localization, relation to tumor infiltrating immune cell composition, and prognostic significance in breast cancer using publicly available datasets. Our results suggest an inverse correlation between TOX expression and DNA methylation in tumor cells. However, its expression is elevated in tumor infiltrating immune cells (TIICs), which may compensates for the total TOX levels in the tumor as a whole. Furthermore, higher TOX levels in tumors are associated with T cell exhaustion signatures along with presence of active inflammatory response, including elevated levels of T cell effector cytokines. Survival analysis also confirmed that higher expression of TOX is associated with better prognosis in breast cancer. Therefore, expression of TOX may serve as a novel prognostic marker for this malignancy.
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31
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Sekine T, Perez-Potti A, Nguyen S, Gorin JB, Wu VH, Gostick E, Llewellyn-Lacey S, Hammer Q, Falck-Jones S, Vangeti S, Yu M, Smed-Sörensen A, Gaballa A, Uhlin M, Sandberg JK, Brander C, Nowak P, Goepfert PA, Price DA, Betts MR, Buggert M. TOX is expressed by exhausted and polyfunctional human effector memory CD8 + T cells. Sci Immunol 2020; 5:5/49/eaba7918. [PMID: 32620560 DOI: 10.1126/sciimmunol.aba7918] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/22/2020] [Indexed: 12/30/2022]
Abstract
CD8+ T cell exhaustion is a hallmark of many cancers and chronic infections. In mice, T cell factor 1 (TCF-1) maintains exhausted CD8+ T cell responses, whereas thymocyte selection-associated HMG box (TOX) is required for the epigenetic remodeling and survival of exhausted CD8+ T cells. However, it has remained unclear to what extent these transcription factors play analogous roles in humans. In this study, we mapped the expression of TOX and TCF-1 as a function of differentiation and specificity in the human CD8+ T cell landscape. Here, we demonstrate that circulating TOX+ CD8+ T cells exist in most humans, but that TOX is not exclusively associated with exhaustion. Effector memory CD8+ T cells generally expressed TOX, whereas naive and early-differentiated memory CD8+ T cells generally expressed TCF-1. Cytolytic gene and protein expression signatures were also defined by the expression of TOX. In the context of a relentless immune challenge, exhausted HIV-specific CD8+ T cells commonly expressed TOX, often in clusters with various activation markers and inhibitory receptors, and expressed less TCF-1. However, polyfunctional memory CD8+ T cells specific for cytomegalovirus (CMV) or Epstein-Barr virus (EBV) also expressed TOX, either with or without TCF-1. A similar phenotype was observed among HIV-specific CD8+ T cells from individuals who maintained exceptional immune control of viral replication. Collectively, these data demonstrate that TOX is expressed by most circulating effector memory CD8+ T cell subsets and not exclusively linked to exhaustion.
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Affiliation(s)
- Takuya Sekine
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - André Perez-Potti
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Son Nguyen
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jean-Baptiste Gorin
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Vincent H Wu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Emma Gostick
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff, UK
| | - Sian Llewellyn-Lacey
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff, UK
| | - Quirin Hammer
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Sara Falck-Jones
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Sindhu Vangeti
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Meng Yu
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Anna Smed-Sörensen
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Ahmed Gaballa
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Michael Uhlin
- Department of Applied Physics, Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden.,Department of Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Johan K Sandberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Christian Brander
- IrsiCaixa AIDS Research Institute, Badalona, Spain.,Universitat de Vic-Universitat Central de Catalunya, Vic, Spain.,Institució Catalana de Recerca i Estudis Avançats, ICREA, Barcelona, Spain
| | - Piotr Nowak
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Paul A Goepfert
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff, UK.,Systems Immunity Research Institute, Cardiff University School of Medicine, University Hospital of Wales, Cardiff, UK
| | - Michael R Betts
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marcus Buggert
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.
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32
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Balkhi MY. Receptor signaling, transcriptional, and metabolic regulation of T cell exhaustion. Oncoimmunology 2020; 9:1747349. [PMID: 32363117 PMCID: PMC7185212 DOI: 10.1080/2162402x.2020.1747349] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 02/11/2020] [Accepted: 02/28/2020] [Indexed: 12/23/2022] Open
Abstract
Exhaustion cripples T cell effector responses against metastatic cancers and chronic infections alike. There has been considerable interest in understanding the molecular and cellular mechanisms driving T cell exhaustion in human cancers fueled by the success of immunotherapy drugs especially the checkpoint receptor blockade (CRB) inhibitory antibodies that reverses T cell functional exhaustion. The current understanding of molecular mechanism of T cell exhaustion has been elucidated from the studies utilizing murine models of chronic viral infections. These studies have formed the basis for much of our understanding of the process of exhaustion and proven vital to developing anti-exhaustion therapies against human cancers. In this review, we discuss the T cell exhaustion differentiation pathway in cancers and chronic viral infections and explore how the transcription factors expression dynamics play role in T cell exhaustion fate choices and maturation. Finally, we summarize the role of some of the most important transcription factors involved in T cell functional exhaustion and construct exhaustion specific signaling pathway maps.
