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Mishto M, Takala I, Bonfanti P, Liepe J. Proteasome isoforms in human thymi and mouse models. Immunol Lett 2024; 269:106899. [PMID: 39019403 DOI: 10.1016/j.imlet.2024.106899] [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: 04/30/2024] [Revised: 07/02/2024] [Accepted: 07/13/2024] [Indexed: 07/19/2024]
Abstract
The thymus is the organ where functional and self-tolerant T cells are selected through processes of positive and negative selection before migrating to the periphery. The antigenic peptides presented on MHC class I molecules of thymic epithelial cells (TECs) in the cortex and medulla of the thymus are key players in these processes. It has been theorized that these cells express different proteasome isoforms, which generate MHC class I immunopeptidomes with features that differentiate cortex and medulla, and hence positive and negative CD8+ T cell selection. This theory is largely based on mouse models and does not consider the large variety of noncanonical antigenic peptides that could be produced by proteasomes and presented on MHC class I molecules. Here, we review the multi-omics, biochemical and cellular studies carried out on mouse models and human thymi to investigate their content of proteasome isoforms, briefly summarize the implication that noncanonical antigenic peptide presentation in the thymus could have on CD8+ T cell repertoire and put these aspects in the larger framework of anatomical and immunological differences between these two species.
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Affiliation(s)
- Michele Mishto
- Molecular Immunology laboratory, the Francis Crick Institute, NW1 1AT London, United Kingdom; Centre for Inflammation Biology and Cancer Immunology & Peter Gorer Department of Immunobiology, King's College London, SE1 1UL London, United Kingdom.
| | - Iina Takala
- Research group of Quantitative System Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Paola Bonfanti
- Epithelial Stem Cell Biology & Regenerative Medicine laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom; Institute of Immunity & Transplantation, Division of Infection & Immunity, UCL, Pears Building, London NW3 2PP, United Kingdom
| | - Juliane Liepe
- Research group of Quantitative System Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
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Galassi C, Esteller M, Vitale I, Galluzzi L. Epigenetic control of immunoevasion in cancer stem cells. Trends Cancer 2024:S2405-8033(24)00171-7. [PMID: 39244477 DOI: 10.1016/j.trecan.2024.08.004] [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: 03/30/2024] [Revised: 07/24/2024] [Accepted: 08/12/2024] [Indexed: 09/09/2024]
Abstract
Cancer stem cells (CSCs) are a poorly differentiated population of malignant cells that (at least in some neoplasms) is responsible for tumor progression, resistance to therapy, and disease relapse. According to a widely accepted model, all stages of cancer progression involve the ability of neoplastic cells to evade recognition or elimination by the host immune system. In line with this notion, CSCs are not only able to cope with environmental and therapy-elicited stress better than their more differentiated counterparts but also appear to better evade tumor-targeting immune responses. We summarize epigenetic modifications of DNA and histones through which CSCs evade immune recognition or elimination, and propose that such alterations constitute promising therapeutic targets to increase the sensitivity of some malignancies to immunotherapy.
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Affiliation(s)
- Claudia Galassi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
| | - Manel Esteller
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain; Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain; Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
| | - Ilio Vitale
- Italian Institute for Genomic Medicine, Istituto di Ricovero e Cura a Carattere Scientifico (IRCSS) Candiolo, Torino, Italy; Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Italy.
| | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA; Sandra and Edward Meyer Cancer Center, New York, NY, USA; Caryl and Israel Englander Institute for Precision Medicine, New York, NY, USA.
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3
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Hu Z, Guo X, Li Z, Meng Z, Huang S. The neoantigens derived from transposable elements - A hidden treasure for cancer immunotherapy. Biochim Biophys Acta Rev Cancer 2024; 1879:189126. [PMID: 38849060 DOI: 10.1016/j.bbcan.2024.189126] [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: 01/16/2024] [Revised: 05/26/2024] [Accepted: 06/02/2024] [Indexed: 06/09/2024]
Abstract
Neoantigen-based therapy is a promising approach that selectively activates the immune system of the host to recognize and eradicate cancer cells. Preliminary clinical trials have validated the feasibility, safety, and immunogenicity of personalized neoantigen-directed vaccines, enhancing their effectiveness and broad applicability in immunotherapy. While many ongoing oncological trials concentrate on neoantigens derived from mutations, these targets do not consistently provoke an immune response in all patients harboring the mutations. Additionally, tumors like ovarian cancer, which have a low tumor mutational burden (TMB), may be less amenable to mutation-based neoantigen therapies. Recent advancements in next-generation sequencing and bioinformatics have uncovered a rich source of neoantigens from non-canonical RNAs associated with transposable elements (TEs). Considering the substantial presence of TEs in the human genome and the proven immunogenicity of TE-derived neoantigens in various tumor types, this review investigates the latest findings on TE-derived neoantigens, examining their clinical implications, challenges, and unique advantages in enhancing tumor immunotherapy.
