1
|
Roider E, Lakatos AIT, McConnell AM, Wang P, Mueller A, Kawakami A, Tsoi J, Szabolcs BL, Ascsillán AA, Suita Y, Igras V, Lo JA, Hsiao JJ, Lapides R, Pál DMP, Lengyel AS, Navarini A, Okazaki A, Iliopoulos O, Németh I, Graeber TG, Zon L, Giese RW, Kemeny LV, Fisher DE. MITF regulates IDH1, NNT, and a transcriptional program protecting melanoma from reactive oxygen species. Sci Rep 2024; 14:21527. [PMID: 39277608 DOI: 10.1038/s41598-024-72031-9] [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: 03/26/2024] [Accepted: 09/03/2024] [Indexed: 09/17/2024] Open
Abstract
Microphthalmia-associated transcription factor (MITF) is a master regulator of melanocyte function, development and plays a significant role in melanoma pathogenesis. MITF genomic amplification promotes melanoma development, and it can facilitate resistance to multiple therapies. Here, we show that MITF regulates a global antioxidant program that increases survival of melanoma cell lines by protecting the cells from reactive oxygen species (ROS)-induced damage. In addition, this redox program is correlated with MITF expression in human melanoma cell lines and patient-derived melanoma samples. Using a zebrafish melanoma model, we show that MITF decreases ROS-mediated DNA damage in vivo. Some of the MITF target genes involved, such as IDH1 and NNT, are regulated through direct MITF binding to canonical enhancer box (E-BOX) sequences proximal to their promoters. Utilizing functional experiments, we demonstrate the role of MITF and its target genes in reducing cytosolic and mitochondrial ROS. Collectively, our data identify MITF as a significant driver of the cellular antioxidant state.
Collapse
Affiliation(s)
- Elisabeth Roider
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, USA.
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, USA.
- Department of Dermatology, University Hospital of Basel, Basel, Switzerland.
| | - Alexandra I T Lakatos
- HCEMM-SU Translational Dermatology Research Group, Semmelweis University, Budapest, Hungary
- Department of Physiology, Semmelweis University, Budapest, Hungary
- Department of Dermatology, Venereology, and Dermatooncology, Semmelweis University, Budapest, Hungary
| | - Alicia M McConnell
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Massachusetts and the Howard Hughes Medical Institute, Boston, USA
| | - Poguang Wang
- Department of Pharmaceutical Sciences, Department of Chemistry and Chemical Biology, and Barnett Institute, Bouve College, Northeastern University, Boston, MA, 02115, USA
| | - Alina Mueller
- Department of Dermatology, University Hospital of Basel, Basel, Switzerland
| | - Akinori Kawakami
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
| | - Jennifer Tsoi
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- UCLA Metabolomics Center, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Botond L Szabolcs
- HCEMM-SU Translational Dermatology Research Group, Semmelweis University, Budapest, Hungary
- Department of Physiology, Semmelweis University, Budapest, Hungary
- Department of Dermatology, Venereology, and Dermatooncology, Semmelweis University, Budapest, Hungary
| | - Anna A Ascsillán
- HCEMM-SU Translational Dermatology Research Group, Semmelweis University, Budapest, Hungary
- Department of Physiology, Semmelweis University, Budapest, Hungary
- Department of Dermatology, Venereology, and Dermatooncology, Semmelweis University, Budapest, Hungary
| | - Yusuke Suita
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
| | - Vivien Igras
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
| | - Jennifer A Lo
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
| | - Jennifer J Hsiao
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
| | - Rebecca Lapides
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
- Robert Larner, College of Medicine at the University of Vermont, Burlington, USA
| | - Dorottya M P Pál
- HCEMM-SU Translational Dermatology Research Group, Semmelweis University, Budapest, Hungary
- Department of Physiology, Semmelweis University, Budapest, Hungary
- Department of Dermatology, Venereology, and Dermatooncology, Semmelweis University, Budapest, Hungary
| | - Anna S Lengyel
- HCEMM-SU Translational Dermatology Research Group, Semmelweis University, Budapest, Hungary
- Department of Physiology, Semmelweis University, Budapest, Hungary
- Department of Dermatology, Venereology, and Dermatooncology, Semmelweis University, Budapest, Hungary
| | - Alexander Navarini
- Department of Dermatology, University Hospital of Basel, Basel, Switzerland
| | - Arimichi Okazaki
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, USA
| | - Othon Iliopoulos
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, USA
| | - István Németh
- Department of Dermatology and Allergology, University of Szeged, Szeged, Hungary
| | - Thomas G Graeber
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- UCLA Metabolomics Center, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- Crump Institute for Molecular Imaging, UCLA, Los Angeles, CA, USA
| | - Leonard Zon
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Massachusetts and the Howard Hughes Medical Institute, Boston, USA
| | - Roger W Giese
- Department of Pharmaceutical Sciences, Department of Chemistry and Chemical Biology, and Barnett Institute, Bouve College, Northeastern University, Boston, MA, 02115, USA
| | - Lajos V Kemeny
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, USA.
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, USA.
- HCEMM-SU Translational Dermatology Research Group, Semmelweis University, Budapest, Hungary.
- Department of Physiology, Semmelweis University, Budapest, Hungary.
- Department of Dermatology, Venereology, and Dermatooncology, Semmelweis University, Budapest, Hungary.
| | - David E Fisher
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, USA.
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, USA.
- Lancer Professorship of Dermatology, Harvard Medical School, Boston, USA.
| |
Collapse
|
2
|
Lim SY, Lin Y, Lee JH, Pedersen B, Stewart A, Scolyer RA, Long GV, Yang JYH, Rizos H. Single-cell RNA sequencing reveals melanoma cell state-dependent heterogeneity of response to MAPK inhibitors. EBioMedicine 2024; 107:105308. [PMID: 39216232 DOI: 10.1016/j.ebiom.2024.105308] [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: 04/23/2024] [Revised: 08/11/2024] [Accepted: 08/12/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND Melanoma is a heterogeneous cancer influenced by the plasticity of melanoma cells and their dynamic adaptations to microenvironmental cues. Melanoma cells transition between well-defined transcriptional cell states that impact treatment response and resistance. METHODS In this study, we applied single-cell RNA sequencing to interrogate the molecular features of immunotherapy-naive and immunotherapy-resistant melanoma tumours in response to ex vivo BRAF/MEK inhibitor treatment. FINDINGS We confirm the presence of four distinct melanoma cell states - melanocytic, transitory, neural-crest like and undifferentiated, and identify enrichment of neural crest-like and undifferentiated melanoma cells in immunotherapy-resistant tumours. Furthermore, we introduce an integrated computational approach to identify subsets of responding and nonresponding melanoma cells within the transcriptional cell states. INTERPRETATION Nonresponding melanoma cells are identified in all transcriptional cell states and are predisposed to BRAF/MEK inhibitor resistance due to pro-inflammatory IL6 and TNFɑ signalling. Our study provides a framework to study treatment response within distinct melanoma cell states and indicate that tumour-intrinsic pro-inflammatory signalling contributes to BRAF/MEK inhibitor resistance. FUNDING This work was supported by Macquarie University, Melanoma Institute Australia, and the National Health and Medical Research Council of Australia (NHMRC; grant 2012860, 2028055).
Collapse
Affiliation(s)
- Su Yin Lim
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Australia; Melanoma Institute Australia, Australia.
| | - Yingxin Lin
- School of Mathematics and Statistics, The University of Sydney, Australia; Charles Perkins Centre, The University of Sydney, Australia
| | - Jenny H Lee
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Australia; Melanoma Institute Australia, Australia; Department of Neurosurgery, Chris O'Brien Lifehouse, Sydney, NSW, Australia
| | - Bernadette Pedersen
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Australia; Melanoma Institute Australia, Australia
| | - Ashleigh Stewart
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Australia; Melanoma Institute Australia, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, Australia; Charles Perkins Centre, The University of Sydney, Australia; Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, Australia; Faculty of Medicine and Health, The University of Sydney, Australia
| | - Georgina V Long
- Melanoma Institute Australia, Australia; Charles Perkins Centre, The University of Sydney, Australia; Royal North Shore and Mater Hospitals, Sydney, Australia; Faculty of Medicine and Health, The University of Sydney, Australia
| | - Jean Y H Yang
- School of Mathematics and Statistics, The University of Sydney, Australia; Charles Perkins Centre, The University of Sydney, Australia
| | - Helen Rizos
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Australia; Melanoma Institute Australia, Australia
| |
Collapse
|
3
|
Ma Y, Tagore M, Hunter MV, Huang TH, Montal E, Weiss JM, White RM. Restraint of melanoma progression by cells in the local skin environment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.15.608067. [PMID: 39229155 PMCID: PMC11370352 DOI: 10.1101/2024.08.15.608067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Keratinocytes, the dominant cell type in the melanoma microenvironment during tumor initiation, exhibit diverse effects on melanoma progression. Using a zebrafish model of melanoma and human cell co-cultures, we observed that keratinocytes undergo an Epithelial-Mesenchymal Transition (EMT)-like transformation in the presence of melanoma, reminiscent of their behavior during wound healing. Surprisingly, overexpression of the EMT transcription factor Twist in keratinocytes led to improved overall survival in zebrafish melanoma models, despite no change in tumor initiation rates. This survival benefit was attributed to reduced melanoma invasion, as confirmed by human cell co-culture assays. Single-cell RNA-sequencing revealed a unique melanoma cell cluster in the Twist-overexpressing condition, exhibiting a more differentiated, less invasive phenotype. Further analysis nominated homotypic jam3b-jam3b and pgrn-sort1a interactions between Twist-overexpressing keratinocytes and melanoma cells as potential mediators of the invasive restraint. Our findings suggest that EMT in the tumor microenvironment (TME) may limit melanoma invasion through altered cell-cell interactions.
Collapse
Affiliation(s)
- Yilun Ma
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Cell and Developmental Biology Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Mohita Tagore
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Miranda V Hunter
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ting-Hsiang Huang
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emily Montal
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joshua M Weiss
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Cell and Developmental Biology Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Richard M White
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Nuffield Department of Medicine, Ludwig Cancer Research, University of Oxford, Oxford, UK
| |
Collapse
|
4
|
Dufau C, Genais M, Mucher E, Jung B, Garcia V, Montfort A, Tosolini M, Clarke CJ, Medin JA, Levade T, Delord JP, Meyer N, Pancaldi V, Andrieu-Abadie N, Ségui B. Ceramide metabolism alterations contribute to Tumor Necrosis Factor-induced melanoma dedifferentiation and predict resistance to immune checkpoint inhibitors in advanced melanoma patients. Front Immunol 2024; 15:1421432. [PMID: 39136013 PMCID: PMC11317267 DOI: 10.3389/fimmu.2024.1421432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 07/08/2024] [Indexed: 08/15/2024] Open
Abstract
Introduction Advanced cutaneous melanoma is a skin cancer characterized by a poor prognosis and high metastatic potential. During metastatic spread, melanoma cells often undergo dedifferentiation toward an invasive phenotype, resulting in reduced expression of microphthalmia-associated transcription factor (MITF)-dependent melanoma antigens and facilitating immune escape. Tumor Necrosis Factor (TNF) is known to be a key factor in melanoma dedifferentiation. Interestingly, accumulating evidence suggests that TNF may play a role in melanoma progression and resistance to immunotherapies. Additionally, TNF has been identified as a potent regulator of sphingolipid metabolism, which could contribute to melanoma aggressiveness and the process of melanoma dedifferentiation. Methods We conducted RNA sequencing and mass spectrometry analyses to investigate TNF-induced dedifferentiation in two melanoma cell lines. In vitro experiments were performed to manipulate sphingolipid metabolism using genetic or pharmacologic alterations in combination with TNF treatment, aiming to elucidate the potential involvement of this metabolism in TNF-induced dedifferentiation. Lastly, to evaluate the clinical significance of our findings, we performed unsupervised analysis of plasma sphingolipid levels in 48 patients receiving treatment with immune checkpoint inhibitors, either alone or in combination with anti-TNF therapy. Results Herein, we demonstrate that TNF-induced melanoma cell dedifferentiation is associated with a global modulation of sphingolipid metabolism. Specifically, TNF decreases the expression and activity of acid ceramidase (AC), encoded by the ASAH1 gene, while increasing the expression of glucosylceramide synthase (GCS), encoded by the UGCG gene. Remarkably, knockdown of AC alone via RNA interference is enough to induce melanoma cell dedifferentiation. Furthermore, treatment with Eliglustat, a GCS inhibitor, inhibits TNF-induced melanoma cell dedifferentiation. Lastly, analysis of plasma samples from patients treated with immune checkpoint inhibitors, with or without anti-TNF therapy, revealed significant predictive sphingolipids. Notably, the top 8 predictive sphingolipids, including glycosphingolipids, were associated with a poor response to immunotherapy. Discussion Our study highlights that ceramide metabolism alterations are causally involved in TNF-induced melanoma cell dedifferentiation and suggests that the evolution of specific ceramide metabolites in plasma may be considered as predictive biomarkers of resistance to immunotherapy.