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Affiliation(s)
- Mumtaz Y Balkhi
- Department of Molecular & Biomedical Sciences, University of Maine, Orono, ME, USA.,Division of Hematology/Oncology Tufts Medical Center and Tufts University School of Medicine, Boston, MA, USA.,Immune Therapy Bio, Nest.Bio Labs, Vassar St. Cambridge, MA, USA
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33
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Association of the functional genetic variants of TOX3 gene with breast cancer in Iran: A case-control study. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2019.100511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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34
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Maestre L, García-García JF, Jiménez S, Reyes-García AI, García-González Á, Montes-Moreno S, Arribas AJ, González-García P, Caleiras E, Banham AH, Piris MÁ, Roncador G. High-mobility group box (TOX) antibody a useful tool for the identification of B and T cell subpopulations. PLoS One 2020; 15:e0229743. [PMID: 32106280 PMCID: PMC7046285 DOI: 10.1371/journal.pone.0229743] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 02/13/2020] [Indexed: 11/19/2022] Open
Abstract
Thymocyte selection-associated high-mobility group box (TOX) is a DNA-binding factor that is able to regulate transcription by modifying local chromatin structure and modulating the formation of multi-protein complexes. TOX has multiple roles in the development of the adaptive immune system including development of CD4 T cells, NK cells and lymph node organogenesis. However very few antibodies recognizing this molecule have been reported and no extensive study of the expression of TOX in reactive and neoplastic lymphoid tissue has been performed to date. In the present study, we have investigated TOX expression in normal and neoplastic lymphoid tissues using a novel rat monoclonal antibody that recognizes its target molecule in paraffin-embedded tissue sections. A large series of normal tissues and B- and T-cell lymphomas was studied, using whole sections and tissue microarrays. We found that the majority of precursor B/T lymphoblastic, follicular and diffuse large B-cell lymphomas, nodular lymphocyte-predominant Hodgkin lymphomas and angioimmunoblastic T-cell lymphomas strongly expressed the TOX protein. Burkitt and mantle cell lymphomas showed TOX expression in a small percentage of cases. TOX was not found in the majority of chronic lymphocytic leukemia, myelomas, marginal zone lymphomas and classical Hodgkin lymphomas. In conclusion, we describe for the first time the expression of TOX in normal and neoplastic lymphoid tissues. The co-expression of TOX and PD-1 identified in normal and neoplastic T cells is consistent with recent studies identifying TOX as a critical regulator of T-cell exhaustion and a potential immunotherapy target. Its differential expression may be of diagnostic relevance in the differential diagnosis of follicular lymphoma, the identification of the phenotype of diffuse large B-cell lymphoma and the recognition of peripheral T-cell lymphoma with a follicular helper T phenotype.
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MESH Headings
- Animals
- Antibodies, Monoclonal, Murine-Derived/immunology
- Antibody Specificity
- B-Lymphocyte Subsets/immunology
- B-Lymphocyte Subsets/metabolism
- B-Lymphocyte Subsets/pathology
- Cell Line, Tumor
- Female
- Gene Expression
- High Mobility Group Proteins/genetics
- High Mobility Group Proteins/immunology
- High Mobility Group Proteins/metabolism
- Humans
- Lymphoid Tissue/immunology
- Lymphoid Tissue/metabolism
- Lymphoma, B-Cell/immunology
- Lymphoma, B-Cell/metabolism
- Lymphoma, B-Cell/pathology
- Lymphoma, T-Cell/immunology
- Lymphoma, T-Cell/metabolism
- Lymphoma, T-Cell/pathology
- Male
- Mice
- Mice, Inbred C57BL
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Rats
- Rats, Wistar
- T-Lymphocyte Subsets/immunology
- T-Lymphocyte Subsets/metabolism
- T-Lymphocyte Subsets/pathology
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Affiliation(s)
| | | | | | | | | | | | - Alberto J. Arribas
- Università della Svizzera Italiana, Institute of Oncology Research, Bellinzona, Switzerland
| | | | | | - Alison H. Banham
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Miguel Ángel Piris
- Department of Pathology, Fundación Jiménez Díaz, CIBERONC, Madrid, Spain
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35
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Bakhashab S, Ahmed N. Genotype based Risk Predictors for Polycystic Ovary Syndrome in Western Saudi Arabia. Bioinformation 2019; 15:812-819. [PMID: 31902981 PMCID: PMC6936662 DOI: 10.6026/97320630015812] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 11/28/2019] [Accepted: 12/07/2019] [Indexed: 02/02/2023] Open
Abstract
Polycystic ovary syndrome (PCOS) is the most common endocrine disease among premenopausal women. The genetic risk of PCOS in the Saudi population is still unclear. Therefore, it is of interest to study the genotype and allele frequency for six gene variants (THADA rs13429458, TOX3 rs4784165, FSHR rs2268361, YAP1 rs1894116, RAB5B rs705702, and HMGA2 rs2272046) in patients with PCOS in western Saudi population. The study included 95 PCOS patients and 94 normal ovulatory females as controls. Genotyping was performed using TaqMan™ real-time polymerase chain reaction assays. There was significant link between the THADA rs13429458 variant and PCOS. Homozygosity in allele A of the rs13429458 variant was correlated with hyperandrogenism (HA) risk. Homozygosity in the T allele of the FSHR rs2268361 variant was associated with normal levels of AMH among non-PCOS women. The THADA rs13429458 and TOX3 rs4784165 variants were significantly associated with the combined oligo/amenorrhea (OA) and polycystic ovarian morphology subgroups while the HMGA2 rs2272046 variant was significantly associated with the combined HA and OA subgroup. Thus, results show the genetic risk of the THADA rs13429458, TOX3 rs4784165, and HMGA2 rs2272046 variants on PCOS patients in the western Saudi population.
