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Heim K, Sagar, Sogukpinar Ö, Llewellyn-Lacey S, Price DA, Emmerich F, Kraft ARM, Cornberg M, Kielbassa S, Knolle P, Wohlleber D, Bengsch B, Boettler T, Neumann-Haefelin C, Thimme R, Hofmann M. Attenuated effector T cells are linked to control of chronic HBV infection. Nat Immunol 2024; 25:1650-1662. [PMID: 39198634 PMCID: PMC11362014 DOI: 10.1038/s41590-024-01928-4] [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: 04/19/2024] [Accepted: 07/12/2024] [Indexed: 09/01/2024]
Abstract
Hepatitis B virus (HBV)-specific CD8+ T cells play a dominant role during acute-resolving HBV infection but are functionally impaired during chronic HBV infection in humans. These functional deficits have been linked with metabolic and phenotypic heterogeneity, but it has remained unclear to what extent different subsets of HBV-specific CD8+ T cells still suppress viral replication. We addressed this issue by deep profiling, functional testing and perturbation of HBV-specific CD8+ T cells during different phases of chronic HBV infection. Our data revealed a mechanism of effector CD8+ T cell attenuation that emerges alongside classical CD8+ T cell exhaustion. Attenuated HBV-specific CD8+ T cells were characterized by cytotoxic properties and a dampened effector differentiation program, determined by antigen recognition and TGFβ signaling, and were associated with viral control during chronic HBV infection. These observations identify a distinct subset of CD8+ T cells linked with immune efficacy in the context of a chronic human viral infection with immunotherapeutic potential.
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Affiliation(s)
- Kathrin Heim
- Department of Medicine II, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sagar
- Department of Medicine II, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Özlem Sogukpinar
- Department of Medicine II, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sian Llewellyn-Lacey
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff, UK
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff, UK
- Systems Immunity Research Institute, Cardiff University School of Medicine, University Hospital of Wales, Cardiff, UK
| | - Florian Emmerich
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Institute for Transfusion Medicine and Gene Therapy, University Medical Center, University of Freiburg, Freiburg, Germany
| | - Anke R M Kraft
- Department of Gastroenterology, Hepatology, Infectious Diseases and Endocrinology, Hannover Medical School, Hannover, Germany
- German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, Germany
- Centre for Individualised Infection Medicine (CiiM), Hannover, Germany
- Cluster of Excellence Resolving Infection Susceptibility (RESIST; EXC), Hannover Medical School, Hannover, Germany
| | - Markus Cornberg
- Department of Gastroenterology, Hepatology, Infectious Diseases and Endocrinology, Hannover Medical School, Hannover, Germany
- German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, Germany
- Centre for Individualised Infection Medicine (CiiM), Hannover, Germany
- Cluster of Excellence Resolving Infection Susceptibility (RESIST; EXC), Hannover Medical School, Hannover, Germany
| | - Sophie Kielbassa
- Department of Medicine II, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Percy Knolle
- Institute of Molecular Immunology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
- German Center for Infection Research, Munich, Germany
- Institute of Molecular Immunology, School of Life Science, TUM, Munich, Germany
| | - Dirk Wohlleber
- Institute of Molecular Immunology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Bertram Bengsch
- Department of Medicine II, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Signaling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Tobias Boettler
- Department of Medicine II, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Christoph Neumann-Haefelin
- Department of Medicine II, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Robert Thimme
- Department of Medicine II, Medical Center - University of Freiburg, Freiburg, Germany.
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Maike Hofmann
- Department of Medicine II, Medical Center - University of Freiburg, Freiburg, Germany.
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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2
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Brockmueller A, Ruiz de Porras V, Shakibaei M. Curcumin and its anti-colorectal cancer potential: From mechanisms of action to autophagy. Phytother Res 2024; 38:3525-3551. [PMID: 38699926 DOI: 10.1002/ptr.8220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/06/2024] [Accepted: 04/10/2024] [Indexed: 05/05/2024]
Abstract
Colorectal cancer (CRC) development and progression, one of the most common cancers globally, is supported by specific mechanisms to escape cell death despite chemotherapy, including cellular autophagy. Autophagy is an evolutionarily highly conserved degradation pathway involved in a variety of cellular processes, such as the maintenance of cellular homeostasis and clearance of foreign bodies, and its imbalance is associated with many diseases. However, the role of autophagy in CRC progression remains controversial, as it has a dual function, affecting either cell death or survival, and is associated with cellular senescence in tumor therapy. Indeed, numerous data have been presented that autophagy in cancers serves as an alternative to cell apoptosis when the latter is ineffective or in apoptosis-resistant cells, which is why it is also referred to as programmed cell death type II. Curcumin, one of the active constituents of Curcuma longa, has great potential to combat CRC by influencing various cellular signaling pathways and epigenetic regulation in a safe and cost-effective approach. This review discusses the efficacy of curcumin against CRC in vitro and in vivo, particularly its modulation of autophagy and apoptosis in various cellular pathways. While clinical studies have assessed the potential of curcumin in cancer prevention and treatment, none have specifically examined its role in autophagy. Nonetheless, we offer an overview of potential correlations to support the use of this polyphenol as a prophylactic or co-therapeutic agent in CRC.
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Affiliation(s)
- Aranka Brockmueller
- Chair of Vegetative Anatomy, Institute of Anatomy, Faculty of Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Vicenç Ruiz de Porras
- CARE Program, Germans Trias i Pujol Research Institute (IGTP), Barcelona, Spain
- Catalan Institute of Oncology, Badalona Applied Research Group in Oncology (B·ARGO), Barcelona, Spain
- GRET and Toxicology Unit, Department of Pharmacology, Toxicology and Therapeutic Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Mehdi Shakibaei
- Chair of Vegetative Anatomy, Institute of Anatomy, Faculty of Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
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3
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Ahn T, Bae EA, Seo H. Decoding and overcoming T cell exhaustion: Epigenetic and transcriptional dynamics in CAR-T cells against solid tumors. Mol Ther 2024; 32:1617-1627. [PMID: 38582965 PMCID: PMC11184340 DOI: 10.1016/j.ymthe.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 02/14/2024] [Accepted: 04/03/2024] [Indexed: 04/08/2024] Open
Abstract
T cell exhaustion, which is observed in various chronic infections and malignancies, is characterized by elevated expression of multiple inhibitory receptors, impaired effector functions, decreased proliferation, and reduced cytokine production. Notably, while adoptive T cell therapies, such as chimeric antigen receptor (CAR)-T therapy, have shown promise in treating cancer and other diseases, the efficacy of these therapies is often compromised by T cell exhaustion. It is imperative, therefore, to understand the mechanisms underlying this exhaustion to promote advances in T cell-related therapies. Here, we divided exhausted T cells into three distinct subsets according to their developmental and functional profiles: stem-like progenitor cells, intermediately exhausted cells, and terminally exhausted cells. These subsets are carefully regulated by synergistic mechanisms that involve transcriptional and epigenetic modulators. Key transcription factors, such as TCF1, BACH2, and TOX, are crucial for defining and sustaining exhaustion phenotypes. Concurrently, epigenetic regulators, such as TET2 and DNMT3A, shape the chromatin dynamics that direct T cell fate. The interplay of these molecular drivers has recently been highlighted in CAR-T research, revealing promising therapeutic directions. Thus, a profound understanding of exhausted T cell hierarchies and their molecular complexities may reveal innovative and improved tumor treatment strategies.
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Affiliation(s)
- Taeyoung Ahn
- Laboratory of Cell & Gene Therapy, Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Eun-Ah Bae
- Laboratory of Immunology, Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyungseok Seo
- Laboratory of Cell & Gene Therapy, Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Republic of Korea.
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4
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Jin L, Zhang L, Yan C, Liu M, Dean DC, Liu Y. Corneal injury repair and the potential involvement of ZEB1. EYE AND VISION (LONDON, ENGLAND) 2024; 11:20. [PMID: 38822380 PMCID: PMC11143703 DOI: 10.1186/s40662-024-00387-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 05/07/2024] [Indexed: 06/03/2024]
Abstract
The cornea, consisting of three cellular and two non-cellular layers, is the outermost part of the eyeball and frequently injured by external physical, chemical, and microbial insults. The epithelial-to-mesenchymal transition (EMT) plays a crucial role in the repair of corneal injuries. Zinc finger E-box binding homeobox 1 (ZEB1), an important transcription factor involved in EMT, is expressed in the corneal tissues. It regulates cell activities like migration, transformation, and proliferation, and thereby affects tissue inflammation, fibrosis, tumor metastasis, and necrosis by mediating various major signaling pathways, including transforming growth factor (TGF)-β. Dysfunction of ZEB1 would impair corneal tissue repair leading to epithelial healing delay, interstitial fibrosis, neovascularization, and squamous cell metaplasia. Understanding the mechanism underlying ZEB1 regulation of corneal injury repair will help us to formulate a therapeutic approach to enhance corneal injury repair.
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Affiliation(s)
- Lin Jin
- Department of Ophthalmology, The Third People's Hospital of Dalian, Dalian Medical University, Dalian, 116033, China
| | - Lijun Zhang
- Department of Ophthalmology, The Third People's Hospital of Dalian, Dalian Medical University, Dalian, 116033, China
| | - Chunxiao Yan
- Department of Ophthalmology, The Third People's Hospital of Dalian, Dalian Medical University, Dalian, 116033, China
| | - Mengxin Liu
- Department of Ophthalmology, The Third People's Hospital of Dalian, Dalian Medical University, Dalian, 116033, China
| | - Douglas C Dean
- James Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
| | - Yongqing Liu
- James Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
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5
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Do KK, Wang F, Sun X, Zhang Y, Liang W, Liu JY, Jiang DY, Lu X, Wang W, Zhang L, Dean DC, Liu Y. Conditional deletion of Zeb1 in Csf1r + cells reduces inflammatory response of the cornea to alkali burn. iScience 2024; 27:109694. [PMID: 38660397 PMCID: PMC11039400 DOI: 10.1016/j.isci.2024.109694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/29/2024] [Accepted: 04/05/2024] [Indexed: 04/26/2024] Open
Abstract
ZEB1 is an essential factor in embryonic development. In adults, it is often highly expressed in malignant tumors with low expression in normal tissues. The major biological function of ZEB1 in developing embryos and progressing cancers is to transdifferentiate cells from an epithelial to mesenchymal phenotype; but what roles ZEB1 plays in normal adult tissues are largely unknown. We previously reported that the reduction of Zeb1 in monoallelic global knockout (Zeb1+/-) mice reduced corneal inflammation-associated neovascularization following alkali burn. To uncover the cellular mechanism underlying the Zeb1 regulation of corneal inflammation, we functionally deleted Zeb1 alleles in Csf1r+ myeloid cells using a conditional knockout (cKO) strategy and found that Zeb1 cKO reduced leukocytes in the cornea after alkali burn. The reduction of immune cells was due to their increased apoptotic rate and linked to a Zeb1-downregulated apoptotic pathway. We conclude that Zeb1 facilitates corneal inflammatory response by maintaining Csf1r+ cell viability.
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Affiliation(s)
- Khoi K. Do
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Fuhua Wang
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Eye Institute and Eye Hospital of Shangdong First Medical University, Jinan 250021, China
| | - Xiaolei Sun
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Eye Institute and Eye Hospital of Shangdong First Medical University, Jinan 250021, China
| | - Yingnan Zhang
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
- The Rosenberg School of Optometry, University of the Incarnate Word, San Antonio, TX 78229, USA
| | - Wei Liang
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Department of Ophthalmology, Third People’s Hospital of Dalian, Dalian Medical University, Dalian 116033, China
| | - John Y. Liu
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Daniel Y. Jiang
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Xiaoqin Lu
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Wei Wang
- Department of Ophthalmology and Visual Sciences, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Lijun Zhang
- Department of Ophthalmology, Third People’s Hospital of Dalian, Dalian Medical University, Dalian 116033, China
| | - Douglas C. Dean
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Department of Ophthalmology and Visual Sciences, University of Louisville School of Medicine, Louisville, KY 40202, USA
- James Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Yongqing Liu
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Department of Ophthalmology and Visual Sciences, University of Louisville School of Medicine, Louisville, KY 40202, USA
- James Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
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6
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Lin CP, Levy PL, Alflen A, Apriamashvili G, Ligtenberg MA, Vredevoogd DW, Bleijerveld OB, Alkan F, Malka Y, Hoekman L, Markovits E, George A, Traets JJH, Krijgsman O, van Vliet A, Poźniak J, Pulido-Vicuña CA, de Bruijn B, van Hal-van Veen SE, Boshuizen J, van der Helm PW, Díaz-Gómez J, Warda H, Behrens LM, Mardesic P, Dehni B, Visser NL, Marine JC, Markel G, Faller WJ, Altelaar M, Agami R, Besser MJ, Peeper DS. Multimodal stimulation screens reveal unique and shared genes limiting T cell fitness. Cancer Cell 2024; 42:623-645.e10. [PMID: 38490212 PMCID: PMC11003465 DOI: 10.1016/j.ccell.2024.02.016] [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: 07/07/2023] [Revised: 01/03/2024] [Accepted: 02/22/2024] [Indexed: 03/17/2024]
Abstract
Genes limiting T cell antitumor activity may serve as therapeutic targets. It has not been systematically studied whether there are regulators that uniquely or broadly contribute to T cell fitness. We perform genome-scale CRISPR-Cas9 knockout screens in primary CD8 T cells to uncover genes negatively impacting fitness upon three modes of stimulation: (1) intense, triggering activation-induced cell death (AICD); (2) acute, triggering expansion; (3) chronic, causing dysfunction. Besides established regulators, we uncover genes controlling T cell fitness either specifically or commonly upon differential stimulation. Dap5 ablation, ranking highly in all three screens, increases translation while enhancing tumor killing. Loss of Icam1-mediated homotypic T cell clustering amplifies cell expansion and effector functions after both acute and intense stimulation. Lastly, Ctbp1 inactivation induces functional T cell persistence exclusively upon chronic stimulation. Our results functionally annotate fitness regulators based on their unique or shared contribution to traits limiting T cell antitumor activity.