Collapse
Affiliation(s)
- Carine Dufau
- Unité Mixte de Recherche Intitut National de la Santé et de la Recherche Médicale (INSERM) 1037, Centre National de la Recherche Scientifique (CNRS) 5071, Université Toulouse III - Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
- Équipe labellisée Fondation Association (ARC), Toulouse, France
| | - Matthieu Genais
- Unité Mixte de Recherche Intitut National de la Santé et de la Recherche Médicale (INSERM) 1037, Centre National de la Recherche Scientifique (CNRS) 5071, Université Toulouse III - Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
- Équipe labellisée Fondation Association (ARC), Toulouse, France
| | - Elodie Mucher
- Unité Mixte de Recherche Intitut National de la Santé et de la Recherche Médicale (INSERM) 1037, Centre National de la Recherche Scientifique (CNRS) 5071, Université Toulouse III - Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
- Équipe labellisée Fondation Association (ARC), Toulouse, France
| | - Benjamin Jung
- Unité Mixte de Recherche Intitut National de la Santé et de la Recherche Médicale (INSERM) 1037, Centre National de la Recherche Scientifique (CNRS) 5071, Université Toulouse III - Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
- Équipe labellisée Fondation Association (ARC), Toulouse, France
| | - Virginie Garcia
- Unité Mixte de Recherche Intitut National de la Santé et de la Recherche Médicale (INSERM) 1037, Centre National de la Recherche Scientifique (CNRS) 5071, Université Toulouse III - Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
- Équipe labellisée Fondation Association (ARC), Toulouse, France
| | - Anne Montfort
- Unité Mixte de Recherche Intitut National de la Santé et de la Recherche Médicale (INSERM) 1037, Centre National de la Recherche Scientifique (CNRS) 5071, Université Toulouse III - Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
- Équipe labellisée Fondation Association (ARC), Toulouse, France
| | - Marie Tosolini
- Unité Mixte de Recherche Intitut National de la Santé et de la Recherche Médicale (INSERM) 1037, Centre National de la Recherche Scientifique (CNRS) 5071, Université Toulouse III - Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
- Équipe labellisée Fondation Association (ARC), Toulouse, France
| | - Christopher J. Clarke
- Stony Brook Cancer Center, and Department of Medicine, Stony Brook University, New York, NY, United States
| | - Jeffrey A. Medin
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, United States
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Thierry Levade
- Unité Mixte de Recherche Intitut National de la Santé et de la Recherche Médicale (INSERM) 1037, Centre National de la Recherche Scientifique (CNRS) 5071, Université Toulouse III - Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
- Équipe labellisée Fondation Association (ARC), Toulouse, France
- Laboratoire de Biochimie, Institut Fédératif de Biologie, Centre Hospitalier Universitaire (CHU) Purpan, Toulouse, France
| | - Jean-Pierre Delord
- Unité Mixte de Recherche Intitut National de la Santé et de la Recherche Médicale (INSERM) 1037, Centre National de la Recherche Scientifique (CNRS) 5071, Université Toulouse III - Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
- Oncopole Claudius Regaud, Toulouse, France
| | - Nicolas Meyer
- Unité Mixte de Recherche Intitut National de la Santé et de la Recherche Médicale (INSERM) 1037, Centre National de la Recherche Scientifique (CNRS) 5071, Université Toulouse III - Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
- Équipe labellisée Fondation Association (ARC), Toulouse, France
- Service d’Oncodermatologie, Institut Universitaire du Cancer (IUCT-O), Centre Hospitalier Universitaire (CHU) de Toulouse, Toulouse, France
| | - Vera Pancaldi
- Unité Mixte de Recherche Intitut National de la Santé et de la Recherche Médicale (INSERM) 1037, Centre National de la Recherche Scientifique (CNRS) 5071, Université Toulouse III - Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
| | - Nathalie Andrieu-Abadie
- Unité Mixte de Recherche Intitut National de la Santé et de la Recherche Médicale (INSERM) 1037, Centre National de la Recherche Scientifique (CNRS) 5071, Université Toulouse III - Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
- Équipe labellisée Fondation Association (ARC), Toulouse, France
| | - Bruno Ségui
- Unité Mixte de Recherche Intitut National de la Santé et de la Recherche Médicale (INSERM) 1037, Centre National de la Recherche Scientifique (CNRS) 5071, Université Toulouse III - Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
- Équipe labellisée Fondation Association (ARC), Toulouse, France
| |
Collapse
|
5
|
Vasilevska J, Cheng PF, Lehmann J, Ramelyte E, Gómez JM, Dimitriou F, Sella F, Ferretti D, Salas-Bastos A, Jordaan WS, Levesque MP, Dummer R, Sommer L. Monitoring melanoma patients on treatment reveals a distinct macrophage population driving targeted therapy resistance. Cell Rep Med 2024; 5:101611. [PMID: 38942020 PMCID: PMC11293307 DOI: 10.1016/j.xcrm.2024.101611] [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: 08/30/2023] [Revised: 04/09/2024] [Accepted: 05/20/2024] [Indexed: 06/30/2024]
Abstract
Resistance to targeted therapy remains a major clinical challenge in melanoma. To uncover resistance mechanisms, we perform single-cell RNA sequencing on fine-needle aspirates from resistant and responding tumors of patients undergoing BRAFi/MEKi treatment. Among the genes most prominently expressed in resistant tumors is POSTN, predicted to signal to a macrophage population associated with targeted therapy resistance (TTR). Accordingly, tumors from patients with fast disease progression after therapy exhibit high POSTN expression levels and high numbers of TTR macrophages. POSTN polarizes human macrophages toward a TTR phenotype and promotes resistance to targeted therapy in a melanoma mouse model, which is associated with a phenotype change in intratumoral macrophages. Finally, polarized TTR macrophages directly protect human melanoma cells from MEKi-induced killing via CD44 receptor expression on melanoma cells. Thus, interfering with the protective activity of TTR macrophages may offer a strategy to overcome resistance to targeted therapy in melanoma.
Collapse
Affiliation(s)
- Jelena Vasilevska
- Institute of Anatomy, University of Zurich, 8057 Zurich, Switzerland
| | - Phil Fang Cheng
- Department of Dermatology, University of Zurich Hospital and Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Julia Lehmann
- Institute of Anatomy, University of Zurich, 8057 Zurich, Switzerland
| | - Egle Ramelyte
- Department of Dermatology, University of Zurich Hospital and Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Julia Martínez Gómez
- Department of Dermatology, University of Zurich Hospital and Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Florentia Dimitriou
- Department of Dermatology, University of Zurich Hospital and Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Federica Sella
- Department of Dermatology, University of Zurich Hospital and Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Daria Ferretti
- Institute of Anatomy, University of Zurich, 8057 Zurich, Switzerland
| | | | | | - Mitchell Paul Levesque
- Department of Dermatology, University of Zurich Hospital and Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Reinhard Dummer
- Department of Dermatology, University of Zurich Hospital and Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Lukas Sommer
- Institute of Anatomy, University of Zurich, 8057 Zurich, Switzerland.
| |
Collapse
|
6
|
Di Leo L, Pagliuca C, Kishk A, Rizza S, Tsiavou C, Pecorari C, Dahl C, Pacheco MP, Tholstrup R, Brewer JR, Berico P, Hernando E, Cecconi F, Ballotti R, Bertolotto C, Filomeni G, Gjerstorff MF, Sauter T, Lovat P, Guldberg P, De Zio D. AMBRA1 levels predict resistance to MAPK inhibitors in melanoma. Proc Natl Acad Sci U S A 2024; 121:e2400566121. [PMID: 38870061 PMCID: PMC11194594 DOI: 10.1073/pnas.2400566121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 05/20/2024] [Indexed: 06/15/2024] Open
Abstract
Intrinsic and acquired resistance to mitogen-activated protein kinase inhibitors (MAPKi) in melanoma remains a major therapeutic challenge. Here, we show that the clinical development of resistance to MAPKi is associated with reduced tumor expression of the melanoma suppressor Autophagy and Beclin 1 Regulator 1 (AMBRA1) and that lower expression levels of AMBRA1 predict a poor response to MAPKi treatment. Functional analyses show that loss of AMBRA1 induces phenotype switching and orchestrates an extracellular signal-regulated kinase (ERK)-independent resistance mechanism by activating focal adhesion kinase 1 (FAK1). In both in vitro and in vivo settings, melanomas with low AMBRA1 expression exhibit intrinsic resistance to MAPKi therapy but higher sensitivity to FAK1 inhibition. Finally, we show that the rapid development of resistance in initially MAPKi-sensitive melanomas can be attributed to preexisting subclones characterized by low AMBRA1 expression and that cotreatment with MAPKi and FAK1 inhibitors (FAKi) effectively prevents the development of resistance in these tumors. In summary, our findings underscore the value of AMBRA1 expression for predicting melanoma response to MAPKi and supporting the therapeutic efficacy of FAKi to overcome MAPKi-induced resistance.
Collapse
Affiliation(s)
- Luca Di Leo
- Melanoma Research Team, Center for Autophagy, Recycling and Disease, Danish Cancer Institute, Copenhagen2100, Denmark
| | - Chiara Pagliuca
- Melanoma Research Team, Center for Autophagy, Recycling and Disease, Danish Cancer Institute, Copenhagen2100, Denmark
| | - Ali Kishk
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux4365, Luxembourg
| | - Salvatore Rizza
- Redox Biology Group, Danish Cancer Institute, Copenhagen2100, Denmark
| | - Christina Tsiavou
- Melanoma Research Team, Center for Autophagy, Recycling and Disease, Danish Cancer Institute, Copenhagen2100, Denmark
| | - Chiara Pecorari
- Redox Biology Group, Danish Cancer Institute, Copenhagen2100, Denmark
| | - Christina Dahl
- Molecular Diagnostics Group, Danish Cancer Institute, Copenhagen2100, Denmark
| | - Maria Pires Pacheco
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux4365, Luxembourg
| | - Rikke Tholstrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense5230, Denmark
| | - Jonathan Richard Brewer
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense5230, Denmark
| | - Pietro Berico
- Department of Pathology, New York University Grossman School of Medicine, New York, NY10016
| | - Eva Hernando
- Department of Pathology, New York University Grossman School of Medicine, New York, NY10016
| | - Francesco Cecconi
- Cell Stress and Survival, Center for Autophagy, Recycling and Disease, Danish Cancer Institute, Copenhagen2100, Denmark
- Faculty of Medicine and Surgery, Università Cattolica del “Sacro Cuore”, Fondazione Policlinico Gemelli—Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome00136, Italy
| | - Robert Ballotti
- Université Côte d’Azur, Nice06200, France
- Inserm, Biology and Pathologies of melanocytes, team1, Equipe labellisée Ligue 2020, Centre Méditerranéen de Médecine Moléculaire, Nice06200, France
| | - Corine Bertolotto
- Université Côte d’Azur, Nice06200, France
- Inserm, Biology and Pathologies of melanocytes, team1, Equipe labellisée Ligue 2020, Centre Méditerranéen de Médecine Moléculaire, Nice06200, France
| | - Giuseppe Filomeni
- Redox Biology Group, Danish Cancer Institute, Copenhagen2100, Denmark
| | - Morten Frier Gjerstorff
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense5230, Denmark
- Department of Oncology, Odense University Hospital, Odense5000, Denmark
| | - Thomas Sauter
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux4365, Luxembourg
| | - Penny Lovat
- Translational and Clinical Research Institute, Medical School, Newcastle University, Newcastle upon TyneNE2 4HH, United Kingdom
| | - Per Guldberg
- Molecular Diagnostics Group, Danish Cancer Institute, Copenhagen2100, Denmark
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense5230, Denmark
| | - Daniela De Zio
- Melanoma Research Team, Center for Autophagy, Recycling and Disease, Danish Cancer Institute, Copenhagen2100, Denmark
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense5230, Denmark
| |
Collapse
|
7
|
Patel AS, Yanai I. A developmental constraint model of cancer cell states and tumor heterogeneity. Cell 2024; 187:2907-2918. [PMID: 38848676 PMCID: PMC11256907 DOI: 10.1016/j.cell.2024.04.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/29/2023] [Accepted: 04/24/2024] [Indexed: 06/09/2024]
Abstract
Cancer is a disease that stems from a fundamental liability inherent to multicellular life forms in which an individual cell is capable of reneging on the interests of the collective organism. Although cancer is commonly described as an evolutionary process, a less appreciated aspect of tumorigenesis may be the constraints imposed by the organism's developmental programs. Recent work from single-cell transcriptomic analyses across a range of cancer types has revealed the recurrence, plasticity, and co-option of distinct cellular states among cancer cell populations. Here, we note that across diverse cancer types, the observed cell states are proximate within the developmental hierarchy of the cell of origin. We thus posit a model by which cancer cell states are directly constrained by the organism's "developmental map." According to this model, a population of cancer cells traverses the developmental map, thereby generating a heterogeneous set of states whose interactions underpin emergent tumor behavior.