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Affiliation(s)
- Sherin Bakhashab
- Biochemistry Department, King Abdulaziz University, Jeddah, P.O. Box 80218, Saudi Arabia
- Centre of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah, P.O. Box 80216, Saudi Arabia
| | - Nada Ahmed
- Biochemistry Department, King Abdulaziz University, Jeddah, P.O. Box 80218, Saudi Arabia
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36
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Akhtar M, Jamal T, Din JU, Hayat C, Rauf M, Ul Haq SM, Sher Khan R, Shah AA, Jamal M, Jalil F. An in silico approach to characterize nonsynonymous SNPs and regulatory SNPs in human TOX3 gene. J Genet 2019; 98:104. [PMID: 31819019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cancer is one of the deadliest complex diseases having multigene nature where the role of single-nucleotide polymorphism (SNP) has been well explored in multiple genes. TOX high mobility group box family member 3 (TOX3) is one such gene, in which SNPs have been found to be associated with breast cancer. In this study, we have examined the potentially damaging nonsynonymous SNPs(nsSNPs) in TOX3 gene using in silico tools, namely PolyPhen2, SNP&GO, PhD-SNP and PROVEAN, which were further confirmed by I-Mutant, MutPred1.2 and ConSurf for their stability, functional and structural effects. nsSNPs rs368713418 (A266D), rs751141352 (P273S, P273T), rs200878352 (A275T) have been found to be the most deleterious that may have a vital role in breast cancer. Premature stop codon producing SNPs (Q527STOP), rs1259790811 (G495STOP), rs1294465822 (S395STOP) and rs1335372738 (G8STOP) were also found having prime importance in truncated and malfunctional protein formation. We also characterized regulatory SNPs for its potential effect on TOX3 gene regulation and found nine SNPs that may affect the gene regulation. Further, we have also designed 3D models using I-TASSER for the wild type and four mutant TOX3 proteins. Our study concludes that these SNPs can be of prime importance while studying breast cancer and other associated diseases as well. They are required to be studied in model organisms and cell cultures, and may have potential importance in personalized medicines and gene therapy.
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Affiliation(s)
- Mehran Akhtar
- Department of Biotechnology, Abdul Wali Khan University, Mardan 23200, Pakistan.
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37
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An in silico approach to characterize nonsynonymous SNPs and regulatory SNPs in human TOX3 gene. J Genet 2019. [DOI: 10.1007/s12041-019-1153-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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38
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Vanheer L, Song J, De Geest N, Janiszewski A, Talon I, Provenzano C, Oh T, Chappell J, Pasque V. Tox4 modulates cell fate reprogramming. J Cell Sci 2019; 132:jcs.232223. [PMID: 31519808 PMCID: PMC6826012 DOI: 10.1242/jcs.232223] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 09/06/2019] [Indexed: 01/05/2023] Open
Abstract
Reprogramming to induced pluripotency induces the switch of somatic cell identity to induced pluripotent stem cells (iPSCs). However, the mediators and mechanisms of reprogramming remain largely unclear. To elucidate the mediators and mechanisms of reprogramming, we used a siRNA-mediated knockdown approach for selected candidate genes during the conversion of somatic cells into iPSCs. We identified Tox4 as a novel factor that modulates cell fate through an assay that determined the efficiency of iPSC reprogramming. We found that Tox4 is needed early in reprogramming to efficiently generate early reprogramming intermediates, irrespective of the reprogramming conditions used. Tox4 enables proper exogenous reprogramming factor expression, and the closing and opening of putative somatic and pluripotency enhancers early during reprogramming, respectively. We show that the TOX4 protein assembles into a high molecular form. Moreover, Tox4 is also required for the efficient conversion of fibroblasts towards the neuronal fate, suggesting a broader role of Tox4 in modulating cell fate. Our study reveals Tox4 as a novel transcriptional modulator of cell fate that mediates reprogramming from the somatic state to the pluripotent and neuronal fate.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Lotte Vanheer
- KU Leuven - University of Leuven, Department of Development and Regeneration, Herestraat 49, B-3000 Leuven, Belgium
| | - Juan Song
- KU Leuven - University of Leuven, Department of Development and Regeneration, Herestraat 49, B-3000 Leuven, Belgium
| | - Natalie De Geest
- KU Leuven - University of Leuven, Department of Development and Regeneration, Herestraat 49, B-3000 Leuven, Belgium
| | - Adrian Janiszewski
- KU Leuven - University of Leuven, Department of Development and Regeneration, Herestraat 49, B-3000 Leuven, Belgium
| | - Irene Talon
- KU Leuven - University of Leuven, Department of Development and Regeneration, Herestraat 49, B-3000 Leuven, Belgium
| | - Caterina Provenzano
- KU Leuven - University of Leuven, Department of Development and Regeneration, Herestraat 49, B-3000 Leuven, Belgium
| | - Taeho Oh
- KU Leuven - University of Leuven, Department of Development and Regeneration, Herestraat 49, B-3000 Leuven, Belgium
| | - Joel Chappell
- KU Leuven - University of Leuven, Department of Development and Regeneration, Herestraat 49, B-3000 Leuven, Belgium
| | - Vincent Pasque
- KU Leuven - University of Leuven, Department of Development and Regeneration, Herestraat 49, B-3000 Leuven, Belgium
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39
