1
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Scholda J, Nguyen TTA, Kopp F. Long noncoding RNAs as versatile molecular regulators of cellular stress response and homeostasis. Hum Genet 2024; 143:813-829. [PMID: 37782337 PMCID: PMC11294412 DOI: 10.1007/s00439-023-02604-7] [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: 05/31/2023] [Accepted: 09/12/2023] [Indexed: 10/03/2023]
Abstract
Normal cell and body functions need to be maintained and protected against endogenous and exogenous stress conditions. Different cellular stress response pathways have evolved that are utilized by mammalian cells to recognize, process and overcome numerous stress stimuli in order to maintain homeostasis and to prevent pathophysiological processes. Although these stress response pathways appear to be quite different on a molecular level, they all have in common that they integrate various stress inputs, translate them into an appropriate stress response and eventually resolve the stress by either restoring homeostasis or inducing cell death. It has become increasingly appreciated that non-protein-coding RNA species, such as long noncoding RNAs (lncRNAs), can play critical roles in the mammalian stress response. However, the precise molecular functions and underlying modes of action for many of the stress-related lncRNAs remain poorly understood. In this review, we aim to provide a framework for the categorization of mammalian lncRNAs in stress response and homeostasis based on their experimentally validated modes of action. We describe the molecular functions and physiological roles of selected lncRNAs and develop a concept of how lncRNAs can contribute as versatile players in mammalian stress response and homeostasis. These concepts may be used as a starting point for the identification of novel lncRNAs and lncRNA functions not only in the context of stress, but also in normal physiology and disease.
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Affiliation(s)
- Julia Scholda
- Faculty of Life Sciences, Department of Pharmaceutical Sciences, Clinical Pharmacy Group, University of Vienna, Josef-Holaubek-Platz 2, 1090, Vienna, Austria
| | - Thi Thuy Anh Nguyen
- Faculty of Life Sciences, Department of Pharmaceutical Sciences, Clinical Pharmacy Group, University of Vienna, Josef-Holaubek-Platz 2, 1090, Vienna, Austria
| | - Florian Kopp
- Faculty of Life Sciences, Department of Pharmaceutical Sciences, Clinical Pharmacy Group, University of Vienna, Josef-Holaubek-Platz 2, 1090, Vienna, Austria.
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2
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Wang Y, Zhang J, Shi H, Wang M, Yu D, Fu M, Qian Y, Zhang X, Ji R, Wang S, Gu J, Zhang X. M2 Tumor-Associated Macrophages-Derived Exosomal MALAT1 Promotes Glycolysis and Gastric Cancer Progression. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309298. [PMID: 38639382 PMCID: PMC11199979 DOI: 10.1002/advs.202309298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 04/01/2024] [Indexed: 04/20/2024]
Abstract
M2-polarized tumor-associated macrophages (M2 TAMs) promote cancer progression. Exosomes mediate cellular communication in the tumor microenvironment (TME). However, the roles of exosomes from M2 TAMs in gastric cancer progression are unclear. Herein, it is reported that M2 TAMs-derived exosomes induced aerobic glycolysis in gastric cancer cells and enhanced their proliferation, metastasis, and chemoresistance in a glycolysis-dependent manner. It is identified that MALAT1 (metastasis-associated lung adenocarcinoma transcript 1) is enriched in M2 TAM exosomes and confirmed that MALAT1 transfer from M2 TAMs to gastric cancer cells via exosomes mediates this effect. Mechanistically, MALAT1 interacted with the δ-catenin protein and suppressed its ubiquitination and degradation by β-TRCP. In addition, MALAT1 upregulated HIF-1α expression by acting as a sponge for miR-217-5p. The activation of β-catenin and HIF-1α signaling pathways by M2 TAM exosomes collectively led to enhanced aerobic glycolysis in gastric cancer cells. Finally, a dual-targeted inhibition of MALAT1 in both gastric cancer cells and macrophages by exosome-mediated delivery of siRNA remarkably suppressed gastric cancer growth and improved chemosensitivity in mouse tumor models. Taken together, these results suggest that M2 TAMs-derived exosomes promote gastric cancer progression via MALAT1-mediated regulation of glycolysis. The findings offer a potential target for gastric cancer therapy.
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Affiliation(s)
- Yanzheng Wang
- Department of Laboratory MedicineSchool of MedicineJiangsu UniversityZhenjiang212013China
| | - Jiahui Zhang
- Department of Laboratory MedicineSchool of MedicineJiangsu UniversityZhenjiang212013China
| | - Hui Shi
- Department of Laboratory MedicineSchool of MedicineJiangsu UniversityZhenjiang212013China
| | - Maoye Wang
- Department of Laboratory MedicineSchool of MedicineJiangsu UniversityZhenjiang212013China
| | - Dan Yu
- Department of Laboratory MedicineSchool of MedicineJiangsu UniversityZhenjiang212013China
| | - Min Fu
- Department of Laboratory MedicineSchool of MedicineJiangsu UniversityZhenjiang212013China
| | - Yu Qian
- Department of Laboratory MedicineSchool of MedicineJiangsu UniversityZhenjiang212013China
| | - Xiaoxin Zhang
- Department of Laboratory MedicineSchool of MedicineJiangsu UniversityZhenjiang212013China
| | - Runbi Ji
- Department of Laboratory MedicineSchool of MedicineJiangsu UniversityZhenjiang212013China
| | - Shouyu Wang
- Jiangsu Key Laboratory of Molecular MedicineMedical School of Nanjing UniversityNanjing210000China
| | - Jianmei Gu
- Department of Clinical Laboratory MedicineNantong Tumor Hospital/Affiliated Tumor Hospital of Nantong UniversityNantong226300China
| | - Xu Zhang
- Department of Laboratory MedicineSchool of MedicineJiangsu UniversityZhenjiang212013China
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3
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Minnie SA, Waltner OG, Zhang P, Takahashi S, Nemychenkov NS, Ensbey KS, Schmidt CR, Legg SRW, Comstock M, Boiko JR, Nelson E, Bhise SS, Wilkens AB, Koyama M, Dhodapkar MV, Chesi M, Riddell SR, Green DJ, Spencer A, Furlan SN, Hill GR. TIM-3 + CD8 T cells with a terminally exhausted phenotype retain functional capacity in hematological malignancies. Sci Immunol 2024; 9:eadg1094. [PMID: 38640253 PMCID: PMC11093588 DOI: 10.1126/sciimmunol.adg1094] [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: 12/02/2022] [Accepted: 03/27/2024] [Indexed: 04/21/2024]
Abstract
Chronic antigen stimulation is thought to generate dysfunctional CD8 T cells. Here, we identify a CD8 T cell subset in the bone marrow tumor microenvironment that, despite an apparent terminally exhausted phenotype (TPHEX), expressed granzymes, perforin, and IFN-γ. Concurrent gene expression and DNA accessibility revealed that genes encoding these functional proteins correlated with BATF expression and motif accessibility. IFN-γ+ TPHEX effectively killed myeloma with comparable efficacy to transitory effectors, and disease progression correlated with numerical deficits in IFN-γ+ TPHEX. We also observed IFN-γ+ TPHEX within CD19-targeted chimeric antigen receptor T cells, which killed CD19+ leukemia cells. An IFN-γ+ TPHEX gene signature was recapitulated in TEX cells from human cancers, including myeloma and lymphoma. Here, we characterize a TEX subset in hematological malignancies that paradoxically retains function and is distinct from dysfunctional TEX found in chronic viral infections. Thus, IFN-γ+ TPHEX represent a potential target for immunotherapy of blood cancers.
