1
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Fey SK, Vaquero-Siguero N, Jackstadt R. Dark force rising: Reawakening and targeting of fetal-like stem cells in colorectal cancer. Cell Rep 2024; 43:114270. [PMID: 38787726 DOI: 10.1016/j.celrep.2024.114270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/14/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Stem cells play pivotal roles in maintaining intestinal homeostasis, orchestrating regeneration, and in key steps of colorectal cancer (CRC) initiation and progression. Intriguingly, adult stem cells are reduced during many of these processes. On the contrary, primitive fetal programs, commonly detected in development, emerge during tissue repair, CRC metastasis, and therapy resistance. Recent findings indicate a dynamic continuum between adult and fetal stem cell programs. We discuss critical mechanisms facilitating the plasticity between stem cell states and highlight the heterogeneity observed upon the appearance of fetal-like states. We focus on therapeutic opportunities that arise by targeting fetal-like CRC cells and how those concepts can be translated into the clinic.
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Affiliation(s)
- Sigrid K Fey
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; Cancer Progression and Metastasis Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Nuria Vaquero-Siguero
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; Cancer Progression and Metastasis Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Rene Jackstadt
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; Cancer Progression and Metastasis Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), DKFZ, Core Center Heidelberg, 69120 Heidelberg, Germany.
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2
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Wohlfarth J, Kosnopfel C, Faber D, Berthold M, Siedel C, Bernhardt M, Schlosser A, Aprati T, Liu D, Schrama D, Houben R, Schadendorf D, Goebeler M, Meierjohann S, Schilling B. Loss of p14 diminishes immunogenicity in melanoma via non-canonical Wnt signaling by reducing the peptide surface density. Mol Oncol 2024. [PMID: 38807304 DOI: 10.1002/1878-0261.13660] [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: 01/03/2024] [Revised: 03/04/2024] [Accepted: 04/26/2024] [Indexed: 05/30/2024] Open
Abstract
Immunotherapy has achieved tremendous success in melanoma. However, only around 50% of advanced melanoma patients benefit from immunotherapy. Cyclin-dependent kinase inhibitor 2A (CDKN2A), encoding the two tumor-suppressor proteins p14ARF and p16INK4a, belongs to the most frequently inactivated gene loci in melanoma and leads to decreased T cell infiltration. While the role of p16INK4a has been extensively investigated, knowledge about p14ARF in melanoma is scarce. In this study, we elucidate the impact of reduced p14ARF expression on melanoma immunogenicity. Knockdown of p14ARF in melanoma cell lines diminished their recognition and killing by melanoma differentiation antigen (MDA)-specific T cells. Resistance was caused by a reduction of the peptide surface density of presented MDAs. Immunopeptidomic analyses revealed that antigen presentation via human leukocyte antigen class I (HLA-I) molecules was enhanced upon p14ARF downregulation in general, but absolute and relative expression of cognate peptides was decreased. However, this phenotype is associated with a favorable outcome for melanoma patients. Limiting Wnt5a signaling reverted this phenotype, suggesting an involvement of non-canonical Wnt signaling. Taken together, our data indicate a new mechanism limiting MDA-specific T cell responses by decreasing both absolute and relative MDA-peptide presentation in melanoma.
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Affiliation(s)
- Jonas Wohlfarth
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Germany
| | - Corinna Kosnopfel
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Germany
| | - Dominic Faber
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Germany
| | - Marion Berthold
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Germany
| | - Claudia Siedel
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Germany
| | - Melissa Bernhardt
- Rudolf-Virchow-Centre for Integrative and Translational Bioimaging, University of Würzburg, Germany
| | - Andreas Schlosser
- Rudolf-Virchow-Centre for Integrative and Translational Bioimaging, University of Würzburg, Germany
| | - Tyler Aprati
- Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - David Liu
- Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - David Schrama
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Germany
| | - Roland Houben
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Germany
| | - Dirk Schadendorf
- Department of Dermatology, Comprehensive Cancer Center (Westdeutsches Tumorzentrum), German Cancer Consortium (DKTK, partner site Essen) and University Hospital Essen, Germany
| | - Matthias Goebeler
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Germany
| | | | - Bastian Schilling
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Germany
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3
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Yapp C, Nirmal AJ, Zhou F, Maliga Z, Tefft JB, Llopis PM, Murphy GF, Lian CG, Danuser G, Santagata S, Sorger PK. Multiplexed 3D Analysis of Immune States and Niches in Human Tissue. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.10.566670. [PMID: 38014052 PMCID: PMC10680601 DOI: 10.1101/2023.11.10.566670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Tissue homeostasis and the emergence of disease are controlled by changes in the proportions of resident and recruited cells, their organization into cellular neighbourhoods, and their interactions with acellular tissue components. Highly multiplexed tissue profiling (spatial omics)1 makes it possible to study this microenvironment in situ, usually in 4-5 micron thick sections (the standard histopathology format)2. Microscopy-based tissue profiling is commonly performed at a resolution sufficient to determine cell types but not to detect subtle morphological features associated with cytoskeletal reorganisation, juxtracrine signalling, or membrane trafficking3. Here we describe a high-resolution 3D imaging approach able to characterize a wide variety of organelles and structures at sub-micron scale while simultaneously quantifying millimetre-scale spatial features. This approach combines cyclic immunofluorescence (CyCIF) imaging4 of over 50 markers with confocal microscopy of archival human tissue thick enough (30-40 microns) to fully encompass two or more layers of intact cells. 3D imaging of entire cell volumes substantially improves the accuracy of cell phenotyping and allows cell proximity to be scored using plasma membrane apposition, not just nuclear position. In pre-invasive melanoma in situ5, precise phenotyping shows that adjacent melanocytic cells are plastic in state and participate in tightly localised niches of interferon signalling near sites of initial invasion into the underlying dermis. In this and metastatic melanoma, mature and precursor T cells engage in an unexpectedly diverse array of juxtracrine and membrane-membrane interactions as well as looser "neighbourhood" associations6 whose morphologies reveal functional states. These data provide new insight into the transitions occurring during early tumour formation and immunoediting and demonstrate the potential for phenotyping of tissues at a level of detail previously restricted to cultured cells and organoids.
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Affiliation(s)
- Clarence Yapp
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Ludwig Centre at Harvard, Harvard Medical School, Boston, MA, 02115, USA
| | - Ajit J. Nirmal
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Ludwig Centre at Harvard, Harvard Medical School, Boston, MA, 02115, USA
- Department of Dermatology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Felix Zhou
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Zoltan Maliga
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Juliann B. Tefft
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Ludwig Centre at Harvard, Harvard Medical School, Boston, MA, 02115, USA
| | - Paula Montero Llopis
- Microscopy Resources on the North Quad (MicRoN), Harvard Medical School, Boston, MA 02115, USA
| | - George F. Murphy
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Christine G. Lian
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Gaudenz Danuser
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Sandro Santagata
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Ludwig Centre at Harvard, Harvard Medical School, Boston, MA, 02115, USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Peter K. Sorger
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Ludwig Centre at Harvard, Harvard Medical School, Boston, MA, 02115, USA
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
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4
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Rosenbaum SR, Caksa S, Stefanski CD, Trachtenberg IV, Wilson HP, Wilski NA, Ott CA, Purwin TJ, Haj JI, Pomante D, Kotas D, Chervoneva I, Capparelli C, Aplin AE. SOX10 Loss Sensitizes Melanoma Cells to Cytokine-Mediated Inflammatory Cell Death. Mol Cancer Res 2024; 22:209-220. [PMID: 37847239 PMCID: PMC10842433 DOI: 10.1158/1541-7786.mcr-23-0290] [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: 04/21/2023] [Revised: 08/30/2023] [Accepted: 10/13/2023] [Indexed: 10/18/2023]
Abstract
The transcription factor, SOX10, plays an important role in the differentiation of neural crest precursors to the melanocytic lineage. Malignant transformation of melanocytes leads to the development of melanoma, and SOX10 promotes melanoma cell proliferation and tumor formation. SOX10 expression in melanomas is heterogeneous, and loss of SOX10 causes a phenotypic switch toward an invasive, mesenchymal-like cell state and therapy resistance; hence, strategies to target SOX10-deficient cells are an active area of investigation. The impact of cell state and SOX10 expression on antitumor immunity is not well understood but will likely have important implications for immunotherapeutic interventions. To this end, we tested whether SOX10 status affects the response to CD8+ T cell-mediated killing and T cell-secreted cytokines, TNFα and IFNγ, which are critical effectors in the cytotoxic killing of cancer cells. We observed that genetic ablation of SOX10 rendered melanoma cells more sensitive to CD8+ T cell-mediated killing and cell death induction by either TNFα or IFNγ. Cytokine-mediated cell death in SOX10-deficient cells was associated with features of caspase-dependent pyroptosis, an inflammatory form of cell death that has the potential to increase immune responses. IMPLICATIONS These data support a role for SOX10 expression altering the response to T cell-mediated cell death and contribute to a broader understanding of the interaction between immune cells and melanoma cells.