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TOX: a rediscovered master molecular actor to enhance immuno-oncology interventions. Cell Mol Immunol 2019; 17:558-560. [PMID: 31515505 DOI: 10.1038/s41423-019-0276-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 08/08/2019] [Indexed: 11/08/2022] Open
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40
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Johnson ND, Huang L, Li R, Li Y, Yang Y, Kim HR, Grant C, Wu H, Whitsel EA, Kiel DP, Baccarelli AA, Jin P, Murabito JM, Conneely KN. Age-related DNA hydroxymethylation is enriched for gene expression and immune system processes in human peripheral blood. Epigenetics 2019; 15:294-306. [PMID: 31506003 DOI: 10.1080/15592294.2019.1666651] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
DNA methylation (DNAm) has a well-established association with age in many tissues, including peripheral blood mononuclear cells (PBMCs). Compared to DNAm, the closely related epigenetic modification known as DNA hydroxymethylation (DNAhm) was much more recently discovered in mammals. Preliminary investigations have observed a positive correlation between gene body DNAhm and cis-gene expression. While some of these studies have observed an association between age and global DNAhm, none have investigated region-specific age-related DNAhm in human blood samples. In this study, we investigated DNAhm and gene expression in PBMCs of 10 young and 10 old, healthy female volunteers. Thousands of regions were differentially hydroxymethylated in the old vs. young individuals in gene bodies, exonic regions, enhancers, and promoters. Consistent with previous work, we observed directional consistency between age-related differences in DNAhm and gene expression. Further, age-related DNAhm and genes with high levels of DNAhm were enriched for immune system processes which may support a role of age-related DNAhm in immunosenescence.
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Affiliation(s)
- Nicholas D Johnson
- Department of Human Genetics, Emory University, Atlanta, GA, USA.,Population Biology, Ecology, and Evolution Program, Emory University, Atlanta, GA, USA
| | - Luoxiu Huang
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Ronghua Li
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Yun Li
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA.,Department of Biostatistics, Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
| | - Yuchen Yang
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Hye Rim Kim
- Department of Human Genetics, Emory University, Atlanta, GA, USA.,Cancer Biology Graduate Program, Emory University, Atlanta, GA, USA
| | - Crystal Grant
- Department of Human Genetics, Emory University, Atlanta, GA, USA.,Genetics and Molecular Biology Graduate Program, Emory University, Atlanta, GA, USA
| | - Hao Wu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA
| | - Eric A Whitsel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA.,Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Douglas P Kiel
- Hebrew SeniorLife, Department of Medicine Beth Israel Deaconess Medical Center and Harvard Medical School, Hinda and Arthur Marcus Institute for Aging Research, Boston, MA, USA
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Peng Jin
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Joanne M Murabito
- National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA, USA.,Section of General Internal Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Karen N Conneely
- Department of Human Genetics, Emory University, Atlanta, GA, USA.,Population Biology, Ecology, and Evolution Program, Emory University, Atlanta, GA, USA
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41
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Tajbakhsh A, Farjami Z, Darroudi S, Ayati SH, Vakili F, Asghari M, Alimardani M, Abedini S, Kushyar MM, Pasdar A. Association of rs4784227-CASC16 (LOC643714 locus) and rs4782447-ACSF3 polymorphisms and their association with breast cancer risk among Iranian population. EXCLI JOURNAL 2019; 18:429-438. [PMID: 31338012 PMCID: PMC6635718 DOI: 10.17179/excli2019-1374] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 06/11/2019] [Indexed: 12/22/2022]
Abstract
TOX3 and FOXA1 proteins are believed to be involved in the susceptibility of breast cancer. rs4784227-CASC16 and rs4782447-ACSF3, as single nucleotide polymorphisms (SNPs), located at the 16q may affect the FOXA1 DNA binding sequence change and therefore may enhance the FOXA1-binding affinity to the promoter of TOX3 gene. This study aimed to investigate the association of these SNPs/haplotypes with breast cancer susceptibility in an Iranian population. We conducted a case-control study of 1072 blood samples (505 breast cancer patients and 567 controls). Genotyping of rs4784227-CASC16 and rs4782447-ACSF3 SNPs was carried out by ARMS-PCR. Moreover, statistical analysis was done using SPSS version 20.0 (IBM Inc., Chicago, IL, USA), PHASE v 2.1 and SNP analyser 2.0. There was a strongly significant statistical association between alleles and genotypes of rs4784227-CASC16 with breast cancer risk in our study population (p<0.05). Moreover, a significant association was demonstrated between TA haplotype and breast cancer risk (OR=0.78; 95% CI (0.62-0.96); P-value=0.025). In this respect, although we did not observe a statistically significant association between rs4782447-ACSF3 with breast cancer susceptibility, the combination of the effects of rs4784227-CASC16 and rs4782447-ACSF3 SNPs may also affect the risk. This is in line with other studies suggesting these SNPs as risk-associated polymorphisms which may lead to a change in the affinity of FOXA1, as a distal enhancer, to TOX3 and thus change in TOX3 expression, which can eventually affect the risk of breast cancer.