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Affiliation(s)
- Chun-Pu Lin
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Pierre L Levy
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Tumor Immunology and Immunotherapy Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | - Astrid Alflen
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Hematology and Medical Oncology, University Medical Center, Johannes Gutenberg-University, 55131 Mainz, Germany; Research Center for Immunotherapy (FZI), University Medical Center, Johannes Gutenberg-University, 55131 Mainz, Germany
| | - Georgi Apriamashvili
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Maarten A Ligtenberg
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - David W Vredevoogd
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Onno B Bleijerveld
- Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Ferhat Alkan
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Yuval Malka
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Liesbeth Hoekman
- Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Ettai Markovits
- Ella Lemelbaum Institute for Immuno-oncology and Melanoma, Sheba Medical Center, Ramat Gan 52612, Israel; Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel-Aviv 6997801, Israel
| | - Austin George
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Joleen J H Traets
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Oscar Krijgsman
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Alex van Vliet
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Joanna Poźniak
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, 3000 Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Carlos Ariel Pulido-Vicuña
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, 3000 Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Beaunelle de Bruijn
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Susan E van Hal-van Veen
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Julia Boshuizen
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Pim W van der Helm
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Judit Díaz-Gómez
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Hamdy Warda
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Leonie M Behrens
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Paula Mardesic
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Bilal Dehni
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Nils L Visser
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, 3000 Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Gal Markel
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel-Aviv 6997801, Israel; Davidoff Cancer Center and Samueli Integrative Cancer Pioneering Institute, Rabin Medical Center, Petach Tikva 4941492, Israel
| | - William J Faller
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Maarten Altelaar
- Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Biomolecular Mass Spectrometry and Proteomics, Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Reuven Agami
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Michal J Besser
- Ella Lemelbaum Institute for Immuno-oncology and Melanoma, Sheba Medical Center, Ramat Gan 52612, Israel; Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel-Aviv 6997801, Israel; Davidoff Cancer Center and Samueli Integrative Cancer Pioneering Institute, Rabin Medical Center, Petach Tikva 4941492, Israel; Felsenstein Medical Research Center, Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Daniel S Peeper
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Pathology, VU University Amsterdam, 1081 HV Amsterdam, the Netherlands.
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7
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Chen XJ, Guo CH, Wang ZC, Yang Y, Pan YH, Liang JY, Sun MG, Fan LS, Liang L, Wang W. Hypoxia-induced ZEB1 promotes cervical cancer immune evasion by strengthening the CD47-SIRPα axis. Cell Commun Signal 2024; 22:15. [PMID: 38183060 PMCID: PMC10768116 DOI: 10.1186/s12964-023-01450-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 12/19/2023] [Indexed: 01/07/2024] Open
Abstract
BACKGROUND The dynamic interaction between cancer cells and tumour-associated macrophages (TAMs) in the hypoxic tumour microenvironment (TME) is an active barrier to the effector arm of the antitumour immune response. Cancer-secreted exosomes are emerging mediators of this cancer-stromal cross-talk in the TME; however, the mechanisms underlying this interaction remain unclear. METHODS Exosomes were isolated with ExoQuick exosome precipitation solution. The polarizing effect of TAMs was evaluated by flow cytometry, western blot analysis, immunofluorescence staining and in vitro phagocytosis assays. Clinical cervical cancer specimens and an in vivo xenograft model were also employed. RESULTS Our previous study showed that hypoxia increased the expression of ZEB1 in cervical squamous cell carcinoma (CSCC) cells, which resulted in increased infiltration of TAMs. Here, we found that hypoxia-induced ZEB1 expression is closely correlated with CD47-SIRPα axis activity in CSCC, which enables cancer cells to evade phagocytosis by macrophages and promotes tumour progression. ZEB1 was found to directly activate the transcription of the CD47 gene in hypoxic CSCC cells. We further showed that endogenous ZEB1 was characteristically enriched in hypoxic CSCC cell-derived exosomes and transferred into macrophages via these exosomes to promote SIRPα+ TAM polarization. Intriguingly, exosomal ZEB1 retained transcriptional activity and reprogrammed SIRPα+ TAMs via activation of the STAT3 signalling pathway in vitro and in vivo. STAT3 inhibition reduced the polarizing effect induced by exosomal ZEB1. Knockdown of ZEB1 increased the phagocytosis of CSCC cells by macrophages via decreasing CD47 and SIRPα expression. CONCLUSIONS Our results suggest that hypoxia-induced ZEB1 promotes immune evasion in CSCC by strengthening the CD47-SIRPα axis. ZEB1-targeted therapy in combination with CD47-SIRPα checkpoint immunotherapy may improve the outcomes of CSCC patients in part by disinhibiting innate immunity.
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Affiliation(s)
- Xiao-Jing Chen
- Guangzhou Medical University/Department of Obstetrics and Gynecology, The First Affiliated Hospital of Guangzhou Medical University, 151 Yanjiang West Road, Yuexiu District, Guangzhou, 510120, People's Republic of China
| | - Chu-Hong Guo
- Guangzhou Medical University/Department of Obstetrics and Gynecology, The First Affiliated Hospital of Guangzhou Medical University, 151 Yanjiang West Road, Yuexiu District, Guangzhou, 510120, People's Republic of China
| | - Zi-Ci Wang
- Guangzhou Medical University/Department of Obstetrics and Gynecology, The First Affiliated Hospital of Guangzhou Medical University, 151 Yanjiang West Road, Yuexiu District, Guangzhou, 510120, People's Republic of China
| | - Yang Yang
- Guangzhou Medical University/Department of Obstetrics and Gynecology, The First Affiliated Hospital of Guangzhou Medical University, 151 Yanjiang West Road, Yuexiu District, Guangzhou, 510120, People's Republic of China
| | - Yu-Hua Pan
- Guangzhou Medical University/Department of Obstetrics and Gynecology, The First Affiliated Hospital of Guangzhou Medical University, 151 Yanjiang West Road, Yuexiu District, Guangzhou, 510120, People's Republic of China
| | - Jie-Ying Liang
- Guangzhou Medical University/Department of Obstetrics and Gynecology, The First Affiliated Hospital of Guangzhou Medical University, 151 Yanjiang West Road, Yuexiu District, Guangzhou, 510120, People's Republic of China
| | - Mei-Ge Sun
- Guangzhou Medical University/Department of Obstetrics and Gynecology, The First Affiliated Hospital of Guangzhou Medical University, 151 Yanjiang West Road, Yuexiu District, Guangzhou, 510120, People's Republic of China
| | - Liang-Sheng Fan
- Guangzhou Medical University/Department of Obstetrics and Gynecology, The First Affiliated Hospital of Guangzhou Medical University, 151 Yanjiang West Road, Yuexiu District, Guangzhou, 510120, People's Republic of China.
| | - Li Liang
- Department of Pathology, Nanfang Hospital, Southern Medical University, 1838 Guangzhou Avenue North, Baiyun District, Guangzhou, 510515, People's Republic of China.
| | - Wei Wang
- Guangzhou Medical University/Department of Obstetrics and Gynecology, The First Affiliated Hospital of Guangzhou Medical University, 151 Yanjiang West Road, Yuexiu District, Guangzhou, 510120, People's Republic of China.
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8
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Agrawal P, Upadhyay A, Kumar A. microRNA as biomarkers in tuberculosis: a new emerging molecular diagnostic solution. Diagn Microbiol Infect Dis 2024; 108:116082. [PMID: 37839161 DOI: 10.1016/j.diagmicrobio.2023.116082] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 08/29/2023] [Accepted: 09/04/2023] [Indexed: 10/17/2023]
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis is a lethal infectious disease that is prevalent worldwide. During TB infection, host microRNAs change their expression in the form of up/down-regulation. The identification of unique host microRNAs during TB could serve as potential biomarkers in the early detection of TB. microRNAs fulfill the required criteria for being an ideal biomarker, such as sensitivity, high specificity, and accessibility. Therefore, the recognition of potential host microRNAs can be valuable for the diagnosis of TB. The field of miRNA biomarkers in TB requires more extensive research to identify potential biomarkers. This review provides an overview of the biogenesis and biological functions of microRNAs and presents the findings of various studies on the identification of potential biomarkers for TB. Research momentum is gaining in this field and we anticipate that miRNAs will become a routine approach in the development of reliable diagnostic and specific therapeutic interventions in future.
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Affiliation(s)
- Piyush Agrawal
- Department of Biotechnology, National Institute of Technology, Raipur (CG), India
| | - Aditya Upadhyay
- Department of Biotechnology, National Institute of Technology, Raipur (CG), India
| | - Awanish Kumar
- Department of Biotechnology, National Institute of Technology, Raipur (CG), India.
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9
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Abdel-Reheim MA, Nomier Y, Zaki MB, Abulsoud AI, Mohammed OA, Rashad AA, Oraby MA, Elballal MS, Tabaa MME, Elazazy O, Abd-Elmawla MA, El-Dakroury WA, Abdel Mageed SS, Abdelmaksoud NM, Elrebehy MA, Helal GK, Doghish AS. Unveiling the regulatory role of miRNAs in stroke pathophysiology and diagnosis. Pathol Res Pract 2024; 253:155085. [PMID: 38183822 DOI: 10.1016/j.prp.2023.155085] [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: 12/14/2023] [Revised: 12/28/2023] [Accepted: 12/30/2023] [Indexed: 01/08/2024]
Abstract
Stroke, a major global cause of mortality, leads to a range of problems for those who survive. Besides its brutal events, stroke also tends to have a characteristic of recurrence, making it a complex disease involving intricate regulatory networks. One of the major cellular regulators is the non-coding RNAs (ncRNA), specifically microRNAs (miRNAs), thus the possible functions of miRNAs in the pathogenesis of stroke are discussed as well as the possibility of using miRNA-based therapeutic approaches. Firstly, the molecular mechanisms by which miRNAs regulate vital physiological processes, including synaptic plasticity, oxidative stress, apoptosis, and the integrity of the blood-brain barrier (BBB) are reviewed. The miRNA indirectly impacts stroke outcomes by regulating BBB function and angiogenesis through the targeting of transcription factors and angiogenic factors. In addition, the tendency for some miRNAs to be upregulated in response to hypoxia, which is a prevalent phenomenon in stroke and various neurological disorders, highlights the possibility that it controls hypoxia-inducible factor (HIF) signaling and angiogenesis, thereby influencing the integrity of the BBB as examples of the discussed mechanisms. Furthermore, this review explores the potential therapeutic targets that miRNAs may offer for stroke recovery and highlights their promising capacity to alleviate post-stroke complications. This review provides researchers and clinicians with valuable resources since it attempts to decipher the complex network of miRNA-mediated mechanisms in stroke. Additionally, the review addresses the interplay between miRNAs and stroke risk factors as well as clinical applications of miRNAs as diagnostic and prognostic markers.
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Affiliation(s)
- Mustafa Ahmed Abdel-Reheim
- Department of Pharmaceutical Sciences, College of Pharmacy, Shaqra University, Shaqra 11961, Saudi Arabia; Department of Pharmacology and Toxicology, Faculty of Pharmacy, Beni-Suef University, Beni Suef 62521, Egypt.
| | - Yousra Nomier
- Department of Pharmacology and Clinical Pharmacy, College of Medicine and health sciences, Sultan Qaboos University, Muscat, Oman
| | - Mohamed Bakr Zaki
- Biochemistry, Department of Biochemistry, Faculty of Pharmacy, University of Sadat City, Menoufia 32897, Egypt
| | - Ahmed I Abulsoud
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt; Biochemistry Department, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | - Osama A Mohammed
- Department of Pharmacology, College of Medicine, University of Bisha, Bisha 61922, Saudi Arabia
| | - Ahmed A Rashad
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Mamdouh A Oraby
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Mohammed S Elballal
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Manar Mohammed El Tabaa
- Pharmacology & Environmental Toxicology, Environmental Studies & Research Institute (ESRI), University of Sadat City, Sadat City 32897, Menoufia, Egypt
| | - Ola Elazazy
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Mai A Abd-Elmawla
- Biochemistry, Department of Biochemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Walaa A El-Dakroury
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Sherif S Abdel Mageed
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | | | - Mahmoud A Elrebehy
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Gouda Kamel Helal
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Al-Azhar University, Cairo 11231, Egypt; Department of Pharmacology and Toxicology, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | - Ahmed S Doghish
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt; Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt.
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10
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Cortés M, Brischetto A, Martinez-Campanario MC, Ninfali C, Domínguez V, Fernández S, Celis R, Esteve-Codina A, Lozano JJ, Sidorova J, Garrabou G, Siegert AM, Enrich C, Pintado B, Morales-Ruiz M, Castro P, Cañete JD, Postigo A. Inflammatory macrophages reprogram to immunosuppression by reducing mitochondrial translation. Nat Commun 2023; 14:7471. [PMID: 37978290 PMCID: PMC10656499 DOI: 10.1038/s41467-023-42277-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/05/2023] [Indexed: 11/19/2023] Open
Abstract
Acute inflammation can either resolve through immunosuppression or persist, leading to chronic inflammation. These transitions are driven by distinct molecular and metabolic reprogramming of immune cells. The anti-diabetic drug Metformin inhibits acute and chronic inflammation through mechanisms still not fully understood. Here, we report that the anti-inflammatory and reactive-oxygen-species-inhibiting effects of Metformin depend on the expression of the plasticity factor ZEB1 in macrophages. Using mice lacking Zeb1 in their myeloid cells and human patient samples, we show that ZEB1 plays a dual role, being essential in both initiating and resolving inflammation by inducing macrophages to transition into an immunosuppressed state. ZEB1 mediates these diverging effects in inflammation and immunosuppression by modulating mitochondrial content through activation of autophagy and inhibition of mitochondrial protein translation. During the transition from inflammation to immunosuppression, Metformin mimics the metabolic reprogramming of myeloid cells induced by ZEB1. Mechanistically, in immunosuppression, ZEB1 inhibits amino acid uptake, leading to downregulation of mTORC1 signalling and a decrease in mitochondrial translation in macrophages. These results identify ZEB1 as a driver of myeloid cell metabolic plasticity, suggesting that targeting its expression and function could serve as a strategy to modulate dysregulated inflammation and immunosuppression.