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Affiliation(s)
- Sheera R. Rosenbaum
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Signe Caksa
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Casey D. Stefanski
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Isabella V. Trachtenberg
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Haley P. Wilson
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Nicole A. Wilski
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Connor A. Ott
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Timothy J. Purwin
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Jelan I. Haj
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Danielle Pomante
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Daniel Kotas
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Inna Chervoneva
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
- Division of Biostatistics, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Claudia Capparelli
- Department of Medical Oncology, Thomas Jefferson University, Philadelphia, PA 19107, USA
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Andrew E. Aplin
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
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5
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Chuang YM, Tzeng SF, Ho PC, Tsai CH. Immunosurveillance encounters cancer metabolism. EMBO Rep 2024; 25:471-488. [PMID: 38216787 PMCID: PMC10897436 DOI: 10.1038/s44319-023-00038-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: 02/10/2023] [Revised: 12/02/2023] [Accepted: 12/12/2023] [Indexed: 01/14/2024] Open
Abstract
Tumor cells reprogram nutrient acquisition and metabolic pathways to meet their energetic, biosynthetic, and redox demands. Similarly, metabolic processes in immune cells support host immunity against cancer and determine differentiation and fate of leukocytes. Thus, metabolic deregulation and imbalance in immune cells within the tumor microenvironment have been reported to drive immune evasion and to compromise therapeutic outcomes. Interestingly, emerging evidence indicates that anti-tumor immunity could modulate tumor heterogeneity, aggressiveness, and metabolic reprogramming, suggesting that immunosurveillance can instruct cancer progression in multiple dimensions. This review summarizes our current understanding of how metabolic crosstalk within tumors affects immunogenicity of tumor cells and promotes cancer progression. Furthermore, we explain how defects in the metabolic cascade can contribute to developing dysfunctional immune responses against cancers and discuss the contribution of immunosurveillance to these defects as a feedback mechanism. Finally, we highlight ongoing clinical trials and new therapeutic strategies targeting cellular metabolism in cancer.
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Affiliation(s)
- Yu-Ming Chuang
- Department of Fundamental Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Sheue-Fen Tzeng
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Ping-Chih Ho
- Department of Fundamental Oncology, University of Lausanne, Lausanne, Switzerland.
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.
| | - Chin-Hsien Tsai
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan.
- Department and Graduate Institute of Biochemistry, National Defense Medical Center, Taipei, Taiwan.
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6
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Lazar I, Livneh I, Ciechanover A, Fabre B. Tryptophanyl-Transfer RNA Synthetase Is Involved in a Negative Feedback Loop Mitigating Interferon-γ-Induced Gene Expression. Cells 2024; 13:180. [PMID: 38247871 PMCID: PMC10813977 DOI: 10.3390/cells13020180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/23/2024] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are essential enzymes responsible for linking a transfer RNA (tRNA) with its cognate amino acid present in all the kingdoms of life. Besides their aminoacyl-tRNA synthetase activity, it was described that many of these enzymes can carry out non-canonical functions. They were shown to be involved in important biological processes such as metabolism, immunity, development, angiogenesis and tumorigenesis. In the present work, we provide evidence that tryptophanyl-tRNA synthetase might be involved in a negative feedback loop mitigating the expression of certain interferon-γ-induced genes. Mining the available TCGA and Gtex data, we found that WARS was highly expressed in cutaneous melanoma (SKCM) compared to other cancers and is of good prognosis for this particular cancer type. WARS expression correlates with genes involved in antigen processing and presentation but also transcription factors involved in IFN-γ signaling such as STAT1. In addition, WARS was found in complex with STAT1 in A375 cells treated with IFN-γ. Finally, we showed that knocking down WARS expression during IFN-γ stimulation further increases the expression of GBP2, APOL1, ISG15, HLA-A and IDO1.
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Affiliation(s)
- Ikrame Lazar
- The Rappaport Technion Integrated Cancer Center (R-TICC) and the Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 3109601, Israel; (I.L.); (I.L.); (A.C.)
- MCD, Centre de Biologie Intégrative (CBI), CNRS, UT3, Université de Toulouse, 31400 Toulouse, France
| | - Ido Livneh
- The Rappaport Technion Integrated Cancer Center (R-TICC) and the Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 3109601, Israel; (I.L.); (I.L.); (A.C.)
| | - Aaron Ciechanover
- The Rappaport Technion Integrated Cancer Center (R-TICC) and the Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 3109601, Israel; (I.L.); (I.L.); (A.C.)
| | - Bertrand Fabre
- The Rappaport Technion Integrated Cancer Center (R-TICC) and the Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 3109601, Israel; (I.L.); (I.L.); (A.C.)
- Laboratoire de Recherche en Sciences Végétales (LRSV), CNRS/UT3/INPT, 31320 Auzeville-Tolosane, France
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7
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Mehta A, Stanger BZ. Lineage Plasticity: The New Cancer Hallmark on the Block. Cancer Res 2024; 84:184-191. [PMID: 37963209 PMCID: PMC10841583 DOI: 10.1158/0008-5472.can-23-1067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 09/12/2023] [Accepted: 11/07/2023] [Indexed: 11/16/2023]
Abstract
Plasticity refers to the ability of cells to adopt a spectrum of states or phenotypes. In cancer, it is a critical contributor to tumor initiation, progression, invasiveness, and therapy resistance, and it has recently been recognized as an emerging cancer hallmark. Plasticity can occur as a result of cell-intrinsic factors (e.g., genetic, transcriptional, or epigenetic fluctuations), or through cell-extrinsic cues (e.g., signaling from components of the tumor microenvironment or selective pressure from therapy). Over the past decade, technological advances, analysis of patient samples, and studies in mouse model systems have led to a deeper understanding of how such plastic states come about. In this review, we discuss: (i) the definition of plasticity; (ii) methods to measure and quantify plasticity; (iii) the clinical relevance of plasticity; and (iv) therapeutic hypotheses to modulate plasticity in the clinic.
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Affiliation(s)
- Arnav Mehta
- Department of Medicine, Massachusetts General Hospital, Boston, MA
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Boston, MA
- Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Ben Z. Stanger
- Abramson Family Cancer Research Institute, Perelman School of Medicine at University of Pennsylvania, Philadelphia, PA
- Department of Medicine, Perelman School of Medicine at University of Pennsylvania, Philadelphia, PA
- Department of Cell and Developmental Biology, Perelman School of Medicine at University of Pennsylvania, Philadelphia, PA
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8
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Maltas J, Killarney ST, Singleton KR, Strobl MAR, Washart R, Wood KC, Wood KB. Drug dependence in cancer is exploitable by optimally constructed treatment holidays. Nat Ecol Evol 2024; 8:147-162. [PMID: 38012363 PMCID: PMC10918730 DOI: 10.1038/s41559-023-02255-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 10/19/2023] [Indexed: 11/29/2023]
Abstract
Cancers with acquired resistance to targeted therapy can become simultaneously dependent on the presence of the targeted therapy drug for survival, suggesting that intermittent therapy may slow resistance. However, relatively little is known about which tumours are likely to become dependent and how to schedule intermittent therapy optimally. Here we characterized drug dependence across a panel of over 75 MAPK-inhibitor-resistant BRAFV600E mutant melanoma models at the population and single-clone levels. Melanocytic differentiated models exhibited a much greater tendency to give rise to drug-dependent progeny than their dedifferentiated counterparts. Mechanistically, acquired loss of microphthalmia-associated transcription factor in differentiated melanoma models drives ERK-JunB-p21 signalling to enforce drug dependence. We identified the optimal scheduling of 'drug holidays' using simple mathematical models that we validated across short and long timescales. Without detailed knowledge of tumour characteristics, we found that a simple adaptive therapy protocol can produce near-optimal outcomes using only measurements of total population size. Finally, a spatial agent-based model showed that optimal schedules derived from exponentially growing cells in culture remain nearly optimal in the context of tumour cell turnover and limited environmental carrying capacity. These findings may guide the implementation of improved evolution-inspired treatment strategies for drug-dependent cancers.
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Affiliation(s)
- Jeff Maltas
- Department of Biophysics, University of Michigan, Ann Arbor, MI, USA
| | - Shane T Killarney
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | | | - Maximilian A R Strobl
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - Rachel Washart
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Kris C Wood
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA.
| | - Kevin B Wood
- Department of Biophysics, University of Michigan, Ann Arbor, MI, USA.
- Department of Physics, University of Michigan, Ann Arbor, MI, USA.
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9
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Emmons MF, Bennett RL, Riva A, Gupta K, Carvalho LADC, Zhang C, Macaulay R, Dupéré-Richér D, Fang B, Seto E, Koomen JM, Li J, Chen YA, Forsyth PA, Licht JD, Smalley KSM. HDAC8-mediated inhibition of EP300 drives a transcriptional state that increases melanoma brain metastasis. Nat Commun 2023; 14:7759. [PMID: 38030596 PMCID: PMC10686983 DOI: 10.1038/s41467-023-43519-1] [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: 08/24/2022] [Accepted: 11/13/2023] [Indexed: 12/01/2023] Open
Abstract
Melanomas can adopt multiple transcriptional states. Little is known about the epigenetic drivers of these cell states, limiting our ability to regulate melanoma heterogeneity. Here, we identify stress-induced HDAC8 activity as driving melanoma brain metastasis development. Exposure of melanocytes and melanoma cells to multiple stresses increases HDAC8 activation leading to a neural crest-stem cell transcriptional state and an amoeboid, invasive phenotype that increases seeding to the brain. Using ATAC-Seq and ChIP-Seq we show that increased HDAC8 activity alters chromatin structure by increasing H3K27ac and enhancing accessibility at c-Jun binding sites. Functionally, HDAC8 deacetylates the histone acetyltransferase EP300, causing its enzymatic inactivation. This, in turn, increases binding of EP300 to Jun-transcriptional sites and decreases binding to MITF-transcriptional sites. Inhibition of EP300 increases melanoma cell invasion, resistance to stress and increases melanoma brain metastasis development. HDAC8 is identified as a mediator of transcriptional co-factor inactivation and chromatin accessibility that drives brain metastasis.