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Affiliation(s)
- Simone A. Minnie
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Olivia G. Waltner
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Ping Zhang
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Shuichiro Takahashi
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Nicole S. Nemychenkov
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Kathleen S. Ensbey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Christine R. Schmidt
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Samuel RW. Legg
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Melissa Comstock
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Julie R. Boiko
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
- Department of Pediatrics, University of Washington; WA, UNITED STATES
| | - Ethan Nelson
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Shruti S. Bhise
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Alec B. Wilkens
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Motoko Koyama
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Madhav V. Dhodapkar
- Department of Hematology/Medical Oncology, Atlanta, GA, UNITED STATES
- Winship Cancer Institute, Emory University, Atlanta, GA, UNITED STATES
| | - Marta Chesi
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, AZ, UNITED STATES
| | - Stanley R. Riddell
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
- Division of Medical Oncology, University of Washington; Seattle, WA, UNITED STATES
| | - Damian J. Green
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
- Division of Medical Oncology, University of Washington; Seattle, WA, UNITED STATES
| | - Andrew Spencer
- Australian Center for Blood Diseases, Monash University/The Alfred Hospital, Melbourne, VIC, AUSTRALIA
- Malignant Haematology and Stem Cell Transplantation, The Alfred Hospital, Melbourne, VIC, AUSTRALIA
- Department of Clinical Haematology, Monash University, Melbourne, VIC
| | - Scott N. Furlan
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
- Department of Pediatrics, University of Washington; WA, UNITED STATES
| | - Geoffrey R. Hill
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
- Division of Medical Oncology, University of Washington; Seattle, WA, UNITED STATES
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4
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Wang S, Prieux M, de Bernard S, Dubois M, Laubreton D, Djebali S, Zala M, Arpin C, Genestier L, Leverrier Y, Gandrillon O, Crauste F, Jiang W, Marvel J. Exogenous IL-2 delays memory precursors generation and is essential for enhancing memory cells effector functions. iScience 2024; 27:109411. [PMID: 38510150 PMCID: PMC10952031 DOI: 10.1016/j.isci.2024.109411] [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: 07/27/2023] [Revised: 11/27/2023] [Accepted: 02/29/2024] [Indexed: 03/22/2024] Open
Abstract
To investigate the impact of paracrine IL-2 signals on memory precursor (MP) cell differentiation, we activated CD8 T cell in vitro in the presence or absence of exogenous IL-2 (ex-IL-2). We assessed memory differentiation by transferring these cells into virus-infected mice. Both conditions generated CD8 T cells that participate in the ongoing response and gave rise to similar memory cells. Nevertheless, when transferred into a naive host, T cells activated with ex-IL-2 generated a higher frequency of memory cells displaying increased functional memory traits. Single-cell RNA-seq analysis indicated that without ex-IL-2, cells rapidly acquire an MP signature, while in its presence they adopted an effector signature. This was confirmed at the protein level and in a functional assay. Overall, ex-IL-2 delays the transition into MP cells, allowing the acquisition of effector functions that become imprinted in their progeny. These findings may help to optimize the generation of therapeutic T cells.
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Affiliation(s)
- Shaoying Wang
- Centre International de Recherche en Infectiologie, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Université de Lyon, Lyon, France
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Margaux Prieux
- Centre International de Recherche en Infectiologie, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Université de Lyon, Lyon, France
- Laboratoire de Biologie et de Modélisation de la Cellule, Université de Lyon, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Lyon, France
| | | | - Maxence Dubois
- Centre International de Recherche en Infectiologie, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Université de Lyon, Lyon, France
| | - Daphne Laubreton
- Centre International de Recherche en Infectiologie, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Université de Lyon, Lyon, France
| | - Sophia Djebali
- Centre International de Recherche en Infectiologie, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Université de Lyon, Lyon, France
| | - Manon Zala
- Centre International de Recherche en Infectiologie, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Université de Lyon, Lyon, France
- Faculté de Médecine Lyon-Sud, Université de Lyon, Oullins, France
| | - Christophe Arpin
- Centre International de Recherche en Infectiologie, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Université de Lyon, Lyon, France
- Laboratoire de Biologie et de Modélisation de la Cellule, Université de Lyon, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Lyon, France
| | - Laurent Genestier
- Centre International de Recherche en Infectiologie, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Université de Lyon, Lyon, France
- Faculté de Médecine Lyon-Sud, Université de Lyon, Oullins, France
| | - Yann Leverrier
- Centre International de Recherche en Infectiologie, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Université de Lyon, Lyon, France
| | - Olivier Gandrillon
- Inria, Villeurbanne, France
- Laboratoire de Biologie et de Modélisation de la Cellule, Université de Lyon, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Lyon, France
| | - Fabien Crauste
- Laboratoire MAP5 (UMR CNRS 8145), Université Paris Cité, Paris, France
| | - Wenzheng Jiang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Jacqueline Marvel
- Centre International de Recherche en Infectiologie, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Université de Lyon, Lyon, France
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5
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Zhao Y, Ning J, Teng H, Deng Y, Sheldon M, Shi L, Martinez C, Zhang J, Tian A, Sun Y, Nakagawa S, Yao F, Wang H, Ma L. Long noncoding RNA Malat1 protects against osteoporosis and bone metastasis. Nat Commun 2024; 15:2384. [PMID: 38493144 PMCID: PMC10944492 DOI: 10.1038/s41467-024-46602-3] [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: 01/19/2023] [Accepted: 03/04/2024] [Indexed: 03/18/2024] Open
Abstract
MALAT1, one of the few highly conserved nuclear long noncoding RNAs (lncRNAs), is abundantly expressed in normal tissues. Previously, targeted inactivation and genetic rescue experiments identified MALAT1 as a suppressor of breast cancer lung metastasis. On the other hand, Malat1-knockout mice are viable and develop normally. On a quest to discover the fundamental roles of MALAT1 in physiological and pathological processes, we find that this lncRNA is downregulated during osteoclastogenesis in humans and mice. Remarkably, Malat1 deficiency in mice promotes osteoporosis and bone metastasis of melanoma and mammary tumor cells, which can be rescued by genetic add-back of Malat1. Mechanistically, Malat1 binds to Tead3 protein, a macrophage-osteoclast-specific Tead family member, blocking Tead3 from binding and activating Nfatc1, a master regulator of osteoclastogenesis, which results in the inhibition of Nfatc1-mediated gene transcription and osteoclast differentiation. Notably, single-cell transcriptome analysis of clinical bone samples reveals that reduced MALAT1 expression in pre-osteoclasts and osteoclasts is associated with osteoporosis and metastatic bone lesions. Altogether, these findings identify Malat1 as a lncRNA that protects against osteoporosis and bone metastasis.
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Affiliation(s)
- Yang Zhao
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jingyuan Ning
- Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100010, China
| | - Hongqi Teng
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yalan Deng
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Marisela Sheldon
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Lei Shi
- Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Consuelo Martinez
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jie Zhang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Annie Tian
- Department of Kinesiology, Rice University, Houston, TX, 77005, USA
| | - Yutong Sun
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| | - Fan Yao
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Hai Wang
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Li Ma
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, 77030, USA.