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Affiliation(s)
- Amir Tajbakhsh
- Department of Modern Sciences & Technologies, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Young Researchers and Elite Club, Yasooj Branch, Islamic Azad University, Yasooj, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Farjami
- Department of Modern Sciences & Technologies, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Susan Darroudi
- Department of Modern Sciences & Technologies, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Hasan Ayati
- Immunology Research Center, Department of Immunology, Medical School, Mashhad University of Medical Sciences. Mashhad, Iran
| | - Fatemeh Vakili
- Midwifery department, Faculty of Nursing and Midwifery, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahla Asghari
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Maliheh Alimardani
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Soheila Abedini
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Mahdi Kushyar
- Department of Haematology-Oncology, Imam Reza Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alireza Pasdar
- Department of Modern Sciences & Technologies, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Division of Applied Medicine, Faculty of Medicine, University of Aberdeen, Foresterhill, Aberdeen, UK
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42
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Scott AC, Dündar F, Zumbo P, Chandran SS, Klebanoff CA, Shakiba M, Trivedi P, Menocal L, Appleby H, Camara S, Zamarin D, Walther T, Snyder A, Femia MR, Comen EA, Wen HY, Hellmann MD, Anandasabapathy N, Liu Y, Altorki NK, Lauer P, Levy O, Glickman MS, Kaye J, Betel D, Philip M, Schietinger A. TOX is a critical regulator of tumour-specific T cell differentiation. Nature 2019; 571:270-274. [PMID: 31207604 PMCID: PMC7698992 DOI: 10.1038/s41586-019-1324-y] [Citation(s) in RCA: 650] [Impact Index Per Article: 130.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 06/04/2019] [Indexed: 01/18/2023]
Abstract
Tumour-specific CD8 T cell dysfunction is a differentiation state that is distinct from the functional effector or memory T cell states1–6. Here we identify the nuclear factor TOX as a crucial regulator of the differentiation of tumour-specific T (TST) cells. We show that TOX is highly expressed in dysfunctional TST cells from tumours and in exhausted T cells during chronic viral infection. Expression of TOX is driven by chronic T cell receptor stimulation and NFAT activation. Ectopic expression of TOX in effector T cells in vitro induced a transcriptional program associated with T cell exhaustion. Conversely, deletion of Tox in TST cells in tumours abrogated the exhaustion program: Tox-deleted TST cells did not upregulate genes for inhibitory receptors (such as Pdcd1, Entpd1, Havcr2, Cd244 and Tigit), the chromatin of which remained largely inaccessible, and retained high expression of transcription factors such as TCF-1. Despite their normal, ‘non-exhausted’ immunophenotype, Tox-deleted TST cells remained dysfunctional, which suggests that the regulation of expression of inhibitory receptors is uncoupled from the loss of effector function. Notably, although Tox-deleted CD8 T cells differentiated normally to effector and memory states in response to acute infection, Tox-deleted TST cells failed to persist in tumours. We hypothesize that the TOX-induced exhaustion program serves to prevent the overstimulation of T cells and activation-induced cell death in settings of chronic antigen stimulation such as cancer.
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Affiliation(s)
- Andrew C Scott
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Friederike Dündar
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.,Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, USA
| | - Paul Zumbo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.,Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, USA
| | - Smita S Chandran
- Parker Institute for Cancer Immunotherapy, New York, NY, USA.,Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher A Klebanoff
- Parker Institute for Cancer Immunotherapy, New York, NY, USA.,Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell Medical College, New York, NY, USA
| | - Mojdeh Shakiba
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Prerak Trivedi
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Laura Menocal
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Heather Appleby
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Steven Camara
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dmitriy Zamarin
- Parker Institute for Cancer Immunotherapy, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tyler Walther
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexandra Snyder
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew R Femia
- Parker Institute for Cancer Immunotherapy, New York, NY, USA.,Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elizabeth A Comen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell Medical College, New York, NY, USA
| | - Hannah Y Wen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew D Hellmann
- Parker Institute for Cancer Immunotherapy, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell Medical College, New York, NY, USA
| | - Niroshana Anandasabapathy
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA.,Department of Dermatology, Weill Cornell Medical College, New York, NY, USA
| | - Yong Liu
- Department of Dermatology, Weill Cornell Medical College, New York, NY, USA
| | - Nasser K Altorki
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, New York Presbyterian Hospital, New York, NY, USA
| | | | - Olivier Levy
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael S Glickman
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Jonathan Kaye
- Research Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Doron Betel
- Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, USA.,Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Mary Philip
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Andrea Schietinger
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA. .,Parker Institute for Cancer Immunotherapy, New York, NY, USA.