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Affiliation(s)
- Michael F Emmons
- Department of Tumor Biology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Richard L Bennett
- UF Health Cancer Center, 2033 Mowry Road, University of Florida, Gainesville, FL, 32610, USA
| | - Alberto Riva
- Bioinformatics Core, Interdisciplinary Center for Biotechnology Research, University of Florida, 2033 Mowry Road, Gainesville, FL, 32610, USA
| | - Kanchan Gupta
- UF Health Cancer Center, 2033 Mowry Road, University of Florida, Gainesville, FL, 32610, USA
| | | | - Chao Zhang
- Department of Tumor Biology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Robert Macaulay
- Department of Neuro-Oncology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Daphne Dupéré-Richér
- UF Health Cancer Center, 2033 Mowry Road, University of Florida, Gainesville, FL, 32610, USA
| | - Bin Fang
- Proteomics & Metabolomics Core, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Edward Seto
- Department of Biochemistry & Molecular Medicine, School of Medicine & Health Sciences, George Washington Cancer Center, George Washington University, 2300 Eye Street, Washington, DC, 20037, USA
| | - John M Koomen
- Department of Molecular Oncology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Jiannong Li
- Department of Bioinformatics and Biostatistics, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Y Ann Chen
- Department of Bioinformatics and Biostatistics, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Peter A Forsyth
- Department of Neuro-Oncology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Jonathan D Licht
- UF Health Cancer Center, 2033 Mowry Road, University of Florida, Gainesville, FL, 32610, USA
| | - Keiran S M Smalley
- Department of Tumor Biology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA.
- Department of Cutaneous Oncology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA.
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10
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James JL, Taylor BC, Axelrod ML, Sun X, Guerin LN, Gonzalez-Ericsson PI, Wang Y, Sanchez V, Fahey CC, Sanders ME, Xu Y, Hodges E, Johnson DB, Balko JM. Polycomb repressor complex 2 suppresses interferon-responsive MHC-II expression in melanoma cells and is associated with anti-PD-1 resistance. J Immunother Cancer 2023; 11:e007736. [PMID: 38315170 PMCID: PMC10660662 DOI: 10.1136/jitc-2023-007736] [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] [Accepted: 10/17/2023] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND Despite the remarkable success of immunotherapy in treating melanoma, understanding of the underlying mechanisms of resistance remains limited. Emerging evidence suggests that upregulation of tumor-specific major histocompatibility complex-II (tsMHC-II) serves as a predictive marker for the response to anti-programmed death-1 (PD-1)/programmed death ligand 1 (PD-L1) therapy in various cancer types. The genetic and epigenetic pathways modulating tsMHC-II expression remain incompletely characterized. Here, we provide evidence that polycomb repressive complex 2 (PRC2)/EZH2 signaling and resulting H3K27 hypermethylation suppresses tsMHC-II. METHODS RNA sequencing data from tumor biopsies from patients with cutaneous melanoma treated with or without anti-PD-1, targeted inhibition assays, and assays for transposase-accessible chromatin with sequencing were used to observe the relationship between EZH2 inhibition and interferon (IFN)-γ inducibility within the MHC-II pathway. RESULTS We find that increased EZH2 pathway messenger RNA (mRNA) expression correlates with reduced mRNA expression of both presentation and T-cell genes. Notably, targeted inhibition assays revealed that inhibition of EZH2 influences the expression dynamics and inducibility of the MHC-II pathway following IFN-γ stimulation. Additionally, our analysis of patients with metastatic melanoma revealed a significant inverse association between PRC2-related gene expression and response to anti-PD-1 therapy. CONCLUSIONS Collectively, our findings demonstrate that EZH2 inhibition leads to enhanced MHC-II expression potentially resulting from improved chromatin accessibility at CIITA, the master regulator of MHC-II. These insights shed light on the molecular mechanisms involved in tsMHC-II suppression and highlight the potential of targeting EZH2 as a therapeutic strategy to improve immunotherapy efficacy.
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Affiliation(s)
- Jamaal L James
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Brandie C Taylor
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Margaret L Axelrod
- Department of Medicine, Washington University in St Louis, St Louis, Missouri, USA
| | - Xiaopeng Sun
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Lindsey N Guerin
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Paula I Gonzalez-Ericsson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Breast Cancer Research Program, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Yu Wang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Violeta Sanchez
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Catherine C Fahey
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Hematology/Oncology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Melinda E Sanders
- Breast Cancer Research Program, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Yaomin Xu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Emily Hodges
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
- Genetics Institute, Vanderbilt University, Nashville, Tennessee, USA
| | - Douglas B Johnson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Justin M Balko
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Breast Cancer Research Program, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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11
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Jain P, Pillai M, Duddu AS, Somarelli JA, Goyal Y, Jolly MK. Dynamical hallmarks of cancer: Phenotypic switching in melanoma and epithelial-mesenchymal plasticity. Semin Cancer Biol 2023; 96:48-63. [PMID: 37788736 DOI: 10.1016/j.semcancer.2023.09.007] [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: 04/19/2023] [Revised: 09/24/2023] [Accepted: 09/28/2023] [Indexed: 10/05/2023]
Abstract
Phenotypic plasticity was recently incorporated as a hallmark of cancer. This plasticity can manifest along many interconnected axes, such as stemness and differentiation, drug-sensitive and drug-resistant states, and between epithelial and mesenchymal cell-states. Despite growing acceptance for phenotypic plasticity as a hallmark of cancer, the dynamics of this process remains poorly understood. In particular, the knowledge necessary for a predictive understanding of how individual cancer cells and populations of cells dynamically switch their phenotypes in response to the intensity and/or duration of their current and past environmental stimuli remains far from complete. Here, we present recent investigations of phenotypic plasticity from a systems-level perspective using two exemplars: epithelial-mesenchymal plasticity in carcinomas and phenotypic switching in melanoma. We highlight how an integrated computational-experimental approach has helped unravel insights into specific dynamical hallmarks of phenotypic plasticity in different cancers to address the following questions: a) how many distinct cell-states or phenotypes exist?; b) how reversible are transitions among these cell-states, and what factors control the extent of reversibility?; and c) how might cell-cell communication be able to alter rates of cell-state switching and enable diverse patterns of phenotypic heterogeneity? Understanding these dynamic features of phenotypic plasticity may be a key component in shifting the paradigm of cancer treatment from reactionary to a more predictive, proactive approach.
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Affiliation(s)
- Paras Jain
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India
| | - Maalavika Pillai
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India; Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Center for Synthetic Biology, Northwestern University, Chicago, IL 60611, USA
| | | | - Jason A Somarelli
- Department of Medicine, Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - Yogesh Goyal
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Center for Synthetic Biology, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Mohit Kumar Jolly
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India.
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12
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Fazilaty H, Basler K. Reactivation of embryonic genetic programs in tissue regeneration and disease. Nat Genet 2023; 55:1792-1806. [PMID: 37904052 DOI: 10.1038/s41588-023-01526-4] [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: 01/10/2023] [Accepted: 09/11/2023] [Indexed: 11/01/2023]
Abstract
Embryonic genetic programs are reactivated in response to various types of tissue damage, providing cell plasticity for tissue regeneration or disease progression. In acute conditions, these programs remedy the damage and then halt to allow a return to homeostasis. In chronic situations, including inflammatory diseases, fibrosis and cancer, prolonged activation of embryonic programs leads to disease progression and tissue deterioration. Induction of progenitor identity and cell plasticity, for example, epithelial-mesenchymal plasticity, are critical outcomes of reactivated embryonic programs. In this Review, we describe molecular players governing reactivated embryonic genetic programs, their role during disease progression, their similarities and differences and lineage reversion in pathology and discuss associated therapeutics and drug-resistance mechanisms across many organs. We also discuss the diversity of reactivated programs in different disease contexts. A comprehensive overview of commonalities between development and disease will provide better understanding of the biology and therapeutic strategies.
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Affiliation(s)
- Hassan Fazilaty
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland.
| | - Konrad Basler
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
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13
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Subhadarshini S, Sahoo S, Debnath S, Somarelli JA, Jolly MK. Dynamical modeling of proliferative-invasive plasticity and IFNγ signaling in melanoma reveals mechanisms of PD-L1 expression heterogeneity. J Immunother Cancer 2023; 11:e006766. [PMID: 37678920 PMCID: PMC10496669 DOI: 10.1136/jitc-2023-006766] [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] [Accepted: 07/17/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND Phenotypic heterogeneity of melanoma cells contributes to drug tolerance, increased metastasis, and immune evasion in patients with progressive disease. Diverse mechanisms have been individually reported to shape extensive intra-tumor and inter-tumor phenotypic heterogeneity, such as IFNγ signaling and proliferative to invasive transition, but how their crosstalk impacts tumor progression remains largely elusive. METHODS Here, we integrate dynamical systems modeling with transcriptomic data analysis at bulk and single-cell levels to investigate underlying mechanisms behind phenotypic heterogeneity in melanoma and its impact on adaptation to targeted therapy and immune checkpoint inhibitors. We construct a minimal core regulatory network involving transcription factors implicated in this process and identify the multiple 'attractors' in the phenotypic landscape enabled by this network. Our model predictions about synergistic control of PD-L1 by IFNγ signaling and proliferative to invasive transition were validated experimentally in three melanoma cell lines-MALME3, SK-MEL-5 and A375. RESULTS We demonstrate that the emergent dynamics of our regulatory network comprising MITF, SOX10, SOX9, JUN and ZEB1 can recapitulate experimental observations about the co-existence of diverse phenotypes (proliferative, neural crest-like, invasive) and reversible cell-state transitions among them, including in response to targeted therapy and immune checkpoint inhibitors. These phenotypes have varied levels of PD-L1, driving heterogeneity in immunosuppression. This heterogeneity in PD-L1 can be aggravated by combinatorial dynamics of these regulators with IFNγ signaling. Our model predictions about changes in proliferative to invasive transition and PD-L1 levels as melanoma cells evade targeted therapy and immune checkpoint inhibitors were validated in multiple RNA-seq data sets from in vitro and in vivo experiments. CONCLUSION Our calibrated dynamical model offers a platform to test combinatorial therapies and provide rational avenues for the treatment of metastatic melanoma. This improved understanding of crosstalk among PD-L1 expression, proliferative to invasive transition and IFNγ signaling can be leveraged to improve the clinical management of therapy-resistant and metastatic melanoma.