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6
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Gibson A, Ram R, Gangula R, Li Y, Mukherjee E, Palubinsky AM, Campbell CN, Thorne M, Konvinse KC, Choshi P, Deshpande P, Pedretti S, O’Neil RT, Wanjalla CN, Kalams SA, Gaudieri S, Lehloenya RJ, Bailin SS, Chopra A, Mallal SA, Phillips EJ. Multiomic single-cell sequencing defines tissue-specific responses in Stevens-Johnson Syndrome and Toxic epidermal necrolysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.26.568771. [PMID: 38405793 PMCID: PMC10888802 DOI: 10.1101/2023.11.26.568771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Stevens-Johnson syndrome and toxic epidermal necrolysis (SJS/TEN) is a rare but life-threatening cutaneous drug reaction mediated by human leukocyte antigen (HLA) class I-restricted CD8+ T-cells. To obtain an unbiased assessment of SJS/TEN cellular immunopathogenesis, we performed single-cell (sc) transcriptome, surface proteome, and TCR sequencing on unaffected skin, affected skin, and blister fluid from 17 SJS/TEN patients. From 119,784 total cells, we identified 16 scRNA-defined subsets, confirmed by subset-defining surface protein expression. Keratinocytes upregulated HLA and IFN-response genes in the affected skin. Cytotoxic CD8+ T-cell subpopulations of expanded and unexpanded TCRαβ clonotypes were shared in affected skin and blister fluid but absent or unexpanded in SJS/TEN unaffected skin. SJS/TEN blister fluid is a rich reservoir of oligoclonal CD8+ T-cells with an effector phenotype driving SJS/TEN pathogenesis. This multiomic database will act as the basis to define antigen-reactivity, HLA restriction, and signatures of drug-antigen-reactive T-cell clonotypes at a tissue level.
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Affiliation(s)
- Andrew Gibson
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
| | - Ramesh Ram
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
| | - Rama Gangula
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Yueran Li
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
| | - Eric Mukherjee
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Amy M Palubinsky
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Chelsea N Campbell
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Michael Thorne
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
| | - Katherine C Konvinse
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Phuti Choshi
- Allergy and Immunology Unit, University of Cape Town Lung Institute, Cape Town, South Africa
| | - Pooja Deshpande
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
| | - Sarah Pedretti
- Allergy and Immunology Unit, University of Cape Town Lung Institute, Cape Town, South Africa
| | - Richard T O’Neil
- Department of Veterans Affairs, Ralph H Johnson VA Medical Center and Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Celestine N Wanjalla
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Spyros A Kalams
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Silvana Gaudieri
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
- School of Human Sciences, The University of Western Australia, Western Australia, Australia
| | - Rannakoe J Lehloenya
- Allergy and Immunology Unit, University of Cape Town Lung Institute, Cape Town, South Africa
- Division of Dermatology, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - Samuel S Bailin
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Jason A Trubiano on behalf of the AUS-SCAR study group
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria, Australia
- Centre for Antibiotic Allergy and Research, Department of Infectious Diseases, Austin Health, Victoria, Australia
| | | | - Simon A Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Elizabeth J Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
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7
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Qi Y, Xu R, Song C, Hao M, Gao Y, Xin M, Liu Q, Chen H, Wu X, Sun R, Zhang Y, He D, Dai Y, Kong C, Ning S, Guo Q, Zhang G, Wang P. A comprehensive database of exosome molecular biomarkers and disease-gene associations. Sci Data 2024; 11:210. [PMID: 38360815 PMCID: PMC10869824 DOI: 10.1038/s41597-024-03015-7] [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: 05/15/2023] [Accepted: 01/29/2024] [Indexed: 02/17/2024] Open
Abstract
Exosomes play a crucial role in intercellular communication and can be used as biomarkers for diagnostic and therapeutic clinical applications. However, systematic studies in cancer-associated exosomal nucleic acids remain a big challenge. Here, we developed ExMdb, a comprehensive database of exosomal nucleic acid biomarkers and disease-gene associations curated from published literature and high-throughput datasets. We performed a comprehensive curation of exosome properties including 4,586 experimentally supported gene-disease associations, 13,768 diagnostic and therapeutic biomarkers, and 312,049 nucleic acid subcellular locations. To characterize expression variation of exosomal molecules and identify causal factors of complex diseases, we have also collected 164 high-throughput datasets, including bulk and single-cell RNA sequencing (scRNA-seq) data. Based on these datasets, we performed various bioinformatics and statistical analyses to support our conclusions and advance our knowledge of exosome biology. Collectively, our dataset will serve as an essential resource for investigating the regulatory mechanisms of complex diseases and improving the development of diagnostic and therapeutic biomarkers.
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Affiliation(s)
- Yue Qi
- Department of Gynecology of the First Affiliated Hospital, Harbin Medical University, Harbin, 150081, China
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Rongji Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Chengxin Song
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Ming Hao
- Department of Gynecology of the First Affiliated Hospital, Harbin Medical University, Harbin, 150081, China
| | - Yue Gao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Mengyu Xin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Qian Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Hongyan Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Xiaoting Wu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Rui Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yuanfu Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Danni He
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yifan Dai
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Congcong Kong
- Department of Gynecology of the First Affiliated Hospital, Harbin Medical University, Harbin, 150081, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Qiuyan Guo
- Department of Gynecology of the First Affiliated Hospital, Harbin Medical University, Harbin, 150081, China.
| | - Guangmei Zhang
- Department of Gynecology of the First Affiliated Hospital, Harbin Medical University, Harbin, 150081, China.
| | - Peng Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
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8
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Jaeger-Ruckstuhl CA, Lo Y, Fulton E, Waltner OG, Shabaneh TB, Simon S, Muthuraman PV, Correnti CE, Newsom OJ, Engstrom IA, Kanaan SB, Bhise SS, Peralta JMC, Ruff R, Price JP, Stull SM, Stevens AR, Bugos G, Kluesner MG, Voillet V, Muhunthan V, Morrish F, Olson JM, Gottardo R, Sarthy JF, Henikoff S, Sullivan LB, Furlan SN, Riddell SR. Signaling via a CD27-TRAF2-SHP-1 axis during naive T cell activation promotes memory-associated gene regulatory networks. Immunity 2024; 57:287-302.e12. [PMID: 38354704 DOI: 10.1016/j.immuni.2024.01.011] [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: 02/27/2023] [Revised: 09/26/2023] [Accepted: 01/11/2024] [Indexed: 02/16/2024]
Abstract
The interaction of the tumor necrosis factor receptor (TNFR) family member CD27 on naive CD8+ T (Tn) cells with homotrimeric CD70 on antigen-presenting cells (APCs) is necessary for T cell memory fate determination. Here, we examined CD27 signaling during Tn cell activation and differentiation. In conjunction with T cell receptor (TCR) stimulation, ligation of CD27 by a synthetic trimeric CD70 ligand triggered CD27 internalization and degradation, suggesting active regulation of this signaling axis. Internalized CD27 recruited the signaling adaptor TRAF2 and the phosphatase SHP-1, thereby modulating TCR and CD28 signals. CD27-mediated modulation of TCR signals promoted transcription factor circuits that induced memory rather than effector associated gene programs, which are induced by CD28 costimulation. CD27-costimulated chimeric antigen receptor (CAR)-engineered T cells exhibited improved tumor control compared with CD28-costimulated CAR-T cells. Thus, CD27 signaling during Tn cell activation promotes memory properties with relevance to T cell immunotherapy.
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Affiliation(s)
- Carla A Jaeger-Ruckstuhl
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
| | - Yun Lo
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Elena Fulton
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Olivia G Waltner
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Tamer B Shabaneh
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Sylvain Simon
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Pranav V Muthuraman
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Colin E Correnti
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Oliver J Newsom
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Ian A Engstrom
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Sami B Kanaan
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Shruti S Bhise
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Jobelle M C Peralta
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Raymond Ruff
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Jason P Price
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Sylvia M Stull
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Andrew R Stevens
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Grace Bugos
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Mitchell G Kluesner
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Valentin Voillet
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Vishaka Muhunthan
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Fionnuala Morrish
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - James M Olson
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Raphaël Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Statistics, University of Washington, Seattle, WA 98195, USA; Swiss Institute of Bioinformatics, University of Lausanne and Lausanne University Hospital, Lausanne 1011, Switzerland
| | - Jay F Sarthy
- Seattle Children's Hospital, Seattle, WA 98105, USA; Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Steven Henikoff
- Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Lucas B Sullivan
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Scott N Furlan
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Stanley R Riddell
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98195, USA.