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43
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Alfei F, Kanev K, Hofmann M, Wu M, Ghoneim HE, Roelli P, Utzschneider DT, von Hoesslin M, Cullen JG, Fan Y, Eisenberg V, Wohlleber D, Steiger K, Merkler D, Delorenzi M, Knolle PA, Cohen CJ, Thimme R, Youngblood B, Zehn D. TOX reinforces the phenotype and longevity of exhausted T cells in chronic viral infection. Nature 2019; 571:265-269. [DOI: 10.1038/s41586-019-1326-9] [Citation(s) in RCA: 396] [Impact Index Per Article: 79.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 05/30/2019] [Indexed: 02/07/2023]
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44
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Yao C, Sun HW, Lacey NE, Ji Y, Moseman EA, Shih HY, Heuston EF, Kirby M, Anderson S, Cheng J, Khan O, Handon R, Reilley J, Fioravanti J, Hu J, Gossa S, Wherry EJ, Gattinoni L, McGavern DB, O'Shea JJ, Schwartzberg PL, Wu T. Single-cell RNA-seq reveals TOX as a key regulator of CD8 + T cell persistence in chronic infection. Nat Immunol 2019; 20:890-901. [PMID: 31209400 PMCID: PMC6588409 DOI: 10.1038/s41590-019-0403-4] [Citation(s) in RCA: 328] [Impact Index Per Article: 65.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 04/16/2019] [Indexed: 02/06/2023]
Abstract
Progenitor-like CD8+ T cells mediate long-term immunity to chronic infection and cancer and respond potently to immune checkpoint blockade. These cells share transcriptional regulators with memory precursor cells, including TCF1, but it is unclear whether they adopt distinct programs to adapt to the immunosuppressive environment. By comparing single-cell transcriptomes and epigenetic profiles of CD8+ T cells responding to acute and chronic viral infections, we found that progenitor-like CD8+ T cells became distinct from memory precursors before the peak of the T-cell response. We discovered a co-expression gene module containing Tox that exhibited higher transcriptional activity associated with more abundant active histone marks in progenitor-like cells than memory precursors. Moreover, TOX promoted persistence of antiviral CD8+ T cells and was required for the programming of progenitor-like CD8+ T cells. Thus, long-term CD8+ T-cell immunity to chronic viral infection requires unique transcriptional and epigenetic programs associated with the transcription factor TOX.
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Affiliation(s)
- Chen Yao
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Hong-Wei Sun
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Neal E Lacey
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yun Ji
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.,Cellular Biomedicine Group, Gaithersburg, MD, USA
| | - E Ashley Moseman
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.,Department of Immunology, Duke University School of Medicine, Durham, NC, USA
| | - Han-Yu Shih
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Elisabeth F Heuston
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Martha Kirby
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stacie Anderson
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jun Cheng
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Omar Khan
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School Medicine, Philadelphia, PA, USA
| | - Robin Handon
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Julie Reilley
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.,National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jessica Fioravanti
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jinhui Hu
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Selamawit Gossa
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School Medicine, Philadelphia, PA, USA
| | - Luca Gattinoni
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dorian B McGavern
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - John J O'Shea
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Pamela L Schwartzberg
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA. .,National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Tuoqi Wu
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA. .,National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. .,Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA.
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45
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Fernando TM, Marullo R, Pera Gresely B, Phillip JM, Yang SN, Lundell-Smith G, Torregroza I, Ahn H, Evans T, Győrffy B, Privé GG, Hirano M, Melnick AM, Cerchietti L. BCL6 Evolved to Enable Stress Tolerance in Vertebrates and Is Broadly Required by Cancer Cells to Adapt to Stress. Cancer Discov 2019; 9:662-679. [PMID: 30777872 DOI: 10.1158/2159-8290.cd-17-1444] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 11/19/2018] [Accepted: 02/13/2019] [Indexed: 11/16/2022]
Abstract
Several lines of evidence link the canonical oncogene BCL6 to stress response. Here we demonstrate that BCL6 evolved in vertebrates as a component of the HSF1-driven stress response, which has been co-opted by the immune system to support germinal center formation and may have been decisive in the convergent evolution of humoral immunity in jawless and jawed vertebrates. We find that the highly conserved BTB corepressor binding site of BCL6 mediates stress adaptation across vertebrates. We demonstrate that pan-cancer cells hijack this stress tolerance mechanism to aberrantly express BCL6. Targeting the BCL6 BTB domain in cancer cells induces apoptosis and increases susceptibility to repeated doses of cytotoxic therapy. The chemosensitization effect upon BCL6 BTB inhibition is dependent on the derepression of TOX, implicating modulation of DNA repair as a downstream mechanism. Collectively, these data suggest a form of adaptive nononcogene addiction rooted in the natural selection of BCL6 during vertebrate evolution. SIGNIFICANCE: We demonstrate that HSF1 drives BCL6 expression to enable stress tolerance in vertebrates. We identify an HSF1-BCL6-TOX stress axis that is required by cancer cells to tolerate exposure to cytotoxic agents and points toward BCL6-targeted therapy as a way to more effectively kill a wide variety of solid tumors.This article is highlighted in the In This Issue feature, p. 565.