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Affiliation(s)
| | - Sarthak Sahoo
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Shibjyoti Debnath
- Department of Medicine, Duke University, Durham, North Carolina, USA
| | - Jason A Somarelli
- Department of Medicine, Duke University, Durham, North Carolina, USA
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
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14
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Kim H, Feng Y, Murad R, Pozniak J, Pelz C, Chen Y, Dalal B, Sears R, Sergienko E, Jackson M, Ruppin E, Herlyn M, Harris C, Marine JC, Klepsch V, Baier G, Ronai ZA. Melanoma-intrinsic NR2F6 activity regulates antitumor immunity. SCIENCE ADVANCES 2023; 9:eadf6621. [PMID: 37406115 DOI: 10.1126/sciadv.adf6621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 05/30/2023] [Indexed: 07/07/2023]
Abstract
Nuclear receptors (NRs) are implicated in the regulation of tumors and immune cells. We identify a tumor-intrinsic function of the orphan NR, NR2F6, regulating antitumor immunity. NR2F6 was selected from 48 candidate NRs based on an expression pattern in melanoma patient specimens (i.e., IFN-γ signature) associated with positive responses to immunotherapy and favorable patient outcomes. Correspondingly, genetic ablation of NR2F6 in a mouse melanoma model conferred a more effective response to PD-1 therapy. NR2F6 loss in B16F10 and YUMM1.7 melanoma cells attenuated tumor development in immune-competent but not -incompetent mice via the increased abundance of effector and progenitor-exhausted CD8+ T cells. Inhibition of NACC1 and FKBP10, identified as NR2F6 effectors, phenocopied NR2F6 loss. Inoculation of NR2F6 KO mice with NR2F6 KD melanoma cells further decreased tumor growth compared with NR2F6 WT mice. Tumor-intrinsic NR2F6 function complements its tumor-extrinsic role and justifies the development of effective anticancer therapies.
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Affiliation(s)
- Hyungsoo Kim
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Yongmei Feng
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Rabi Murad
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | - Carl Pelz
- Department of Molecular and Medical Genetics, Brenden Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, OR, USA
| | - Yeqing Chen
- Molecular and Cellular Oncogenesis Program and Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
| | - Bhavik Dalal
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Rosalie Sears
- Department of Molecular and Medical Genetics, Brenden Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, OR, USA
| | - Eduard Sergienko
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Michael Jackson
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Eytan Ruppin
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Meenhard Herlyn
- Molecular and Cellular Oncogenesis Program and Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
| | - Curtis Harris
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | | | - Victoria Klepsch
- Division of Translational Cell Genetics, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Gottfried Baier
- Division of Translational Cell Genetics, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Ze'ev A Ronai
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
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15
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Hench J, Mihic-Probst D, Agaimy A, Frank S, Meyer P, Hultschig C, Simi S, Alos L, Balamurugan T, Blokx W, Bosisio F, Cappellesso R, Griewank K, Hadaschik E, van Kempen LC, Kempf W, Lentini M, Mazzucchelli L, Rinaldi G, Rutkowski P, Schadendorf D, Schilling B, Szumera-Cieckiewicz A, van den Oord J, Mandalà M, Massi D. Clinical, histopathological and molecular features of dedifferentiated melanomas: An EORTC Melanoma Group Retrospective Analysis. Eur J Cancer 2023; 187:7-14. [PMID: 37098294 DOI: 10.1016/j.ejca.2023.03.032] [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: 01/26/2023] [Revised: 03/26/2023] [Accepted: 03/28/2023] [Indexed: 04/04/2023]
Abstract
PURPOSE Dedifferentiated melanoma (DedM) poses significant diagnostic challenges. We aimed to investigate the clinical, histopathological and molecular features of DedM. Methylation signature (MS) and copy number profiling (CNP) were carried out in a subgroup of cases. PATIENTS AND METHODS A retrospective series of 78 DedM tissue samples from 61 patients retrieved from EORTC (European Organisation for Research and Treatment of Cancer) Melanoma Group centres were centrally reviewed. Clinical and histopathological features were retrieved. In a subgroup of patients, genotyping through Infinium Methylation microarray and CNP analysis was carried out. RESULTS Most patients (60/61) had a metastatic DedM showing most frequently an unclassified pleomorphic, spindle cell, or small round cell morphology akin to undifferentiated soft tissue sarcoma, rarely associated with heterologous elements. Overall, among 20 successfully analysed tissue samples from 16 patients, we found retained melanoma-like MS in only 7 tissue samples while a non-melanoma-like MS was observed in 13 tissue samples. In two patients from whom multiple specimens were analysed, some of the samples had a preserved cutaneous melanoma MS while other specimens exhibited an epigenetic shift towards a mesenchymal/sarcoma-like profile, matching the histological features. In these two patients, CNP was largely identical across all analysed specimens, in line with their common clonal origin, despite significant modification of their epigenome. CONCLUSIONS Our study further highlights that DedM represents a real diagnostic challenge. While MS and genomic CNP may help pathologists to diagnose DedM, we provide proof-of-concept that dedifferentiation in melanoma is frequently associated with epigenetic modifications.
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Affiliation(s)
- Juergen Hench
- Institute of Medical Genetics and Pathology, Division of Neuropathology, University Hospital Basel, Basel, Switzerland
| | - Daniela Mihic-Probst
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Abbas Agaimy
- Institute of Pathology, Friedrich-Alexander-University Erlangen-Nürnberg, University Hospital, Erlangen, Germany
| | - Stephan Frank
- Institute of Medical Genetics and Pathology, Division of Neuropathology, University Hospital Basel, Basel, Switzerland
| | - Peter Meyer
- Institute of Medical Genetics and Pathology, Division of Neuropathology, University Hospital Basel, Basel, Switzerland
| | - Claus Hultschig
- Institute of Medical Genetics and Pathology, Division of Neuropathology, University Hospital Basel, Basel, Switzerland
| | - Sara Simi
- Section of Pathology, Department of Health Sciences, University of Florence, Florence, Italy
| | - Lucia Alos
- Department of Pathology, Hospital Clinic of Barcelona, Barcelona, Spain
| | | | - Willeke Blokx
- Department of Pathology, Division of Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Francesca Bosisio
- Department of Imaging & Pathology, Laboratory of Translational Cell & Tissue Research and Department of Pathology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Rocco Cappellesso
- Pathological Anatomy Unit, Padua University Hospital, 35121 Padua, Italy
| | - Klaus Griewank
- Department of Dermatology, University Hospital of Essen, West German Cancer Center, University Duisburg-Essen and the German Cancer Consortium (DKTK), Essen, Germany
| | - Eva Hadaschik
- Department of Dermatology, University Hospital of Essen, West German Cancer Center, University Duisburg-Essen and the German Cancer Consortium (DKTK), Essen, Germany
| | - Leon C van Kempen
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Pathology, University Hospital Antwerp, Antwerp, Belgium
| | - Werner Kempf
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
| | - Maria Lentini
- Department of Human Pathology, University of Messina, Messina, Italy
| | - Luca Mazzucchelli
- Laboratory of Molecular Pathology, Institute of Pathology, Ente Ospedaliero Cantonale, Locarno, Switzerland
| | - Gaetana Rinaldi
- Sezione di Oncologia, Dipartimento di Discipline Chirurgiche, Oncologiche e Stomatologiche (Di.Chir.On.S.), Università degli Studi di Palermo, Palermo, Italy
| | - Piotr Rutkowski
- Maria Sklodowska-Curie National Research Institute of Oncology, Department of Soft Tissue/Bone Sarcoma and Melanoma, Warsaw, Poland
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital of Essen, West German Cancer Center, University Duisburg-Essen and the German Cancer Consortium (DKTK), Essen, Germany
| | - Bastian Schilling
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Würzburg, Germany
| | - Anna Szumera-Cieckiewicz
- Maria Sklodowska-Curie National Research Institute of Oncology, Department of Soft Tissue/Bone Sarcoma and Melanoma, Warsaw, Poland
| | - Joost van den Oord
- Department of Imaging & Pathology, Laboratory of Translational Cell & Tissue Research and Department of Pathology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Mario Mandalà
- University of Perugia, Unit of Medical Oncology, Santa Maria della Misericordia Hospital, Perugia, Italy.
| | - Daniela Massi
- Section of Pathology, Department of Health Sciences, University of Florence, Florence, Italy
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16
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Subhadarshini S, Sahoo S, Debnath S, Somarelli JA, Jolly MK. Dynamical modelling of proliferative-invasive plasticity and IFNγ signaling in melanoma reveals mechanisms of PD-L1 expression heterogeneity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.09.523355. [PMID: 37398358 PMCID: PMC10312429 DOI: 10.1101/2023.01.09.523355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Phenotypic heterogeneity of melanoma cells contributes to drug tolerance, increased metastasis, and immune evasion in patients with progressive disease. Diverse mechanisms have been individually reported to shape extensive intra- and inter-tumoral phenotypic heterogeneity, such as IFNγ signaling and proliferative to invasive transition, but how their crosstalk impacts tumor progression remains largely elusive. Here, we integrate dynamical systems modeling with transcriptomic data analysis at bulk and single-cell levels to investigate underlying mechanisms behind phenotypic heterogeneity in melanoma and its impact on adaptation to targeted therapy and immune checkpoint inhibitors. We construct a minimal core regulatory network involving transcription factors implicated in this process and identify the multiple "attractors" in the phenotypic landscape enabled by this network. Our model predictions about synergistic control of PD-L1 by IFNγ signaling and proliferative to invasive transition were validated experimentally in three melanoma cell lines - MALME3, SK-MEL-5 and A375. We demonstrate that the emergent dynamics of our regulatory network comprising MITF, SOX10, SOX9, JUN and ZEB1 can recapitulate experimental observations about the co-existence of diverse phenotypes (proliferative, neural crest-like, invasive) and reversible cell-state transitions among them, including in response to targeted therapy and immune checkpoint inhibitors. These phenotypes have varied levels of PD-L1, driving heterogeneity in immune-suppression. This heterogeneity in PD-L1 can be aggravated by combinatorial dynamics of these regulators with IFNγ signaling. Our model predictions about changes in proliferative to invasive transition and PD-L1 levels as melanoma cells evade targeted therapy and immune checkpoint inhibitors were validated in multiple data sets from in vitro and in vivo experiments. Our calibrated dynamical model offers a platform to test combinatorial therapies and provide rational avenues for the treatment of metastatic melanoma. This improved understanding of crosstalk among PD-L1 expression, proliferative to invasive transition and IFNγ signaling can be leveraged to improve the clinical management of therapy-resistant and metastatic melanoma.