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9
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Weghorst F, Torres Marcén M, Faridi G, Lee YCG, Cramer KS. Deep Conservation and Unexpected Evolutionary History of Neighboring lncRNAs MALAT1 and NEAT1. J Mol Evol 2024; 92:30-41. [PMID: 38189925 PMCID: PMC10869381 DOI: 10.1007/s00239-023-10151-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 11/29/2023] [Indexed: 01/09/2024]
Abstract
Long non-coding RNAs (lncRNAs) have begun to receive overdue attention for their regulatory roles in gene expression and other cellular processes. Although most lncRNAs are lowly expressed and tissue-specific, notable exceptions include MALAT1 and its genomic neighbor NEAT1, two highly and ubiquitously expressed oncogenes with roles in transcriptional regulation and RNA splicing. Previous studies have suggested that NEAT1 is found only in mammals, while MALAT1 is present in all gnathostomes (jawed vertebrates) except birds. Here we show that these assertions are incomplete, likely due to the challenges associated with properly identifying these two lncRNAs. Using phylogenetic analysis and structure-aware annotation of publicly available genomic and RNA-seq coverage data, we show that NEAT1 is a common feature of tetrapod genomes except birds and squamates. Conversely, we identify MALAT1 in representative species of all major gnathostome clades, including birds. Our in-depth examination of MALAT1, NEAT1, and their genomic context in a wide range of vertebrate species allows us to reconstruct the series of events that led to the formation of the locus containing these genes in taxa from cartilaginous fish to mammals. This evolutionary history includes the independent loss of NEAT1 in birds and squamates, since NEAT1 is found in the closest living relatives of both clades (crocodilians and tuataras, respectively). These data clarify the origins and relationships of MALAT1 and NEAT1 and highlight an opportunity to study the change and continuity in lncRNA structure and function over deep evolutionary time.
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Affiliation(s)
- Forrest Weghorst
- Department of Neurobiology and Behavior, University of California, Irvine, USA
| | - Martí Torres Marcén
- Department of Neurobiology and Behavior, University of California, Irvine, USA
| | - Garrison Faridi
- Department of Neurobiology and Behavior, University of California, Irvine, USA
| | - Yuh Chwen G Lee
- Department of Ecology and Evolutionary Biology, University of California, Irvine, USA
| | - Karina S Cramer
- Department of Neurobiology and Behavior, University of California, Irvine, USA.
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10
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Li Z, Wang D, Zhang W, Shi H, Zhu M. Novel PBMC LncRNA signatures as diagnostic biomarkers for colorectal cancer. Pathol Res Pract 2024; 253:154985. [PMID: 38039742 DOI: 10.1016/j.prp.2023.154985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/20/2023] [Accepted: 11/23/2023] [Indexed: 12/03/2023]
Abstract
The expression of long non-coding RNAs (LncRNAs) in peripheral blood mononuclear cell (PBMC) and its clinical relevance in colorectal cancer (CRC) remains largely uncharacterized. To address these gaps, we investigated the expression profiles of lncRNAs in PBMC from CRC and healthy controls (HC) by RNA sequencing. The expression level of differentially expressed lncRNAs (DElncRNAs) were evaluated by quantitative PCR in PBMC samples from CRC patients and HC. A total of 447 DElncRNAs were identified, with 178 elevated lncRNAs and 269 decreased lncRNAs in PBMC from CRC patients as compared with that from HC. RT-PCR results supported a significant elevation of NEAT1:11, lnc-PDZD8-1:5 and LINC00910:16 in 98 CRC patients and 82 HC. The clinical implication of NEAT1:11, lnc-PDZD8-1:5 and LINC00910:16 as CRC diagnostic biomarker were determined by receiver operating characteristic (ROC) curve, showing sensitivity 74.5% and specificity 84.5% for joint detection the three lncRNAs. Notably, NEAT1:11 was closely related with the size and extent of primary tumor, with higher relative expression of NEAT1:11 in higher T stage (P = 0.0047). Moreover, NEAT1:11 was related with grade (P = 0.012). Collectively, PBMC from patients with CRC show significantly variable expression profiles of lncRNAs, and detection of these differential expression lncRNAs may provide useful information for basic and clinical research.
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Affiliation(s)
- Zhaosheng Li
- Department of Clinical Laboratory, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Dongfeng Wang
- Department of General Surgery, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Wenjun Zhang
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
| | - Huina Shi
- Department of Clinical Laboratory, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Mingchen Zhu
- Department of Clinical Laboratory, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China.
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11
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Wheeler BD, Gagnon JD, Zhu WS, Muñoz-Sandoval P, Wong SK, Simeonov DS, Li Z, DeBarge R, Spitzer MH, Marson A, Ansel KM. The lncRNA Malat1 inhibits miR-15/16 to enhance cytotoxic T cell activation and memory cell formation. eLife 2023; 12:RP87900. [PMID: 38127070 PMCID: PMC10735224 DOI: 10.7554/elife.87900] [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] [Indexed: 12/23/2023] Open
Abstract
Proper activation of cytotoxic T cells via the T cell receptor and the costimulatory receptor CD28 is essential for adaptive immunity against viruses, intracellular bacteria, and cancers. Through biochemical analysis of RNA:protein interactions, we uncovered a non-coding RNA circuit regulating activation and differentiation of cytotoxic T cells composed of the long non-coding RNA Malat1 (Metastasis Associated Lung Adenocarcinoma Transcript 1) and the microRNA family miR-15/16. miR-15/16 is a widely and highly expressed tumor suppressor miRNA family important for cell proliferation and survival. miR-15/16 play important roles in T cell responses to viral infection, including the regulation of antigen-specific T cell expansion and memory. Comparative Argonaute-2 high-throughput sequencing of crosslinking immunoprecipitation (AHC) combined with gene expression profiling in normal and miR-15/16-deficient mouse T cells revealed a large network of hundreds of direct miR-15/16 target mRNAs, many with functional relevance for T cell activation, survival and memory formation. Among these targets, Malat1 contained the largest absolute magnitude miR-15/16-dependent AHC peak. This binding site was among the strongest lncRNA:miRNA interactions detected in the T cell transcriptome. We used CRISPR targeting with homology directed repair to generate mice with a 5-nucleotide mutation in the miR-15/16-binding site in Malat1. This mutation interrupted Malat1:miR-15/16 interaction, and enhanced the repression of other miR-15/16 target genes, including CD28. Interrupting Malat1 interaction with miR-15/16 decreased cytotoxic T cell activation, including the expression of interleukin 2 (IL-2) and a broader CD28-responsive gene program. Accordingly, Malat1 mutation diminished memory cell persistence in mice following LCMV Armstrong and Listeria monocytogenes infection. This study marks a significant advance in the study of long non-coding RNAs in the immune system by ascribing cell-intrinsic, sequence-specific in vivo function to Malat1. These findings have implications for T cell-mediated autoimmune diseases, antiviral and anti-tumor immunity, as well as lung adenocarcinoma and other malignancies where Malat1 is overexpressed.