Collapse
Affiliation(s)
- Ayushi S Patel
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA; Department of Biochemistry & Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA; Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Itai Yanai
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA; Department of Biochemistry & Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA; Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
| |
Collapse
|
8
|
Kosemehmetoglu K, Mosaieby E, Šteiner P, Vaněček T, Baranovska-Andrigo V, Michal M. Calcifying Spindle Cell Soft Tissue Tumor With SOX10::PLAG1 Fusion: A Case Report of a Morphologically Distinctive and Potentially Novel Soft Tissue Tumor. Genes Chromosomes Cancer 2024; 63:e23249. [PMID: 38884173 DOI: 10.1002/gcc.23249] [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: 02/09/2024] [Revised: 04/02/2024] [Accepted: 05/14/2024] [Indexed: 06/18/2024] Open
Abstract
The widespread use of advanced molecular techniques has led to the identification of several tumor types with PLAG1 gene fusions some of which also affect the skin and soft tissues. Herein, we present a 38-year-old female with a subcutaneous tumor affecting her forearm, which does not seem to fit into any currently recognized entity. It was a well-circumscribed tumor measuring 6 × 4,5 × 4 cm. It had a thick capsule composed of bland spindle cells forming palisades and Verocay body-like structures within a myxocollagenous background. Scattered calcifications were dispersed throughout the lesion. No cytological atypia, mitotic activity, or necrosis were present. Targeted NGS revealed a SOX10::PLAG1 fusion and fluorescent in situ hybridization confirmed the presence of PLAG1 gene rearrangement. The neoplastic cells showed a diffuse immunohistochemical expression of S100, SOX10, and PLAG1, as well as patchy desmin and CD34 positivity. The methylation profile of this tumor did not match any other entity covered by the DKFZ sarcoma classifier and apart from the gain of chromosome 12, the copy number profile was normal. The tumor was completely excised, and the patient has been free of disease for 4 years since the excision. While more cases are needed to confirm this tumor as a distinct entity, we propose a provisional name "SOX10::PLAG1-rearranged calcifying spindle cell tumor."
Collapse
Affiliation(s)
- Kemal Kosemehmetoglu
- Department of Pathology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | | | - Petr Šteiner
- Bioptica Laboratory, Ltd., Plzen, Czech Republic
| | | | - Vira Baranovska-Andrigo
- Department of Pathology, Charles University, Faculty of Medicine in Plzen, Plzen, Czech Republic
| | - Michael Michal
- Bioptica Laboratory, Ltd., Plzen, Czech Republic
- Department of Pathology, Charles University, Faculty of Medicine in Plzen, Plzen, Czech Republic
| |
Collapse
|
9
|
Durand S, Tang Y, Pommier RM, Benboubker V, Grimont M, Boivin F, Barbollat-Boutrand L, Cumunel E, Dupeuble F, Eberhardt A, Plaschka M, Dalle S, Caramel J. ZEB1 controls a lineage-specific transcriptional program essential for melanoma cell state transitions. Oncogene 2024; 43:1489-1505. [PMID: 38519642 PMCID: PMC11090790 DOI: 10.1038/s41388-024-03010-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/06/2024] [Indexed: 03/25/2024]
Abstract
Cell plasticity sustains intra-tumor heterogeneity and treatment resistance in melanoma. Deciphering the transcriptional mechanisms governing reversible phenotypic transitions between proliferative/differentiated and invasive/stem-like states is required. Expression of the ZEB1 transcription factor is frequently activated in melanoma, where it fosters adaptive resistance to targeted therapies. Here, we performed a genome-wide characterization of ZEB1 transcriptional targets, by combining ChIP-sequencing and RNA-sequencing, upon phenotype switching in melanoma models. We identified and validated ZEB1 binding peaks in the promoter of key lineage-specific genes crucial for melanoma cell identity. Mechanistically, ZEB1 negatively regulates SOX10-MITF dependent proliferative/melanocytic programs and positively regulates AP-1 driven invasive and stem-like programs. Comparative analyses with breast carcinoma cells revealed lineage-specific ZEB1 binding, leading to the design of a more reliable melanoma-specific ZEB1 regulon. We then developed single-cell spatial multiplexed analyses to characterize melanoma cell states intra-tumoral heterogeneity in human melanoma samples. Combined with scRNA-Seq analyses, our findings confirmed increased ZEB1 expression in Neural-Crest-like cells and mesenchymal cells, underscoring its significance in vivo in both populations. Overall, our results define ZEB1 as a major transcriptional regulator of cell states transitions and provide a better understanding of lineage-specific transcriptional programs sustaining intra-tumor heterogeneity in melanoma.
Collapse
Affiliation(s)
- Simon Durand
- "Cancer cell Plasticity in Melanoma" lab, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon1, 69008, Lyon, France
| | - Yaqi Tang
- "Cancer cell Plasticity in Melanoma" lab, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon1, 69008, Lyon, France
| | - Roxane M Pommier
- Fondation Synergie Lyon Cancer, Plateforme de bio-informatique Gilles Thomas, Centre de Recherche en Cancérologie de Lyon, Centre Léon Bérard, INSERM U1052-CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon1, 69008, Lyon, France
| | - Valentin Benboubker
- "Cancer cell Plasticity in Melanoma" lab, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon1, 69008, Lyon, France
| | - Maxime Grimont
- "Cancer cell Plasticity in Melanoma" lab, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon1, 69008, Lyon, France
| | - Felix Boivin
- "Cancer cell Plasticity in Melanoma" lab, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon1, 69008, Lyon, France
| | - Laetitia Barbollat-Boutrand
- "Cancer cell Plasticity in Melanoma" lab, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon1, 69008, Lyon, France
| | - Eric Cumunel
- Fondation Synergie Lyon Cancer, Plateforme de bio-informatique Gilles Thomas, Centre de Recherche en Cancérologie de Lyon, Centre Léon Bérard, INSERM U1052-CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon1, 69008, Lyon, France
| | - Florian Dupeuble
- "Cancer cell Plasticity in Melanoma" lab, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon1, 69008, Lyon, France
| | - Anaïs Eberhardt
- "Cancer cell Plasticity in Melanoma" lab, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon1, 69008, Lyon, France
- Dermatology Unit, Hospices Civils de Lyon, CH Lyon Sud, 165 chemin du Grand Revoyet, 69495, Pierre Bénite, Cedex, France
| | - Maud Plaschka
- "Cancer cell Plasticity in Melanoma" lab, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon1, 69008, Lyon, France
| | - Stéphane Dalle
- "Cancer cell Plasticity in Melanoma" lab, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon1, 69008, Lyon, France
- Dermatology Unit, Hospices Civils de Lyon, CH Lyon Sud, 165 chemin du Grand Revoyet, 69495, Pierre Bénite, Cedex, France
| | - Julie Caramel
- "Cancer cell Plasticity in Melanoma" lab, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon1, 69008, Lyon, France.
| |
Collapse
|
10
|
Carvalho LADC, Noma IHY, Uehara AH, Siena ÁDD, Osaki LH, Mori MP, Pinto NCDS, Freitas VM, Junior WAS, Smalley KSM, Maria-Engler SS. Modeling Melanoma Heterogeneity In Vitro: Redox, Resistance and Pigmentation Profiles. Antioxidants (Basel) 2024; 13:555. [PMID: 38790661 PMCID: PMC11118096 DOI: 10.3390/antiox13050555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/21/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
Microenvironment and transcriptional plasticity generate subpopulations within the tumor, and the use of BRAF inhibitors (BRAFis) contributes to the rise and selection of resistant clones. We stochastically isolated subpopulations (C1, C2, and C3) from naïve melanoma and found that the clones demonstrated distinct morphology, phenotypic, and functional profiles: C1 was less proliferative, more migratory and invasive, less sensitive to BRAFis, less dependent on OXPHOS, more sensitive to oxidative stress, and less pigmented; C2 was more proliferative, less migratory and invasive, more sensitive to BRAFis, less sensitive to oxidative stress, and more pigmented; and C3 was less proliferative, more migratory and invasive, less sensitive to BRAFis, more dependent on OXPHOS, more sensitive to oxidative stress, and more pigmented. Hydrogen peroxide plays a central role in oxidative stress and cell signaling, and PRDXs are one of its main consumers. The intrinsically resistant C1 and C3 clones had lower MITF, PGC-1α, and PRDX1 expression, while C1 had higher AXL and decreased pigmentation markers, linking PRDX1 to clonal heterogeneity and resistance. PRDX2 is depleted in acquired BRAFi-resistant cells and acts as a redox sensor. Our results illustrate that decreased pigmentation markers are related to therapy resistance and decreased antioxidant defense.
Collapse
Affiliation(s)
- Larissa Anastacio da Costa Carvalho
- Department of Tumor Biology, Moffitt Cancer Center, Tampa, FL 33612, USA; (L.A.d.C.C.); (K.S.M.S.)
- Department of Clinical and Toxicological Analysis, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, SP, Brazil; (I.H.Y.N.); (A.H.U.)
| | - Isabella Harumi Yonehara Noma
- Department of Clinical and Toxicological Analysis, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, SP, Brazil; (I.H.Y.N.); (A.H.U.)
| | - Adriana Hiromi Uehara
- Department of Clinical and Toxicological Analysis, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, SP, Brazil; (I.H.Y.N.); (A.H.U.)
| | - Ádamo Davi Diógenes Siena
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil; (Á.D.D.S.); (W.A.S.J.)
| | - Luciana Harumi Osaki
- Department of Cell Biology and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, SP, Brazil; (L.H.O.); (V.M.F.)
| | - Mateus Prates Mori
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, SP, Brazil; (M.P.M.); (N.C.d.S.P.)
| | - Nadja Cristhina de Souza Pinto
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, SP, Brazil; (M.P.M.); (N.C.d.S.P.)
| | - Vanessa Morais Freitas
- Department of Cell Biology and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, SP, Brazil; (L.H.O.); (V.M.F.)
| | - Wilson Araújo Silva Junior
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil; (Á.D.D.S.); (W.A.S.J.)
| | - Keiran S. M. Smalley
- Department of Tumor Biology, Moffitt Cancer Center, Tampa, FL 33612, USA; (L.A.d.C.C.); (K.S.M.S.)
| | - Silvya Stuchi Maria-Engler
- Department of Clinical and Toxicological Analysis, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, SP, Brazil; (I.H.Y.N.); (A.H.U.)
| |
Collapse
|
11
|
Runel G, Lopez-Ramirez N, Barbollat-Boutrand L, Cario M, Durand S, Grimont M, Schartl M, Dalle S, Caramel J, Chlasta J, Masse I. Cancer Cell Biomechanical Properties Accompany Tspan8-Dependent Cutaneous Melanoma Invasion. Cancers (Basel) 2024; 16:694. [PMID: 38398085 PMCID: PMC10887418 DOI: 10.3390/cancers16040694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 01/27/2024] [Accepted: 01/29/2024] [Indexed: 02/25/2024] Open
Abstract
The intrinsic biomechanical properties of cancer cells remain poorly understood. To decipher whether cell stiffness modulation could increase melanoma cells' invasive capacity, we performed both in vitro and in vivo experiments exploring cell stiffness by atomic force microscopy (AFM). We correlated stiffness properties with cell morphology adaptation and the molecular mechanisms underlying epithelial-to-mesenchymal (EMT)-like phenotype switching. We found that melanoma cell stiffness reduction was systematically associated with the acquisition of invasive properties in cutaneous melanoma cell lines, human skin reconstructs, and Medaka fish developing spontaneous MAP-kinase-induced melanomas. We observed a systematic correlation of stiffness modulation with cell morphological changes towards mesenchymal characteristic gains. We accordingly found that inducing melanoma EMT switching by overexpressing the ZEB1 transcription factor, a major regulator of melanoma cell plasticity, was sufficient to decrease cell stiffness and transcriptionally induce tetraspanin-8-mediated dermal invasion. Moreover, ZEB1 expression correlated with Tspan8 expression in patient melanoma lesions. Our data suggest that intrinsic cell stiffness could be a highly relevant marker for human cutaneous melanoma development.
Collapse
Affiliation(s)
- Gaël Runel
- Cancer Research Center of Lyon, CNRS UMR5286, Inserm U1052, University of Lyon, University Lyon 1, 69000 Lyon, France; (G.R.); (N.L.-R.)
- BioMeca, 60F, Bioserra 2, Av. Rockefeller, 69008 Lyon, France
| | - Noémie Lopez-Ramirez
- Cancer Research Center of Lyon, CNRS UMR5286, Inserm U1052, University of Lyon, University Lyon 1, 69000 Lyon, France; (G.R.); (N.L.-R.)
| | - Laetitia Barbollat-Boutrand
- Cancer Research Center of Lyon, CNRS UMR5286, Inserm U1052, University of Lyon, University Lyon 1, 69000 Lyon, France; (G.R.); (N.L.-R.)
| | - Muriel Cario
- National Reference Center for Rare Skin Disease, Department of Dermatology, University Hospital, INSERM 1035, 33000 Bordeaux, France
- AquiDerm, University Bordeaux, 33076 Bordeaux, France
| | - Simon Durand
- Cancer Research Center of Lyon, CNRS UMR5286, Inserm U1052, University of Lyon, University Lyon 1, 69000 Lyon, France; (G.R.); (N.L.-R.)
| | - Maxime Grimont
- Cancer Research Center of Lyon, CNRS UMR5286, Inserm U1052, University of Lyon, University Lyon 1, 69000 Lyon, France; (G.R.); (N.L.-R.)
| | - Manfred Schartl
- Developmental Biochemistry, University of Würzburg, 97074 Würzburg, Germany
- Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX 78666, USA
| | - Stéphane Dalle
- Cancer Research Center of Lyon, CNRS UMR5286, Inserm U1052, University of Lyon, University Lyon 1, 69000 Lyon, France; (G.R.); (N.L.-R.)