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Affiliation(s)
- Marlies Cortés
- Group of Gene Regulation in Stem Cells, Cell Plasticity, Differentiation, and Cancer, IDIBAPS, 08036, Barcelona, Spain.
| | - Agnese Brischetto
- Group of Gene Regulation in Stem Cells, Cell Plasticity, Differentiation, and Cancer, IDIBAPS, 08036, Barcelona, Spain
| | - M C Martinez-Campanario
- Group of Gene Regulation in Stem Cells, Cell Plasticity, Differentiation, and Cancer, IDIBAPS, 08036, Barcelona, Spain
| | - Chiara Ninfali
- Group of Gene Regulation in Stem Cells, Cell Plasticity, Differentiation, and Cancer, IDIBAPS, 08036, Barcelona, Spain
| | - Verónica Domínguez
- National Center of Biotechnology (CSIC-CNB) and Center for Molecular Biology Severo Ochoa (CSIC/UAM-CBMSO) Transgenesis Facility, Higher Research Council (CSIC) and Autonomous University of Madrid (UAM), Cantoblanco, 28049, Madrid, Spain
| | - Sara Fernández
- Medical Intensive Care Unit and Department of Internal Medicine, Hospital Clínic of Barcelona, Group of Muscle Research and Mitochondrial Function, IDIBAPS, and CIBERER, 08036, Barcelona, Spain
| | - Raquel Celis
- Arthritis Unit, Dept. of Rheumathology, Hospital Clínic and IDIBAPS, 08036, Barcelona, Spain
| | | | - Juan J Lozano
- Biomedical Research Networking Centers in Digestive and Hepatic Diseases (CIBERehd), Carlos III Health Institute, 08036, Barcelona, Spain
| | - Julia Sidorova
- Biomedical Research Networking Centers in Digestive and Hepatic Diseases (CIBERehd), Carlos III Health Institute, 08036, Barcelona, Spain
| | - Gloria Garrabou
- Medical Intensive Care Unit and Department of Internal Medicine, Hospital Clínic of Barcelona, Group of Muscle Research and Mitochondrial Function, IDIBAPS, and CIBERER, 08036, Barcelona, Spain
| | - Anna-Maria Siegert
- MRC Metabolic Diseases Unit, University of Cambridge Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, CB1 0QQ, UK
| | - Carlos Enrich
- Department of Biomedicine, University of Barcelona School of Medicine and Health Sciences, 08036, Barcelona, Spain
| | - Belén Pintado
- National Center of Biotechnology (CSIC-CNB) and Center for Molecular Biology Severo Ochoa (CSIC/UAM-CBMSO) Transgenesis Facility, Higher Research Council (CSIC) and Autonomous University of Madrid (UAM), Cantoblanco, 28049, Madrid, Spain
| | - Manuel Morales-Ruiz
- Biomedical Research Networking Centers in Digestive and Hepatic Diseases (CIBERehd), Carlos III Health Institute, 08036, Barcelona, Spain
- Department of Biomedicine, University of Barcelona School of Medicine and Health Sciences, 08036, Barcelona, Spain
- Department of Biochemistry and Molecular Genetics, Hospital Clínic of Barcelona and IDIBAPS, 08036, Barcelona, Spain
| | - Pedro Castro
- Medical Intensive Care Unit and Department of Internal Medicine, Hospital Clínic of Barcelona, Group of Muscle Research and Mitochondrial Function, IDIBAPS, and CIBERER, 08036, Barcelona, Spain
| | - Juan D Cañete
- Arthritis Unit, Dept. of Rheumathology, Hospital Clínic and IDIBAPS, 08036, Barcelona, Spain
| | - Antonio Postigo
- Group of Gene Regulation in Stem Cells, Cell Plasticity, Differentiation, and Cancer, IDIBAPS, 08036, Barcelona, Spain.
- Biomedical Research Networking Centers in Digestive and Hepatic Diseases (CIBERehd), Carlos III Health Institute, 08036, Barcelona, Spain.
- Molecular Targets Program, Division of Oncology, Department of Medicine, J.G. Brown Cancer Center, Louisville, KY, 40202, USA.
- ICREA, 08010, Barcelona, Spain.
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11
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Hou W, Ji Z, Chen Z, Wherry EJ, Hicks SC, Ji H. A statistical framework for differential pseudotime analysis with multiple single-cell RNA-seq samples. Nat Commun 2023; 14:7286. [PMID: 37949861 PMCID: PMC10638410 DOI: 10.1038/s41467-023-42841-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 10/24/2023] [Indexed: 11/12/2023] Open
Abstract
Pseudotime analysis with single-cell RNA-sequencing (scRNA-seq) data has been widely used to study dynamic gene regulatory programs along continuous biological processes. While many methods have been developed to infer the pseudotemporal trajectories of cells within a biological sample, it remains a challenge to compare pseudotemporal patterns with multiple samples (or replicates) across different experimental conditions. Here, we introduce Lamian, a comprehensive and statistically-rigorous computational framework for differential multi-sample pseudotime analysis. Lamian can be used to identify changes in a biological process associated with sample covariates, such as different biological conditions while adjusting for batch effects, and to detect changes in gene expression, cell density, and topology of a pseudotemporal trajectory. Unlike existing methods that ignore sample variability, Lamian draws statistical inference after accounting for cross-sample variability and hence substantially reduces sample-specific false discoveries that are not generalizable to new samples. Using both real scRNA-seq and simulation data, including an analysis of differential immune response programs between COVID-19 patients with different disease severity levels, we demonstrate the advantages of Lamian in decoding cellular gene expression programs in continuous biological processes.
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Affiliation(s)
- Wenpin Hou
- Department of Biostatistics, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
| | - Zhicheng Ji
- Department of Biostatistics, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Zeyu Chen
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Stephanie C Hicks
- Department of Biostatistics, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA.
| | - Hongkai Ji
- Department of Biostatistics, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA.
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12
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Rithvik A, Samarpita S, Rasool M. Unleashing the pathological imprinting of cancer in autoimmunity: Is ZEB1 the answer? Life Sci 2023; 332:122115. [PMID: 37739160 DOI: 10.1016/j.lfs.2023.122115] [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: 06/30/2023] [Revised: 09/05/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
The intriguing scientific relationship between autoimmunity and cancer immunology have been traditionally indulged to throw spotlight on novel pathological targets. Understandably, these "slowly killing" diseases are on the opposite ends of the immune spectrum. However, the immune regulatory mechanisms between autoimmunity and cancer are not always contradictory and sometimes mirror each other based on disease stage, location, and timepoint. Moreover, the blockade of immune checkpoint molecules or signalling pathways that unleashes the immune response against cancer is being leveraged to preserve self-tolerance and treat many autoimmune disorders. Therefore, understanding the common crucial factors involved in cancer is of paramount importance to paint the autoimmune disease spectrum and validate novel drug candidates. In the current review, we will broadly describe how ZEB1, or Zinc-finger E-box Binding Homeobox 1, reinforces immune exhaustion in cancer or contributes to loss of self-tolerance in auto-immune conditions. We made an effort to exchange information about the molecular pathways and pathological responses (immune regulation, cell proliferation, senescence, autophagy, hypoxia, and circadian rhythm) that can be regulated by ZEB1 in the context of autoimmunity. This will help untwine the intricate and closely postured pathogenesis of ZEB1, that is less explored from the perspective of autoimmunity than its counterpart, cancer. This review will further consider several approaches for targeting ZEB1 in autoimmunity.
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Affiliation(s)
- Arulkumaran Rithvik
- Immunopathology Lab, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632 014, Tamil Nādu, India
| | - Snigdha Samarpita
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Mahaboobkhan Rasool
- Immunopathology Lab, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632 014, Tamil Nādu, India.
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13
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Liu J, Li J, Tuo Z, Hu W, Liu J. BATF2 inhibits PD-L1 expression and regulates CD8+ T-cell infiltration in non-small cell lung cancer. J Biol Chem 2023; 299:105302. [PMID: 37777155 PMCID: PMC10641166 DOI: 10.1016/j.jbc.2023.105302] [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: 07/18/2023] [Revised: 08/29/2023] [Accepted: 09/11/2023] [Indexed: 10/02/2023] Open
Abstract
Immune checkpoint blockades have made huge breakthrough among some cancer types including lung cancer. However, only a small proportion of patients will benefit from immune checkpoint blockades; other patients have no or minor response to immunotherapy. The underlying mechanisms and efficient biomarkers to predict immunotherapy resistances remain unclear and lacking. In this study, BATF2 knockout mice, human xenograft mice, were used for in vivo studies. Relevant RNA and protein levels were analyzed by RT-quantitative PCR and Western blotting. As a result, we found that the expression of BATF2 is negatively correlated with expression of programmed death-ligand 1 in the plasma of patients. Mechanically, we showed that BATF2 inhibits programmed death-ligand 1 expression in cancer cells by inhibiting the PI3K-AKT pathway where ZEB2 plays an important role in this process. Based on bioinformatics analysis, we found that the function of BATF2 in promoting antitumor immune response in patients with non-small cell lung cancer, which is mediated by BATF2, enhances CD8+ T-cell infiltration as well as activation. The expression of BATF2 from circulating tumor cells and tissues can be serve as an efficient biomarker to predict diagnosis, prognosis, and immunotherapy efficacy.
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Affiliation(s)
- Junwei Liu
- Department of Thoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jie Li
- Department of Immunology, University of South Florida, Tampa, Florida, USA
| | - Zhan Tuo
- Department of Immunotherapy, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, P.R. China
| | - Weidong Hu
- Department of Thoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China.
| | - Jun Liu
- Department of Thoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China.
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14
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Ninfali C, Siles L, Esteve-Codina A, Postigo A. The mesodermal and myogenic specification of hESCs depend on ZEB1 and are inhibited by ZEB2. Cell Rep 2023; 42:113222. [PMID: 37819755 DOI: 10.1016/j.celrep.2023.113222] [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: 03/12/2022] [Revised: 08/02/2023] [Accepted: 09/20/2023] [Indexed: 10/13/2023] Open
Abstract
Human embryonic stem cells (hESCs) can differentiate into any cell lineage. Here, we report that ZEB1 and ZEB2 promote and inhibit mesodermal-to-myogenic specification of hESCs, respectively. Knockdown and/or overexpression experiments of ZEB1, ZEB2, or PAX7 in hESCs indicate that ZEB1 is required for hESC Nodal/Activin-mediated mesodermal specification and PAX7+ human myogenic progenitor (hMuP) generation, while ZEB2 inhibits these processes. ZEB1 downregulation induces neural markers, while ZEB2 downregulation induces mesodermal/myogenic markers. Mechanistically, ZEB1 binds to and transcriptionally activates the PAX7 promoter, while ZEB2 binds to and activates the promoter of the neural OTX2 marker. Transplanting ZEB1 or ZEB2 knocked down hMuPs into the muscles of a muscular dystrophy mouse model, showing that hMuP engraftment and generation of dystrophin-positive myofibers depend on ZEB1 and are inhibited by ZEB2. The mouse model results suggest that ZEB1 expression and/or downregulating ZEB2 in hESCs may also enhance hESC regenerative capacity for human muscular dystrophy therapy.
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Affiliation(s)
- Chiara Ninfali
- Group of Gene Regulation in Stem Cells, Cell Plasticity, Differentiation, and Cancer, IDIBAPS, 08036 Barcelona, Spain
| | - Laura Siles
- Group of Gene Regulation in Stem Cells, Cell Plasticity, Differentiation, and Cancer, IDIBAPS, 08036 Barcelona, Spain
| | | | - Antonio Postigo
- Group of Gene Regulation in Stem Cells, Cell Plasticity, Differentiation, and Cancer, IDIBAPS, 08036 Barcelona, Spain; Molecular Targets Program, J.G. Brown Center, Louisville University Healthcare Campus, Louisville, KY 40202, USA; ICREA, 08010 Barcelona, Spain.
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15
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Iyoda T, Shimizu K, Endo T, Watanabe T, Taniuchi I, Aoshima H, Satoh M, Nakazato H, Yamasaki S, Fujii SI. Zeb2 regulates differentiation of long-lived effector of invariant natural killer T cells. Commun Biol 2023; 6:1070. [PMID: 37903859 PMCID: PMC10616117 DOI: 10.1038/s42003-023-05421-w] [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: 04/04/2023] [Accepted: 10/04/2023] [Indexed: 11/01/2023] Open
Abstract
After activation, some invariant natural killer T (iNKT) cells are differentiated into Klrg1+ long-lived effector NKT1 cells. However, the regulation from the effector phase to the memory phase has not been elucidated. Zeb2 is a zinc finger E homeobox-binding transcription factor and is expressed in a variety of immune cells, but its function in iNKT cell differentiation remains also unknown. Here, we show that Zeb2 is dispensable for development of iNKT cells in the thymus and their maintenance in steady state peripheral tissues. After ligand stimulation, Zeb2 plays essential roles in the differentiation to and maintenance of Klrg1+ Cx3cr1+GzmA+ iNKT cell population derived from the NKT1 subset. Our results including single-cell-RNA-seq analysis indicate that Zeb2 regulates Klrg1+ long-lived iNKT cell differentiation by preventing apoptosis. Collectively, this study reveals the crucial transcriptional regulation by Zeb2 in establishment of the memory iNKT phase through driving differentiation of Klrg1+ Cx3cr1+GzmA+ iNKT population.
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Affiliation(s)
- Tomonori Iyoda
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
| | - Kanako Shimizu
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
- Program for Drug Discovery and Medical Technology Platforms, RIKEN, Yokohama, Kanagawa, Japan
| | - Takaho Endo
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
| | - Takashi Watanabe
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
| | - Ichiro Taniuchi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
| | - Honoka Aoshima
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
| | - Mikiko Satoh
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
| | - Hiroshi Nakazato
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
| | - Satoru Yamasaki
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
| | - Shin-Ichiro Fujii
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan.
- Program for Drug Discovery and Medical Technology Platforms, RIKEN, Yokohama, Kanagawa, Japan.
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16
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Rudloff MW, Zumbo P, Favret NR, Roetman JJ, Detrés Román CR, Erwin MM, Murray KA, Jonnakuti ST, Dündar F, Betel D, Philip M. Hallmarks of CD8 + T cell dysfunction are established within hours of tumor antigen encounter before cell division. Nat Immunol 2023; 24:1527-1539. [PMID: 37537361 PMCID: PMC10878719 DOI: 10.1038/s41590-023-01578-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 07/07/2023] [Indexed: 08/05/2023]
Abstract
Tumor-specific CD8+ T cells (TST) in patients with cancer are dysfunctional and unable to halt cancer progression. TST dysfunction, also known as exhaustion, is thought to be driven by chronic T cell antigen receptor (TCR) stimulation over days to weeks. However, we know little about the interplay between CD8+ T cell function, cell division and epigenetic remodeling within hours of activation. Here, we assessed early CD8+ T cell differentiation, cell division, chromatin accessibility and transcription in tumor-bearing mice and acutely infected mice. Surprisingly, despite robust activation and proliferation, TST had near complete effector function impairment even before undergoing cell division and had acquired hallmark chromatin accessibility features previously associated with later dysfunction/exhaustion. Moreover, continued tumor/antigen exposure drove progressive epigenetic remodeling, 'imprinting' the dysfunctional state. Our study reveals the rapid divergence of T cell fate choice before cell division in the context of tumors versus infection.
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Affiliation(s)
- Michael W Rudloff
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Paul Zumbo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, USA
| | - Natalie R Favret
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Jessica J Roetman
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Carlos R Detrés Román
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Megan M Erwin
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Kristen A Murray
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Sriya T Jonnakuti
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Friederike Dündar
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, USA
| | - Doron Betel
- Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Mary Philip
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA.
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN, USA.
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.
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17
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Wu JE, Manne S, Ngiow SF, Baxter AE, Huang H, Freilich E, Clark ML, Lee JH, Chen Z, Khan O, Staupe RP, Huang YJ, Shi J, Giles JR, Wherry EJ. In vitro modeling of CD8 + T cell exhaustion enables CRISPR screening to reveal a role for BHLHE40. Sci Immunol 2023; 8:eade3369. [PMID: 37595022 DOI: 10.1126/sciimmunol.ade3369] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 07/07/2023] [Indexed: 08/20/2023]
Abstract
Identifying molecular mechanisms of exhausted CD8 T cells (Tex) is a key goal of improving immunotherapy of cancer and other diseases. However, high-throughput interrogation of in vivo Tex can be costly and inefficient. In vitro models of Tex are easily customizable and quickly generate high cellular yield, enabling CRISPR screening and other high-throughput assays. We established an in vitro model of chronic stimulation and benchmarked key phenotypic, functional, transcriptional, and epigenetic features against bona fide in vivo Tex. We leveraged this model of in vitro chronic stimulation in combination with CRISPR screening to identify transcriptional regulators of T cell exhaustion. This approach identified several transcription factors, including BHLHE40. In vitro and in vivo validation defined a role for BHLHE40 in regulating a key differentiation checkpoint between progenitor and intermediate Tex subsets. By developing and benchmarking an in vitro model of Tex, then applying high-throughput CRISPR screening, we demonstrate the utility of mechanistically annotated in vitro models of Tex.