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Affiliation(s)
- Benjamin D Wheeler
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
- Sandler Asthma Basic Research Program, University of California, San FranciscoSan FranciscoUnited States
| | - John D Gagnon
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
- Sandler Asthma Basic Research Program, University of California, San FranciscoSan FranciscoUnited States
| | - Wandi S Zhu
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
- Sandler Asthma Basic Research Program, University of California, San FranciscoSan FranciscoUnited States
| | - Priscila Muñoz-Sandoval
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
- Sandler Asthma Basic Research Program, University of California, San FranciscoSan FranciscoUnited States
| | - Simon K Wong
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
| | - Dimitre S Simeonov
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
| | - Zhongmei Li
- Gladstone-UCSF Institute of Genomic ImmunologySan FranciscoUnited States
| | - Rachel DeBarge
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
- Gladstone-UCSF Institute of Genomic ImmunologySan FranciscoUnited States
- Department of Otolaryngology-Head and Neck Surgery, University of California San FranciscoSan FranciscoUnited States
| | - Matthew H Spitzer
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
- Gladstone-UCSF Institute of Genomic ImmunologySan FranciscoUnited States
- Department of Otolaryngology-Head and Neck Surgery, University of California San FranciscoSan FranciscoUnited States
- Parker Institute for Cancer Immunotherapy, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Alexander Marson
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
- Gladstone-UCSF Institute of Genomic ImmunologySan FranciscoUnited States
- Department of Medicine, University of California San FranciscoLexingtonUnited States
| | - K Mark Ansel
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
- Sandler Asthma Basic Research Program, University of California, San FranciscoSan FranciscoUnited States
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12
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Zhu WS, Wheeler BD, Ansel KM. RNA circuits and RNA-binding proteins in T cells. Trends Immunol 2023; 44:792-806. [PMID: 37599172 PMCID: PMC10890840 DOI: 10.1016/j.it.2023.07.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 08/22/2023]
Abstract
RNA is integral to the regulatory circuits that control cell identity and behavior. Cis-regulatory elements in mRNAs interact with RNA-binding proteins (RBPs) that can alter RNA sequence, stability, and translation into protein. Similarly, long noncoding RNAs (lncRNAs) scaffold ribonucleoprotein complexes that mediate transcriptional and post-transcriptional regulation of gene expression. Indeed, cell programming is fundamental to multicellular life and, in this era of cellular therapies, it is of particular interest in T cells. Here, we review key concepts and recent advances in our understanding of the RNA circuits and RBPs that govern mammalian T cell differentiation and immune function.
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Affiliation(s)
- Wandi S Zhu
- Department of Microbiology & Immunology, Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA 94143, USA
| | - Benjamin D Wheeler
- Department of Microbiology & Immunology, Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA 94143, USA
| | - K Mark Ansel
- Department of Microbiology & Immunology, Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA 94143, USA.
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13
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Alluli A, Rijnbout St James W, Eidelman DH, Baglole CJ. Dynamic relationship between the aryl hydrocarbon receptor and long noncoding RNA balances cellular and toxicological responses. Biochem Pharmacol 2023; 216:115745. [PMID: 37597813 DOI: 10.1016/j.bcp.2023.115745] [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: 06/07/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 08/21/2023]
Abstract
The aryl hydrocarbon receptor (AhR) is a cytosolic transcription factor activated by endogenous ligands and xenobiotic chemicals. Once the AhR is activated, it translocates to the nucleus, dimerizes with the AhR nuclear translator (ARNT) and binds to xenobiotic response elements (XRE) to promote gene transcription, notably the cytochrome P450 CYP1A1. The AhR not only mediates the toxic effects of environmental chemicals, but also has numerous putative physiological functions. This dichotomy in AhR biology may be related to reciprocal regulation of long non-coding RNA (lncRNA). lncRNA are defined as transcripts more than 200 nucleotides in length that do not encode a protein but are implicated in many physiological processes such as cell differentiation, cell proliferation, and apoptosis. lncRNA are also linked to disease pathogenesis, particularly the development of cancer. Recent studies have revealed that AhR activation by environmental chemicals affects the expression and function of lncRNA. In this article, we provide an overview of AhR signaling pathways activated by diverse ligands and highlight key differences in the putative biological versus toxicological response of AhR activation. We also detail the functions of lncRNA and provide current data on their regulation by the AhR. Finally, we outline how overlap in function between AhR and lncRNA may be one way in which AhR can be both a regulator of endogenous functions but also a mediator of toxicological responses to environmental chemicals. Overall, more research is still needed to fully understand the dynamic interplay between the AhR and lncRNA.
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Affiliation(s)
- Aeshah Alluli
- Meakins-Christie Laboratories, McGill University, Canada; Translational Research in Respiratory Diseases Program at the Research Institute of the McGill University Health Centre, Canada; Department of Pathology, McGill University, Canada
| | - Willem Rijnbout St James
- Meakins-Christie Laboratories, McGill University, Canada; Translational Research in Respiratory Diseases Program at the Research Institute of the McGill University Health Centre, Canada; Department of Pathology, McGill University, Canada
| | - David H Eidelman
- Meakins-Christie Laboratories, McGill University, Canada; Department of Medicine, McGill University, Canada
| | - Carolyn J Baglole
- Meakins-Christie Laboratories, McGill University, Canada; Translational Research in Respiratory Diseases Program at the Research Institute of the McGill University Health Centre, Canada; Department of Pathology, McGill University, Canada; Department of Medicine, McGill University, Canada; Department of Pharmacology and Therapeutics, McGill University, Canada.
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14
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Alahdal M, Elkord E. Non-coding RNAs in cancer immunotherapy: Predictive biomarkers and targets. Clin Transl Med 2023; 13:e1425. [PMID: 37735815 PMCID: PMC10514379 DOI: 10.1002/ctm2.1425] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/06/2023] [Accepted: 09/10/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND To date, standardising clinical predictive biomarkers for assessing the response to immunotherapy remains challenging due to variations in personal genetic signatures, tumour microenvironment complexities and epigenetic onco-mechanisms. MAIN BODY Early monitoring of key non-coding RNA (ncRNA) biomarkers may help in predicting the clinical efficacy of cancer immunotherapy and come up with standard predictive ncRNA biomarkers. For instance, reduced miR-125b-5p level in the plasma of non-small cell lung cancer patients treated with anti-PD-1 predicts a positive outcome. The level of miR-153 in the plasma of colorectal cancer patients treated with chimeric antigen receptor T lymphocyte (CAR-T) cell therapy may indicate the activation of T-cell killing activity. miR-148a-3p and miR-375 levels may forecast favourable responses to CAR-T-cell therapy in B-cell acute lymphoblastic leukaemia. In cancer patients treated with the GPC3 peptide vaccine, serum levels of miR-1228-5p, miR-193a-5p and miR-375-3p were reported as predictive biomarkers of good response and improved overall survival. Therefore, there is a critical need for further studies to elaborate on the key ncRNA biomarkers that have the potential to predict early clinical responses to immunotherapy. CONCLUSION This review summarises important predictive ncRNA biomarkers that were reported in cancer patients treated with different immunotherapeutic modalities, including monoclonal antibodies, small molecule inhibitors, cancer vaccines and CAR-T cells. In addition, a concise discussion on forthcoming perspectives is provided, outlining technical approaches for the optimal utilisation of immunomodulatory ncRNA biomarkers as predictive tools and therapeutic targets.