- Dermatology Department, Hôpital Universitaire Lyon Sud, Hospices Civils de Lyon, 69495 Pierre-Bénite, France
| | - Julie Caramel
- Cancer Research Center of Lyon, CNRS UMR5286, Inserm U1052, University of Lyon, University Lyon 1, 69000 Lyon, France; (G.R.); (N.L.-R.)
| | - Julien Chlasta
- BioMeca, 60F, Bioserra 2, Av. Rockefeller, 69008 Lyon, France
| | - Ingrid Masse
- Cancer Research Center of Lyon, CNRS UMR5286, Inserm U1052, University of Lyon, University Lyon 1, 69000 Lyon, France; (G.R.); (N.L.-R.)
| |
Collapse
|
12
|
Wu M, Hanly A, Gibson F, Fisher R, Rogers S, Park K, Zuger A, Kuang K, Kalin JH, Nocco S, Cole M, Xiao A, Agus F, Labadorf A, Beck S, Collard M, Cole PA, Alani RM. The CoREST repressor complex mediates phenotype switching and therapy resistance in melanoma. J Clin Invest 2024; 134:e171063. [PMID: 38300709 PMCID: PMC10940100 DOI: 10.1172/jci171063] [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: 04/03/2023] [Accepted: 01/22/2024] [Indexed: 02/03/2024] Open
Abstract
Virtually all patients with BRAF-mutant melanoma develop resistance to MAPK inhibitors largely through nonmutational events. Although the epigenetic landscape is shown to be altered in therapy-resistant melanomas and other cancers, a specific targetable epigenetic mechanism has not been validated. Here, we evaluated the corepressor for element 1-silencing transcription factor (CoREST) epigenetic repressor complex and the recently developed bivalent inhibitor corin within the context of melanoma phenotype plasticity and therapeutic resistance. We found that CoREST was a critical mediator of the major distinct melanoma phenotypes and that corin treatment of melanoma cells led to phenotype reprogramming. Global assessment of transcript and chromatin changes conferred by corin revealed specific effects on histone marks connected to epithelial-mesenchymal transition-associated (EMT-associated) transcription factors and the dual-specificity phosphatases (DUSPs). Remarkably, treatment of BRAF inhibitor-resistant (BRAFi-R) melanomas with corin promoted resensitization to BRAFi therapy. DUSP1 was consistently downregulated in BRAFi-R melanomas, which was reversed by corin treatment and associated with inhibition of p38 MAPK activity and resensitization to BRAFi therapies. Moreover, this activity was recapitulated by the p38 MAPK inhibitor BIRB 796. These findings identify the CoREST repressor complex as a central mediator of melanoma phenotype plasticity and resistance to targeted therapy and suggest that CoREST inhibitors may prove beneficial for patients with BRAFi-resistant melanoma.
Collapse
Affiliation(s)
- Muzhou Wu
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Ailish Hanly
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Frederick Gibson
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Robert Fisher
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Samantha Rogers
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Kihyun Park
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Angelina Zuger
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Kevin Kuang
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Jay H. Kalin
- Division of Genetics, Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Sarah Nocco
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Matthew Cole
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Amy Xiao
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Filisia Agus
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
| | - Adam Labadorf
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Samuel Beck
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Marianne Collard
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Philip A. Cole
- Division of Genetics, Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Rhoda M. Alani
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| |
Collapse
|
13
|
Lim SY, Rizos H. Single-cell RNA sequencing in melanoma: what have we learned so far? EBioMedicine 2024; 100:104969. [PMID: 38241976 PMCID: PMC10831183 DOI: 10.1016/j.ebiom.2024.104969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/18/2023] [Accepted: 01/03/2024] [Indexed: 01/21/2024] Open
Abstract
Over the past decade, there have been remarkable improvements in the treatment and survival rates of melanoma patients. Treatment resistance remains a persistent challenge, however, and is partly attributable to intratumoural heterogeneity. Melanoma cells can transition through a series of phenotypic and transcriptional cell states that vary in invasiveness and treatment responsiveness. The diverse stromal and immune contexture of the tumour microenvironment also contributes to intratumoural heterogeneity and disparities in treatment response in melanoma patients. Recent advances in single-cell sequencing technologies have enabled a more detailed understanding of melanoma heterogeneity and the underlying transcriptional programs that regulate melanoma cell diversity and behaviour. In this review, we examine the concept of intratumoural heterogeneity and the challenges it poses to achieving long-lasting treatment responses. We focus on the significance of next generation single-cell sequencing in advancing our understanding of melanoma diversity and the unique insights gained from single-cell studies.
Collapse
Affiliation(s)
- Su Yin Lim
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Australia; Melanoma Institute Australia, Sydney, Australia.
| | - Helen Rizos
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Australia; Melanoma Institute Australia, Sydney, Australia
| |
Collapse
|
14
|
Balderson B, Fane M, Harvey TJ, Piper M, Smith A, Bodén M. Systematic analysis of the transcriptional landscape of melanoma reveals drug-target expression plasticity. Brief Funct Genomics 2024:elad055. [PMID: 38183207 DOI: 10.1093/bfgp/elad055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 10/25/2023] [Accepted: 12/04/2023] [Indexed: 01/07/2024] Open
Abstract
Metastatic melanoma originates from melanocytes of the skin. Melanoma metastasis results in poor treatment prognosis for patients and is associated with epigenetic and transcriptional changes that reflect the developmental program of melanocyte differentiation from neural crest stem cells. Several studies have explored melanoma transcriptional heterogeneity using microarray, bulk and single-cell RNA-sequencing technologies to derive data-driven models of the transcriptional-state change which occurs during melanoma progression. No study has systematically examined how different models of melanoma progression derived from different data types, technologies and biological conditions compare. Here, we perform a cross-sectional study to identify averaging effects of bulk-based studies that mask and distort apparent melanoma transcriptional heterogeneity; we describe new transcriptionally distinct melanoma cell states, identify differential co-expression of genes between studies and examine the effects of predicted drug susceptibilities of different cell states between studies. Importantly, we observe considerable variability in drug-target gene expression between studies, indicating potential transcriptional plasticity of melanoma to down-regulate these drug targets and thereby circumvent treatment. Overall, observed differences in gene co-expression and predicted drug susceptibility between studies suggest bulk-based transcriptional measurements do not reliably gauge heterogeneity and that melanoma transcriptional plasticity is greater than described when studies are considered in isolation.
Collapse
Affiliation(s)
- Brad Balderson
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072 Queensland, Australia
| | - Mitchell Fane
- Fox Chase Cancer Centre, Philadelphia, 19019 Pennsylvania, United States of America
| | - Tracey J Harvey
- School of Biomedical Sciences, University of Queensland, Brisbane, 4072 Queensland, Australia
| | - Michael Piper
- School of Biomedical Sciences, University of Queensland, Brisbane, 4072 Queensland, Australia
| | - Aaron Smith
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, 4072 Queensland, Australia
| | - Mikael Bodén
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072 Queensland, Australia
| |
Collapse
|
15
|
Bahar ME, Kim HJ, Kim DR. Targeting the RAS/RAF/MAPK pathway for cancer therapy: from mechanism to clinical studies. Signal Transduct Target Ther 2023; 8:455. [PMID: 38105263 PMCID: PMC10725898 DOI: 10.1038/s41392-023-01705-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/03/2023] [Accepted: 11/12/2023] [Indexed: 12/19/2023] Open
Abstract
Metastatic dissemination of solid tumors, a leading cause of cancer-related mortality, underscores the urgent need for enhanced insights into the molecular and cellular mechanisms underlying metastasis, chemoresistance, and the mechanistic backgrounds of individuals whose cancers are prone to migration. The most prevalent signaling cascade governed by multi-kinase inhibitors is the mitogen-activated protein kinase (MAPK) pathway, encompassing the RAS-RAF-MAPK kinase (MEK)-extracellular signal-related kinase (ERK) pathway. RAF kinase is a primary mediator of the MAPK pathway, responsible for the sequential activation of downstream targets, such as MEK and the transcription factor ERK, which control numerous cellular and physiological processes, including organism development, cell cycle control, cell proliferation and differentiation, cell survival, and death. Defects in this signaling cascade are associated with diseases such as cancer. RAF inhibitors (RAFi) combined with MEK blockers represent an FDA-approved therapeutic strategy for numerous RAF-mutant cancers, including melanoma, non-small cell lung carcinoma, and thyroid cancer. However, the development of therapy resistance by cancer cells remains an important barrier. Autophagy, an intracellular lysosome-dependent catabolic recycling process, plays a critical role in the development of RAFi resistance in cancer. Thus, targeting RAF and autophagy could be novel treatment strategies for RAF-mutant cancers. In this review, we delve deeper into the mechanistic insights surrounding RAF kinase signaling in tumorigenesis and RAFi-resistance. Furthermore, we explore and discuss the ongoing development of next-generation RAF inhibitors with enhanced therapeutic profiles. Additionally, this review sheds light on the functional interplay between RAF-targeted therapies and autophagy in cancer.
Collapse
Affiliation(s)
- Md Entaz Bahar
- Department of Biochemistry and Convergence Medical Sciences and Institute of Medical Science, Gyeongsang National University, College of Medicine, Jinju, South Korea
| | - Hyun Joon Kim
- Department of Anatomy and Convergence Medical Sciences and Institute of Medical Science, Gyeongsang National University, College of Medicine, Jinju, South Korea
| | - Deok Ryong Kim
- Department of Biochemistry and Convergence Medical Sciences and Institute of Medical Science, Gyeongsang National University, College of Medicine, Jinju, South Korea.
| |
Collapse
|
16
|
Santasusagna S, Zhu S, Jawalagatti V, Carceles-Cordon M, Ertel A, Garcia-Longarte S, Song WM, Fujiwara N, Li P, Mendizabal I, Petrylak DP, Kelly WK, Reddy EP, Wang L, Schiewer MJ, Lujambio A, Karnes J, Knudsen KE, Cordon-Cardo C, Dong H, Huang H, Carracedo A, Hoshida Y, Rodriguez-Bravo V, Domingo-Domenech J. Master Transcription Factor Reprogramming Unleashes Selective Translation Promoting Castration Resistance and Immune Evasion in Lethal Prostate Cancer. Cancer Discov 2023; 13:2584-2609. [PMID: 37676710 PMCID: PMC10714140 DOI: 10.1158/2159-8290.cd-23-0306] [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: 03/15/2023] [Revised: 07/28/2023] [Accepted: 09/05/2023] [Indexed: 09/08/2023]
Abstract
Signaling rewiring allows tumors to survive therapy. Here we show that the decrease of the master regulator microphthalmia transcription factor (MITF) in lethal prostate cancer unleashes eukaryotic initiation factor 3B (eIF3B)-dependent translation reprogramming of key mRNAs conferring resistance to androgen deprivation therapy (ADT) and promoting immune evasion. Mechanistically, MITF represses through direct promoter binding eIF3B, which in turn regulates the translation of specific mRNAs. Genome-wide eIF3B enhanced cross-linking immunoprecipitation sequencing (eCLIP-seq) showed specialized binding to a UC-rich motif present in subsets of 5' untranslated regions. Indeed, translation of the androgen receptor and major histocompatibility complex I (MHC-I) through this motif is sensitive to eIF3B amount. Notably, pharmacologic targeting of eIF3B-dependent translation in preclinical models sensitizes prostate cancer to ADT and anti-PD-1 therapy. These findings uncover a hidden connection between transcriptional and translational rewiring promoting therapy-refractory lethal prostate cancer and provide a druggable mechanism that may transcend into effective combined therapeutic strategies. SIGNIFICANCE Our study shows that specialized eIF3B-dependent translation of specific mRNAs released upon downregulation of the master transcription factor MITF confers castration resistance and immune evasion in lethal prostate cancer. Pharmacologic targeting of this mechanism delays castration resistance and increases immune-checkpoint efficacy. This article is featured in Selected Articles from This Issue, p. 2489.