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Affiliation(s)
- Tharu M Fernando
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York.,Department of Pharmacology, Weill Cornell Medicine, New York, New York
| | - Rossella Marullo
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Benet Pera Gresely
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Jude M Phillip
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Shao Ning Yang
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | | | | | - Haelee Ahn
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Todd Evans
- Department of Surgery, Weill Cornell Medicine, New York, New York
| | - Balázs Győrffy
- MTA TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Budapest, Hungary.,Semmelweis University 2nd Department of Pediatrics, Budapest, Hungary
| | - Gilbert G Privé
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Masayuki Hirano
- Emory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia
| | - Ari M Melnick
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York. .,Department of Pharmacology, Weill Cornell Medicine, New York, New York
| | - Leandro Cerchietti
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York.
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46
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TOX3 inhibits cancer cell migration and invasion via transcriptional regulation of SNAI1 and SNAI2 in clear cell renal cell carcinoma. Cancer Lett 2019; 449:76-86. [PMID: 30772441 DOI: 10.1016/j.canlet.2019.02.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/07/2019] [Accepted: 02/10/2019] [Indexed: 12/13/2022]
Abstract
Studies on the mechanism of clear cell renal cell carcinoma (ccRCC) progression are lacking. In this study, TOX3 was identified as a novel cancer suppressor gene in ccRCC. Hypermethylation of CpG probes in the promoter region was associated with the functional loss of TOX3 in ccRCC cancer tissues. Downregulation of TOX3 mRNA was strongly associated with poor clinical outcomes in ccRCC. Immunohistochemistry confirmed TOX3 was downregulated in primary tumors without metastasis (n = 126) and further downregulated in primary metastatic tumors (n = 23) compared with adjacent noncancerous tissues (n = 92). In vitro, overexpression of TOX3 inhibited RCC cell growth, migration and invasion. Mechanistic investigations showed that TOX3 deficiency facilitates the epithelial-mesenchymal transition due to impairment of transcriptional repression of SNAIL members SNAI1 and SNAI2 and promotes cancer cell migration and invasion. In vivo, restoring TOX3 expression reduced lung metastatic lesions and prolonged survival of mice. TOX3 combined with SNAI1 or SNAI2 predicted overall survival in ccRCC patients. Blockage of this pathway could be a promising therapeutic target for advanced ccRCC.
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47
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Zeng X, Vonk JM, van der Plaat DA, Faiz A, Paré PD, Joubert P, Nickle D, Brandsma CA, Kromhout H, Vermeulen R, Xu X, Huo X, de Jong K, Boezen HM. Genome-wide interaction study of gene-by-occupational exposures on respiratory symptoms. ENVIRONMENT INTERNATIONAL 2019; 122:263-269. [PMID: 30449631 DOI: 10.1016/j.envint.2018.11.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 11/05/2018] [Accepted: 11/08/2018] [Indexed: 02/05/2023]
Abstract
Respiratory symptoms are important indicators of respiratory diseases. Both genetic and environmental factors contribute to respiratory symptoms development but less is known about gene-environment interactions. We aimed to assess interactions between single nucleotide polymorphisms (SNPs) and occupational exposures on respiratory symptoms cough, dyspnea and phlegm. As identification cohort LifeLines I (n = 7976 subjects) was used. Job-specific exposure was estimated using the ALOHA + job exposure matrix. SNP-by-occupational exposure interactions on respiratory symptoms were tested using logistic regression adjusted for gender, age, and current smoking. SNP-by-exposure interactions with a p-value <10-4 were tested for replication in two independent cohorts: LifeLines II (n = 5260) and the Vlagtwedde-Vlaardingen cohort (n = 1529). The interaction estimates of the replication cohorts were meta-analyzed using PLINK. Replication was achieved when the meta-analysis p-value was <0.05 and the interaction effect had the same direction as in the identification cohort. Additionally, we assessed whether replicated SNPs associated with gene expression by analyzing if they were cis-acting expression quantitative trait loci (eQTL) in lung tissue. In the replication meta-analysis, sixteen out of 477 identified SNP-by-occupational exposure interactions had a p-value <0.05 and 9 of these interactions had the same direction as in the identification cohort. Several identified loci were plausible candidates for respiratory symptoms, such as TMPRSS9, SERPINH1, TOX3, and ARHGAP18. Three replicated SNPs were cis-eQTLs for FCER1A, CHN1, and TIMM13 in lung tissue. Taken together, this genome-wide SNP-by-occupational exposure interaction study in relation to cough, dyspnea, and phlegm identified several suggestive susceptibility genes. Further research should determine if these genes are true susceptibility loci for respiratory symptoms in relation to occupational exposures.
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Affiliation(s)
- Xiang Zeng
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands; Shantou University Medical College, Laboratory of Environmental Medicine and Developmental Toxicology, Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou, China; Xinxiang Medical University, School of Public Health, Department of Epidemiology and Health Statistics, Xinxiang, China
| | - Judith M Vonk
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands
| | - Diana A van der Plaat
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands
| | - Alen Faiz
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, the Netherlands
| | - Peter D Paré
- University of British Columbia, Department of Medicine, Center for Heart Lung Innovation and Institute for Heart and Lung Health, St. Paul's Hospital, Vancouver, BC, Canada
| | - Philippe Joubert
- Institut universitaire de cardiologie et de pneumologie de Québec, Laval University, Québec, QC, Canada
| | | | - Corry-Anke Brandsma
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, the Netherlands
| | - Hans Kromhout
- University of Utrecht, Institute for Risk Assessment Sciences, Division of Environmental Epidemiology, Utrecht, the Netherlands
| | - Roel Vermeulen
- University of Utrecht, Institute for Risk Assessment Sciences, Division of Environmental Epidemiology, Utrecht, the Netherlands
| | - Xijin Xu
- Shantou University Medical College, Laboratory of Environmental Medicine and Developmental Toxicology, Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou, China
| | - Xia Huo
- Jinan University, School of Environment, Guangdong Key Laboratory of Environmental Pollution and Health, Guangzhou Key Laboratory of Environmental Exposure and Health, Guangzhou, China
| | - Kim de Jong
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands
| | - H Marike Boezen
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands.