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Affiliation(s)
- Murad Alahdal
- Johns Hopkins All Children's Hospital, StPetersburgFloridaUSA
- Department of OncologySydney Kimmel Cancer CenterSchool of MedicineJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Eyad Elkord
- Department of Applied BiologyCollege of ScienceUniversity of SharjahUniversity CitySharjahUnited Arab Emirates
- Biomedical Research CenterSchool of ScienceEngineering and EnvironmentUniversity of SalfordManchesterUK
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15
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Gallardo-Dodd CJ, Oertlin C, Record J, Galvani RG, Sommerauer C, Kuznetsov NV, Doukoumopoulos E, Ali L, Oliveira MMS, Seitz C, Percipalle M, Nikić T, Sadova AA, Shulgina SM, Shmarov VA, Kutko OV, Vlasova DD, Orlova KD, Rykova MP, Andersson J, Percipalle P, Kutter C, Ponomarev SA, Westerberg LS. Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells. SCIENCE ADVANCES 2023; 9:eadg1610. [PMID: 37624890 PMCID: PMC10456848 DOI: 10.1126/sciadv.adg1610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 07/25/2023] [Indexed: 08/27/2023]
Abstract
The next steps of deep space exploration are manned missions to Moon and Mars. For safe space missions for crew members, it is important to understand the impact of space flight on the immune system. We studied the effects of 21 days dry immersion (DI) exposure on the transcriptomes of T cells isolated from blood samples of eight healthy volunteers. Samples were collected 7 days before DI, at day 7, 14, and 21 during DI, and 7 days after DI. RNA sequencing of CD3+ T cells revealed transcriptional alterations across all time points, with most changes occurring 14 days after DI exposure. At day 21, T cells showed evidence of adaptation with a transcriptional profile resembling that of 7 days before DI. At 7 days after DI, T cells again changed their transcriptional profile. These data suggest that T cells adapt by rewiring their transcriptomes in response to simulated weightlessness and that remodeling cues persist when reexposed to normal gravity.
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Affiliation(s)
- Carlos J. Gallardo-Dodd
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Christian Oertlin
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Julien Record
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Rômulo G. Galvani
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
- Universidade Veiga de Almeida, Rio de Janeiro, Brazil
- Laboratory for Thymus Research (LPT), Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Christian Sommerauer
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Nikolai V. Kuznetsov
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Russian Federation State Research Center Institute of Biomedical Problems RAS, Moscow, Russia
| | | | - Liaqat Ali
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates
- Core Technology Platform, NYUAD, Abu Dhabi, United Arab Emirates
| | - Mariana M. S. Oliveira
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Christina Seitz
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Mathias Percipalle
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Tijana Nikić
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Anastasia A. Sadova
- Russian Federation State Research Center Institute of Biomedical Problems RAS, Moscow, Russia
| | - Sofia M. Shulgina
- Russian Federation State Research Center Institute of Biomedical Problems RAS, Moscow, Russia
| | - Vjacheslav A. Shmarov
- Russian Federation State Research Center Institute of Biomedical Problems RAS, Moscow, Russia
| | - Olga V. Kutko
- Russian Federation State Research Center Institute of Biomedical Problems RAS, Moscow, Russia
| | - Daria D. Vlasova
- Russian Federation State Research Center Institute of Biomedical Problems RAS, Moscow, Russia
| | - Kseniya D. Orlova
- Russian Federation State Research Center Institute of Biomedical Problems RAS, Moscow, Russia
| | - Marina P. Rykova
- Russian Federation State Research Center Institute of Biomedical Problems RAS, Moscow, Russia
| | - John Andersson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Piergiorgio Percipalle
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates
- Center for Genomics and Systems Biology, NYUAD, Abu Dhabi, United Arab Emirates
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Claudia Kutter
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Sergey A. Ponomarev
- Russian Federation State Research Center Institute of Biomedical Problems RAS, Moscow, Russia
| | - Lisa S. Westerberg
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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16
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Baghdadi H, Heidari R, Zavvar M, Ahmadi N, Shakouri Khomartash M, Vahidi M, Mohammadimehr M, Bashash D, Ghorbani M. Long Non-Coding RNA Signatures in Lymphopoiesis and Lymphoid Malignancies. Noncoding RNA 2023; 9:44. [PMID: 37624036 PMCID: PMC10458434 DOI: 10.3390/ncrna9040044] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/09/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023] Open
Abstract
Lymphoid cells play a critical role in the immune system, which includes three subgroups of T, B, and NK cells. Recognition of the complexity of the human genetics transcriptome in lymphopoiesis has revolutionized our understanding of the regulatory potential of RNA in normal lymphopoiesis and lymphoid malignancies. Long non-coding RNAs (lncRNAs) are a class of RNA molecules greater than 200 nucleotides in length. LncRNAs have recently attracted much attention due to their critical roles in various biological processes, including gene regulation, chromatin organization, and cell cycle control. LncRNAs can also be used for cell differentiation and cell fate, as their expression patterns are often specific to particular cell types or developmental stages. Additionally, lncRNAs have been implicated in lymphoid differentiation, such as regulating T-cell and B-cell development, and their expression has been linked to immune-associated diseases such as leukemia and lymphoma. In addition, lncRNAs have been investigated as potential biomarkers for diagnosis, prognosis, and therapeutic response to disease management. In this review, we provide an overview of the current knowledge about the regulatory role of lncRNAs in physiopathology processes during normal lymphopoiesis and lymphoid leukemia.
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Affiliation(s)
- Hamed Baghdadi
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, AJA University of Medical Sciences, Tehran 1411718541, Iran; (H.B.); (M.V.); (M.M.)
| | - Reza Heidari
- Research Center for Cancer Screening and Epidemiology, AJA University of Medical Sciences, Tehran 1411718541, Iran;
- Medical Biotechnology Research Center, AJA University of Medical Sciences, Tehran 1411718541, Iran;
| | - Mahdi Zavvar
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran 443614177, Iran;
| | - Nazanin Ahmadi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran 1985717443, Iran;
| | | | - Mahmoud Vahidi
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, AJA University of Medical Sciences, Tehran 1411718541, Iran; (H.B.); (M.V.); (M.M.)
- Medical Biotechnology Research Center, AJA University of Medical Sciences, Tehran 1411718541, Iran;
| | - Mojgan Mohammadimehr
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, AJA University of Medical Sciences, Tehran 1411718541, Iran; (H.B.); (M.V.); (M.M.)
- Medical Biotechnology Research Center, AJA University of Medical Sciences, Tehran 1411718541, Iran;
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran 1985717443, Iran;
| | - Mahdi Ghorbani
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, AJA University of Medical Sciences, Tehran 1411718541, Iran; (H.B.); (M.V.); (M.M.)
- Medical Biotechnology Research Center, AJA University of Medical Sciences, Tehran 1411718541, Iran;
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17
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Yao W, Wang L, Liu F, Xia L. The role of long non-coding RNAs in breast cancer microenvironment. Pathol Res Pract 2023; 248:154707. [PMID: 37506626 DOI: 10.1016/j.prp.2023.154707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023]
Abstract
The tumor microenvironment (TME), which includes tumor cells, fibroblasts, endothelial cells, immune cells, and blood vessels, can affect tumor growth and metastasis. Studies have shown that tumor cells, fibroblasts, and macrophages can promote the development of tumors, while T and B cells can inhibit tumor progression. The crosstalk among different cells within the TME needs further study. Long non-coding RNAs (lncRNAs) are involved in biological processes, including cell proliferation, migration, and differentiation. The abnormal expression of certain lncRNAs is correlated with the progression of breast cancer and has been proven as diagnostic markers in various cancers, including breast cancer. In breast cancer, recent studies have shown that tumor cell- and non-tumor cell-derived lncRNAs can affect various facets of tumor progression, including growth, proliferation, and migration of tumor cells. Interestingly, in addition to being regulated by lncRNAs derived from tumor and non-tumor cells, the TME can regulate the expression of lncRNAs in tumor cells, fibroblasts, and macrophages, influencing their phenotype and function. However, the detailed molecular mechanisms of these phenomena remain unclear in the breast cancer microenvironment. Currently, many studies have shown that TME-associated lncRNAs are potential diagnostic and therapeutic targets for breast cancer. Considering that TME and lncRNAs can regulate each other, we summarize the role of lncRNAs in the breast cancer microenvironment and the potential of lncRNAs as valuable diagnostic markers.