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Affiliation(s)
- Zhixiang Hu
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xinyi Guo
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ziteng Li
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhiqiang Meng
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Shenglin Huang
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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4
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Hao K, Gao KM, Strauss M, Subramanian S, Marshak-Rothstein A. IFNγ initiates TLR9-dependent autoimmune hepatitis in DNase II deficient mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.10.602775. [PMID: 39071327 PMCID: PMC11275780 DOI: 10.1101/2024.07.10.602775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Patients with biallelic hypomorphic mutation in DNASE2 develop systemic autoinflammation and early-onset liver fibrosis. Prior studies showed that Dnase2 -/- Ifnar -/- double knockout (DKO) mice develop Type I IFN-independent liver inflammation, but immune mechanisms were unclear. We now show that DKO mice recapitulate many features of human autoimmune hepatitis (AIH), including periportal and interstitial inflammation and fibrosis and elevated ALT. Infiltrating cells include CD8+ tissue resident memory T cells, type I innate lymphoid cells, and inflammatory monocyte/macrophage cells that replace the Kupffer cell pool. Importantly, TLR9 expression by bone marrow-derived cells is required for the the development of AIH. TLR9 is highly expressed by inflammatory myeloid cells but not long-lived Kupffer cells. Furthermore, the initial recruitment of TLR9 expressing monocytes and subsequent activation of lymphocytes requires IFNγ signaling. These findings highlight a critical role of feed forward loop between TLR9 expressing monocyte-lineage cells and IFNg producing lymphocytes in autoimmune hepatitis.
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Nanaware PP, Khan ZN, Clement CC, Shetty M, Mota I, Seltzer ES, Dzieciatkowska M, Gamboni F, D'Alessandro A, Ng C, Nagayama M, Lichti CF, Soni RK, Jacob B Geri, Matei I, Lyden D, Longman R, Lu TT, Wan X, Unanue ER, Stern LJ, Santambrogio L. Role of the afferent lymph as an immunological conduit to analyze tissue antigenic and inflammatory load. Cell Rep 2024; 43:114311. [PMID: 38848214 PMCID: PMC11233987 DOI: 10.1016/j.celrep.2024.114311] [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: 10/16/2023] [Revised: 04/03/2024] [Accepted: 05/16/2024] [Indexed: 06/09/2024] Open
Abstract
The lymphatic fluid is the conduit by which part of the tissue "omics" is transported to the draining lymph node for immunosurveillance. Following cannulation of the pre-nodal cervical and mesenteric afferent lymphatics, herein we investigate the lymph proteomic composition, uncovering that its composition varies according to the tissue of origin. Tissue specificity is also reflected in the dendritic cell-major histocompatibility complex class II-eluted immunopeptidome harvested from the cervical and mesenteric nodes. Following inflammatory disruption of the gut barrier, the lymph antigenic and inflammatory loads are analyzed in both mice and subjects with inflammatory bowel diseases. Gastrointestinal tissue damage reflects the lymph inflammatory and damage-associated molecular pattern signatures, microbiome-derived by-products, and immunomodulatory molecules, including metabolites of the gut-brain axis, mapped in the afferent mesenteric lymph. Our data point to the relevance of the lymphatic fluid to probe the tissue-specific antigenic and inflammatory load transported to the draining lymph node for immunosurveillance.