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48
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NickAria S, Haghpanah S, Ramzi M, Karimi M. Relationship of the Interaction Between Two Quantitative Trait Loci with γ-Globin Expression in β-Thalassemia Intermedia Patients. Hemoglobin 2018; 42:108-112. [PMID: 29745274 DOI: 10.1080/03630269.2018.1463915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Globin switching is a significant factor on blood hemoglobin (Hb) level but its molecular mechanisms have not yet been identified, however, several quantitative trait loci (QTL) and polymorphisms involved regions on chromosomes 2p, 6q, 8q and X account for variation in the γ-globin expression level. We studied the effect of interaction between a region on intron six of the TOX gene, chromosome 8q (chr8q) and XmnI locus on the γ-globin promoter, chr11p on γ-globin expression in 150 β-thalassemia intermedia (β-TI) patients, evaluated by statistical interaction analysis. Our results showed a significant interaction between one QTL on intron six of the TOX gene (rs9693712) and XmnI locus that effect γ-globin expression. Interchromosomal interaction mediates through transcriptional machanisms to preserve true genome architectural features, chromosomes localization and DNA bending. This interaction can be a part of the unknown molecular mechanism of globin switching and regulation of gene expression.
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Affiliation(s)
- Shiva NickAria
- a Hematology Research Center , Shiraz University of Medical Sciences , Shiraz , Iran
| | - Sezaneh Haghpanah
- a Hematology Research Center , Shiraz University of Medical Sciences , Shiraz , Iran
| | - Mani Ramzi
- a Hematology Research Center , Shiraz University of Medical Sciences , Shiraz , Iran
| | - Mehran Karimi
- a Hematology Research Center , Shiraz University of Medical Sciences , Shiraz , Iran
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49
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Pan-cancer screen for mutations in non-coding elements with conservation and cancer specificity reveals correlations with expression and survival. NPJ Genom Med 2018; 3:1. [PMID: 29354286 PMCID: PMC5765157 DOI: 10.1038/s41525-017-0040-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 11/22/2017] [Accepted: 11/29/2017] [Indexed: 01/01/2023] Open
Abstract
Cancer develops by accumulation of somatic driver mutations, which impact cellular function. Mutations in non-coding regulatory regions can now be studied genome-wide and further characterized by correlation with gene expression and clinical outcome to identify driver candidates. Using a new two-stage procedure, called ncDriver, we first screened 507 ICGC whole-genomes from 10 cancer types for non-coding elements, in which mutations are both recurrent and have elevated conservation or cancer specificity. This identified 160 significant non-coding elements, including the TERT promoter, a well-known non-coding driver element, as well as elements associated with known cancer genes and regulatory genes (e.g., PAX5, TOX3, PCF11, MAPRE3). However, in some significant elements, mutations appear to stem from localized mutational processes rather than recurrent positive selection in some cases. To further characterize the driver potential of the identified elements and shortlist candidates, we identified elements where presence of mutations correlated significantly with expression levels (e.g., TERT and CDH10) and survival (e.g., CDH9 and CDH10) in an independent set of 505 TCGA whole-genome samples. In a larger pan-cancer set of 4128 TCGA exomes with expression profiling, we identified mutational correlation with expression for additional elements (e.g., near GATA3, CDC6, ZNF217, and CTCF transcription factor binding sites). Survival analysis further pointed to MIR122, a known marker of poor prognosis in liver cancer. In conclusion, the screen for significant mutation patterns coupled with correlative mutational analysis identified new individual driver candidates and suggest that some non-coding mutations recurrently affect expression and play a role in cancer development. Mutations in the “non-coding” part of the genome have been identified that could be involved in driving cancer development. Jakob Pedersen, Henrik Hornshøj and colleagues from Aarhus University Hospital in Denmark and MIT in the United States developed a two-stage procedure to identify elements that could be driving cancer development in the part of DNA that does not code for proteins. They conducted statisical analyses on catalogs of tumor genomes to identify recurrent mutations. They then evaluated how specific these mutations were to different cancer types, their predicted functional impact, and their association with gene expression and patient survival. The analyses identified mutations in the non-coding part of cancer genomes that could be driving tumor development, but further analyses on larger sample sets need to be conducted to validate the results, which could provide a basis for biomarker discovery and precision medical treatment.
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50
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TOX as a diagnostic and prognostic marker for mycosis fungoides. JOURNAL OF THE EGYPTIAN WOMENʼS DERMATOLOGIC SOCIETY 2018. [DOI: 10.1097/01.ewx.0000525982.47129.30] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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