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Affiliation(s)
| | - Sarthak Sahoo
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, 560012, India
| | | | | | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, 560012, India
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17
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Alicea GM, Portuallo ME, Patel P, Fane ME, Carey AE, Speicher D, Tang HY, Kossenkov AV, Rebecca VW, Wirtz DG, Weeraratna AT. Age-related increases in IGFBP2 increase melanoma cell invasion and lipid synthesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.539059. [PMID: 37205503 PMCID: PMC10187234 DOI: 10.1101/2023.05.02.539059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Aged melanoma patients (>65 years old) have more aggressive disease relative to young patients (<55 years old) for reasons that are not completely understood. Analysis of the young and aged secretome from human dermal fibroblasts identified >5-fold levels of insulin-like growth factor binding protein 2 (IGFBP2) in the aged fibroblast secretome. IGFBP2 functionally triggers upregulation of the PI3K-dependent fatty acid biosynthesis program in melanoma cells through increases in FASN. Melanoma cells co-cultured with aged dermal fibroblasts have higher levels of lipids relative to young dermal fibroblasts, which can be lowered by silencing IGFBP2 expression in fibroblasts, prior to treating with conditioned media. Conversely, ectopically treating melanoma cells with recombinant IGFBP2 in the presence of conditioned media from young fibroblasts, promoted lipid synthesis and accumulation in the melanoma cells. Neutralizing IGFBP2 in vitro reduces migration and invasion in melanoma cells, and in vivo studies demonstrate that neutralizing IGFBP2 in syngeneic aged mice, ablates tumor growth as well as metastasis. Conversely, ectopic treatment of young mice with IGFBP2 in young mice increases tumor growth and metastasis. Our data reveal that aged dermal fibroblasts increase melanoma cell aggressiveness through increased secretion of IGFBP2, stressing the importance of considering age when designing studies and treatment. Significance The aged microenvironment drives metastasis in melanoma cells. This study reports that IGFBP2 secretion by aged fibroblasts induces FASN in melanoma cells and drives metastasis. Neutralizing IGFBP2 decreases melanoma tumor growth and metastasis.
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18
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Indini A, Lombardo M, Sidoni A, Gianatti A, Mandalà M, Massi D. Pathology of Immunotherapy-induced Responses in Cutaneous Melanoma: Current Evidences and Future Perspectives. Adv Anat Pathol 2023; 30:218-229. [PMID: 36221225 DOI: 10.1097/pap.0000000000000375] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Over the last years, immune checkpoint inhibitors (ICIs) have demonstrated remarkable anti-tumor activity and beneficial effects in patients with early and advanced melanoma. However, ICIs provide clinical benefit only in a minority of patients due to primary and/or acquired resistance mechanisms. Immunotherapy resistance is a complex phenomenon relying on genetic and epigenetic factors, which ultimately influence the interplay between cancer cells and the tumor microenvironment. Information is accumulating on the cellular and molecular mechanisms underlying the production of resistance and the resulting diminished therapeutic efficacy. In addition, current knowledge on predictors of response and toxicity to immunotherapy and on biomarkers that reliably identify resistant patients is in progress. In this review, we will focus on the tumor microenvironment changes induced by ICIs in melanoma, summarizing the available evidence of clinical trials in the neoadjuvant and metastatic setting. We will also overview the role of potential biomarkers in predicting disease response to ICIs, providing insight into current and future research in this field.
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Affiliation(s)
| | - Maurizio Lombardo
- Division of Dermatology, Department of Medicine and Surgery, Ospedale di Circolo e Fondazione Macchi, ASST dei Sette Laghi, Varese
| | - Angelo Sidoni
- Section of Anatomic Pathology and Histology, Department of Medicine and Surgery, University of Perugia
| | | | - Mario Mandalà
- Unit of Medical Oncology, Department of Medicine and Surgery, University of Perugia, Perugia
| | - Daniela Massi
- Section of Pathological Anatomy, Department of Health Sciences, University of Florence, Florence, Italy
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19
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Gruen C, Yang HH, Sassano A, Wu E, Gopalan V, Marie KL, Castro A, Mehrabadi FR, Wu CH, Church I, Needle GA, Smith C, Chin S, Ebersole J, Marcelus C, Fon A, Liu H, Malikic S, Sahinalp C, Carter H, Hannenhalli S, Day CP, Lee MP, Merlino G, Pérez-Guijarro E. Melanoma clonal subline analysis uncovers heterogeneity-driven immunotherapy resistance mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.03.535074. [PMID: 37333132 PMCID: PMC10274874 DOI: 10.1101/2023.04.03.535074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Intratumoral heterogeneity (ITH) can promote cancer progression and treatment failure, but the complexity of the regulatory programs and contextual factors involved complicates its study. To understand the specific contribution of ITH to immune checkpoint blockade (ICB) response, we generated single cell-derived clonal sublines from an ICB-sensitive and genetically and phenotypically heterogeneous mouse melanoma model, M4. Genomic and single cell transcriptomic analyses uncovered the diversity of the sublines and evidenced their plasticity. Moreover, a wide range of tumor growth kinetics were observed in vivo , in part associated with mutational profiles and dependent on T cell-response. Further inquiry into melanoma differentiation states and tumor microenvironment (TME) subtypes of untreated tumors from the clonal sublines demonstrated correlations between highly inflamed and differentiated phenotypes with the response to anti-CTLA-4 treatment. Our results demonstrate that M4 sublines generate intratumoral heterogeneity at both levels of intrinsic differentiation status and extrinsic TME profiles, thereby impacting tumor evolution during therapeutic treatment. These clonal sublines proved to be a valuable resource to study the complex determinants of response to ICB, and specifically the role of melanoma plasticity in immune evasion mechanisms.
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20
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Kato S, Maeda Y, Sugiyama D, Watanabe K, Nishikawa H, Hinohara K. The cancer epigenome: Non-cell autonomous player in tumor immunity. Cancer Sci 2023; 114:730-740. [PMID: 36468774 PMCID: PMC9986067 DOI: 10.1111/cas.15681] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/28/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Dysregulation of the tumor-intrinsic epigenetic circuit is a key driver event for the development of cancer. Accumulating evidence suggests that epigenetic and/or genetic drivers stimulate intrinsic oncogenic pathways as well as extrinsic factors that modulate the immune system. These modulations indeed shape the tumor microenvironment (TME), allowing pro-oncogenic factors to become oncogenic, thereby contributing to cancer development and progression. Here we review the epigenetic dysregulation arising in cancer cells that disseminates throughout the TME and beyond. Recent CRISPR screening has elucidated key epigenetic drivers that play important roles in the proliferation of cancer cells (intrinsic) and inhibition of antitumor immunity (extrinsic), which lead to the development and progression of cancer. These epigenetic players can serve as promising targets for cancer therapy as a dual (two-in-one)-targeted approach. Considering the interplay between cancer and the immune system as a key determinant of immunotherapy, we discuss a novel lineage-tracing technology that enables longitudinal monitoring of cancer and immune phenotypic heterogeneity and fate paths during cancer development, progression, and therapeutic interventions.
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Affiliation(s)
- Shinichiro Kato
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Center for 5D Cell Dynamics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuka Maeda
- Division of Cancer Immunology, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Research Institute, Tokyo, Japan
| | - Daisuke Sugiyama
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Keisuke Watanabe
- Division of Cancer Immunology, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Research Institute, Tokyo, Japan
| | - Hiroyoshi Nishikawa
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Center for 5D Cell Dynamics, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Division of Cancer Immunology, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Research Institute, Tokyo, Japan.,Institute for Advanced Study, Nagoya University, Nagoya, Japan
| | - Kunihiko Hinohara
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Center for 5D Cell Dynamics, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Institute for Advanced Study, Nagoya University, Nagoya, Japan
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21
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Tsai CH, Chuang YM, Li X, Yu YR, Tzeng SF, Teoh ST, Lindblad KE, Di Matteo M, Cheng WC, Hsueh PC, Kao KC, Imrichova H, Duan L, Gallart-Ayala H, Hsiao PW, Mazzone M, Ivanesevic J, Liu X, de Visser KE, Lujambio A, Lunt SY, Kaech SM, Ho PC. Immunoediting instructs tumor metabolic reprogramming to support immune evasion. Cell Metab 2023; 35:118-133.e7. [PMID: 36599297 PMCID: PMC10375941 DOI: 10.1016/j.cmet.2022.12.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 10/06/2022] [Accepted: 11/30/2022] [Indexed: 01/05/2023]
Abstract
Immunoediting sculpts immunogenicity and thwarts host anti-tumor responses in tumor cells during tumorigenesis; however, it remains unknown whether metabolic programming of tumor cells can be guided by immunosurveillance. Here, we report that T cell-mediated immunosurveillance in early-stage tumorigenesis instructs c-Myc upregulation and metabolic reprogramming in tumor cells. This previously unexplored tumor-immune interaction is controlled by non-canonical interferon gamma (IFNγ)-STAT3 signaling and supports tumor immune evasion. Our findings uncover that immunoediting instructs deregulated bioenergetic programs in tumor cells to empower them to disarm the T cell-mediated immunosurveillance by imposing metabolic tug-of-war between tumor and infiltrating T cells and forming the suppressive tumor microenvironment.