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Affiliation(s)
- Padma P Nanaware
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY 10065, USA; Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Zohaib N Khan
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Cristina C Clement
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Madhur Shetty
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ines Mota
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ethan S Seltzer
- Pediatric Rheumatology and Autoimmunity and Inflammation Program, Hospital for Special Surgery Research Institute, New York NY 100021, USA
| | - Monika Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Fabia Gamboni
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Charles Ng
- Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital and Weill Cornell Medicine, New York, NY 10065, USA
| | - Manabu Nagayama
- Division of Gastroenterology and Hepatology, New York-Presbyterian Hospital and Weill Cornell Medicine, New York, NY 10065, USA
| | - Cheryl F Lichti
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Rajesh K Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York 10032, NY, USA
| | - Jacob B Geri
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics and Cell and Developmental Biology, Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY 10065, USA
| | - Irina Matei
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics and Cell and Developmental Biology, Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY 10065, USA; Sandra and Edward Meyer Cancer Center, New York, NY 10065, USA
| | - David Lyden
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics and Cell and Developmental Biology, Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY 10065, USA; Sandra and Edward Meyer Cancer Center, New York, NY 10065, USA
| | - Randy Longman
- Division of Gastroenterology and Hepatology, New York-Presbyterian Hospital and Weill Cornell Medicine, New York, NY 10065, USA
| | - Theresa T Lu
- Pediatric Rheumatology and Autoimmunity and Inflammation Program, Hospital for Special Surgery Research Institute, New York NY 100021, USA
| | - Xiaoxiao Wan
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Emil R Unanue
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Lawrence J Stern
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Laura Santambrogio
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY 10065, USA; Sandra and Edward Meyer Cancer Center, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, New York, NY 10065, USA.
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Paparoditis P, Shulman Z. The tumor-driven antibody-mediated immune response in cancer. Curr Opin Immunol 2024; 88:102431. [PMID: 38866666 DOI: 10.1016/j.coi.2024.102431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 05/21/2024] [Accepted: 05/27/2024] [Indexed: 06/14/2024]
Abstract
Immune cells in the tumor microenvironment play a crucial role in cancer prognosis and response to immunotherapy. Recent studies highlight the significance of tumor-infiltrating B cells and tertiary lymphoid structures as markers of favorable prognosis and patient-positive response to immune checkpoint blockers in some types of cancer. Although the presence of germinal center B cells and plasma cells in the tumor microenvironment has been established, determining their tumor reactivity remains challenging. The few known tumor targets range from viral proteins to self and altered self-proteins. The emergence of self-reactive antibodies in patients with cancer, involves the opposing forces of antigen-driven affinity increase and peripheral tolerance mechanisms. Here, B cell tumor antigen specificity and affinity maturation in tumor-directed immune responses in cancer are discussed.
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Affiliation(s)
- Philipp Paparoditis
- Department of Systems Immunology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ziv Shulman
- Department of Systems Immunology, The Weizmann Institute of Science, Rehovot 7610001, Israel.
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Catanzaro E, Demuynck R, Naessens F, Galluzzi L, Krysko DV. Immunogenicity of ferroptosis in cancer: a matter of context? Trends Cancer 2024; 10:407-416. [PMID: 38368244 DOI: 10.1016/j.trecan.2024.01.013] [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: 12/12/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/19/2024]
Abstract
Ferroptosis is a variant of regulated cell death (RCD) elicited by an imbalance of cellular redox homeostasis that culminates with extensive lipid peroxidation and rapid plasma membrane breakdown. Since other necrotic forms of RCD, such as necroptosis, are highly immunogenic, ferroptosis inducers have attracted considerable attention as potential tools to selectively kill malignant cells while eliciting therapeutically relevant tumor-targeting immune responses. However, rather than being consistently immunogenic, ferroptosis mediates context-dependent effects on anticancer immunity. The inability of ferroptotic cancer cells to elicit adaptive immune responses may arise from contextual deficiencies in intrinsic aspects of the process, such as adjuvanticity and antigenicity, or from microenvironmental defects imposed by ferroptotic cancer cells themselves or elicited by the induction of ferroptosis in immune cells.
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Affiliation(s)
- Elena Catanzaro
- Cell Death Investigation and Therapy (CDIT) Laboratory, Anatomy and Embryology Unit, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Robin Demuynck
- Cell Death Investigation and Therapy (CDIT) Laboratory, Anatomy and Embryology Unit, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Faye Naessens
- Cell Death Investigation and Therapy (CDIT) Laboratory, Anatomy and Embryology Unit, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA; Sandra and Edward Meyer Cancer Center, New York, NY, USA; Caryl and Israel Englander Institute for Precision Medicine, New York, NY, USA
| | - Dmitri V Krysko
- Cell Death Investigation and Therapy (CDIT) Laboratory, Anatomy and Embryology Unit, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent, Ghent University, Ghent, Belgium.
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