Collapse
Affiliation(s)
- Sandra Santasusagna
- Department of Urology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
- Department of Biochemistry and Molecular Biology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
| | - Shijia Zhu
- Department of Medicine, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota
| | - Vijayakumar Jawalagatti
- Department of Urology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
- Department of Biochemistry and Molecular Biology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
| | | | - Adam Ertel
- Department of Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Saioa Garcia-Longarte
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Won-Min Song
- Department of Genetics and Genome Sciences, Tisch Cancer Center, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Naoto Fujiwara
- Department of Medicine, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Peiyao Li
- Department of Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Isabel Mendizabal
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Daniel P. Petrylak
- Department of Oncology, Yale Comprehensive Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - William Kevin Kelly
- Department of Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - E. Premkumar Reddy
- Department of Oncological Sciences, Tisch Cancer Center, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Liguo Wang
- Department of Biochemistry and Molecular Biology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
| | - Matthew J. Schiewer
- Department of Pharmacology, Physiology, and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Amaia Lujambio
- Department of Oncological Sciences, Tisch Cancer Center, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jeffrey Karnes
- Department of Urology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
| | - Karen E. Knudsen
- Department of Pharmacology, Physiology, and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Carlos Cordon-Cardo
- Department of Pathology. Tisch Cancer Center, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Haidong Dong
- Department of Urology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
- Department of Immunology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
| | - Haojie Huang
- Department of Urology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
- Department of Biochemistry and Molecular Biology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
| | - Arkaitz Carracedo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Traslational prostate cancer Research Lab, CIC bioGUNE-Basurto, Biocruces Bizkaia Health Research Institute CIC bioGUNE, Bizkaia Technology Park, Derio, Spain
- CIBERONC, Madrid, Spain
- Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Yujin Hoshida
- Department of Medicine, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Veronica Rodriguez-Bravo
- Department of Urology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
- Department of Biochemistry and Molecular Biology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
| | - Josep Domingo-Domenech
- Department of Urology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
- Department of Biochemistry and Molecular Biology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
| |
Collapse
|
17
|
Godoy PM, Oyedeji A, Mudd JL, Morikis VA, Zarov AP, Longmore GD, Fields RC, Kaufman CK. Functional analysis of recurrent CDC20 promoter variants in human melanoma. Commun Biol 2023; 6:1216. [PMID: 38030698 PMCID: PMC10686982 DOI: 10.1038/s42003-023-05526-2] [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: 09/05/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023] Open
Abstract
Small nucleotide variants in non-coding regions of the genome can alter transcriptional regulation, leading to changes in gene expression which can activate oncogenic gene regulatory networks. Melanoma is heavily burdened by non-coding variants, representing over 99% of total genetic variation, including the well-characterized TERT promoter mutation. However, the compendium of regulatory non-coding variants is likely still functionally under-characterized. We developed a pipeline to identify hotspots, i.e. recurrently mutated regions, in melanoma containing putatively functional non-coding somatic variants that are located within predicted melanoma-specific regulatory regions. We identified hundreds of statistically significant hotspots, including the hotspot containing the TERT promoter variants, and focused on a hotspot in the promoter of CDC20. We found that variants in the promoter of CDC20, which putatively disrupt an ETS motif, lead to lower transcriptional activity in reporter assays. Using CRISPR/Cas9, we generated an indel in the CDC20 promoter in human A375 melanoma cell lines and observed decreased expression of CDC20, changes in migration capabilities, increased growth of xenografts, and an altered transcriptional state previously associated with a more proliferative and less migratory state. Overall, our analysis prioritized several recurrent functional non-coding variants that, through downregulation of CDC20, led to perturbation of key melanoma phenotypes.
Collapse
Affiliation(s)
- Paula M Godoy
- Division of Medical Oncology, Department of Medicine and Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Abimbola Oyedeji
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in Saint Louis, St. Louis, MO, USA
| | - Jacqueline L Mudd
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in Saint Louis, St. Louis, MO, USA
| | - Vasilios A Morikis
- Departments of Medicine (Oncology) and Cell Biology and Physiology and the ICCE Institute, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Anna P Zarov
- Division of Medical Oncology, Department of Medicine and Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Gregory D Longmore
- Siteman Cancer Center, Washington University in Saint Louis, St. Louis, MO, USA
- Departments of Medicine (Oncology) and Cell Biology and Physiology and the ICCE Institute, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ryan C Fields
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in Saint Louis, St. Louis, MO, USA
| | - Charles K Kaufman
- Division of Medical Oncology, Department of Medicine and Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University in Saint Louis, St. Louis, MO, USA.
| |
Collapse
|
18
|
Dutriaux A, Diazzi S, Bresesti C, Hardouin S, Deshayes F, Collignon J, Flagiello D. LADON, a Natural Antisense Transcript of NODAL, Promotes Tumour Progression and Metastasis in Melanoma. Noncoding RNA 2023; 9:71. [PMID: 37987367 PMCID: PMC10661258 DOI: 10.3390/ncrna9060071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/02/2023] [Accepted: 11/10/2023] [Indexed: 11/22/2023] Open
Abstract
The TGFβ family member NODAL, repeatedly required during embryonic development, has also been associated with tumour progression. Our aim was to clarify the controversy surrounding its involvement in melanoma tumour progression. We found that the deletion of the NODAL exon 2 in a metastatic melanoma cell line impairs its ability to form tumours and colonize distant tissues. However, we show that this phenotype does not result from the absence of NODAL, but from a defect in the expression of a natural antisense transcript of NODAL, here called LADON. We show that LADON expression is specifically activated in metastatic melanoma cell lines, that its transcript is packaged in exosomes secreted by melanoma cells, and that, via its differential impact on the expression of oncogenes and tumour suppressors, it promotes the mesenchymal to amoeboid transition that is critical for melanoma cell invasiveness. LADON is, therefore, a new player in the regulatory network governing tumour progression in melanoma and possibly in other types of cancer.
Collapse
Affiliation(s)
| | | | | | | | | | - Jérôme Collignon
- Institut Jacques Monod, Université Paris Cité, CNRS, F-75013 Paris, France; (A.D.); (S.D.)
| | - Domenico Flagiello
- Institut Jacques Monod, Université Paris Cité, CNRS, F-75013 Paris, France; (A.D.); (S.D.)
| |
Collapse
|
19
|
Roider E, Lakatos AIT, McConnell AM, Wang P, Mueller A, Kawakami A, Tsoi J, Szabolcs BL, Ascsillán AA, Suita Y, Igras V, Lo JA, Hsiao JJ, Lapides R, Pál DMP, Lengyel AS, Navarini A, Okazaki A, Iliopoulos O, Németh I, Graeber TG, Zon L, Giese RW, Kemeny LV, Fisher DE. MITF regulates IDH1 and NNT and drives a transcriptional program protecting cutaneous melanoma from reactive oxygen species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.10.564582. [PMID: 38014031 PMCID: PMC10680652 DOI: 10.1101/2023.11.10.564582] [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
Microphthalmia-associated transcription factor (MITF) plays pivotal roles in melanocyte development, function, and melanoma pathogenesis. MITF amplification occurs in melanoma and has been associated with resistance to targeted therapies. Here, we show that MITF regulates a global antioxidant program that increases survival of melanoma cell lines by protecting the cells from reactive oxygen species (ROS)-induced damage. In addition, this redox program is correlated with MITF expression in human melanoma cell lines and patient-derived melanoma samples. Using a zebrafish melanoma model, we show that MITF decreases ROS-mediated DNA damage in vivo . Some of the MITF target genes involved, such as IDH1 and NNT , are regulated through direct MITF binding to canonical enhancer box (E-BOX) sequences proximal to their promoters. Utilizing functional experiments, we demonstrate the role of MITF and its target genes in reducing cytosolic and mitochondrial ROS. Collectively, our data identify MITF as a significant driver of the cellular antioxidant state. One Sentence Summary MITF promote melanoma survival via increasing ROS tolerance.
Collapse
|
20
|
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.
Collapse
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.
| |
Collapse
|
21
|
Muccioli S, Brillo V, Varanita T, Rossin F, Zaltron E, Velle A, Alessio G, Angi B, Severin F, Tosi A, D'Eletto M, Occhigrossi L, Falasca L, Checchetto V, Ciaccio R, Fascì A, Chieregato L, Rebelo AP, Giacomello M, Rosato A, Szabò I, Romualdi C, Piacentini M, Leanza L. Transglutaminase Type 2-MITF axis regulates phenotype switching in skin cutaneous melanoma. Cell Death Dis 2023; 14:704. [PMID: 37898636 PMCID: PMC10613311 DOI: 10.1038/s41419-023-06223-y] [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: 07/12/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 10/30/2023]
Abstract
Skin cutaneous melanoma (SKCM) is the deadliest form of skin cancer due to its high heterogeneity that drives tumor aggressiveness. Melanoma plasticity consists of two distinct phenotypic states that co-exist in the tumor niche, the proliferative and the invasive, respectively associated with a high and low expression of MITF, the master regulator of melanocyte lineage. However, despite efforts, melanoma research is still far from exhaustively dissecting this phenomenon. Here, we discovered a key function of Transglutaminase Type-2 (TG2) in regulating melanogenesis by modulating MITF transcription factor expression and its transcriptional activity. Importantly, we demonstrated that TG2 expression affects melanoma invasiveness, highlighting its positive value in SKCM. These results suggest that TG2 may have implications in the regulation of the phenotype switching by promoting melanoma differentiation and impairing its metastatic potential. Our findings offer potential perspectives to unravel melanoma vulnerabilities via tuning intra-tumor heterogeneity.
Collapse
Affiliation(s)
- Silvia Muccioli
- Department of Biology, University of Padua, Padua, Italy
- Laboratory of Translational Research, Azienda USL - IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | | | | | - Federica Rossin
- Department of Biology, University of Rome 'Tor Vergata', Rome, Italy
| | | | - Angelo Velle
- Department of Biology, University of Padua, Padua, Italy
| | | | - Beatrice Angi
- Department of Biology, University of Padua, Padua, Italy
| | | | - Anna Tosi
- Immunology and Molecular Oncology Diagnostics, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Manuela D'Eletto
- Department of Biology, University of Rome 'Tor Vergata', Rome, Italy
| | - Luca Occhigrossi
- Department of Biology, University of Rome 'Tor Vergata', Rome, Italy
| | - Laura Falasca
- National Institute for Infectious Diseases IRCCS "Lazzaro Spallanzani", Rome, Italy
| | | | | | - Amelia Fascì
- Department of Biology, University of Padua, Padua, Italy
| | | | | | | | - Antonio Rosato
- Immunology and Molecular Oncology Diagnostics, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
- Department of Surgery, Oncology and Gastroenterology (DiSCOG), University of Padua, Padua, Italy
| | - Ildikò Szabò
- Department of Biology, University of Padua, Padua, Italy
| | | | - Mauro Piacentini
- Department of Biology, University of Rome 'Tor Vergata', Rome, Italy
- National Institute for Infectious Diseases IRCCS "Lazzaro Spallanzani", Rome, Italy
| | - Luigi Leanza
- Department of Biology, University of Padua, Padua, Italy.
| |
Collapse
|
22
|
Tagore M, Hergenreder E, Perlee SC, Cruz NM, Menocal L, Suresh S, Chan E, Baron M, Melendez S, Dave A, Chatila WK, Nsengimana J, Koche RP, Hollmann TJ, Ideker T, Studer L, Schietinger A, White RM. GABA Regulates Electrical Activity and Tumor Initiation in Melanoma. Cancer Discov 2023; 13:2270-2291. [PMID: 37553760 PMCID: PMC10551668 DOI: 10.1158/2159-8290.cd-23-0389] [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: 04/05/2023] [Revised: 06/27/2023] [Accepted: 08/02/2023] [Indexed: 08/10/2023]
Abstract
Oncogenes can initiate tumors only in certain cellular contexts, which is referred to as oncogenic competence. In melanoma, whether cells in the microenvironment can endow such competence remains unclear. Using a combination of zebrafish transgenesis coupled with human tissues, we demonstrate that GABAergic signaling between keratinocytes and melanocytes promotes melanoma initiation by BRAFV600E. GABA is synthesized in melanoma cells, which then acts on GABA-A receptors in keratinocytes. Electron microscopy demonstrates specialized cell-cell junctions between keratinocytes and melanoma cells, and multielectrode array analysis shows that GABA acts to inhibit electrical activity in melanoma/keratinocyte cocultures. Genetic and pharmacologic perturbation of GABA synthesis abrogates melanoma initiation in vivo. These data suggest that GABAergic signaling across the skin microenvironment regulates the ability of oncogenes to initiate melanoma. SIGNIFICANCE This study shows evidence of GABA-mediated regulation of electrical activity between melanoma cells and keratinocytes, providing a new mechanism by which the microenvironment promotes tumor initiation. This provides insights into the role of the skin microenvironment in early melanomas while identifying GABA as a potential therapeutic target in melanoma. See related commentary by Ceol, p. 2128. This article is featured in Selected Articles from This Issue, p. 2109.