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Affiliation(s)
- Chin-Hsien Tsai
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland; Graduate Institute of Life Sciences, National Defense Medical Center, Taipei City, Taiwan
| | - Yu-Ming Chuang
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Xiaoyun Li
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Yi-Ru Yu
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Sheue-Fen Tzeng
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland; Graduate Institute of Life Sciences, National Defense Medical Center, Taipei City, Taiwan
| | - Shao Thing Teoh
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Katherine E Lindblad
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences at Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mario Di Matteo
- Laboratory of Tumor Inflammation and angiogenesis, Vesalius Research Center, VIB, Leuven, Belgium; Laboratory of Tumor Inflammation and angiogenesis, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Wan-Chen Cheng
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Pei-Chun Hsueh
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Kung-Chi Kao
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Hana Imrichova
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Wien, Austria
| | - Likun Duan
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
| | - Hector Gallart-Ayala
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Pei-Wen Hsiao
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei City, Taiwan
| | - Massimiliano Mazzone
- Laboratory of Tumor Inflammation and angiogenesis, Vesalius Research Center, VIB, Leuven, Belgium; Laboratory of Tumor Inflammation and angiogenesis, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Julijana Ivanesevic
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Wien, Austria
| | - Xiaojing Liu
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
| | - Karin E de Visser
- Division of Tumor Biology and Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Amaia Lujambio
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences at Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sophia Y Lunt
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA; Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
| | - Susan M Kaech
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Ping-Chih Ho
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland.
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22
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Rubanov A, Berico P, Hernando E. Epigenetic Mechanisms Underlying Melanoma Resistance to Immune and Targeted Therapies. Cancers (Basel) 2022; 14:cancers14235858. [PMID: 36497341 PMCID: PMC9738385 DOI: 10.3390/cancers14235858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 11/22/2022] [Indexed: 11/30/2022] Open
Abstract
Melanoma is an aggressive skin cancer reliant on early detection for high likelihood of successful treatment. Solar UV exposure transforms melanocytes into highly mutated tumor cells that metastasize to the liver, lungs, and brain. Even upon resection of the primary tumor, almost thirty percent of patients succumb to melanoma within twenty years. Identification of key melanoma genetic drivers led to the development of pharmacological BRAFV600E and MEK inhibitors, significantly improving metastatic patient outcomes over traditional cytotoxic chemotherapy or pioneering IFN-α and IL-2 immune therapies. Checkpoint blockade inhibitors releasing the immunosuppressive effects of CTLA-4 or PD-1 proved to be even more effective and are the standard first-line treatment. Despite these major improvements, durable responses to immunotherapy and targeted therapy have been hindered by intrinsic or acquired resistance. In addition to gained or selected genetic alterations, cellular plasticity conferred by epigenetic reprogramming is emerging as a driver of therapy resistance. Epigenetic regulation of chromatin accessibility drives gene expression and establishes distinct transcriptional cell states. Here we review how aberrant chromatin, transcriptional, and epigenetic regulation contribute to therapy resistance and discuss how targeting these programs sensitizes melanoma cells to immune and targeted therapies.
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Affiliation(s)
- Andrey Rubanov
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Pietro Berico
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Eva Hernando
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
- Correspondence:
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23
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Pillai M, Rajaram G, Thakur P, Agarwal N, Muralidharan S, Ray A, Barbhaya D, Somarelli JA, Jolly MK. Mapping phenotypic heterogeneity in melanoma onto the epithelial-hybrid-mesenchymal axis. Front Oncol 2022; 12:913803. [PMID: 36003764 PMCID: PMC9395132 DOI: 10.3389/fonc.2022.913803] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/11/2022] [Indexed: 11/25/2022] Open
Abstract
Epithelial to mesenchymal transition (EMT) is a well-studied hallmark of epithelial-like cancers that is characterized by loss of epithelial markers and gain of mesenchymal markers. Melanoma, which is derived from melanocytes of the skin, also undergo phenotypic plasticity toward mesenchymal-like phenotypes under the influence of various micro-environmental cues. Our study connects EMT to the phenomenon of de-differentiation (i.e., transition from proliferative to more invasive phenotypes) observed in melanoma cells during drug treatment. By analyzing 78 publicly available transcriptomic melanoma datasets, we found that de-differentiation in melanoma is accompanied by upregulation of mesenchymal genes, but not necessarily a concomitant loss of an epithelial program, suggesting a more “one-dimensional” EMT that leads to a hybrid epithelial/mesenchymal phenotype. Samples lying in the hybrid epithelial/mesenchymal phenotype also correspond to the intermediate phenotypes in melanoma along the proliferative-invasive axis - neural crest and transitory ones. As melanoma cells progress along the invasive axis, the mesenchymal signature does not increase monotonically. Instead, we observe a peak in mesenchymal scores followed by a decline, as cells further de-differentiate. This biphasic response recapitulates the dynamics of melanocyte development, suggesting close interactions among genes controlling differentiation and mesenchymal programs in melanocytes. Similar trends were noted for metabolic changes often associated with EMT in carcinomas in which progression along mesenchymal axis correlates with the downregulation of oxidative phosphorylation, while largely maintaining glycolytic capacity. Overall, these results provide an explanation for how EMT and de-differentiation axes overlap with respect to their transcriptional and metabolic programs in melanoma.
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Affiliation(s)
- Maalavika Pillai
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
- Undergraduate Programme, Indian Institute of Science, Bangalore, India
| | - Gouri Rajaram
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, India
| | - Pradipti Thakur
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, India
| | - Nilay Agarwal
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
- Undergraduate Programme, Indian Institute of Science, Bangalore, India
| | - Srinath Muralidharan
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Ankita Ray
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, India
| | - Dev Barbhaya
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India
| | | | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
- *Correspondence: Mohit Kumar Jolly,
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24
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Lim SY, Pedersen B, Rizos H. Protein-based classification of melanoma differentiation subtypes. Pigment Cell Melanoma Res 2022; 35:471-473. [PMID: 35452161 DOI: 10.1111/pcmr.13041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 03/29/2022] [Accepted: 04/18/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Su Yin Lim
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia.,Melanoma Institute Australia, Sydney, New South Wales, Australia
| | - Bernadette Pedersen
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia.,Melanoma Institute Australia, Sydney, New South Wales, Australia
| | - Helen Rizos
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia.,Melanoma Institute Australia, Sydney, New South Wales, Australia
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25
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Lv H, Liu X, Zeng X, Liu Y, Zhang C, Zhang Q, Xu J. Comprehensive Analysis of Cuproptosis-Related Genes in Immune Infiltration and Prognosis in Melanoma. Front Pharmacol 2022; 13:930041. [PMID: 35837286 PMCID: PMC9273972 DOI: 10.3389/fphar.2022.930041] [Citation(s) in RCA: 125] [Impact Index Per Article: 62.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/19/2022] [Indexed: 12/16/2022] Open
Abstract
Skin cutaneous melanoma (SKCM, hereafter referred to as melanoma) is the most lethal skin cancer with increasing incidence. Regulated cell death plays an important role in tumorigenesis and serves as an important target for almost all treatment strategies. Cuproptosis is the most recently identified copper-dependent regulated cell death form that relies on mitochondria respiration. However, its role in tumorigenesis remains unknown. The correlation of cuproptosis-related genes with tumor prognosis is far to be understood, either. In the present study, we explored the correlation between cuproptosis-related genes with the prognosis of melanoma by accessing and analyzing a public database and found 11 out 12 genes were upregulated in melanoma tissues and three genes (LIPT1, PDHA1, and SLC31A1) have predictive value for the prognosis. The subgroup of melanoma patients with higher cuproptosis-related gene expression showed longer overall survival than those with lower gene expression. We chose LIPT1 for further exploration. LIPT1 expression was increased in melanoma biopsies and was an independent favorable prognostic indicator for melanoma patients. Moreover, LIPT1 expression was positively correlated with PD-L1 expression and negatively associated with Treg cell infiltration. The melanoma patients with higher LIPT1 expression showed longer overall survival than those with lower LIPT1 expression after receiving immunotherapy, indicating the prognostic predictive value of LIPT1. Finally, a pan-cancer analysis indicated that LIPT1 was differentially expressed in diverse cancers as compared to normal tissues and correlated with the expression of multiple immune checkpoints, especially PD-L1. It could serve as a favorable prognosis indicator in some cancer types. In conclusion, our study demonstrated the prognostic value of cuproptosis-related genes, especially LIPT1, in melanoma, and revealed the correlation between LIPT1 expression and immune infiltration in melanoma, thus providing new clues on the prognostic assessment of melanoma patients and providing a new target for the immunotherapy of melanoma.