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Affiliation(s)
- Wenwu Yao
- Institute of Hematological Disease, Jiangsu University, Zhenjiang 212001, China; International Genome Center, Jiangsu University, Zhenjiang 212013, China
| | - Lin Wang
- Department of Thyroid and Breast Surgery, Affiliated Hospital of Jiangsu University, Zhenjiang 212001, China
| | - Fang Liu
- International Genome Center, Jiangsu University, Zhenjiang 212013, China
| | - Lin Xia
- Institute of Hematological Disease, Jiangsu University, Zhenjiang 212001, China; Department of Laboratory Medicine, Affiliated Hospital of Jiangsu University, Zhenjiang 212001, China.
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18
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Wheeler BD, Gagnon JD, Zhu WS, Muñoz-Sandoval P, Wong SK, Simeonov DR, Li Z, Debarge R, Spitzer MH, Marson A, Ansel KM. The lncRNA Malat1 Inhibits miR-15/16 to Enhance Cytotoxic T Cell Activation and Memory Cell Formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.14.536843. [PMID: 37547023 PMCID: PMC10401941 DOI: 10.1101/2023.04.14.536843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Proper activation of cytotoxic T cells via the T cell receptor and the costimulatory receptor CD28 is essential for adaptive immunity against viruses, many intracellular bacteria and cancers. Through biochemical analysis of RNA:protein interactions, we uncovered a non-coding RNA circuit regulating activation and differentiation of cytotoxic T cells composed of the long non-coding RNA Malat1 (Metastasis Associated Lung Adenocarcinoma Transcript 1) and the microRNA family miR-15/16. miR-15/16 is a widely and highly expressed tumor suppressor miRNA family important for cell proliferation and survival. miR-15/16 also play important roles in T cell responses to viral infection, including the regulation of antigen-specific T cell expansion and T cell memory. Comparative Argonaute-2 high throughput sequencing of crosslinking immunoprecipitation (Ago2 HITS-CLIP, or AHC) combined with gene expression profiling in normal and miR-15/16-deficient T cells revealed a large network of several hundred direct miR-15/16 target mRNAs, many with functional relevance for T cell activation, survival and memory formation. Among these targets, the long non-coding RNA Malat1 contained the largest absolute magnitude miR-15/16-dependent AHC peak in T cells. This binding site was also among the strongest lncRNA:miRNA interactions detected in the T cell transcriptome. We used CRISPR targeting with homology directed repair to generate mice with a 5-nucleotide mutation in the miR-15/16 binding site in Malat1. This mutation interrupted Malat1:miR-15/16 interaction, and enhanced the repression of other miR-15/16 target genes, including CD28. Interrupting Malat1 interaction with miR-15/16 decreased cytotoxic T cell activation, including the expression of IL-2 and a broader CD28-responsive gene program. Accordingly, Malat1 mutation diminished memory cell persistence following LCMV Armstrong and Listeria monocytogenes infection. This study marks a significant advance in the study of long noncoding RNAs in the immune system by ascribing cell-intrinsic, sequence-specific in vivo function to Malat1. These findings have implications for T cell-mediated autoimmune diseases, antiviral and anti-tumor immunity, as well as lung adenocarcinoma and other malignancies where Malat1 is overexpressed.
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Affiliation(s)
- Benjamin D Wheeler
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- Sandler Asthma Basic Research Program, University of California, San Francisco, San Francisco, CA, USA
| | - John D Gagnon
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- Sandler Asthma Basic Research Program, University of California, San Francisco, San Francisco, CA, USA
| | - Wandi S Zhu
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- Sandler Asthma Basic Research Program, University of California, San Francisco, San Francisco, CA, USA
| | - Priscila Muñoz-Sandoval
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- Sandler Asthma Basic Research Program, University of California, San Francisco, San Francisco, CA, USA
| | - Simon K Wong
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Dimitre R Simeonov
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Zhongmei Li
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Rachel Debarge
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
- Department of Otolaryngology-Head and Neck Surgery, University of California San Francisco, San Francisco, CA 94143, USA
| | - Matthew H Spitzer
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
- Department of Otolaryngology-Head and Neck Surgery, University of California San Francisco, San Francisco, CA 94143, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129
- Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - Alexander Marson
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - K Mark Ansel
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- Sandler Asthma Basic Research Program, University of California, San Francisco, San Francisco, CA, USA
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19
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Louis TL, Wong WH, Yao P, Kurd NS, Tysl T, Indralingam CS, Ma S, Huang WJM, Chang JT. Regulation of CD8 T Cell Differentiation by the RNA-Binding Protein DDX5. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:241-251. [PMID: 37265401 PMCID: PMC10373580 DOI: 10.4049/jimmunol.2200778] [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: 10/24/2022] [Accepted: 05/05/2023] [Indexed: 06/03/2023]
Abstract
The RNA-binding protein DEAD-box protein 5 (DDX5) is a polyfunctional regulator of gene expression, but its role in CD8+ T cell biology has not been extensively investigated. In this study, we demonstrate that deletion of DDX5 in murine CD8+ T cells reduced the differentiation of terminal effector, effector memory T, and terminal effector memory cells while increasing the generation of central memory T cells, whereas forced expression of DDX5 elicited the opposite phenotype. DDX5-deficient CD8+ T cells exhibited increased expression of genes that promote central memory T cell differentiation, including Tcf7 and Eomes. Taken together, these findings reveal a role for DDX5 in regulating the differentiation of effector and memory CD8+ T cell subsets in response to microbial infection.
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Affiliation(s)
- Tiani L. Louis
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - William H. Wong
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Priscilla Yao
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Nadia S. Kurd
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Tiffani Tysl
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - Shengyun Ma
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Wendy Jia Men Huang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - John T. Chang
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Medicine, Jennifer Moreno Department of Veteran Affairs Medical Center, San Diego, CA, USA
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20
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Erber J, Herndler-Brandstetter D. Regulation of T cell differentiation and function by long noncoding RNAs in homeostasis and cancer. Front Immunol 2023; 14:1181499. [PMID: 37346034 PMCID: PMC10281531 DOI: 10.3389/fimmu.2023.1181499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/02/2023] [Indexed: 06/23/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) increase in genomes of complex organisms and represent the largest group of RNA genes transcribed in mammalian cells. Previously considered only transcriptional noise, lncRNAs comprise a heterogeneous class of transcripts that are emerging as critical regulators of T cell-mediated immunity. Here we summarize the lncRNA expression landscape of different T cell subsets and highlight recent advances in the role of lncRNAs in regulating T cell differentiation, function and exhaustion during homeostasis and cancer. We discuss the different molecular mechanisms of lncRNAs and highlight lncRNAs that can serve as novel targets to modulate T cell function or to improve the response to cancer immunotherapies by modulating the immunosuppressive tumor microenvironment.