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Affiliation(s)
- Jennifer E Wu
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, USA
| | - Sasikanth Manne
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Shin Foong Ngiow
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, USA
| | - Amy E Baxter
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hua Huang
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elizabeth Freilich
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Megan L Clark
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joanna H Lee
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zeyu Chen
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Omar Khan
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ryan P Staupe
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yinghui J Huang
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Junwei Shi
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Josephine R Giles
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, USA
| | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, USA
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Zwijnenburg AJ, Pokharel J, Varnaitė R, Zheng W, Hoffer E, Shryki I, Comet NR, Ehrström M, Gredmark-Russ S, Eidsmo L, Gerlach C. Graded expression of the chemokine receptor CX3CR1 marks differentiation states of human and murine T cells and enables cross-species interpretation. Immunity 2023; 56:1955-1974.e10. [PMID: 37490909 DOI: 10.1016/j.immuni.2023.06.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 02/02/2023] [Accepted: 06/29/2023] [Indexed: 07/27/2023]
Abstract
T cells differentiate into functionally distinct states upon antigen encounter. These states are delineated by different cell surface markers for murine and human T cells, which hamper cross-species translation of T cell properties. We aimed to identify surface markers that reflect the graded nature of CD8+ T cell differentiation and delineate functionally comparable states in mice and humans. CITEseq analyses revealed that graded expression of CX3CR1, encoding the chemokine receptor CX3CR1, correlated with the CD8+ T cell differentiation gradient. CX3CR1 expression distinguished human and murine CD8+ and CD4+ T cell states, as defined by migratory and functional properties. Graded CX3CR1 expression, refined with CD62L, accurately captured the high-dimensional T cell differentiation continuum. Furthermore, the CX3CR1 expression gradient delineated states with comparable properties in humans and mice in steady state and on longitudinally tracked virus-specific CD8+ T cells in both species. Thus, graded CX3CR1 expression provides a strategy to translate the behavior of distinct T cell differentiation states across species.
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Affiliation(s)
- Anthonie Johan Zwijnenburg
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Center for Molecular Medicine, 17176 Stockholm, Sweden
| | - Jyoti Pokharel
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Center for Molecular Medicine, 17176 Stockholm, Sweden
| | - Renata Varnaitė
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Wenning Zheng
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Center for Molecular Medicine, 17176 Stockholm, Sweden
| | - Elena Hoffer
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Center for Molecular Medicine, 17176 Stockholm, Sweden
| | - Iman Shryki
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Center for Molecular Medicine, 17176 Stockholm, Sweden
| | - Natalia Ramirez Comet
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Center for Molecular Medicine, 17176 Stockholm, Sweden
| | - Marcus Ehrström
- Department of Reconstructive Plastic Surgery, Karolinska University Hospital, 17176 Stockholm, Sweden; Nordiska Kliniken, 11151 Stockholm, Sweden
| | - Sara Gredmark-Russ
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, 17176 Stockholm, Sweden; Department of Infectious Diseases, Karolinska University Hospital, 17176 Stockholm, Sweden; Laboratory for Molecular Infection Medicine Sweden, 90187 Umeå, Sweden
| | - Liv Eidsmo
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Center for Molecular Medicine, 17176 Stockholm, Sweden; Leo Foundation Skin Immunology Center, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Carmen Gerlach
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Center for Molecular Medicine, 17176 Stockholm, Sweden.
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Radhakrishnan K, Truong L, Carmichael CL. An "unexpected" role for EMT transcription factors in hematological development and malignancy. Front Immunol 2023; 14:1207360. [PMID: 37600794 PMCID: PMC10435889 DOI: 10.3389/fimmu.2023.1207360] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/14/2023] [Indexed: 08/22/2023] Open
Abstract
The epithelial to mesenchymal transition (EMT) is a fundamental developmental process essential for normal embryonic development. It is also important during various pathogenic processes including fibrosis, wound healing and epithelial cancer cell metastasis and invasion. EMT is regulated by a variety of cell signalling pathways, cell-cell interactions and microenvironmental cues, however the key drivers of EMT are transcription factors of the ZEB, TWIST and SNAIL families. Recently, novel and unexpected roles for these EMT transcription factors (EMT-TFs) during normal blood cell development have emerged, which appear to be largely independent of classical EMT processes. Furthermore, EMT-TFs have also begun to be implicated in the development and pathogenesis of malignant hematological diseases such as leukemia and lymphoma, and now present themselves or the pathways they regulate as possible new therapeutic targets within these malignancies. In this review, we discuss the ZEB, TWIST and SNAIL families of EMT-TFs, focusing on what is known about their normal roles during hematopoiesis as well as the emerging and "unexpected" contribution they play during development and progression of blood cancers.
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Affiliation(s)
- Karthika Radhakrishnan
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia
| | - Lynda Truong
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia
| | - Catherine L. Carmichael
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Monash University, Faculty of Medicine, Nursing and Health Sciences, Clayton, VIC, Australia
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Verma M, Verma D, Sripada AS, Sirohi K, Varma R, Sahu A, Alam R. NFκB1 inhibits memory formation and supports effector function of ILC2s in memory-driven asthma. Front Immunol 2023; 14:1217776. [PMID: 37575259 PMCID: PMC10415221 DOI: 10.3389/fimmu.2023.1217776] [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: 05/05/2023] [Accepted: 07/06/2023] [Indexed: 08/15/2023] Open
Abstract
Background ILC2s are capable of generating memory. The mechanism of memory induction and memory-driven effector function (trained immunity) in ILC2s is unknown. Objective NFκB1 is preferentially expressed at a high level in ILC2s. We examined the role of NFkB1 in memory induction and memory-driven effector function in a mouse model of asthma. Methods Intranasal administration of Alternaria, flexivent, ELISA, histology, real-time PCR, western blot, flow cytometry and immunofluorescence staining. Results NFκB1 was essential for the effector phase of memory-driven asthma. NFκB1 was critical for IL33 production, ILC2 generation, and production of type-2 cytokines, which resulted in eosinophilic inflammation and other features of asthma. NFκB1 induction of type-2 cytokines in ILC2s was independent of GATA3. NFκB1 was important for allergen induction of ILC3s and FoxP3+ Tregs. NFκB1 did not affect Th2 cells or their cytokine production. In contrast to its protagonistic role in the effector phase, NFκB1 had an antagonistic role in the memory phase. NFκB1 inhibited allergen-induced upregulation of memory-associated repressor and preparedness genes in ILC2s. NFκB1 upregulated RUNX1. NFκB1 formed a heterodimer with RUNX1 in ILC2s. Conclusions NFκB1 positively regulated the effector phase but inhibited the induction phase of memory. The foregoing pointed to an interdependent antagonism between the memory induction and the memory effector processes. The NFκB1-RUNX1 heterodimer represented a non-canonical transcriptional activator of type-2 cytokines in ILC2s.
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Affiliation(s)
- Mukesh Verma
- Division of Allergy & Immunology, Department of Medicine, National Jewish Health, Denver, CO, United States
| | - Divya Verma
- Division of Allergy & Immunology, Department of Medicine, National Jewish Health, Denver, CO, United States
| | - Anand Santosh Sripada
- Division of Allergy & Immunology, Department of Medicine, National Jewish Health, Denver, CO, United States
| | - Kapil Sirohi
- Division of Allergy & Immunology, Department of Medicine, National Jewish Health, Denver, CO, United States
| | - Rangati Varma
- Division of Allergy & Immunology, Department of Medicine, National Jewish Health, Denver, CO, United States
| | - Anita Sahu
- Division of Allergy & Immunology, Department of Medicine, National Jewish Health, Denver, CO, United States
| | - Rafeul Alam
- Division of Allergy & Immunology, Department of Medicine, National Jewish Health, Denver, CO, United States
- School of Medicine, University of Colorado Denver, Denver, CO, United States
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21
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Jung IY, Bartoszek RL, Rech AJ, Collins SM, Ooi SK, Williams EF, Hopkins CR, Narayan V, Haas NB, Frey NV, Hexner EO, Siegel DL, Plesa G, Porter DL, Cantu A, Everett JK, Guedan S, Berger SL, Bushman FD, Herbst F, Fraietta JA. Type I Interferon Signaling via the EGR2 Transcriptional Regulator Potentiates CAR T Cell-Intrinsic Dysfunction. Cancer Discov 2023; 13:1636-1655. [PMID: 37011008 PMCID: PMC10330003 DOI: 10.1158/2159-8290.cd-22-1175] [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: 10/16/2022] [Revised: 01/18/2023] [Accepted: 03/03/2023] [Indexed: 04/04/2023]
Abstract
Chimeric antigen receptor (CAR) T cell therapy has shown promise in treating hematologic cancers, but resistance is common and efficacy is limited in solid tumors. We found that CAR T cells autonomously propagate epigenetically programmed type I interferon signaling through chronic stimulation, which hampers antitumor function. EGR2 transcriptional regulator knockout not only blocks this type I interferon-mediated inhibitory program but also independently expands early memory CAR T cells with improved efficacy against liquid and solid tumors. The protective effect of EGR2 deletion in CAR T cells against chronic antigen-induced exhaustion can be overridden by interferon-β exposure, suggesting that EGR2 ablation suppresses dysfunction by inhibiting type I interferon signaling. Finally, a refined EGR2 gene signature is a biomarker for type I interferon-associated CAR T cell failure and shorter patient survival. These findings connect prolonged CAR T cell activation with deleterious immunoinflammatory signaling and point to an EGR2-type I interferon axis as a therapeutically amenable biological system. SIGNIFICANCE To improve CAR T cell therapy outcomes, modulating molecular determinants of CAR T cell-intrinsic resistance is crucial. Editing the gene encoding the EGR2 transcriptional regulator renders CAR T cells impervious to type I interferon pathway-induced dysfunction and improves memory differentiation, thereby addressing major barriers to progress for this emerging class of cancer immunotherapies. This article is highlighted in the In This Issue feature, p. 1501.
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Affiliation(s)
- In-Young Jung
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert L. Bartoszek
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew J. Rech
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sierra M. Collins
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Philadelphia, PA 19104, USA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Soon-Keat Ooi
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erik F. Williams
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Caitlin R. Hopkins
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Vivek Narayan
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Naomi B. Haas
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Noelle V. Frey
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Elizabeth O. Hexner
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Donald L. Siegel
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gabriela Plesa
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David L. Porter
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Adrian Cantu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John K. Everett
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sonia Guedan
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, 08036, Spain
| | - Shelley L. Berger
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Philadelphia, PA 19104, USA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frederic D. Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Friederike Herbst
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joseph A. Fraietta
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lead Contact
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Chandiran K, Cauley LS. The diverse effects of transforming growth factor-β and SMAD signaling pathways during the CTL response. Front Immunol 2023; 14:1199671. [PMID: 37426662 PMCID: PMC10327426 DOI: 10.3389/fimmu.2023.1199671] [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: 04/03/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023] Open
Abstract
Cytotoxic T lymphocytes (CTLs) play an important role in defense against infections with intracellular pathogens and anti-tumor immunity. Efficient migration is required to locate and destroy infected cells in different regions of the body. CTLs accomplish this task by differentiating into specialized subsets of effector and memory CD8 T cells that traffic to different tissues. Transforming growth factor-beta (TGFβ) belongs to a large family of growth factors that elicit diverse cellular responses via canonical and non-canonical signaling pathways. Canonical SMAD-dependent signaling pathways are required to coordinate changes in homing receptor expression as CTLs traffic between different tissues. In this review, we discuss the various ways that TGFβ and SMAD-dependent signaling pathways shape the cellular immune response and transcriptional programming of newly activated CTLs. As protective immunity requires access to the circulation, emphasis is placed on cellular processes that are required for cell-migration through the vasculature.
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Affiliation(s)
- Karthik Chandiran
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, India
| | - Linda S. Cauley
- Department of Immunology, UCONN Health, Farmington, CT, United States
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23
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Sun L, Su Y, Jiao A, Wang X, Zhang B. T cells in health and disease. Signal Transduct Target Ther 2023; 8:235. [PMID: 37332039 PMCID: PMC10277291 DOI: 10.1038/s41392-023-01471-y] [Citation(s) in RCA: 123] [Impact Index Per Article: 123.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 06/20/2023] Open
Abstract
T cells are crucial for immune functions to maintain health and prevent disease. T cell development occurs in a stepwise process in the thymus and mainly generates CD4+ and CD8+ T cell subsets. Upon antigen stimulation, naïve T cells differentiate into CD4+ helper and CD8+ cytotoxic effector and memory cells, mediating direct killing, diverse immune regulatory function, and long-term protection. In response to acute and chronic infections and tumors, T cells adopt distinct differentiation trajectories and develop into a range of heterogeneous populations with various phenotype, differentiation potential, and functionality under precise and elaborate regulations of transcriptional and epigenetic programs. Abnormal T-cell immunity can initiate and promote the pathogenesis of autoimmune diseases. In this review, we summarize the current understanding of T cell development, CD4+ and CD8+ T cell classification, and differentiation in physiological settings. We further elaborate the heterogeneity, differentiation, functionality, and regulation network of CD4+ and CD8+ T cells in infectious disease, chronic infection and tumor, and autoimmune disease, highlighting the exhausted CD8+ T cell differentiation trajectory, CD4+ T cell helper function, T cell contributions to immunotherapy and autoimmune pathogenesis. We also discuss the development and function of γδ T cells in tissue surveillance, infection, and tumor immunity. Finally, we summarized current T-cell-based immunotherapies in both cancer and autoimmune diseases, with an emphasis on their clinical applications. A better understanding of T cell immunity provides insight into developing novel prophylactic and therapeutic strategies in human diseases.
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Affiliation(s)
- Lina Sun
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, 710061, China
- Xi'an Key Laboratory of Immune Related Diseases, Xi'an, Shannxi, 710061, China
| | - Yanhong Su
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, 710061, China
- Xi'an Key Laboratory of Immune Related Diseases, Xi'an, Shannxi, 710061, China
| | - Anjun Jiao
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, 710061, China
- Xi'an Key Laboratory of Immune Related Diseases, Xi'an, Shannxi, 710061, China
| | - Xin Wang
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, 710061, China
- Xi'an Key Laboratory of Immune Related Diseases, Xi'an, Shannxi, 710061, China
| | - Baojun Zhang
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China.
- Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China.
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, 710061, China.
- Xi'an Key Laboratory of Immune Related Diseases, Xi'an, Shannxi, 710061, China.
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Baxter AE, Huang H, Giles JR, Chen Z, Wu JE, Drury S, Dalton K, Park SL, Torres L, Simone BW, Klapholz M, Ngiow SF, Freilich E, Manne S, Alcalde V, Ekshyyan V, Berger SL, Shi J, Jordan MS, Wherry EJ. The SWI/SNF chromatin remodeling complexes BAF and PBAF differentially regulate epigenetic transitions in exhausted CD8 + T cells. Immunity 2023; 56:1320-1340.e10. [PMID: 37315535 DOI: 10.1016/j.immuni.2023.05.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 02/28/2023] [Accepted: 05/11/2023] [Indexed: 06/16/2023]
Abstract
CD8+ T cell exhaustion (Tex) limits disease control during chronic viral infections and cancer. Here, we investigated the epigenetic factors mediating major chromatin-remodeling events in Tex-cell development. A protein-domain-focused in vivo CRISPR screen identified distinct functions for two versions of the SWI/SNF chromatin-remodeling complex in Tex-cell differentiation. Depletion of the canonical SWI/SNF form, BAF, impaired initial CD8+ T cell responses in acute and chronic infection. In contrast, disruption of PBAF enhanced Tex-cell proliferation and survival. Mechanistically, PBAF regulated the epigenetic and transcriptional transition from TCF-1+ progenitor Tex cells to more differentiated TCF-1- Tex subsets. Whereas PBAF acted to preserve Tex progenitor biology, BAF was required to generate effector-like Tex cells, suggesting that the balance of these factors coordinates Tex-cell subset differentiation. Targeting PBAF improved tumor control both alone and in combination with anti-PD-L1 immunotherapy. Thus, PBAF may present a therapeutic target in cancer immunotherapy.
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Affiliation(s)
- Amy E Baxter
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Hua Huang
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Josephine R Giles
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Zeyu Chen
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jennifer E Wu
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Sydney Drury
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Katherine Dalton
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Simone L Park
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Leonel Torres
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Brandon W Simone
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Max Klapholz
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Radiation Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Shin Foong Ngiow
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Elizabeth Freilich
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Sasikanth Manne
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Victor Alcalde
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Viktoriya Ekshyyan
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Shelley L Berger
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Junwei Shi
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
| | - Martha S Jordan
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
| | - E John Wherry
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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Duong HG, Choi EJ, Hsu P, Chiang NR, Patel SA, Olvera JG, Liu YC, Lin YH, Yao P, Wong WH, Indralingam CS, Tsai MS, Boland BS, Wang W, Chang JT. Identification of CD8 + T-Cell-Immune Cell Communications in Ileal Crohn's Disease. Clin Transl Gastroenterol 2023; 14:e00576. [PMID: 36854061 PMCID: PMC10208704 DOI: 10.14309/ctg.0000000000000576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 02/10/2023] [Indexed: 03/02/2023] Open
Abstract
INTRODUCTION Crohn's disease (CD) is a major subtype of inflammatory bowel disease (IBD), a spectrum of chronic intestinal disorders caused by dysregulated immune responses to gut microbiota. Although transcriptional and functional changes in a number of immune cell types have been implicated in the pathogenesis of IBD, the cellular interactions and signals that drive these changes have been less well-studied. METHODS We performed Cellular Indexing of Transcriptomes and Epitopes by sequencing on peripheral blood, colon, and ileal immune cells derived from healthy subjects and patients with CD. We applied a previously published computational approach, NicheNet, to predict immune cell types interacting with CD8 + T-cell subsets, revealing putative ligand-receptor pairs and key transcriptional changes downstream of these cell-cell communications. RESULTS As a number of recent studies have revealed a potential role for CD8 + T-cell subsets in the pathogenesis of IBD, we focused our analyses on identifying the interactions of CD8 + T-cell subsets with other immune cells in the intestinal tissue microenvironment. We identified ligands and signaling pathways that have implicated in IBD, such as interleukin-1β, supporting the validity of the approach, along with unexpected ligands, such as granzyme B, which may play previously unappreciated roles in IBD. DISCUSSION Overall, these findings suggest that future efforts focused on elucidating cell-cell communications among immune and nonimmune cell types may further our understanding of IBD pathogenesis.
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Affiliation(s)
- Han G. Duong
- Department of Medicine, University of California San Diego, La Jolla, California, USA;
| | - Eunice J. Choi
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA;
| | - Paul Hsu
- Department of Medicine, University of California San Diego, La Jolla, California, USA;
| | - Natalie R. Chiang
- Department of Medicine, University of California San Diego, La Jolla, California, USA;
| | - Shefali A. Patel
- Department of Medicine, University of California San Diego, La Jolla, California, USA;
| | - Jocelyn G. Olvera
- Department of Medicine, University of California San Diego, La Jolla, California, USA;
| | - Yi Chia Liu
- Department of Medicine, University of California San Diego, La Jolla, California, USA;
| | - Yun Hsuan Lin
- Department of Medicine, University of California San Diego, La Jolla, California, USA;
| | - Priscilla Yao
- Department of Medicine, University of California San Diego, La Jolla, California, USA;
| | - William H. Wong
- Department of Medicine, University of California San Diego, La Jolla, California, USA;
| | | | - Matthew S. Tsai
- Department of Medicine, University of California San Diego, La Jolla, California, USA;
- Department of Medicine, Jennifer Moreno Department of Veteran Affairs Medical Center, San Diego, California, USA
| | - Brigid S. Boland
- Department of Medicine, University of California San Diego, La Jolla, California, USA;
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA;
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA.
| | - John T. Chang
- Department of Medicine, University of California San Diego, La Jolla, California, USA;
- Department of Medicine, Jennifer Moreno Department of Veteran Affairs Medical Center, San Diego, California, USA
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Wu JE, Manne S, Ngiow SF, Baxter AE, Huang H, Freilich E, Clark ML, Lee JH, Chen Z, Khan O, Staupe RP, Huang YJ, Shi J, Giles JR, Wherry EJ. In Vitro Modeling of CD8 T Cell Exhaustion Enables CRISPR Screening to Reveal a Role for BHLHE40. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.17.537229. [PMID: 37131713 PMCID: PMC10153201 DOI: 10.1101/2023.04.17.537229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Identifying novel molecular mechanisms of exhausted CD8 T cells (T ex ) is a key goal of improving immunotherapy of cancer and other diseases. However, high-throughput interrogation of in vivo T ex can be costly and inefficient. In vitro models of T ex are easily customizable and quickly generate high cellular yield, offering an opportunity to perform CRISPR screening and other high-throughput assays. We established an in vitro model of chronic stimulation and benchmarked key phenotypic, functional, transcriptional, and epigenetic features against bona fide in vivo T ex . We leveraged this model of in vitro chronic stimulation in combination with pooled CRISPR screening to uncover transcriptional regulators of T cell exhaustion. This approach identified several transcription factors, including BHLHE40. In vitro and in vivo validation defined a role for BHLHE40 in regulating a key differentiation checkpoint between progenitor and intermediate subsets of T ex . By developing and benchmarking an in vitro model of T ex , we demonstrate the utility of mechanistically annotated in vitro models of T ex , in combination with high-throughput approaches, as a discovery pipeline to uncover novel T ex biology.
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Affiliation(s)
- Jennifer E. Wu
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy at University of Pennsylvania; Philadelphia, PA, USA
| | - Sasikanth Manne
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Shin Foong Ngiow
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy at University of Pennsylvania; Philadelphia, PA, USA
| | - Amy E. Baxter
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Hua Huang
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Elizabeth Freilich
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Megan L. Clark
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Joanna H. Lee
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Zeyu Chen
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- Present Address: Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School; Boston, MA, USA
| | - Omar Khan
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- Present Address: Department of Laboratory Medicine, University of California, San Francisco; San Francisco, CA, USA
| | - Ryan P. Staupe
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- Present Address: Infectious Diseases and Vaccines, MRL, Merck & Co., Inc, West Point, PA, USA
| | - Yinghui J. Huang
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Junwei Shi
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Josephine R. Giles
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy at University of Pennsylvania; Philadelphia, PA, USA
| | - E. John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy at University of Pennsylvania; Philadelphia, PA, USA
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27
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Sell MC, Ramlogan-Steel CA, Steel JC, Dhungel BP. MicroRNAs in cancer metastasis: biological and therapeutic implications. Expert Rev Mol Med 2023; 25:e14. [PMID: 36927814 PMCID: PMC10407223 DOI: 10.1017/erm.2023.7] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 01/02/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023]
Abstract
Cancer metastasis is the primary cause of cancer-related deaths. The seeding of primary tumours at a secondary site is a highly inefficient process requiring substantial alterations in the genetic architecture of cancer cells. These alterations include significant changes in global gene expression patterns. MicroRNAs are small, non-protein coding RNAs which play a central role in regulating gene expression. Here, we focus on microRNA determinants of cancer metastasis and examine microRNA dysregulation in metastatic cancer cells. We dissect the metastatic process in a step-wise manner and summarise the involvement of microRNAs at each step. We also discuss the advantages and limitations of different microRNA-based strategies that have been used to target metastasis in pre-clinical models. Finally, we highlight current clinical trials that use microRNA-based therapies to target advanced or metastatic tumours.
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Affiliation(s)
- Marie C. Sell
- School of Health, Medical and Applied Sciences, Central Queensland University, Rockhampton, QLD 4701, Australia
| | - Charmaine A. Ramlogan-Steel
- School of Health, Medical and Applied Sciences, Central Queensland University, Rockhampton, QLD 4701, Australia
| | - Jason C. Steel
- School of Health, Medical and Applied Sciences, Central Queensland University, Rockhampton, QLD 4701, Australia
| | - Bijay P. Dhungel
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2050, Australia
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28
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Xiao Z, Liu X, Mo Y, Chen W, Zhang S, Yu Y, Weng H. Prognosis and clinical features analysis of EMT-related signature and tumor Immune microenvironment in glioma. J Med Biochem 2023; 42:122-137. [PMID: 36819132 PMCID: PMC9920870 DOI: 10.5937/jomb0-39234] [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: 03/16/2022] [Accepted: 07/30/2022] [Indexed: 11/02/2022] Open
Abstract
Background As the most common primary malignant intracranial tumor, glioblastoma has a poor prognosis with limited treatment options. It has a high propensity for recurrence, invasion, and poor immune prognosis due to the complex tumor microenvironment. Methods Six groups of samples from four datasets were included in this study. We used consensus ClusterPlus to establish two subgroups by the EMT-related gene. The difference in clinicopathological features, genomic characteristics, immune infiltration, treatment response and prognoses were evaluated by multiple algorithms. By using LASSO regression, multi-factor Cox analysis, stepAIC method, a prognostic risk model was constructed based on the final screened genes. Results The consensusClusterPlus analyses revealed two subtypes of glioblastoma (C1 and C2), which were characterized by different EMT-related gene expression patterns. C2 subtype with the worse prognosis had the more malignant clinical and pathology manifestations, higher Immune infiltration and tumor-associated molecular pathways scores, and poorer response to treatment. Additionally, our EMT-related genes risk prediction model can provide valuable support for clinical evaluations of glioma. Conclusions The assessment system and prediction model displayed good performance in independent prognostic risk assessment and individual patient treatment response prediction. This can help with clinical treatment decisions and the development of effective treatments.
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Affiliation(s)
- Zheng Xiao
- Southern Medical University, Zhujiang Hospital, Department of Neurosurgery, Guangzhou, China
| | - Xiaoyan Liu
- Jinan University, The First Affiliated Hospital of Jinan University, Department of Neurology, Guangzhou, China
| | - Yixiang Mo
- Southern Medical University, Zhujiang Hospital, Department of Neurosurgery, Guangzhou, China
| | - Weibo Chen
- Southern Medical University, Zhujiang Hospital, Department of Neurosurgery, Guangzhou, China
| | - Shizhong Zhang
- Southern Medical University, Zhujiang Hospital, Department of Neurosurgery, Guangzhou, China
| | - Yingwei Yu
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Huiwen Weng
- The First Affiliated Hospital of Sun Yat-sen University, Department of Oncology, Guangzhou, China
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29
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Meng Q, Deng Y, Lu Y, Wu C, Tang S. Tumor-derived miRNAs as tumor microenvironment regulators for synergistic therapeutic options. J Cancer Res Clin Oncol 2023; 149:423-439. [PMID: 36378341 DOI: 10.1007/s00432-022-04432-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022]
Abstract
MicroRNAs (miRNAs) are a class of non-coding RNAs that perform post-transcriptional gene regulation. This review focuses on the role of tumor cell-derived miRNAs in the regulation of the tumor microenvironment (TME) via receptor cell recoding, including angiogenesis, expression of immunosuppressive molecules, formation of radiation resistance, and chemoresistance. Furthermore, we discuss the potential of these molecules as adjuvant therapies in combination with chemotherapy, radiotherapy, or immunotherapy, as well as their advantages as efficacy predictors for personalized therapy. MiRNA-based therapeutic agents for tumors are currently in clinical trials, and while challenges remain, additional research on tumor-derived miRNAs is warranted, which may provide significant clinical benefits to cancer patients.
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Affiliation(s)
- Qiuxing Meng
- Department of Laboratory Medicine, Liuzhou People's Hospital, Liu Zhou, China.,Liuzhou Key Laboratory of Precision Medicine for Viral Diseases, Liu Zhou, China
| | - Yaoming Deng
- Department of Laboratory Medicine, Liuzhou People's Hospital, Liu Zhou, China.,Liuzhou Key Laboratory of Precision Medicine for Viral Diseases, Liu Zhou, China
| | - Yu Lu
- Department of Laboratory Medicine, Liuzhou People's Hospital, Liu Zhou, China.,Liuzhou Key Laboratory of Precision Medicine for Viral Diseases, Liu Zhou, China
| | - Chunfeng Wu
- Department of Laboratory Medicine, Liuzhou People's Hospital, Liu Zhou, China.,Liuzhou Key Laboratory of Precision Medicine for Viral Diseases, Liu Zhou, China
| | - Shifu Tang
- Department of Laboratory Medicine, Liuzhou People's Hospital, Liu Zhou, China. .,Liuzhou Key Laboratory of Precision Medicine for Viral Diseases, Liu Zhou, China.