Collapse
Affiliation(s)
- Mohita Tagore
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Emiliano Hergenreder
- The Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, New York
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, New York
- Weill Graduate School of Medical Sciences of Cornell University, New York, New York
| | - Sarah C. Perlee
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nelly M. Cruz
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Laura Menocal
- Weill Graduate School of Medical Sciences of Cornell University, New York, New York
| | - Shruthy Suresh
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Eric Chan
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maayan Baron
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, California
| | - Stephanie Melendez
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Asim Dave
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Walid K. Chatila
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jeremie Nsengimana
- Biostatistics Research Group, Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Richard P. Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Travis J. Hollmann
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Trey Ideker
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, California
| | - Lorenz Studer
- The Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, New York
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, New York
| | - Andrea Schietinger
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Richard M. White
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
- Nuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
23
|
Kuras M. Exploring the Complex and Multifaceted Interplay between Melanoma Cells and the Tumor Microenvironment. Int J Mol Sci 2023; 24:14403. [PMID: 37762707 PMCID: PMC10531837 DOI: 10.3390/ijms241814403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/17/2023] [Accepted: 09/20/2023] [Indexed: 09/29/2023] Open
Abstract
Malignant melanoma is a very aggressive skin cancer, characterized by a heterogeneous nature and high metastatic potential. The incidence of melanoma is continuously increasing worldwide, and it is one of the most common cancers in young adults. In the past twenty years, our understanding of melanoma biology has increased profoundly, and disease management for patients with disseminated disease has improved due to the emergence of immunotherapy and targeted therapy. However, a significant fraction of patients relapse or do not respond adequately to treatment. This can partly be explained by the complex signaling between the tumor and its microenvironment, giving rise to melanoma phenotypes with different patterns of disease progression. This review focuses on the key aspects and complex relationship between pathogenesis, genetic abnormalities, tumor microenvironment, cellular plasticity, and metabolic reprogramming in melanoma. By acquiring a deeper understanding of the multifaceted features of melanomagenesis, we can reach a point of more individualized and patient-centered disease management and reduced costs of ineffective treatments.
Collapse
Affiliation(s)
- Magdalena Kuras
- Department of Biomedical Engineering, Lund University, 221 00 Lund, Sweden;
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, 205 02 Malmö, Sweden
| |
Collapse
|
24
|
Bravo González-Blas C, De Winter S, Hulselmans G, Hecker N, Matetovici I, Christiaens V, Poovathingal S, Wouters J, Aibar S, Aerts S. SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks. Nat Methods 2023; 20:1355-1367. [PMID: 37443338 PMCID: PMC10482700 DOI: 10.1038/s41592-023-01938-4] [Citation(s) in RCA: 85] [Impact Index Per Article: 85.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 06/06/2023] [Indexed: 07/15/2023]
Abstract
Joint profiling of chromatin accessibility and gene expression in individual cells provides an opportunity to decipher enhancer-driven gene regulatory networks (GRNs). Here we present a method for the inference of enhancer-driven GRNs, called SCENIC+. SCENIC+ predicts genomic enhancers along with candidate upstream transcription factors (TFs) and links these enhancers to candidate target genes. To improve both recall and precision of TF identification, we curated and clustered a motif collection with more than 30,000 motifs. We benchmarked SCENIC+ on diverse datasets from different species, including human peripheral blood mononuclear cells, ENCODE cell lines, melanoma cell states and Drosophila retinal development. Next, we exploit SCENIC+ predictions to study conserved TFs, enhancers and GRNs between human and mouse cell types in the cerebral cortex. Finally, we use SCENIC+ to study the dynamics of gene regulation along differentiation trajectories and the effect of TF perturbations on cell state. SCENIC+ is available at scenicplus.readthedocs.io .
Collapse
Affiliation(s)
- Carmen Bravo González-Blas
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Seppe De Winter
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Gert Hulselmans
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Nikolai Hecker
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Irina Matetovici
- VIB Center for Brain & Disease Research, Leuven, Belgium
- VIB Tech Watch, VIB Headquarters, Ghent, Belgium
| | - Valerie Christiaens
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Jasper Wouters
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Sara Aibar
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Stein Aerts
- VIB Center for Brain & Disease Research, Leuven, Belgium.
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
| |
Collapse
|
25
|
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.
Collapse
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
| |
Collapse
|
26
|
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.
Collapse
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
| |
Collapse
|
27
|
Yang TT, Yu S, Ke CLK, Cheng ST. The Genomic Landscape of Melanoma and Its Therapeutic Implications. Genes (Basel) 2023; 14:genes14051021. [PMID: 37239381 DOI: 10.3390/genes14051021] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/25/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
Melanoma is one of the most aggressive malignancies of the skin. The genetic composition of melanoma is complex and varies among different subtypes. With the aid of recent technologies such as next generation sequencing and single-cell sequencing, our understanding of the genomic landscape of melanoma and its tumor microenvironment has become increasingly clear. These advances may provide explanation to the heterogenic treatment outcomes of melanoma patients under current therapeutic guidelines and provide further insights to the development of potential new therapeutic targets. Here, we provide a comprehensive review on the genetics related to melanoma tumorigenesis, metastasis, and prognosis. We also review the genetics affecting the melanoma tumor microenvironment and its relation to tumor progression and treatment.
Collapse
Affiliation(s)
- Ting-Ting Yang
- Department of Dermatology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Dermatology, Pingtung Hospital, Ministry of Health and Welfare, Pingtung 900, Taiwan
| | - Sebastian Yu
- Department of Dermatology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Dermatology, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Neuroscience Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Chiao-Li Khale Ke
- Department of Psychiatry, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- Department of Psychiatry, Kaohsiung Municipal SiaoGang Hospital, Kaohsiung Medical University, Kaohsiung 812, Taiwan
| | - Shih-Tsung Cheng
- Department of Dermatology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Dermatology, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| |
Collapse
|
28
|
Neuendorf HM, Simmons JL, Boyle GM. Therapeutic targeting of anoikis resistance in cutaneous melanoma metastasis. Front Cell Dev Biol 2023; 11:1183328. [PMID: 37181747 PMCID: PMC10169659 DOI: 10.3389/fcell.2023.1183328] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/14/2023] [Indexed: 05/16/2023] Open
Abstract
The acquisition of resistance to anoikis, the cell death induced by loss of adhesion to the extracellular matrix, is an absolute requirement for the survival of disseminating and circulating tumour cells (CTCs), and for the seeding of metastatic lesions. In melanoma, a range of intracellular signalling cascades have been identified as potential drivers of anoikis resistance, however a full understanding of the process is yet to be attained. Mechanisms of anoikis resistance pose an attractive target for the therapeutic treatment of disseminating and circulating melanoma cells. This review explores the range of small molecule, peptide and antibody inhibitors targeting molecules involved in anoikis resistance in melanoma, and may be repurposed to prevent metastatic melanoma prior to its initiation, potentially improving the prognosis for patients.
Collapse
Affiliation(s)
- Hannah M. Neuendorf
- Cancer Drug Mechanisms Group, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Jacinta L. Simmons
- Cancer Drug Mechanisms Group, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Glen M. Boyle
- Cancer Drug Mechanisms Group, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| |
Collapse
|
29
|
Koziej P, Kluszczynska K, Hartman ML, Czyz M. Trametinib-Resistant Melanoma Cells Displaying MITF high/NGFR low/IL-8 low Phenotype Are Highly Responsive to Alternating Periods of Drug Withdrawal and Drug Rechallenge. Int J Mol Sci 2023; 24:ijms24097891. [PMID: 37175614 PMCID: PMC10178474 DOI: 10.3390/ijms24097891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 04/19/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Despite significant advances in targeted therapies against the hyperactivated BRAFV600/MEK pathway for patients with unresectable metastatic melanoma, acquired resistance remains an unsolved clinical problem. In this study, we focused on melanoma cells resistant to trametinib, an agent broadly used in combination therapies. Molecular and cellular changes were assessed during alternating periods of trametinib withdrawal and rechallenge in trametinib-resistant cell lines displaying either a differentiation phenotype (MITFhigh/NGFRlow) or neural crest stem-like dedifferentiation phenotype (NGFRhigh/MITFlow). Neither drug withdrawal nor drug rechallenge induced cell death, and instead of loss of fitness, trametinib-resistant melanoma cells adapted to altered conditions by phenotype switching. In resistant cells displaying a differentiation phenotype, trametinib withdrawal markedly decreased MITF level and activity, which was associated with reduced cell proliferation capacity, and induced stemness assessed as NGFR-positive cells and senescence features, including IL-8 expression and secretion. All these changes could be reversed by trametinib re-exposure, which emphasizes melanoma cell plasticity. Trametinib-resistant cells displaying a dedifferentiation phenotype were less responsive presumably due to the already low level of MITF, a master regulator of the melanoma phenotype. Considering new directions of the development of anti-melanoma treatment, our study suggests that the phenotype of melanomas resistant to targeted therapy might be a crucial determinant of the selection of second-line therapy for melanoma patients.
Collapse
Affiliation(s)
- Paulina Koziej
- Department of Molecular Biology of Cancer, Medical University of Lodz, 6/8 Mazowiecka Street, 92-215 Lodz, Poland
| | - Katarzyna Kluszczynska
- Department of Molecular Biology of Cancer, Medical University of Lodz, 6/8 Mazowiecka Street, 92-215 Lodz, Poland
| | - Mariusz L Hartman
- Department of Molecular Biology of Cancer, Medical University of Lodz, 6/8 Mazowiecka Street, 92-215 Lodz, Poland
| | - Malgorzata Czyz
- Department of Molecular Biology of Cancer, Medical University of Lodz, 6/8 Mazowiecka Street, 92-215 Lodz, Poland
| |
Collapse
|
30
|
Abstract
Over the past decade, melanoma has led the field in new cancer treatments, with impressive gains in on-treatment survival but more modest improvements in overall survival. Melanoma presents heterogeneity and transcriptional plasticity that recapitulates distinct melanocyte developmental states and phenotypes, allowing it to adapt to and eventually escape even the most advanced treatments. Despite remarkable advances in our understanding of melanoma biology and genetics, the melanoma cell of origin is still fiercely debated because both melanocyte stem cells and mature melanocytes can be transformed. Animal models and high-throughput single-cell sequencing approaches have opened new opportunities to address this question. Here, we discuss the melanocytic journey from the neural crest, where they emerge as melanoblasts, to the fully mature pigmented melanocytes resident in several tissues. We describe a new understanding of melanocyte biology and the different melanocyte subpopulations and microenvironments they inhabit, and how this provides unique insights into melanoma initiation and progression. We highlight recent findings on melanoma heterogeneity and transcriptional plasticity and their implications for exciting new research areas and treatment opportunities. The lessons from melanocyte biology reveal how cells that are present to protect us from the damaging effects of ultraviolet radiation reach back to their origins to become a potentially deadly cancer.
Collapse
Affiliation(s)
- Patricia P Centeno
- Molecular Oncology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, UK
| | - Valeria Pavet
- Molecular Oncology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, UK
| | - Richard Marais
- Molecular Oncology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, UK.
- Oncodrug Ltd, Alderly Park, Macclesfield, UK.
| |
Collapse
|
31
|
Moscona R, Janssen SM, Elchebly M, Papadakis AI, Rubin E, Spatz A. BORIS/CTCFL-mediated chromatin accessibility alterations promote a pro-invasive transcriptional signature in melanoma cells. Pigment Cell Melanoma Res 2023; 36:299-313. [PMID: 37082838 DOI: 10.1111/pcmr.13089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 03/20/2023] [Accepted: 03/30/2023] [Indexed: 04/22/2023]
Abstract
Melanoma is the deadliest form of skin cancer, due to its tendency to metastasize early. Brother of regulator of imprinted sites (BORIS), also known as CCCTC binding factor-like (CTCFL), is a transcription regulator that becomes ectopically expressed in melanoma. We recently showed that BORIS contributes to melanoma phenotype switching by altering the gene expression program of melanoma cells from an intermediate melanocytic state toward a more mesenchymal-like state. However, the mechanism underlying this transcriptional switch remains unclear. Here, ATAC-seq was used to study BORIS-mediated chromatin accessibility alterations in melanoma cells harboring an intermediate melanocytic state. The gene set that gained promoter accessibility, following ectopic BORIS expression, showed enrichment for biological processes associated with melanoma invasion, while promoters of genes associated with proliferation showed reduced accessibility. Integration of ATAC-seq and RNA-seq data demonstrated that increased chromatin accessibility was associated with transcriptional upregulation of genes involved in tumor progression processes, and the aberrant activation of oncogenic transcription factors, while reduced chromatin accessibility and downregulated genes were associated with repressed activity of tumor suppressors and proliferation factors. Together, these findings indicate that BORIS mediates transcriptional reprogramming in melanoma cells by altering chromatin accessibility and gene expression, shifting the cellular transcription landscape of melanoma cells toward a mesenchymal-like genetic signature.
Collapse
Affiliation(s)
- Roy Moscona
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Sanne Marlijn Janssen
- Lady Davis Institute, Montréal, Quebec, Canada
- Department of Pathology, McGill University, Montréal, Quebec, Canada
| | | | | | - Eitan Rubin
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Alan Spatz
- Lady Davis Institute, Montréal, Quebec, Canada
- Department of Pathology, McGill University, Montréal, Quebec, Canada
- Division of Pathology, Department of Laboratory Medicine, McGill University Health Center, Montréal, Quebec, Canada
- Department of Oncology, McGill University, Montréal, Quebec, Canada
| |
Collapse
|
32
|
Howell R, Davies J, Clarke MA, Appios A, Mesquita I, Jayal Y, Ringham-Terry B, Boned Del Rio I, Fisher J, Bennett CL. Localized immune surveillance of primary melanoma in the skin deciphered through executable modeling. SCIENCE ADVANCES 2023; 9:eadd1992. [PMID: 37043573 PMCID: PMC10096595 DOI: 10.1126/sciadv.add1992] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 03/10/2023] [Indexed: 06/19/2023]
Abstract
While skin is a site of active immune surveillance, primary melanomas often escape detection. Here, we have developed an in silico model to determine the local cross-talk between melanomas and Langerhans cells (LCs), the primary antigen-presenting cells at the site of melanoma development. The model predicts that melanomas fail to activate LC migration to lymph nodes until tumors reach a critical size, which is determined by a positive TNF-α feedback loop within melanomas, in line with our observations of murine tumors. In silico drug screening, supported by subsequent experimental testing, shows that treatment of primary tumors with MAPK pathway inhibitors may further prevent LC migration. In addition, our in silico model predicts treatment combinations that bypass LC dysfunction. In conclusion, our combined approach of in silico and in vivo studies suggests a molecular mechanism that explains how early melanomas develop under the radar of immune surveillance by LC.