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21
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Long T, Hernandez JE, Ma S, Steele S, Luo C, Li Y, Xie Q, Telese F, Zhou B, Huang WJM. The long non-coding RNA MALAT1 regulates intestine host-microbe interactions and polyposis. Front Cell Dev Biol 2023; 11:1168693. [PMID: 37325561 PMCID: PMC10265687 DOI: 10.3389/fcell.2023.1168693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/26/2023] [Indexed: 06/17/2023] Open
Abstract
The long non-coding RNA (lncRNA) Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) maintains the integrity of the intestinal epithelial barrier and regulates local inflammation. However, its influences on intestinal microbial communities and tissue susceptibility to cancer development remain unexplored. Here, we report that MALAT1 regulates host anti-microbial response gene expression and the composition of mucosal-associated microbial communities in a region-specific manner. In the APC mutant mouse model of intestine tumorigenesis, knocking out MALAT1 results in higher polyp counts in the small intestine and colon. Interestingly, intestine polyps that developed in the absence of MALAT1 were smaller in size. These findings highlight the unexpected bivalent role of MALAT1 in restricting and promoting cancer progression at different disease stages. Among the 30 MALAT1-targets shared by both the small intestine and colon, ZNF638 and SENP8 levels are predictive of colon adenoma patient overall survival and disease-free survival. Genomic assays further revealed that MALAT1 modulates intestinal target expression and splicing through both direct and indirect mechanisms. This study expands the role of lncRNAs in regulating intestine homeostasis, microbial communities, and cancer pathogenesis.
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Affiliation(s)
- Tianyun Long
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, United States
| | - Juan E. Hernandez
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, United States
| | - Shengyun Ma
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, United States
| | - Scarlet Steele
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, United States
| | - Claire Luo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, United States
| | - Yuxin Li
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, United States
| | - Qinghong Xie
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, United States
| | - Francesca Telese
- Department of Psychiatry, University of California San Diego, La Jolla, CA, United States
| | - Bing Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Wendy Jia Men Huang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, United States
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22
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Pathania AS. Crosstalk between Noncoding RNAs and the Epigenetics Machinery in Pediatric Tumors and Their Microenvironment. Cancers (Basel) 2023; 15:2833. [PMID: 37345170 DOI: 10.3390/cancers15102833] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 06/23/2023] Open
Abstract
According to the World Health Organization, every year, an estimated 400,000+ new cancer cases affect children under the age of 20 worldwide. Unlike adult cancers, pediatric cancers develop very early in life due to alterations in signaling pathways that regulate embryonic development, and environmental factors do not contribute much to cancer development. The highly organized complex microenvironment controlled by synchronized gene expression patterns plays an essential role in the embryonic stages of development. Dysregulated development can lead to tumor initiation and growth. The low mutational burden in pediatric tumors suggests the predominant role of epigenetic changes in driving the cancer phenotype. However, one more upstream layer of regulation driven by ncRNAs regulates gene expression and signaling pathways involved in the development. Deregulation of ncRNAs can alter the epigenetic machinery of a cell, affecting the transcription and translation profiles of gene regulatory networks required for cellular proliferation and differentiation during embryonic development. Therefore, it is essential to understand the role of ncRNAs in pediatric tumor development to accelerate translational research to discover new treatments for childhood cancers. This review focuses on the role of ncRNA in regulating the epigenetics of pediatric tumors and their tumor microenvironment, the impact of their deregulation on driving pediatric tumor progress, and their potential as effective therapeutic targets.
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Affiliation(s)
- Anup S Pathania
- Department of Biochemistry and Molecular Biology & The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
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23
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Zhao Y, Teng H, Deng Y, Sheldon M, Martinez C, Zhang J, Tian A, Sun Y, Nakagawa S, Yao F, Wang H, Ma L. Long noncoding RNA Malat1 inhibits Tead3-Nfatc1-mediated osteoclastogenesis to suppress osteoporosis and bone metastasis. RESEARCH SQUARE 2023:rs.3.rs-2405644. [PMID: 36993303 PMCID: PMC10055520 DOI: 10.21203/rs.3.rs-2405644/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
MALAT1, one of the few highly conserved nuclear long noncoding RNAs (IncRNAs), is abundantly expressed in normal tissues. Previously, targeted inactivation and genetic rescue experiments identified MALAT1 as a suppressor of breast cancer lung metastasis. On the other hand, Malat1-knockout mice are viable and develop normally. On a quest to discover new roles of MALAT1 in physiological and pathological processes, we found that this lncRNA is downregulated during osteoclastogenesis in humans and mice. Notably, Malat1 deficiency in mice promotes osteoporosis and bone metastasis, which can be rescued by genetic add-back of Malat1. Mechanistically, Malat1 binds to Tead3 protein, a macrophage-osteoclast-specific Tead family member, blocking Tead3 from binding and activating Nfatc1, a master regulator of osteoclastogenesis, which results in the inhibition of Nfatc1-mediated gene transcription and osteoclast differentiation. Altogether, these findings identify Malat1 as a lncRNA that suppresses osteoporosis and bone metastasis.
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Affiliation(s)
- Yang Zhao
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Hongqi Teng
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Yalan Deng
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Marisela Sheldon
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Consuelo Martinez
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jie Zhang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Annie Tian
- Department of Kinesiology, Rice University, Houston, Texas 77005, USA
| | - Yutong Sun
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Fan Yao
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Present address: Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Hai Wang
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14263, USA
| | - Li Ma
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, Texas 77030, USA
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24
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Quezada LK, Jin W, Liu YC, Kim ES, He Z, Indralingam CS, Tysl T, Labarta-Bajo L, Wehrens EJ, Jo Y, Kazane KR, Hattori C, Zuniga EI, Yeo GW, Chang JT. Early transcriptional and epigenetic divergence of CD8+ T cells responding to acute versus chronic infection. PLoS Biol 2023; 21:e3001983. [PMID: 36716323 PMCID: PMC9886247 DOI: 10.1371/journal.pbio.3001983] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 01/03/2023] [Indexed: 02/01/2023] Open
Abstract
During a microbial infection, responding CD8+ T cells give rise to effector cells that provide acute host defense and memory cells that provide sustained protection. An alternative outcome is exhaustion, a state of T cell dysfunction that occurs in the context of chronic infections and cancer. Although it is evident that exhausted CD8+ T (TEX) cells are phenotypically and molecularly distinct from effector and memory CD8+ T cells, the factors regulating the earliest events in the differentiation process of TEX cells remain incompletely understood. Here, we performed single-cell RNA-sequencing and single-cell ATAC-sequencing of CD8+ T cells responding to LCMV-Armstrong (LCMV-Arm) or LCMV-Clone 13 (LCMV-Cl13), which result in acute or chronic infections, respectively. Compared to CD8+ T cells that had undergone their first division in response to LCMV-Arm (Div1ARM) cells, CD8+ T cells that had undergone their first division in response to LCMV-Cl13 (Div1CL13) expressed higher levels of genes encoding transcription factors previously associated with exhaustion, along with higher levels of Ezh2, the catalytic component of the Polycomb Repressive Complex 2 (PRC2) complex, which mediates epigenetic silencing. Modulation of Ezh2 resulted in altered expression of exhaustion-associated molecules by CD8+ T cells responding to LCMV-Cl13, though the specific cellular and infectious contexts, rather than simply the level of Ezh2 expression, likely determine the eventual outcome. Taken together, these findings suggest that the differentiation paths of CD8+ T cells responding to acute versus chronic infections may diverge earlier than previously appreciated.
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Affiliation(s)
- Lauren K. Quezada
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Wenhao Jin
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Yi Chia Liu
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Eleanor S. Kim
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Zhaoren He
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Cynthia S. Indralingam
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Tiffani Tysl
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Lara Labarta-Bajo
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Ellen J. Wehrens
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Yeara Jo
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Katelynn R. Kazane
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Christopher Hattori
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Elina I. Zuniga
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Gene W. Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California, United States of America
| | - John T. Chang
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
- Department of Medicine, Jennifer Moreno Department of Veteran Affairs Medical Center, San Diego, California, United States of America
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