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Affiliation(s)
- Haozhen Lv
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiao Liu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xuanhao Zeng
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yating Liu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Canjing Zhang
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Qi Zhang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
- *Correspondence: Qi Zhang, ; Jinhua Xu,
| | - Jinhua Xu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
- Shanghai Institute of Dermatology, Shanghai, China
- *Correspondence: Qi Zhang, ; Jinhua Xu,
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26
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Thier B, Zhao F, Stupia S, Brüggemann A, Koch J, Schulze N, Horn S, Coch C, Hartmann G, Sucker A, Schadendorf D, Paschen A. Innate immune receptor signaling induces transient melanoma dedifferentiation while preserving immunogenicity. J Immunother Cancer 2022; 10:jitc-2021-003863. [PMID: 35697379 PMCID: PMC9196182 DOI: 10.1136/jitc-2021-003863] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2022] [Indexed: 11/21/2022] Open
Abstract
Background Immune-stimulatory agents, like agonists of the innate immune receptor RIG-I, are currently tested in clinical trials as an intratumoral treatment option for patients with unresectable melanoma, aiming to enhance anti-tumor T cell responses. Switching of melanoma toward a dedifferentiated cell state has recently been linked to T cell and therapy resistance. It remains to be determined whether RIG-I agonists affect melanoma differentiation, potentially leading to T cell resistance. Methods Patient metastases-derived melanoma cell lines were treated with the synthetic RIG-I agonist 3pRNA, and effects on tumor cell survival, phenotype and differentiation were determined. Transcriptomic data sets from cell lines and metastases were analyzed for associations between RIG-I (DDX58) and melanoma differentiation markers and used to define signaling pathways involved in RIG-I-driven dedifferentiation. The impact of 3pRNA-induced melanoma dedifferentiation on CD8 T cell activation was studied in autologous tumor T cell models. Results RIG-I activation by 3pRNA induced apoptosis in a subpopulation of melanoma cells, while the majority of tumor cells switched into a non-proliferative cell state. Those persisters displayed a dedifferentiated cell phenotype, marked by downregulation of the melanocytic lineage transcription factor MITF and its target genes, including melanoma differentiation antigens (MDA). Transition into the MITFlow/MDAlow cell state was JAK-dependent, with some cells acquiring nerve growth factor receptor expression. MITFlow/MDAlow persisters switched back to the proliferative differentiated cell state when RIG-I signaling declined. Consistent with our in vitro findings, an association between melanoma dedifferentiation and high RIG-I (DDX58) levels was detected in transcriptomic data from patient metastases. Notably, despite their dedifferentiated cell phenotype, 3pRNA-induced MITFlow/MDAlow persisters were still efficiently targeted by autologous CD8 tumor-infiltrating T lymphocytes (TILs). Conclusions Our results demonstrate that RIG-I signaling in melanoma cells drives a transient phenotypic switch toward a non-proliferative dedifferentiated persister cell state. Despite their dedifferentiation, those persisters are highly immunogenic and sensitive toward autologous TILs, challenging the concept of melanoma dedifferentiation as a general indicator of T cell resistance. In sum, our findings support the application of RIG-I agonists as a therapeutic tool for the generation of long-term clinical benefit in non-resectable melanoma.
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Affiliation(s)
- Beatrice Thier
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Essen, Germany
| | - Fang Zhao
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Essen, Germany
| | - Simone Stupia
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Essen, Germany
| | - Alicia Brüggemann
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Essen, Germany
| | - Johannes Koch
- Imaging Center Campus Essen, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Nina Schulze
- Imaging Center Campus Essen, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Susanne Horn
- Rudolf Schönheimer Institute of Biochemistry, University of Leipzig, Leipzig, Germany
| | - Christoph Coch
- Institute of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany.,Nextevidence GmbH, Grünwald, Germany
| | - Gunther Hartmann
- Institute of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany
| | - Antje Sucker
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Essen, Germany
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Essen, Germany
| | - Annette Paschen
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany .,German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Essen, Germany
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27
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Loick SM, Fröhlich A, Gabrielpillai J, Franzen A, Vogt TJ, Dietrich J, Wiek C, Scheckenbach K, Strieth S, Landsberg J, Dietrich D. DNA Methylation and mRNA Expression of OX40 (TNFRSF4) and GITR (TNFRSF18, AITR) in Head and Neck Squamous Cell Carcinoma Correlates With HPV Status, Mutational Load, an Interferon-γ Signature, Signatures of Immune Infiltrates, and Survival. J Immunother 2022; 45:194-206. [PMID: 34908008 DOI: 10.1097/cji.0000000000000407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 11/08/2021] [Indexed: 11/25/2022]
Abstract
The tumor necrosis factor receptor superfamily members 4 (TNFRSF4, OX40) and 18 (TNFRSF18, GITR, AITR) are under investigation as targets for immunotherapy of various cancers, including head and neck squamous cell carcinomas. Understanding the regulation of OX40 and GITR, particularly on an epigenetic level, might help to develop companion predictive biomarkers. We conducted broad correlation analyses of DNA methylation of 46 CpG sites within the GITR/OX40 gene locus in head and neck squamous cell carcinomas and normal adjacent tissues provided by The Cancer Genome Atlas (TCGA) Research Network. We analyzed methylation levels with regard to transcriptional gene activity (mRNA expression), human papillomavirus (HPV) infection, differential methylation between tumors and normal adjacent tissues, signatures of immune cell infiltrates, an interferon-γ signature, mutational load, and overall survival. Moreover, we investigated methylation levels in HPV-positive and HPV-negative cell lines and in isolated monocytes, granulocytes, CD8+ and CD4+ T cells, and B cells from peripheral blood from healthy donors. Our results revealed a complex and sequence-contextual methylation pattern in accordance with features of epigenetic regulated genes. We detected significant methylation differences between normal adjacent and tumor tissues, between HPV-positive and HPV-negative tumors, between tumor and immune cells, and significant correlations between methylation and mRNA expression. We further found significant correlations of CpG methylation with overall survival, signatures of immune cell infiltrates, an interferon-γ signature, and mutational load. Our study provides a framework to prospectively test specific CpG sites as biomarkers, in particular in the context of immunotherapies.
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Affiliation(s)
- Sophia M Loick
- Department of Otorhinolaryngology, University Medical Center Bonn (UKB)
| | - Anne Fröhlich
- Department of Dermatology, University Hospital Bonn, Bonn
| | | | - Alina Franzen
- Department of Otorhinolaryngology, University Medical Center Bonn (UKB)
| | - Timo J Vogt
- Department of Otorhinolaryngology, University Medical Center Bonn (UKB)
| | - Jörn Dietrich
- Department of Otorhinolaryngology, University Medical Center Bonn (UKB)
| | - Constanze Wiek
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Kathrin Scheckenbach
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Sebastian Strieth
- Department of Otorhinolaryngology, University Medical Center Bonn (UKB)
| | | | - Dimo Dietrich
- Department of Otorhinolaryngology, University Medical Center Bonn (UKB)
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28
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Paschen A, Melero I, Ribas A. Central Role of the Antigen-Presentation and Interferon-γ Pathways in Resistance to Immune Checkpoint Blockade. ANNUAL REVIEW OF CANCER BIOLOGY 2022. [DOI: 10.1146/annurev-cancerbio-070220-111016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Resistance to immunotherapy is due in some instances to the acquired stealth mechanisms of tumor cells that lose expression of MHC class I antigen–presenting molecules or downregulate their class I antigen–presentation pathways. Most dramatically, biallelic β2-microglobulin (B2M) loss leads to complete loss of MHC class I expression and to invisibility to CD8+ T cells. MHC class I expression and antigen presentation are potently upregulated by interferon-γ (IFNγ) in a manner that depends on IFNγ receptor (IFNGR) signaling via JAK1 and JAK2. Mutations in these molecules lead to IFNγ unresponsiveness and mediate loss of recognition and killing by cytotoxic T lymphocytes. Loss of MHC class I augments sensitivity of tumor cells to be killed by natural killer (NK) lymphocytes, and this mechanism could be exploited to revert resistance, for instance, with interleukin-2 (IL-2)-based agents. Moreover, in some experimental models,potent local type I interferon responses, such as those following intratumoral injection of Toll-like receptor 9 (TLR9) or TLR3 agonists, revert resistance due to mutations of JAKs.
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Affiliation(s)
- Annette Paschen
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- German Cancer Consortium (DKTK) Partner Site Essen/Düsseldorf, Essen, Germany
| | - Ignacio Melero
- University Clinic of Navarre (CUN) and Centre of Applied Medical Research (CIMA), University of Navarre, Pamplona, Spain
- CIBERONC (Consorcio Centro de Investigación Biomédica en Red de Cáncer), Madrid, Spain
| | - Antoni Ribas
- Department of Medicine, Department of Surgery, and Jonsson Comprehensive Cancer Center, University of California, Los Angeles, California, USA
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29
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Niebel D, Fröhlich A, Zarbl R, Fietz S, de Vos L, Vogt TJ, Dietrich J, Sirokay J, Kuster P, Saavedra G, Ramírez Valladolid S, Hoffmann F, Strieth S, Landsberg J, Dietrich D. DNA methylation regulates TIGIT expression within the melanoma microenvironment, is prognostic for overall survival, and predicts progression-free survival in patients treated with anti-PD-1 immunotherapy. Clin Epigenetics 2022; 14:50. [PMID: 35410311 PMCID: PMC9004005 DOI: 10.1186/s13148-022-01270-2] [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: 12/18/2021] [Accepted: 04/02/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND TIGIT is an immune checkpoint under investigation as therapeutic target. Understanding the regulation of TIGIT on an epigenetic level might support the development of companion biomarkers. METHODS We correlated TIGIT DNA methylation of single CpG sites with gene expression, signatures of immune infiltrates and interferon-γ, and survival in melanoma. We further analyzed methylation levels in immune cell subsets, melanocyte and melanoma cell lines. TIGIT expression patterns within components of the melanoma microenvironment were analyzed by single cell sequencing. We used quantitative methylation-specific PCR, flow cytometry, and immunohistochemistry for correlations between expression and methylation and to assess the effect of pharmacological demethylation of melanoma cells treated with 5-aza-2-deoxycytidine (decitabine). Finally, we investigated the association of patients' survival with TIGIT mRNA and methylation. RESULTS Depending on the sequence context of the analyzed CpG site, we found a cell type-specific TIGIT gene locus methylation pattern and significant correlations of TIGIT methylation with mRNA expression, an interferon γ signature, and distinct immune cell infiltrates, including TIGIT+ lymphocytes. We detected a melanoma cell-intrinsic TIGIT protein expression. Pharmacological demethylation of the A375 melanoma cell line led to a constitutive TIGIT expression. Low promoter flank methylation and high mRNA expression was associated with patients' prognosis and predicted progression-free survival in patients treated with anti-PD-1 immunotherapy. A high TIGIT+ lymphocyte score was associated with better progression-free survival under anti-PD-1 immunotherapy. CONCLUSIONS Our data demonstrate an epigenetic regulation of TIGIT expression via DNA methylation within the melanoma microenvironment. TIGIT DNA methylation and expression may serve as predictive biomarkers in the context of immunotherapies in melanoma.