Collapse
Affiliation(s)
| | | | - Matthew A. Clarke
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - Anna Appios
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - Inês Mesquita
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - Yashoda Jayal
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - Ben Ringham-Terry
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - Isabel Boned Del Rio
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | | | | |
Collapse
|
33
|
Li M, Wei J, Xue C, Zhou X, Chen S, Zheng L, Duan Y, Deng H, Xiong W, Tang F, Li G, Zhou M. Dissecting the roles and clinical potential of YY1 in the tumor microenvironment. Front Oncol 2023; 13:1122110. [PMID: 37081988 PMCID: PMC10110844 DOI: 10.3389/fonc.2023.1122110] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/13/2023] [Indexed: 04/07/2023] Open
Abstract
Yin-Yang 1 (YY1) is a member of the GLI-Kruppel family of zinc finger proteins and plays a vital dual biological role in cancer as an oncogene or a tumor suppressor during tumorigenesis and tumor progression. The tumor microenvironment (TME) is identified as the “soil” of tumor that has a critical role in both tumor growth and metastasis. Many studies have found that YY1 is closely related to the remodeling and regulation of the TME. Herein, we reviewed the expression pattern of YY1 in tumors and summarized the function and mechanism of YY1 in regulating tumor angiogenesis, immune and metabolism. In addition, we discussed the potential value of YY1 in tumor diagnosis and treatment and provided a novel molecular strategy for the clinical diagnosis and treatment of tumors.
Collapse
Affiliation(s)
- MengNa Li
- Key Laboratory of Carcinogenesis, National Health Commission, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Cancer Research Institute, Central South University, Changsha, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, China
- Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - JianXia Wei
- Key Laboratory of Carcinogenesis, National Health Commission, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Cancer Research Institute, Central South University, Changsha, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, China
| | - ChangNing Xue
- Key Laboratory of Carcinogenesis, National Health Commission, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Cancer Research Institute, Central South University, Changsha, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, China
| | - XiangTing Zhou
- The First Clinical College of Changsha Medical University, Changsha, China
| | - ShiPeng Chen
- Key Laboratory of Carcinogenesis, National Health Commission, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Cancer Research Institute, Central South University, Changsha, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, China
| | - LeMei Zheng
- Key Laboratory of Carcinogenesis, National Health Commission, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Cancer Research Institute, Central South University, Changsha, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, China
| | - YuMei Duan
- Key Laboratory of Carcinogenesis, National Health Commission, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Cancer Research Institute, Central South University, Changsha, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, China
| | - HongYu Deng
- Key Laboratory of Carcinogenesis, National Health Commission, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Cancer Research Institute, Central South University, Changsha, China
- Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Wei Xiong
- Key Laboratory of Carcinogenesis, National Health Commission, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Cancer Research Institute, Central South University, Changsha, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, China
| | - FaQing Tang
- Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - GuiYuan Li
- Key Laboratory of Carcinogenesis, National Health Commission, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Cancer Research Institute, Central South University, Changsha, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, China
| | - Ming Zhou
- Key Laboratory of Carcinogenesis, National Health Commission, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Cancer Research Institute, Central South University, Changsha, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, China
- Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- *Correspondence: Ming Zhou,
| |
Collapse
|
34
|
Lim SY, Shklovskaya E, Lee JH, Pedersen B, Stewart A, Ming Z, Irvine M, Shivalingam B, Saw RPM, Menzies AM, Carlino MS, Scolyer RA, Long GV, Rizos H. The molecular and functional landscape of resistance to immune checkpoint blockade in melanoma. Nat Commun 2023; 14:1516. [PMID: 36934113 PMCID: PMC10024679 DOI: 10.1038/s41467-023-36979-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 02/23/2023] [Indexed: 03/20/2023] Open
Abstract
Resistance to immune checkpoint inhibitor therapies in melanoma is common and remains an intractable clinical challenge. In this study, we comprehensively profile immune checkpoint inhibitor resistance mechanisms in short-term tumor cell lines and matched tumor samples from melanoma patients progressing on immune checkpoint inhibitors. Combining genome, transcriptome, and high dimensional flow cytometric profiling with functional analysis, we identify three distinct programs of immunotherapy resistance. Here we show that resistance programs include (1) the loss of wild-type antigen expression, resulting from tumor-intrinsic IFNγ signaling and melanoma de-differentiation, (2) the disruption of antigen presentation via multiple independent mechanisms affecting MHC expression, and (3) immune cell exclusion associated with PTEN loss. The dominant role of compromised antigen production and presentation in melanoma resistance to immune checkpoint inhibition highlights the importance of treatment salvage strategies aimed at the restoration of MHC expression, stimulation of innate immunity, and re-expression of wild-type differentiation antigens.
Collapse
Affiliation(s)
- Su Yin Lim
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
| | - Elena Shklovskaya
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
| | - Jenny H Lee
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Department of Medical Oncology, Chris O'Brien Lifehouse, Sydney, NSW, Australia
| | - Bernadette Pedersen
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
| | - Ashleigh Stewart
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
| | - Zizhen Ming
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
| | - Mal Irvine
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
| | - Brindha Shivalingam
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Department of Neurosurgery, Chris O'Brien Lifehouse, Sydney, NSW, Australia
- Department of Neurosurgery, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Robyn P M Saw
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Alexander M Menzies
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Department of Medical Oncology, Northern Sydney Cancer Centre, Royal North Shore Hospital, Sydney, NSW, Australia
- Department of Medical Oncology, Mater Hospital, Sydney, NSW, Australia
| | - Matteo S Carlino
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Department of Medical Oncology, Blacktown Cancer and Haematology Centre, Blacktown Hospital, Sydney, NSW, Australia
- Department of Medical Oncology, Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, NSW, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Georgina V Long
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Department of Medical Oncology, Northern Sydney Cancer Centre, Royal North Shore Hospital, Sydney, NSW, Australia
- Department of Medical Oncology, Mater Hospital, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Helen Rizos
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia.
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia.
| |
Collapse
|
35
|
Xu L, Liu Y, Chen X, Zhong H, Wang Y. Ferroptosis in life: To be or not to be. Biomed Pharmacother 2023; 159:114241. [PMID: 36634587 DOI: 10.1016/j.biopha.2023.114241] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 01/12/2023] Open
Abstract
Ferroptosis is a novel type of programmed cell death, characterized by a dysregulated iron metabolism and accumulation of lipid peroxides. It features the alteration of mitochondria and aberrant accumulation of excessive iron as well as loss of the cysteine-glutathione-GPX4 axis. Eventually, the accumulated lipid peroxides result in lethal damage to the cells. Ferroptosis is induced by the overloading of iron and the accumulation of ROS and can be inhibited by the activation of the GPX4 pathway, FS1-CoQ10 pathway, GCH1-BH4 pathway, and the DHODH pathway, it is also regulated by the oncogenes and tumor suppressors. Ferroptosis involves various physiological and pathological processes, and increasing evidence indicates that ferroptosis play a critical role in cancers and other diseases. It inhibits the proliferation of malignant cells in various types of cancers and inducing ferroptosis may become a new method of cancer treatment. Many inhibitors targeting the key factors of ferroptosis such as SLC7A11, GPX4, and iron overload have been developed. The application of ferroptosis is mainly divided into two directions, i.e. to avoid ferroptosis in healthy cells and selectively induce ferroptosis in cancers. In this review, we provide a critical analysis of the concept, and regulation pathways of ferroptosis and explored its roles in various diseases, we also summarized the compounds targeting ferroptosis, aiming to promote the speed of clinical use of ferroptosis induction in cancer treatment.
Collapse
Affiliation(s)
- Ling Xu
- Department of Internal Medicine of Traditional Chinese Medicine, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai 200120, China.
| | - Yu'e Liu
- Tongji University Cancer Center, Shanghai Tenth People's Hospital of Tongji University, School of Medicine, Tongji University, Shanghai 200092, China.
| | - Xi Chen
- Xi Chen, Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hua Zhong
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA 96813
| | - Yi Wang
- Department of Critical Care Medicine, Sichuan Academy of Medical Science and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| |
Collapse
|
36
|
The mechanical phenotypic plasticity of melanoma cell: an emerging driver of therapy cross-resistance. Oncogenesis 2023; 12:7. [PMID: 36774337 PMCID: PMC9922263 DOI: 10.1038/s41389-023-00452-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/13/2023] Open
Abstract
Advanced cutaneous melanoma is the deadliest form of skin cancer and one of the most aggressive human cancers. Targeted therapies (TT) against BRAF mutated melanoma and immune checkpoints blockade therapies (ICB) have been a breakthrough in the treatment of metastatic melanoma. However, therapy-driven resistance remains a major hurdle in the clinical management of the metastatic disease. Besides shaping the tumor microenvironment, current treatments impact transition states to promote melanoma cell phenotypic plasticity and intratumor heterogeneity, which compromise treatment efficacy and clinical outcomes. In this context, mesenchymal-like dedifferentiated melanoma cells exhibit a remarkable ability to autonomously assemble their own extracellular matrix (ECM) and to biomechanically adapt in response to therapeutic insults, thereby fueling tumor relapse. Here, we review recent studies that highlight mechanical phenotypic plasticity of melanoma cells as a hallmark of adaptive and non-genetic resistance to treatment and emerging driver in cross-resistance to TT and ICB. We also discuss how targeting BRAF-mutant dedifferentiated cells and ECM-based mechanotransduction pathways may overcome melanoma cross-resistance.
Collapse
|
37
|
PPARs and the Kynurenine Pathway in Melanoma-Potential Biological Interactions. Int J Mol Sci 2023; 24:ijms24043114. [PMID: 36834531 PMCID: PMC9960262 DOI: 10.3390/ijms24043114] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/28/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Peroxisome proliferator-activated receptors (PPARs) are ligand-activated transcription factors involved in various physiological and pathological processes within the skin. PPARs regulate several processes in one of the most aggressive skin cancers, melanoma, including proliferation, cell cycle, metabolic homeostasis, cell death, and metastasis. In this review, we focused not only on the biological activity of PPAR isoforms in melanoma initiation, progression, and metastasis but also on potential biological interactions between the PPAR signaling and the kynurenine pathways. The kynurenine pathway is a major pathway of tryptophan metabolism leading to nicotinamide adenine dinucleotide (NAD+) production. Importantly, various tryptophan metabolites exert biological activity toward cancer cells, including melanoma. Previous studies confirmed the functional relationship between PPAR and the kynurenine pathway in skeletal muscles. Despite the fact this interaction has not been reported in melanoma to date, some bioinformatics data and biological activity of PPAR ligands and tryptophan metabolites may suggest a potential involvement of these metabolic and signaling pathways in melanoma initiation, progression, and metastasis. Importantly, the possible relationship between the PPAR signaling pathway and the kynurenine pathway may relate not only to the direct biological effect on melanoma cells but also to the tumor microenvironment and the immune system.
Collapse
|
38
|
Mehdi A, Attias M, Arakelian A, Szyf M, Piccirillo CA, Rabbani SA. S-adenosylmethionine blocks tumorigenesis and with immune checkpoint inhibitor enhances anti-cancer efficacy against BRAF mutant and wildtype melanomas. Neoplasia 2023; 36:100874. [PMID: 36638586 PMCID: PMC9840362 DOI: 10.1016/j.neo.2022.100874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/13/2023]
Abstract
Despite marked success in treatment with immune checkpoint inhibitor (CPI), only a third of patients are responsive. Thus, melanoma still has one of the highest prevalence and mortality rates; which has led to a search for novel combination therapies that might complement CPI. Aberrant methylomes are one of the mechanisms of resistance to CPI therapy. S-adenosylmethionine (SAM), methyl donor of important epigenetic processes, has significant anti-cancer effects in several malignancies; however, SAM's effect has never been extensively investigated in melanoma. We demonstrate that SAM modulates phenotype switching of melanoma cells and directs the cells towards differentiation indicated by increased melanogenesis (melanin and melanosome synthesis), melanocyte-like morphology, elevated Mitf and Mitf activators' expression, increased antigen expression, reduced proliferation, and reduced stemness genes' expression. Consistently, providing SAM orally, reduced tumor growth and progression, and metastasis of syngeneic BRAF mutant and wild-type (WT) melanoma mouse models. Of note, SAM and anti-PD-1 antibody combination treatment had enhanced anti-cancer efficacy compared to monotherapies, showed significant reduction in tumor growth and progression, and increased survival. Furthermore, SAM and anti-PD-1 antibody combination triggered significantly higher immune cell infiltration, higher CD8+ T cells infiltration and effector functions, and polyfunctionality of CD8+ T cells in YUMMER1.7 tumors. Therefore, SAM combined with CPI provides a novel therapeutic strategy against BRAF mutant and WT melanomas and provides potential to be translated into clinic.