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30
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Li Y, Liu P, Wang W, Bai Y, Jia H, Yuan Z, Yang Z. Transcriptome analysis reveals the spinal expression profiles of non-coding RNAs involved in anorectal malformations in rat fetuses. J Pediatr Surg 2022; 57:974-985. [PMID: 35725663 DOI: 10.1016/j.jpedsurg.2022.05.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 05/26/2022] [Accepted: 05/28/2022] [Indexed: 11/24/2022]
Abstract
BACKGROUND Despite improvements in anorectal malformation (ARM) therapy, patients might still experience post-operative problems such as fecal incontinence, constipation, and soiling. In particular, the dysplasia of the lumbosacral spinal cord in ARM patients is a major disorder that affects fecal function post-operation. However, the pathological mechanisms involved are still unclear. METHODS The non-coding RNAs (ncRNAs) in the lumbosacral spinal cord of fetal rats with ethylenethiourea-induced ARM were identified using RNA sequencing (RNA-seq) and examined to determine their potential function. The lumbosacral spinal cord was isolated on embryonic day 17 for subsequent RNA extraction and RNA-seq. The transcriptome data was analyzed using bioinformatics analysis, followed by validation using quantitative reverse transcription PCR. RESULTS Compared to the control group, 26 differentially expressed microRNAs (DEMs; 22 upregulated, 4 downregulated) and 112 differentially expressed long non-coding RNAs (63 upregulated, 49 downregulated) were identified in the ARM group. Several DEMs related to development, namely miR-200a-3p, miR-200b-3p, miR-200c-3p, miR-200a-5p, and miR-429, were selected for further analysis. Notably, compared to the control, the relative expression of miR-200 family members was highly upregulated in ARM fetal rats. Furthermore, GO and KEGG enrichment and miRNA-transcription factor-lncRNA/mRNA network analysis was explored to show molecular mechanism underlying DEMs. CONCLUSIONS Our findings suggest the involvement of ncRNAs, especially the miR-200 family members, in the pathogenesis of lumbosacral spinal cord dysplasia in ARM fetal rats.
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Affiliation(s)
- Yue Li
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Peiqi Liu
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Weilin Wang
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yuzuo Bai
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Huimin Jia
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Zhengwei Yuan
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.
| | - Zhonghua Yang
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.
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31
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Giles JR, Ngiow SF, Manne S, Baxter AE, Khan O, Wang P, Staupe R, Abdel-Hakeem MS, Huang H, Mathew D, Painter MM, Wu JE, Huang YJ, Goel RR, Yan PK, Karakousis GC, Xu X, Mitchell TC, Huang AC, Wherry EJ. Shared and distinct biological circuits in effector, memory and exhausted CD8 + T cells revealed by temporal single-cell transcriptomics and epigenetics. Nat Immunol 2022; 23:1600-1613. [PMID: 36271148 PMCID: PMC10408358 DOI: 10.1038/s41590-022-01338-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 09/13/2022] [Indexed: 01/13/2023]
Abstract
Naïve CD8+ T cells can differentiate into effector (Teff), memory (Tmem) or exhausted (Tex) T cells. These developmental pathways are associated with distinct transcriptional and epigenetic changes that endow cells with different functional capacities and therefore therapeutic potential. The molecular circuitry underlying these developmental trajectories and the extent of heterogeneity within Teff, Tmem and Tex populations remain poorly understood. Here, we used the lymphocytic choriomeningitis virus model of acute-resolving and chronic infection to address these gaps by applying longitudinal single-cell RNA-sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) analyses. These analyses uncovered new subsets, including a subpopulation of Tex cells expressing natural killer cell-associated genes that is dependent on the transcription factor Zeb2, as well as multiple distinct TCF-1+ stem/progenitor-like subsets in acute and chronic infection. These data also revealed insights into the reshaping of Tex subsets following programmed death 1 (PD-1) pathway blockade and identified a key role for the cell stress regulator, Btg1, in establishing the Tex population. Finally, these results highlighted how the same biological circuits such as cytotoxicity or stem/progenitor pathways can be used by CD8+ T cell subsets with highly divergent underlying chromatin landscapes generated during different infections.
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Affiliation(s)
- Josephine R Giles
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Shin Foong Ngiow
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sasikanth Manne
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amy E Baxter
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Omar Khan
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ping Wang
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Ryan Staupe
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Infectious Disease & Vaccines, MRL, Merck & Co. Inc., West Point, PA, USA
| | - Mohamed S Abdel-Hakeem
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Hua Huang
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Divij Mathew
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mark M Painter
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer E Wu
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yinghui Jane Huang
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rishi R Goel
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Patrick K Yan
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Immunology Graduate Program, Stanford University, Stanford, CA, USA
| | | | - Xiaowei Xu
- Department of Surgery, University of Pennsylvania, Philadelphia, PA, USA
| | - Tara C Mitchell
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alexander C Huang
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Elghzaly AA, Sun C, Looger LL, Hirose M, Salama M, Khalil NM, Behiry ME, Hegazy MT, Hussein MA, Salem MN, Eltoraby E, Tawhid Z, Alwasefy M, Allam W, El-Shiekh I, Elserafy M, Abdelnaser A, Hashish S, Shebl N, Shahba AA, Elgirby A, Hassab A, Refay K, El-Touchy HM, Youssef A, Shabacy F, Hashim AA, Abdelzaher A, Alshebini E, Fayez D, El-Bakry SA, Elzohri MH, Abdelsalam EN, El-Khamisy SF, Ibrahim S, Ragab G, Nath SK. Genome-wide association study for systemic lupus erythematosus in an egyptian population. Front Genet 2022; 13:948505. [PMID: 36324510 PMCID: PMC9619055 DOI: 10.3389/fgene.2022.948505] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/30/2022] [Indexed: 04/11/2024] Open
Abstract
Systemic lupus erythematosus (SLE) susceptibility has a strong genetic component. Genome-wide association studies (GWAS) across trans-ancestral populations show both common and distinct genetic variants of susceptibility across European and Asian ancestries, while many other ethnic populations remain underexplored. We conducted the first SLE GWAS on Egyptians-an admixed North African/Middle Eastern population-using 537 patients and 883 controls. To identify novel susceptibility loci and replicate previously known loci, we performed imputation-based association analysis with 6,382,276 SNPs while accounting for individual admixture. We validated the association analysis using adaptive permutation tests (n = 109). We identified a novel genome-wide significant locus near IRS1/miR-5702 (Pcorrected = 1.98 × 10-8) and eight novel suggestive loci (Pcorrected < 1.0 × 10-5). We also replicated (Pperm < 0.01) 97 previously known loci with at least one associated nearby SNP, with ITGAM, DEF6-PPARD and IRF5 the top three replicated loci. SNPs correlated (r 2 > 0.8) with lead SNPs from four suggestive loci (ARMC9, DIAPH3, IFLDT1, and ENTPD3) were associated with differential gene expression (3.5 × 10-95 < p < 1.0 × 10-2) across diverse tissues. These loci are involved in cellular proliferation and invasion-pathways prominent in lupus and nephritis. Our study highlights the utility of GWAS in an admixed Egyptian population for delineating new genetic associations and for understanding SLE pathogenesis.
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Affiliation(s)
- Ashraf A. Elghzaly
- Department of Clinical Pathology, Faculty of Medicine, Mansoura University, El-Mansoura, Egypt
| | - Celi Sun
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Loren L. Looger
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, San Diego, CA, United States
| | - Misa Hirose
- Division of Genetics, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Mohamed Salama
- Institute of Global Health and Human Ecology, The American University in Cairo, New Cairo, Egypt
| | - Noha M. Khalil
- Rheumatology and Clinical Immunology Unit, Department of Internal Medicine, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Mervat Essam Behiry
- Rheumatology and Clinical Immunology Unit, Department of Internal Medicine, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Mohamed Tharwat Hegazy
- Rheumatology and Clinical Immunology Unit, Department of Internal Medicine, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Mohamed Ahmed Hussein
- Rheumatology and Clinical Immunology Unit, Department of Internal Medicine, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Mohamad Nabil Salem
- Department of Internal Medicine, Faculty of Medicine, Beni-Suef University, Beni Suef, Egypt
| | - Ehab Eltoraby
- Department of Internal Medicine, Faculty of Medicine, Mansoura University, El-Mansoura, Egypt
| | - Ziyad Tawhid
- Department of Clinical Pathology, Faculty of Medicine, Mansoura University, El-Mansoura, Egypt
| | - Mona Alwasefy
- Department of Clinical Pathology, Faculty of Medicine, Mansoura University, El-Mansoura, Egypt
| | - Walaa Allam
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Iman El-Shiekh
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Menattallah Elserafy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Anwar Abdelnaser
- Institute of Global Health and Human Ecology, The American University in Cairo, New Cairo, Egypt
| | - Sara Hashish
- Institute of Global Health and Human Ecology, The American University in Cairo, New Cairo, Egypt
| | - Nourhan Shebl
- Institute of Global Health and Human Ecology, The American University in Cairo, New Cairo, Egypt
| | | | - Amira Elgirby
- Department of Internal Medicine, Faculty of Medicine, Alexandria University, Bab Sharqi, Egypt
| | - Amina Hassab
- Department of Clinical Pathology, Faculty of Medicine, Alexandria University, Bab Sharqi, Egypt
| | - Khalida Refay
- Department of Internal Medicine, Faculty of Medicine, Al-Azhar University, Cairo, Egypt
| | | | - Ali Youssef
- Department of Rheumatology and Immunology, Faculty of Medicine, Benha University Hospital, Benha, Egypt
| | - Fatma Shabacy
- Department of Rheumatology and Immunology, Faculty of Medicine, Benha University Hospital, Benha, Egypt
| | | | - Asmaa Abdelzaher
- Department of Clinical Pathology, Faculty of Medicine, South Valley University, Qena, Egypt
| | - Emad Alshebini
- Department of Internal Medicine, Faculty of Medicine, Menoufia University, Al Minufiyah, Egypt
| | - Dalia Fayez
- Rheumatology and Clinical Immunology Unit, Department of Internal Medicine, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Samah A. El-Bakry
- Rheumatology and Clinical Immunology Unit, Department of Internal Medicine, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Mona H. Elzohri
- Department of Internal Medicine, Faculty of Medicine, Assiut University, Asyut, Egypt
| | | | - Sherif F. El-Khamisy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- The Healthy Lifespan Institute, University of Sheffield, Sheffield, United Kingdom
- The Institute of Cancer Therapeutics, University of Bradford, Bradford, United Kingdom
| | - Saleh Ibrahim
- Division of Genetics, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Gaafar Ragab
- Rheumatology and Clinical Immunology Unit, Department of Internal Medicine, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Swapan K. Nath
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
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Kasmani MY, Ciecko AE, Brown AK, Petrova G, Gorski J, Chen YG, Cui W. Autoreactive CD8 T cells in NOD mice exhibit phenotypic heterogeneity but restricted TCR gene usage. Life Sci Alliance 2022; 5:5/10/e202201503. [PMID: 35667687 PMCID: PMC9170949 DOI: 10.26508/lsa.202201503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 11/27/2022] Open
Abstract
Paired scRNA-seq and scTCR-seq reveals that diabetogenic CD8 T cells in the islets and spleens of NOD mice exhibit phenotypic and clonal heterogeneity despite restricted TCR gene usage. Expression of certain TCR genes correlates with clonal proliferation and effector phenotype. Type 1 diabetes (T1D) is an autoimmune disorder defined by CD8 T cell–mediated destruction of pancreatic β cells. We have previously shown that diabetogenic CD8 T cells in the islets of non-obese diabetic mice are phenotypically heterogeneous, but clonal heterogeneity remains relatively unexplored. Here, we use paired single-cell RNA and T-cell receptor sequencing (scRNA-seq and scTCR-seq) to characterize autoreactive CD8 T cells from the islets and spleens of non-obese diabetic mice. scTCR-seq demonstrates that CD8 T cells targeting the immunodominant β-cell epitope IGRP206-214 exhibit restricted TCR gene usage. scRNA-seq identifies six clusters of autoreactive CD8 T cells in the islets and six in the spleen, including memory and exhausted cells. Clonal overlap between IGRP206-214–reactive CD8 T cells in the islets and spleen suggests these cells may circulate between the islets and periphery. Finally, we identify correlations between TCR genes and T-cell clonal expansion and effector fate. Collectively, our work demonstrates that IGRP206-214–specific CD8 T cells are phenotypically heterogeneous but clonally restricted, raising the possibility of selectively targeting these TCR structures for therapeutic benefit.
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Affiliation(s)
- Moujtaba Y Kasmani
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA.,Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, USA
| | - Ashley E Ciecko
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA.,Max McGee National Research Center for Juvenile Diabetes, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Ashley K Brown
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA.,Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, USA
| | - Galina Petrova
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jack Gorski
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA.,Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, USA
| | - Yi-Guang Chen
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA .,Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA.,Max McGee National Research Center for Juvenile Diabetes, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Weiguo Cui
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA .,Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, USA
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Suarez-Ramirez JE, Cauley LS, Chandiran K. CTLs Get SMAD When Pathogens Tell Them Where to Go. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:1025-1032. [PMID: 36130123 PMCID: PMC9512391 DOI: 10.4049/jimmunol.2200345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/18/2022] [Indexed: 01/04/2023]
Abstract
Vaccines protect against infections by eliciting both Ab and T cell responses. Because the immunity wanes as protective epitopes get modified by accruing mutations, developing strategies for immunization against new variants is a major priority for vaccine development. CTLs eliminate cells that support viral replication and provide protection against new variants by targeting epitopes from internal viral proteins. This form of protection has received limited attention during vaccine development, partly because reliable methods for directing pathogen-specific memory CD8 T cells to vulnerable tissues are currently unavailable. In this review we examine how recent studies expand our knowledge of mechanisms that contribute to the functional diversity of CTLs as they respond to infection. We discuss the role of TGF-β and the SMAD signaling cascade during genetic programming of pathogen-specific CTLs and the pathways that promote formation of a newly identified subset of terminally differentiated memory CD8 T cells that localize in the vasculature.
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35
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ZEB1: Catalyst of immune escape during tumor metastasis. Biomed Pharmacother 2022; 153:113490. [DOI: 10.1016/j.biopha.2022.113490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/23/2022] [Accepted: 07/27/2022] [Indexed: 11/20/2022] Open
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Chandiran K, Suarez-Ramirez JE, Hu Y, Jellison ER, Ugur Z, Low JS, McDonald B, Kaech SM, Cauley LS. SMAD4 and TGFβ are architects of inverse genetic programs during fate-determination of antiviral CTLs. eLife 2022; 11:76457. [PMID: 35942952 PMCID: PMC9402230 DOI: 10.7554/elife.76457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 08/05/2022] [Indexed: 11/25/2022] Open
Abstract
Transforming growth factor β (TGFβ) is an important differentiation factor for cytotoxic T lymphocytes (CTLs) and alters the expression levels of several of homing receptors during infection. SMAD4 is part of the canonical signaling network used by members of the transforming growth factor family. For this study, genetically modified mice were used to determine how SMAD4 and TGFβ receptor II (TGFβRII) participate in transcriptional programming of pathogen-specific CTLs. We show that these molecules are essential components of opposing signaling mechanisms, and cooperatively regulate a collection of genes that determine whether specialized populations of pathogen-specific CTLs circulate around the body, or settle in peripheral tissues. TGFβ uses a canonical SMAD-dependent signaling pathway to downregulate Eomesodermin (EOMES), KLRG1, and CD62L, while CD103 is induced. Conversely, in vivo and in vitro data show that EOMES, KLRG1, CX3CR1, and CD62L are positively regulated via SMAD4, while CD103 and Hobit are downregulated. Intravascular staining also shows that signaling via SMAD4 promotes formation of long-lived terminally differentiated CTLs that localize in the vasculature. Our data show that inflammatory molecules play a key role in lineage determination of pathogen-specific CTLs, and use SMAD-dependent signaling to alter the expression levels of multiple homing receptors and transcription factors with known functions during memory formation.