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Affiliation(s)
- Dennis Niebel
- Department of Dermatology and Allergy, University Medical Center Bonn (UKB), Venusberg-Campus 1, 53127, Bonn, Germany
| | - Anne Fröhlich
- Department of Dermatology and Allergy, University Medical Center Bonn (UKB), Venusberg-Campus 1, 53127, Bonn, Germany
| | - Romina Zarbl
- Department of Otorhinolaryngology, University Medical Center Bonn (UKB), Venusberg-Campus 1, 53127, Bonn, Germany
| | - Simon Fietz
- Department of Dermatology and Allergy, University Medical Center Bonn (UKB), Venusberg-Campus 1, 53127, Bonn, Germany.,Department of Otorhinolaryngology, University Medical Center Bonn (UKB), Venusberg-Campus 1, 53127, Bonn, Germany
| | - Luka de Vos
- Department of Dermatology and Allergy, University Medical Center Bonn (UKB), Venusberg-Campus 1, 53127, Bonn, Germany
| | - Timo J Vogt
- Department of Otorhinolaryngology, University Medical Center Bonn (UKB), Venusberg-Campus 1, 53127, Bonn, Germany
| | - Jörn Dietrich
- Department of Otorhinolaryngology, University Medical Center Bonn (UKB), Venusberg-Campus 1, 53127, Bonn, Germany
| | - Judith Sirokay
- Department of Dermatology and Allergy, University Medical Center Bonn (UKB), Venusberg-Campus 1, 53127, Bonn, Germany
| | - Pia Kuster
- Department of Dermatology and Allergy, University Medical Center Bonn (UKB), Venusberg-Campus 1, 53127, Bonn, Germany
| | - Gonzalo Saavedra
- Department of Dermatology and Allergy, University Medical Center Bonn (UKB), Venusberg-Campus 1, 53127, Bonn, Germany.,Department of Otorhinolaryngology, University Medical Center Bonn (UKB), Venusberg-Campus 1, 53127, Bonn, Germany
| | - Susana Ramírez Valladolid
- Department of Dermatology and Allergy, University Medical Center Bonn (UKB), Venusberg-Campus 1, 53127, Bonn, Germany
| | - Friederike Hoffmann
- Department of Dermatology and Allergy, University Medical Center Bonn (UKB), Venusberg-Campus 1, 53127, Bonn, Germany
| | - Sebastian Strieth
- Department of Otorhinolaryngology, University Medical Center Bonn (UKB), Venusberg-Campus 1, 53127, Bonn, Germany
| | - Jennifer Landsberg
- Department of Dermatology and Allergy, University Medical Center Bonn (UKB), Venusberg-Campus 1, 53127, Bonn, Germany
| | - Dimo Dietrich
- Department of Otorhinolaryngology, University Medical Center Bonn (UKB), Venusberg-Campus 1, 53127, Bonn, Germany.
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Ladányi A, Rásó E, Barbai T, Vízkeleti L, Puskás LG, Kovács SA, Győrffy B, Tímár J. Identification of a Tumor Cell Associated Type I IFN Resistance Gene Expression Signature of Human Melanoma, the Components of Which Have a Predictive Potential for Immunotherapy. Int J Mol Sci 2022; 23:2704. [PMID: 35269844 PMCID: PMC8911010 DOI: 10.3390/ijms23052704] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 02/04/2023] Open
Abstract
We developed a human melanoma model using the HT168-M1 cell line to induce IFN-α2 resistance in vitro (HT168-M1res), which was proven to be maintained in vivo in SCID mice. Comparing the mRNA profile of in vitro cultured HT168-M1res cells to its sensitive counterpart, we found 79 differentially expressed genes (DEGs). We found that only a 13-gene core of the DEGs was stable in vitro and only a 4-gene core was stable in vivo. Using an in silico cohort of IFN-treated melanoma tissues, we validated a differentially expressed 9-gene core of the DEGs. Furthermore, using an in silico cohort of immune checkpoint inhibitor (ICI)-treated melanoma tissues, we tested the predictive power of the DEGs for the response rate. Analysis of the top four upregulated and top four downregulated genes of the DEGs identified WFDC1, EFNA3, DDX10, and PTBP1 as predictive genes, and analysis of the "stable" genes of DEGs for predictive potential of ICI response revealed another 13 genes, out of which CDCA4, SOX4, DEK, and HSPA1B were identified as IFN-regulated genes. Interestingly, the IFN treatment associated genes and the ICI-therapy predictive genes overlapped by three genes: WFDC1, BCAN, and MT2A, suggesting a connection between the two biological processes.
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Affiliation(s)
- Andrea Ladányi
- Department of Surgical and Molecular Pathology, National Institute of Oncology, 1122 Budapest, Hungary;
| | - Erzsébet Rásó
- 2nd Department of Pathology, Semmelweis University, 1091 Budapest, Hungary; (E.R.); (T.B.); (L.V.)
| | - Tamás Barbai
- 2nd Department of Pathology, Semmelweis University, 1091 Budapest, Hungary; (E.R.); (T.B.); (L.V.)
| | - Laura Vízkeleti
- 2nd Department of Pathology, Semmelweis University, 1091 Budapest, Hungary; (E.R.); (T.B.); (L.V.)
| | | | - Szonja A. Kovács
- Department of Bioinformatics, Semmelweis University, 1094 Budapest, Hungary; (S.A.K.); (B.G.)
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, 1094 Budapest, Hungary; (S.A.K.); (B.G.)
- Research Centre for Natural Sciences, Oncology Biomarkers Research Group, Institute of Enzymology, Eötvös Loránd Research Network, 1117 Budapest, Hungary
| | - József Tímár
- 2nd Department of Pathology, Semmelweis University, 1091 Budapest, Hungary; (E.R.); (T.B.); (L.V.)
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Enhancing Therapeutic Approaches for Melanoma Patients Targeting Epigenetic Modifiers. Cancers (Basel) 2021; 13:cancers13246180. [PMID: 34944799 PMCID: PMC8699560 DOI: 10.3390/cancers13246180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/30/2021] [Accepted: 12/03/2021] [Indexed: 12/25/2022] Open
Abstract
Melanoma is the least common but deadliest type of skin cancer. Melanomagenesis is driven by a series of mutations and epigenetic alterations in oncogenes and tumor suppressor genes that allow melanomas to grow, evolve, and metastasize. Epigenetic alterations can also lead to immune evasion and development of resistance to therapies. Although the standard of care for melanoma patients includes surgery, targeted therapies, and immune checkpoint blockade, other therapeutic approaches like radiation therapy, chemotherapy, and immune cell-based therapies are used for patients with advanced disease or unresponsive to the conventional first-line therapies. Targeted therapies such as the use of BRAF and MEK inhibitors and immune checkpoint inhibitors such as anti-PD-1 and anti-CTLA4 only improve the survival of a small subset of patients. Thus, there is an urgent need to identify alternative standalone or combinatorial therapies. Epigenetic modifiers have gained attention as therapeutic targets as they modulate multiple cellular and immune-related processes. Due to melanoma's susceptibility to extrinsic factors and reversible nature, epigenetic drugs are investigated as a therapeutic avenue and as adjuvants for targeted therapies and immune checkpoint inhibitors, as they can sensitize and/or reverse resistance to these therapies, thus enhancing their therapeutic efficacy. This review gives an overview of the role of epigenetic changes in melanoma progression and resistance. In addition, we evaluate the latest advances in preclinical and clinical research studying combinatorial therapies and discuss the use of epigenetic drugs such as HDAC and DNMT inhibitors as potential adjuvants for melanoma patients.
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Transcriptional Reprogramming and Constitutive PD-L1 Expression in Melanoma Are Associated with Dedifferentiation and Activation of Interferon and Tumour Necrosis Factor Signalling Pathways. Cancers (Basel) 2021; 13:cancers13174250. [PMID: 34503064 PMCID: PMC8428231 DOI: 10.3390/cancers13174250] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/07/2021] [Accepted: 08/13/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Melanoma, an aggressive form of skin cancer, is frequently associated with drug resistance in the advanced stages. For instance, frequently resistance is observed in sequential treatment of melanoma with targeted therapy and immunotherapy. In this research, the authors investigated whether potential transcriptional mechanisms and pathways associated with PD-L1 protein expression could underlie targeted therapy drug resistance in melanoma. The authors found a PD-L1 expression transcriptional pattern underlies resistance to targeted therapy in a subgroup of melanomas. These melanomas were markedly dedifferentiated, as compared to melanomas that were not drug resistant. Understanding changes in transcription and molecular pathways that lead to drug resistance could allow researchers to develop interventions to prevent drug resistance from occurring in melanoma, which could also be relevant to other cancer types. Abstract Melanoma is the most aggressive type of skin cancer, with increasing incidence worldwide. Advances in targeted therapy and immunotherapy have improved the survival of melanoma patients experiencing recurrent disease, but unfortunately treatment resistance frequently reduces patient survival. Resistance to targeted therapy is associated with transcriptomic changes and has also been shown to be accompanied by increased expression of programmed death ligand 1 (PD-L1), a potent inhibitor of immune response. Intrinsic upregulation of PD-L1 is associated with genome-wide DNA hypomethylation and widespread alterations in gene expression in melanoma cell lines. However, an in-depth analysis of the transcriptomic landscape of melanoma cells with intrinsically upregulated PD-L1 expression is lacking. To determine the transcriptomic landscape of intrinsically upregulated PD-L1 expression in melanoma, we investigated transcriptomes in melanomas with constitutive versus inducible PD-L1 expression (referred to as PD-L1CON and PD-L1IND). RNA-Seq analysis was performed on seven PD-L1CON melanoma cell lines and ten melanoma cell lines with low inducible PD-L1IND expression. We observed that PD-L1CON melanoma cells had a reprogrammed transcriptome with a characteristic pattern of dedifferentiated gene expression, together with active interferon (IFN) and tumour necrosis factor (TNF) signalling pathways. Furthermore, we identified key transcription factors that were also differentially expressed in PD-L1CON versus PD-L1IND melanoma cell lines. Overall, our studies describe transcriptomic reprogramming of melanomas with PD-L1CON expression.
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