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Affiliation(s)
- Karthik Chandiran
- Department of Immunology, University of Connecticut Health Center, Farmington, United States
| | - Jenny E Suarez-Ramirez
- Department of Immunology, University of Connecticut Health Center, Farmington, United States
| | - Yinghong Hu
- Department of Microbiology and Immunology, Emory University, Atlanta, United States
| | - Evan R Jellison
- Department of Immunology, University of Connecticut Health Center, Farmington, United States
| | - Zenep Ugur
- Department of Immunology, University of Connecticut Health Center, Farmington, United States
| | - Jun-Siong Low
- Department of Immunobiology, Yale University, Bellinzona, Switzerland
| | - Bryan McDonald
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, San Diego, United States
| | - Susan M Kaech
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, San Diego, United States
| | - Linda S Cauley
- Department of Immunology, University of Connecticut Health Center, Farmington, United States
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37
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Zhang Q, Zhong C, Shen J, Chen S, Jia Y, Duan S. Emerging role of LINC00461 in cancer. Biomed Pharmacother 2022; 152:113239. [PMID: 35679722 DOI: 10.1016/j.biopha.2022.113239] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/28/2022] [Accepted: 06/02/2022] [Indexed: 11/25/2022] Open
Abstract
LINC00461 is located in the intergenic region between the protein-coding genes MEF2C and TMEM161B. LINC00461 upregulation was associated with the risk of 13 tumors and was strongly associated with clinicopathologic features and poor prognosis in 11 tumors. LINC00461 is involved in resistance to four anticancer drugs, including sunitinib for renal cell carcinoma, cisplatin for head and neck squamous cell carcinoma and rectal cancer, temozolomide for glioma, and docetaxel for breast cancer. LINC00461 can sponge 18 miRNAs to form a complex ceRNA network that regulates the expression of a large number of downstream genes. LINC00461 is involved in the MAPK/ERK signaling pathway and PI3K/AKT signaling pathway, thereby promoting tumorigenesis. Notably, knockdown of LINC00461 in exosomes antagonizes tumor cell proliferation in multiple myeloma. This article summarizes the diagnostic, prognostic, and therapeutic value of LINC00461 in various tumors, and systematically describes the ceRNA network and signaling pathways associated with LINC00461, providing potential directions for future LINC00461 research.
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Affiliation(s)
- Qiudan Zhang
- Department of Clinical Medicine, School of Medicine, Zhejiang University City College, Hangzhou, Zhejiang 310015, China; Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Chenming Zhong
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Jinze Shen
- Department of Clinical Medicine, School of Medicine, Zhejiang University City College, Hangzhou, Zhejiang 310015, China
| | - Sang Chen
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Yunhua Jia
- Department of Clinical Medicine, School of Medicine, Zhejiang University City College, Hangzhou, Zhejiang 310015, China.
| | - Shiwei Duan
- Department of Clinical Medicine, School of Medicine, Zhejiang University City College, Hangzhou, Zhejiang 310015, China.
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38
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Rehm A, Wirges A, Hoser D, Fischer C, Herda S, Gerlach K, Sauer S, Willimsky G, Höpken UE. EBAG9 controls CD8+ T cell memory formation responding to tumor challenge in mice. JCI Insight 2022; 7:155534. [PMID: 35482418 PMCID: PMC9220939 DOI: 10.1172/jci.insight.155534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 04/22/2022] [Indexed: 11/17/2022] Open
Abstract
Insight into processes that determine CD8+ T cell memory formation has been obtained from infection models. These models are biased toward an inflammatory milieu and often use high-avidity CD8+ T cells in adoptive-transfer procedures. It is unclear whether these conditions mimic the differentiation processes of an endogenous repertoire that proceed upon noninflammatory conditions prevailing in premalignant tumor lesions. We examined the role of cytolytic capacity on CD8+ T cell fate decisions when primed by tumor cells or by minor histocompatibility antigen–mismatched leukocytes. CD8+ memory commitment was analyzed in Ebag9-deficient mice that exhibited enhanced tumor cell lysis. This property endowed Ebag9–/– mice with extended control of Tcl-1 oncogene–induced chronic lymphocytic leukemia progression. In Ebag9–/– mice, an expanded memory population was obtained for anti-HY and anti–SV-40 T antigen–specific T cells, despite unchanged effector frequencies in the primary response. By comparing the single-cell transcriptomes of CD8+ T cells responding to tumor cell vaccination, we found differential distribution of subpopulations between Ebag9+/+ and Ebag9–/– T cells. In Ebag9–/– cells, these larger clusters contained genes encoding transcription factors regulating memory cell differentiation and anti-apoptotic gene functions. Our findings link EBAG9-controlled cytolytic activity and the commitment to the CD8+ memory lineage.
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Affiliation(s)
- Armin Rehm
- Department of Translational Tumorimmunology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Anthea Wirges
- Department of Translational Tumorimmunology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Dana Hoser
- Institute of Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Cornelius Fischer
- Scientific Infrastructure Department, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Stefanie Herda
- Department of Translational Tumorimmunology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Kerstin Gerlach
- Department of Translational Tumorimmunology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Sascha Sauer
- Scientific Infrastructure Department, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Gerald Willimsky
- Institute of Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Uta E Höpken
- Department of Microenvironmental Regulation of Autoimmunity and Cancer, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
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39
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Vardam-Kaur T, van Dijk S, Peng C, Wanhainen KM, Jameson SC, Borges da Silva H. The Extracellular ATP Receptor P2RX7 Imprints a Promemory Transcriptional Signature in Effector CD8 + T Cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:1686-1699. [PMID: 35264459 PMCID: PMC8976739 DOI: 10.4049/jimmunol.2100555] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 01/25/2022] [Indexed: 12/31/2022]
Abstract
Development of CD8+ central memory T (Tcm) and resident memory T (Trm) cells, which promote immunity in the circulation and in barrier tissues, respectively, is not completely understood. Tcm and Trm cells may arise from common precursors; however, their fate-inducing signals are elusive. We found that virus-specific effector CD8+ T cells display heterogeneous expression of the extracellular ATP sensor P2RX7. P2RX7-high expression is confined, at peak effector phase, to CD62L+ memory precursors, which preferentially form Tcm cells. Among early effector CD8+ T cells, asymmetrical P2RX7 distribution correlated with distinct transcriptional signatures, with P2RX7-high cells enriched for memory and tissue residency sets. P2RX7-high early effectors preferentially form both Tcm and Trm cells. Defective Tcm and Trm cell formation in P2RX7 deficiency is significantly reverted when the transcriptional repressor Zeb2 is ablated. Mechanistically, P2RX7 negatively regulates Zeb2 expression, at least partially through TGF-β sensing in early effector CD8+ T cells. Our study indicates that unequal P2RX7 upregulation in effector CD8+ T cells is a foundational element of the early Tcm/Trm fate.
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Affiliation(s)
| | - Sarah van Dijk
- Department of Immunology, Mayo Clinic Arizona, Scottsdale, AZ; and
| | - Changwei Peng
- Center for Immunology, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | - Kelsey M Wanhainen
- Center for Immunology, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | - Stephen C Jameson
- Center for Immunology, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
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40
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Selective Targeting of Protein Kinase C (PKC)-θ Nuclear Translocation Reduces Mesenchymal Gene Signatures and Reinvigorates Dysfunctional CD8 + T Cells in Immunotherapy-Resistant and Metastatic Cancers. Cancers (Basel) 2022; 14:cancers14061596. [PMID: 35326747 PMCID: PMC8946217 DOI: 10.3390/cancers14061596] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/07/2022] [Accepted: 03/14/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Some important signaling proteins that control how cells grow and behave not only act in the cytoplasm but also in the nucleus, where they tether to chromatin. This is especially true for protein kinase C (PKC)-θ, which acts in the nucleus to mediate cancer hallmarks that drive metastasis and in normal T cells. However, current PKC-θ inhibitors are either non-specific or target only its cytoplasmic function. In a bid to develop a novel class of PKC-θ inhibitor that maintains cytoplasmic signaling but inhibits its nuclear function, here we present a novel PKC-θ inhibitor (nPKC-θi2) that specifically inhibits nuclear translocation of PKC-θ without interrupting normal signaling in healthy T cells. We show for the first time that nPKC-θ mediates immunotherapy resistance via its activity in circulating tumor cells and dysfunctional CD8+ T cells. Our novel inhibitor provides a means to target this process by simultaneously overcoming T-cell exhaustion and cancer stem cell burden. As part of a sequential approach with other therapies, this work paves the way for improving outcomes in cancer patients with immunotherapy-resistant relapse and metastasis. Abstract Protein kinase C (PKC)-θ is a serine/threonine kinase with both cytoplasmic and nuclear functions. Nuclear chromatin-associated PKC-θ (nPKC-θ) is increasingly recognized to be pathogenic in cancer, whereas its cytoplasmic signaling is restricted to normal T-cell function. Here we show that nPKC-θ is enriched in circulating tumor cells (CTCs) in patients with triple-negative breast cancer (TNBC) brain metastases and immunotherapy-resistant metastatic melanoma and is associated with poor survival in immunotherapy-resistant disease. To target nPKC-θ, we designed a novel PKC-θ peptide inhibitor (nPKC-θi2) that selectively inhibits nPKC-θ nuclear translocation but not PKC-θ signaling in healthy T cells. Targeting nPKC-θ reduced mesenchymal cancer stem cell signatures in immunotherapy-resistant CTCs and TNBC xenografts. PKC-θ was also enriched in the nuclei of CD8+ T cells isolated from stage IV immunotherapy-resistant metastatic cancer patients. We show for the first time that nPKC-θ complexes with ZEB1, a key repressive transcription factor in epithelial-to-mesenchymal transition (EMT), in immunotherapy-resistant dysfunctional PD1+/CD8+ T cells. nPKC-θi2 inhibited the ZEB1/PKC-θ repressive complex to induce cytokine production in CD8+ T cells isolated from patients with immunotherapy-resistant disease. These data establish for the first time that nPKC-θ mediates immunotherapy resistance via its activity in CTCs and dysfunctional CD8+ T cells. Disrupting nPKC-θ but retaining its cytoplasmic function may offer a means to target metastases in combination with chemotherapy or immunotherapy.
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Mikuła-Pietrasik J, Rutecki S, Książek K. The functional multipotency of transforming growth factor β signaling at the intersection of senescence and cancer. Cell Mol Life Sci 2022; 79:196. [PMID: 35305149 PMCID: PMC11073081 DOI: 10.1007/s00018-022-04236-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/22/2022] [Accepted: 03/08/2022] [Indexed: 12/12/2022]
Abstract
The transforming growth factor β (TGF-β) family of cytokines comprises a group of proteins, their receptors, and effector molecules that, in a coordinated manner, modulate a plethora of physiological and pathophysiological processes. TGF-β1 is the best known and plausibly most active representative of this group. It acts as an immunosuppressant, contributes to extracellular matrix remodeling, and stimulates tissue fibrosis, differentiation, angiogenesis, and epithelial-mesenchymal transition. In recent years, this cytokine has been established as a vital regulator of organismal aging and cellular senescence. Finally, the role of TGF-β1 in cancer progression is no longer in question. Because this protein is involved in so many, often overlapping phenomena, the question arises whether it can be considered a molecular bridge linking some of these phenomena together and governing their reciprocal interactions. In this study, we reviewed the literature from the perspective of the role of various TGF-β family members as regulators of a complex mutual interplay between senescence and cancer. These aspects are then considered in a broader context of remaining TGF-β-related functions and coexisting processes. The main narrative axis in this work is centered around the interaction between the senescence of normal peritoneal cells and ovarian cancer cells. The discussion also includes examples of TGF-β activity at the interface of other normal and cancer cell types.
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Affiliation(s)
- Justyna Mikuła-Pietrasik
- Department of Pathophysiology of Ageing and Civilization Diseases, Długa ½ Str, Poznań University of Medical Sciences, 61-848, Poznań, Poland
| | - Szymon Rutecki
- Department of Pathophysiology of Ageing and Civilization Diseases, Długa ½ Str, Poznań University of Medical Sciences, 61-848, Poznań, Poland
| | - Krzysztof Książek
- Department of Pathophysiology of Ageing and Civilization Diseases, Długa ½ Str, Poznań University of Medical Sciences, 61-848, Poznań, Poland.
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42
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Pattnaik B, Patnaik N, Mittal S, Mohan A, Agrawal A, Guleria R, Madan K. Micro RNAs as potential biomarkers in tuberculosis: A systematic review. Noncoding RNA Res 2022; 7:16-26. [PMID: 35128217 PMCID: PMC8792429 DOI: 10.1016/j.ncrna.2021.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/24/2021] [Accepted: 12/29/2021] [Indexed: 12/15/2022] Open
Abstract
Tuberculosis (TB) remains a major infectious disease across the globe. With increasing TB infections and a rise in multi-drug resistance, rapid diagnostic modalities are required to achieve TB control. Radiological investigations and microbiological tests (microscopic examination, cartridge-based nucleic acid amplification tests, and cultures) are most commonly used to diagnose TB. Histopathological/cytopathological examinations are also required for an accurate diagnosis in many patients. The causative agent, Mycobacterium tuberculosis (Mtb), is known to circumvent the host's immune system. Circulating microRNAs (miRNAs) play a crucial role in biological pathways and can be used as a potential biomarker to detect tuberculosis. miRNAs are small non-coding RNAs and negatively regulate gene expression during post-transcriptional regulation. The differential expression of miRNAs in multiple clinical samples in tuberculosis patients may be helpful as potential disease biomarkers. This review summarizes the literature on miRNAs in various clinical samples as biomarkers for TB diagnosis.
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Affiliation(s)
- Bijay Pattnaik
- Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Niharika Patnaik
- Centre of Excellence in Asthma & Lung Disease, Molecular Immunogenetics Lab, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
| | - Saurabh Mittal
- Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Anant Mohan
- Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Anurag Agrawal
- Centre of Excellence in Asthma & Lung Disease, Molecular Immunogenetics Lab, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
| | - Randeep Guleria
- Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Karan Madan
- Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, India
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43
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Tcf1 preprograms the mobilization of glycolysis in central memory CD8 + T cells during recall responses. Nat Immunol 2022; 23:386-398. [PMID: 35190717 PMCID: PMC8904300 DOI: 10.1038/s41590-022-01131-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 01/06/2022] [Indexed: 01/09/2023]
Abstract
The mechanisms underlying the heightened protection mediated by central memory CD8+ T (TCM) cells remain unclear. Here we show that the transcription factor Tcf1 was required in resting TCM cells to generate secondary effector CD8+ T cells and to clear pathogens during recall responses. Recall stimulation of CD8+ TCM cells caused extensive reprogramming of the transcriptome and chromatin accessibility, leading to rapid induction of glycolytic enzymes, cell cycle regulators and transcriptional regulators, including Id3. This cluster of genes did not require Tcf1 in resting CD8+ TCM cells, but depended on Tcf1 for optimal induction and chromatin opening in recall-stimulated CD8+ TCM cells. Tcf1 bound extensively to these recall-induced gene loci in resting CD8+ TCM cells and mediated chromatin interactions that positioned these genes in architectural proximity with poised enhancers. Thus, Tcf1 preprogramed a transcriptional program that supported the bioenergetic and proliferative needs of CD8+ TCM cells in case of a secondary challenge.
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44
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Tsuda S, Pipkin ME. Transcriptional Control of Cell Fate Determination in Antigen-Experienced CD8 T Cells. Cold Spring Harb Perspect Biol 2022; 14:a037945. [PMID: 34127445 PMCID: PMC8805646 DOI: 10.1101/cshperspect.a037945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Robust immunity to intracellular infections is mediated by antigen-specific naive CD8 T cells that become activated and differentiate into phenotypically and functionally diverse subsets of effector cells, some of which terminally differentiate and others that give rise to memory cells that provide long-lived protection. This developmental system is an outstanding model with which to elucidate how regulation of chromatin structure and transcriptional control establish gene expression programs that govern cell fate determination, insights from which are likely to be useful for informing the design of immunotherapeutic approaches to engineer durable immunity to infections and tumors. A unifying framework that describes how naive CD8 T cells develop into memory cells is still outstanding. We propose a model that incorporates a common early linear path followed by divergent paths that slowly lose capacity to interconvert and discuss classical and contemporary observations that support these notions, focusing on insights from transcriptional control and chromatin regulation.
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Affiliation(s)
- Shanel Tsuda
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Matthew E Pipkin
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida 33458, USA
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45
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Evrard M, Wynne-Jones E, Peng C, Kato Y, Christo SN, Fonseca R, Park SL, Burn TN, Osman M, Devi S, Chun J, Mueller SN, Kannourakis G, Berzins SP, Pellicci DG, Heath WR, Jameson SC, Mackay LK. Sphingosine 1-phosphate receptor 5 (S1PR5) regulates the peripheral retention of tissue-resident lymphocytes. J Exp Med 2022; 219:e20210116. [PMID: 34677611 PMCID: PMC8546662 DOI: 10.1084/jem.20210116] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 08/16/2021] [Accepted: 10/01/2021] [Indexed: 11/05/2022] Open
Abstract
Tissue-resident memory T (TRM) cells provide long-lasting immune protection. One of the key events controlling TRM cell development is the local retention of TRM cell precursors coupled to downregulation of molecules necessary for tissue exit. Sphingosine-1-phosphate receptor 5 (S1PR5) is a migratory receptor with an uncharted function in T cells. Here, we show that S1PR5 plays a critical role in T cell infiltration and emigration from peripheral organs, as well as being specifically downregulated in TRM cells. Consequentially, TRM cell development was selectively impaired upon ectopic expression of S1pr5, whereas loss of S1pr5 enhanced skin TRM cell formation by promoting peripheral T cell sequestration. Importantly, we found that T-bet and ZEB2 were required for S1pr5 induction and that local TGF-β signaling was necessary to promote coordinated Tbx21, Zeb2, and S1pr5 downregulation. Moreover, S1PR5-mediated control of tissue residency was conserved across innate and adaptive immune compartments. Together, these results identify the T-bet-ZEB2-S1PR5 axis as a previously unappreciated mechanism modulating the generation of tissue-resident lymphocytes.
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Affiliation(s)
- Maximilien Evrard
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Erica Wynne-Jones
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Changwei Peng
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN
| | - Yu Kato
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- The ARC Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria, Australia
| | - Susan N. Christo
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Raissa Fonseca
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Simone L. Park
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Thomas N. Burn
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Maleika Osman
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Sapna Devi
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Jerold Chun
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Scott N. Mueller
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - George Kannourakis
- Federation University Australia and Fiona Elsey Cancer Research Institute, Ballarat, Victoria, Australia
| | - Stuart P. Berzins
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Federation University Australia and Fiona Elsey Cancer Research Institute, Ballarat, Victoria, Australia
| | - Daniel G. Pellicci
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- The ARC Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria, Australia
- Cellular Immunology Group, Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - William R. Heath
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- The ARC Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria, Australia
| | - Stephen C. Jameson
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN
| | - Laura K. Mackay
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- The ARC Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria, Australia
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Hallisey VM, Schwab SR. Blood-thirsty: S1PR5 and TRM. J Exp Med 2022; 219:212737. [PMID: 34714328 PMCID: PMC8574975 DOI: 10.1084/jem.20211971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In this elegant study, Evrard et al. (2021. J. Exp. Med.https://doi.org/10.1084/jem.20210116) find that sphingosine 1-phosphate receptor 5 (S1PR5) powerfully impairs tissue-resident memory T cell (TRM) formation, and that tissue-derived TGF-β limits S1pr5 expression by infiltrating T cells.
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Affiliation(s)
- Victoria M Hallisey
- Skirball Institute of Biomolecular Medicine, New York University Grossman School of Medicine, New York, NY
| | - Susan R Schwab
- Skirball Institute of Biomolecular Medicine, New York University Grossman School of Medicine, New York, NY
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47
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Matsuyama-Kato A, Iseki H, Boodhoo N, Bavananthasivam J, Alqazlan N, Abdul-Careem MF, Plattner BL, Behboudi S, Sharif S. Phenotypic characterization of gamma delta (γδ) T cells in chickens infected with or vaccinated against Marek's disease virus. Virology 2022; 568:115-125. [DOI: 10.1016/j.virol.2022.01.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 12/31/2021] [Accepted: 01/21/2022] [Indexed: 11/24/2022]
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48
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Abstract
Immunological memory and exhaustion are fundamental features of adaptive immunity. Recent advances reveal increasing heterogeneity and diversity among CD8 T-cell subsets, resulting in new subsets to annotate and understand. Here, we review our current knowledge of differentiation and maintenance of memory and exhausted CD8 T cells, including phenotypic classification, developmental paths, transcriptional and epigenetic features, and cell intrinsic and extrinsic factors. Additionally, we use this outline to discuss the nomenclature of effector, memory, and exhausted CD8 T cells. Finally, we discuss how new findings about these cell types may impact the therapeutic efficacy and development of immunotherapies targeting effector, memory, and/or exhausted CD8 T cells in chronic infections and cancer.
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Affiliation(s)
- Yuki Muroyama
- Institute for Immunology
- Department of Systems Pharmacology and Translational Therapeutics
| | - E John Wherry
- Institute for Immunology
- Department of Systems Pharmacology and Translational Therapeutics
- Abramson Cancer Center
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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49
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Zhang M, Zhao Z, Pritykin Y, Hannum M, Scott AC, Kuo F, Sanghvi V, Chan TA, Seshan V, Wendel HG, Schietinger A, Sadelain M, Huse M. Ectopic activation of the miR-200c-EpCAM axis enhances antitumor T cell responses in models of adoptive cell therapy. Sci Transl Med 2021; 13:eabg4328. [PMID: 34524864 PMCID: PMC9374309 DOI: 10.1126/scitranslmed.abg4328] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Adoptive T cell therapy (ACT) is a promising strategy for treating cancer, but it often fails because of cell intrinsic regulatory programs that limit the degree or duration of T cell function. In this study, we found that ectopic expression of microRNA-200c (miR-200c) markedly enhanced the antitumor activity of CD8+ cytotoxic T lymphocytes (CTLs) during ACT in multiple mouse models. CTLs transduced with miR-200c exhibited reduced apoptosis during engraftment and enhanced in vivo persistence, accompanied by up-regulation of the transcriptional regulator T cell factor 1 (TCF1) and the inflammatory cytokine tumor necrosis factor (TNF). miR-200c elicited these changes by suppressing the transcription factor Zeb1 and thereby inducing genes characteristic of epithelial cells. Overexpression of one of these genes, Epcam, was sufficient to augment therapeutic T cell responses against both solid and liquid tumors. These results identify the miR-200c–EpCAM axis as an avenue for improving ACT and demonstrate that select genetic perturbations can produce phenotypically distinct T cells with advantageous therapeutic properties.
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Affiliation(s)
- Minggang Zhang
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Zeguo Zhao
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yuri Pritykin
- Lewis-Sigler Institute for Integrative Genomics and Computer Science Department, Princeton University, Princeton, NJ 08540, USA
| | - Margaret Hannum
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrew C Scott
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Fengshen Kuo
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Viraj Sanghvi
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Venkatraman Seshan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Hans-Guido Wendel
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrea Schietinger
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Michel Sadelain
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Morgan Huse
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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50
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Almotiri A, Alzahrani H, Menendez-Gonzalez JB, Abdelfattah A, Alotaibi B, Saleh L, Greene A, Georgiou M, Gibbs A, Alsayari A, Taha S, Thomas LA, Shah D, Edkins S, Giles P, Stemmler MP, Brabletz S, Brabletz T, Boyd AS, Siebzehnrubl FA, Rodrigues NP. Zeb1 modulates hematopoietic stem cell fates required for suppressing acute myeloid leukemia. J Clin Invest 2021; 131:129115. [PMID: 33108352 PMCID: PMC7773410 DOI: 10.1172/jci129115] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 10/14/2020] [Indexed: 12/12/2022] Open
Abstract
Zeb1, a zinc finger E-box binding homeobox epithelial-mesenchymal transition (EMT) transcription factor, confers properties of "stemness," such as self-renewal, in cancer. Yet little is known about the function of Zeb1 in adult stem cells. Here, we used the hematopoietic system as a well-established paradigm of stem cell biology to evaluate Zeb1-mediated regulation of adult stem cells. We employed a conditional genetic approach using the Mx1-Cre system to specifically knock out (KO) Zeb1 in adult hematopoietic stem cells (HSCs) and their downstream progeny. Acute genetic deletion of Zeb1 led to rapid-onset thymic atrophy and apoptosis-driven loss of thymocytes and T cells. A profound cell-autonomous self-renewal defect and multilineage differentiation block were observed in Zeb1-KO HSCs. Loss of Zeb1 in HSCs activated transcriptional programs of deregulated HSC maintenance and multilineage differentiation genes and of cell polarity consisting of cytoskeleton-, lipid metabolism/lipid membrane-, and cell adhesion-related genes. Notably, epithelial cell adhesion molecule (EpCAM) expression was prodigiously upregulated in Zeb1-KO HSCs, which correlated with enhanced cell survival, diminished mitochondrial metabolism, ribosome biogenesis, and differentiation capacity and an activated transcriptomic signature associated with acute myeloid leukemia (AML) signaling. ZEB1 expression was downregulated in AML patients, and Zeb1 KO in the malignant counterparts of HSCs - leukemic stem cells (LSCs) - accelerated MLL-AF9- and Meis1a/Hoxa9-driven AML progression, implicating Zeb1 as a tumor suppressor in AML LSCs. Thus, Zeb1 acts as a transcriptional regulator in hematopoiesis, critically coordinating HSC self-renewal, apoptotic, and multilineage differentiation fates required to suppress leukemic potential in AML.
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Affiliation(s)
- Alhomidi Almotiri
- European Cancer Stem Cell Research Institute, Cardiff University, School of Biosciences, Cardiff, United Kingdom.,College of Applied Medical Sciences-Dawadmi, Shaqra University, Dawadmi, Saudi Arabia
| | - Hamed Alzahrani
- European Cancer Stem Cell Research Institute, Cardiff University, School of Biosciences, Cardiff, United Kingdom
| | | | - Ali Abdelfattah
- European Cancer Stem Cell Research Institute, Cardiff University, School of Biosciences, Cardiff, United Kingdom
| | - Badi Alotaibi
- European Cancer Stem Cell Research Institute, Cardiff University, School of Biosciences, Cardiff, United Kingdom
| | - Lubaid Saleh
- European Cancer Stem Cell Research Institute, Cardiff University, School of Biosciences, Cardiff, United Kingdom
| | - Adelle Greene
- European Cancer Stem Cell Research Institute, Cardiff University, School of Biosciences, Cardiff, United Kingdom
| | - Mia Georgiou
- European Cancer Stem Cell Research Institute, Cardiff University, School of Biosciences, Cardiff, United Kingdom
| | - Alex Gibbs
- European Cancer Stem Cell Research Institute, Cardiff University, School of Biosciences, Cardiff, United Kingdom
| | - Amani Alsayari
- European Cancer Stem Cell Research Institute, Cardiff University, School of Biosciences, Cardiff, United Kingdom
| | - Sarab Taha
- European Cancer Stem Cell Research Institute, Cardiff University, School of Biosciences, Cardiff, United Kingdom
| | - Leigh-Anne Thomas
- European Cancer Stem Cell Research Institute, Cardiff University, School of Biosciences, Cardiff, United Kingdom
| | - Dhruv Shah
- European Cancer Stem Cell Research Institute, Cardiff University, School of Biosciences, Cardiff, United Kingdom
| | - Sarah Edkins
- Wales Gene Park and Wales Cancer Research Centre, Division of Cancer and Genetics, Cardiff University, School of Medicine, Cardiff, United Kingdom
| | - Peter Giles
- Wales Gene Park and Wales Cancer Research Centre, Division of Cancer and Genetics, Cardiff University, School of Medicine, Cardiff, United Kingdom
| | - Marc P Stemmler
- Department of Experimental Medicine 1, Nikolaus-Fiebiger-Center for Molecular Medicine, FAU University Erlangen-Nürnberg, Erlangen, Germany
| | - Simone Brabletz
- Department of Experimental Medicine 1, Nikolaus-Fiebiger-Center for Molecular Medicine, FAU University Erlangen-Nürnberg, Erlangen, Germany
| | - Thomas Brabletz
- Department of Experimental Medicine 1, Nikolaus-Fiebiger-Center for Molecular Medicine, FAU University Erlangen-Nürnberg, Erlangen, Germany
| | - Ashleigh S Boyd
- Department of Surgical Biotechnology, Division of Surgery and Interventional Science, Royal Free Hospital, and.,Institute of Immunity and Transplantation, University College London, London, United Kingdom
| | - Florian A Siebzehnrubl
- European Cancer Stem Cell Research Institute, Cardiff University, School of Biosciences, Cardiff, United Kingdom
| | - Neil P Rodrigues
- European Cancer Stem Cell Research Institute, Cardiff University, School of Biosciences, Cardiff, United Kingdom
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