Collapse
Affiliation(s)
- A Mehdi
- Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3A 2B4, Canada; Department of Human Genetics, McGill University, Montreal, QC H3A 2B4, Canada; Program in Metabolic Disorders and Complications (MeDiC), Research Institute of the McGill University Health Centre, 1001 Décarie Blvd. (Glen site), Room EM1.3232, Montréal, QC H4A 3J1, Canada
| | - M Attias
- Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3A 2B4, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada; Program in Infectious Diseases and Immunology in Global Health, Centre for Translational Biology, Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada; Centre of Excellence in Translational Immunology (CETI), Montréal, QC H4A 3J1, Canada
| | - A Arakelian
- Program in Metabolic Disorders and Complications (MeDiC), Research Institute of the McGill University Health Centre, 1001 Décarie Blvd. (Glen site), Room EM1.3232, Montréal, QC H4A 3J1, Canada
| | - M Szyf
- Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3A 2B4, Canada; Department of Pharmacology and Therapeutics, McGill University, Montreal, QC H3A 2B4, Canada
| | - C A Piccirillo
- Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3A 2B4, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada; Program in Infectious Diseases and Immunology in Global Health, Centre for Translational Biology, Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada; Centre of Excellence in Translational Immunology (CETI), Montréal, QC H4A 3J1, Canada
| | - S A Rabbani
- Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3A 2B4, Canada; Department of Human Genetics, McGill University, Montreal, QC H3A 2B4, Canada; Department of Experimental Medicine, McGill University, Montreal, QC H3A 2B4, Canada; Department of Oncology, McGill University, Montreal, QC H3A 2B4, Canada; Program in Metabolic Disorders and Complications (MeDiC), Research Institute of the McGill University Health Centre, 1001 Décarie Blvd. (Glen site), Room EM1.3232, Montréal, QC H4A 3J1, Canada.
| |
Collapse
|
39
|
Ziogas DC, Theocharopoulos C, Koutouratsas T, Haanen J, Gogas H. Mechanisms of resistance to immune checkpoint inhibitors in melanoma: What we have to overcome? Cancer Treat Rev 2023; 113:102499. [PMID: 36542945 DOI: 10.1016/j.ctrv.2022.102499] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022]
Abstract
Marching into the second decade after the approval of ipilimumab, it is clear that immune checkpoint inhibitors (ICIs) have dramatically improved the prognosis of melanoma. Although the current edge is already high, with a 4-year OS% of 77.9% for adjuvant nivolumab and a 6.5-year OS% of 49% for nivolumab/ipilimumab combination in the metastatic setting, a high proportion of patients with advanced melanoma have no benefit from immunotherapy, or experience an early disease relapse/progression in the first few months of treatment, surviving much less. Reasonably, the primary and acquired resistance to ICIs has entered into the focus of clinical research with positive (e.g., nivolumab and relatlimab combination) and negative feedbacks (e.g., nivolumab with pegylated-IL2, pembrolizumab with T-VEC, nivolumab with epacadostat, and combinatorial triplets of BRAF/MEK inhibitors with immunotherapy). Many intrinsic (intracellular or intra-tumoral) but also extrinsic (systematic) events are considered to be involved in the development of this resistance to ICIs: i) melanoma cell immunogenicity (e.g., tumor mutational burden, antigen-processing machinery and immunogenic cell death, neoantigen affinity and heterogeneity, genomic instability, melanoma dedifferentiation and phenotypic plasticity), ii) immune cell trafficking, T-cell priming, and cell death evasion, iii) melanoma neovascularization, cellular TME components(e.g., Tregs, CAFs) and extracellular matrix modulation, iv) metabolic antagonism in the TME(highly glycolytic status, upregulated CD39/CD73/adenosine pathway, iDO-dependent tryptophan catabolism), v) T-cell exhaustion and negative immune checkpoints, and vi) gut microbiota. In the present overview, we discuss how these parameters compromise the efficacy of ICIs, with an emphasis on the lessons learned by the latest melanoma studies; and in parallel, we describe the main ongoing approaches to overcome the resistance to immunotherapy. Summarizing this information will improve the understanding of how these complicated dynamics contribute to immune escape and will help to develop more effective strategies on how anti-tumor immunity can surpass existing barriers of ICI-refractory melanoma.
Collapse
Affiliation(s)
- Dimitrios C Ziogas
- First Department of Medicine, National and Kapodistrian University of Athens School of Medicine, Athens, Greece.
| | - Charalampos Theocharopoulos
- First Department of Medicine, National and Kapodistrian University of Athens School of Medicine, Athens, Greece.
| | - Tilemachos Koutouratsas
- First Department of Medicine, National and Kapodistrian University of Athens School of Medicine, Athens, Greece.
| | - John Haanen
- Division of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Helen Gogas
- First Department of Medicine, National and Kapodistrian University of Athens School of Medicine, Athens, Greece.
| |
Collapse
|
40
|
Lasheras-Otero I, Feliu I, Maillo A, Moreno H, Redondo-Muñoz M, Aldaz P, Bocanegra A, Olias-Arjona A, Lecanda F, Fernandez-Irigoyen J, Santamaria E, Larrayoz IM, Gomez-Cabrero D, Wellbrock C, Vicent S, Arozarena I. The Regulators of Peroxisomal Acyl-Carnitine Shuttle CROT and CRAT Promote Metastasis in Melanoma. J Invest Dermatol 2023; 143:305-316.e5. [PMID: 36058299 DOI: 10.1016/j.jid.2022.08.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/26/2022] [Accepted: 08/03/2022] [Indexed: 01/25/2023]
Abstract
Circulating tumor cells are the key link between a primary tumor and distant metastases, but once in the bloodstream, loss of adhesion induces cell death. To identify the mechanisms relevant for melanoma circulating tumor cell survival, we performed RNA sequencing and discovered that detached melanoma cells and isolated melanoma circulating tumor cells rewire lipid metabolism by upregulating fatty acid (FA) transport and FA beta-oxidation‒related genes. In patients with melanoma, high expression of FA transporters and FA beta-oxidation enzymes significantly correlates with reduced progression-free and overall survival. Among the highest expressed regulators in melanoma circulating tumor cells were the carnitine transferases carnitine O-octanoyltransferase and carnitine acetyltransferase, which control the shuttle of peroxisome-derived medium-chain FAs toward mitochondria to fuel mitochondrial FA beta-oxidation. Knockdown of carnitine O-octanoyltransferase or carnitine acetyltransferase and short-term treatment with peroxisomal or mitochondrial FA beta-oxidation inhibitors thioridazine or ranolazine suppressed melanoma metastasis in mice. Carnitine O-octanoyltransferase and carnitine acetyltransferase depletion could be rescued by medium-chain FA supplementation, indicating that the peroxisomal supply of FAs is crucial for the survival of nonadherent melanoma cells. Our study identifies targeting the FA-based cross-talk between peroxisomes and mitochondria as a potential therapeutic opportunity to challenge melanoma progression. Moreover, the discovery of the antimetastatic activity of the Food and Drug Administration‒approved drug ranolazine carries translational potential.
Collapse
Affiliation(s)
- Irene Lasheras-Otero
- Cancer Signaling Unit, Navarrabiomed, University Hospital of Navarra (HUN), Public University of Navarra (UPNA), Pamplona, Spain; IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Iker Feliu
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain; Program in Solid Tumors, Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Alberto Maillo
- Translational Bioinformatics Unit, Navarrabiomed, University Hospital of Navarra (HUN), Public University of Navarra (UPNA), Pamplona, Spain
| | - Haritz Moreno
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain; Program in Solid Tumors, Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Marta Redondo-Muñoz
- Cancer Signaling Unit, Navarrabiomed, University Hospital of Navarra (HUN), Public University of Navarra (UPNA), Pamplona, Spain; IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Paula Aldaz
- Cancer Signaling Unit, Navarrabiomed, University Hospital of Navarra (HUN), Public University of Navarra (UPNA), Pamplona, Spain; IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Ana Bocanegra
- Oncoimmunology Group, Navarrabiomed, Navarrabiomed, University Hospital of Navarra (HUN), Public University of Navarra (UPNA), Pamplona, Spain
| | - Ana Olias-Arjona
- Cancer Signaling Unit, Navarrabiomed, University Hospital of Navarra (HUN), Public University of Navarra (UPNA), Pamplona, Spain; IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Fernando Lecanda
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain; Program in Solid Tumors, Centre for Applied Medical Research, University of Navarra, Pamplona, Spain; Center for Biomedical Research Network on Cancer (CIBERONC), Madrid, Spain; Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, Pamplona, Spain
| | - Joaquin Fernandez-Irigoyen
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain; Proteomics Platform, Navarrabiomed, University Hospital of Navarra (HUN), Public University of Navarra (UPNA), Pamplona, Spain
| | - Enrique Santamaria
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain; Clinical Neuroproteomics Unit, Navarrabiomed, University Hospital of Navarra (HUN), Public University of Navarra (UPNA), Pamplona, Spain
| | - Ignacio M Larrayoz
- Biomarkers and Molecular Signaling Group, Center for Biomedical Research of La Rioja (CIBIR), Foundation Rioja Salud, Logroño, Spain; Pre-departmental Nursing Unit, University of La Rioja (UR), Logroño, La Rioja, Spain
| | - David Gomez-Cabrero
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain; Translational Bioinformatics Unit, Navarrabiomed, University Hospital of Navarra (HUN), Public University of Navarra (UPNA), Pamplona, Spain; Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Claudia Wellbrock
- Cancer Signaling Unit, Navarrabiomed, University Hospital of Navarra (HUN), Public University of Navarra (UPNA), Pamplona, Spain
| | - Silvestre Vicent
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain; Program in Solid Tumors, Centre for Applied Medical Research, University of Navarra, Pamplona, Spain; Center for Biomedical Research Network on Cancer (CIBERONC), Madrid, Spain
| | - Imanol Arozarena
- Cancer Signaling Unit, Navarrabiomed, University Hospital of Navarra (HUN), Public University of Navarra (UPNA), Pamplona, Spain; IdiSNA, Navarra Institute for Health Research, Pamplona, Spain.
| |
Collapse
|
41
|
Kontogianni G, Voutetakis K, Piroti G, Kypreou K, Stefanaki I, Vlachavas EI, Pilalis E, Stratigos A, Chatziioannou A, Papadodima O. A Comprehensive Analysis of Cutaneous Melanoma Patients in Greece Based on Multi-Omic Data. Cancers (Basel) 2023; 15:cancers15030815. [PMID: 36765773 PMCID: PMC9913631 DOI: 10.3390/cancers15030815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 02/01/2023] Open
Abstract
Cutaneous melanoma (CM) is the most aggressive type of skin cancer, and it is characterised by high mutational load and heterogeneity. In this study, we aimed to analyse the genomic and transcriptomic profile of primary melanomas from forty-six Formalin-Fixed, Paraffin-Embedded (FFPE) tissues from Greek patients. Molecular analysis for both germline and somatic variations was performed in genomic DNA from peripheral blood and melanoma samples, respectively, exploiting whole exome and targeted sequencing, and transcriptomic analysis. Detailed clinicopathological data were also included in our analyses and previously reported associations with specific mutations were recognised. Most analysed samples (43/46) were found to harbour at least one clinically actionable somatic variant. A subset of samples was profiled at the transcriptomic level, and it was shown that specific melanoma phenotypic states could be inferred from bulk RNA isolated from FFPE primary melanoma tissue. Integrative bioinformatics analyses, including variant prioritisation, differential gene expression analysis, and functional and gene set enrichment analysis by group and per sample, were conducted and molecular circuits that are implicated in melanoma cell programmes were highlighted. Integration of mutational and transcriptomic data in CM characterisation could shed light on genes and pathways that support the maintenance of phenotypic states encrypted into heterogeneous primary tumours.
Collapse
Affiliation(s)
- Georgia Kontogianni
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
- Centre of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | | | - Georgia Piroti
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Katerina Kypreou
- 1st Department of Dermatology, Andreas Syggros Hospital, Medical School, National and Kapodistrian University of Athens, 16121 Athens, Greece
| | - Irene Stefanaki
- 1st Department of Dermatology, Andreas Syggros Hospital, Medical School, National and Kapodistrian University of Athens, 16121 Athens, Greece
| | | | | | - Alexander Stratigos
- 1st Department of Dermatology, Andreas Syggros Hospital, Medical School, National and Kapodistrian University of Athens, 16121 Athens, Greece
| | - Aristotelis Chatziioannou
- Centre of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
- e-NIOS Applications Private Company, 17671 Kallithea, Greece
- Correspondence: (A.C.); (O.P.); Tel.: +30-210-727-3721 (A.C. & O.P.)
| | - Olga Papadodima
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
- Correspondence: (A.C.); (O.P.); Tel.: +30-210-727-3721 (A.C. & O.P.)
| |
Collapse
|
42
|
Militaru IV, Rus AA, Munteanu CV, Manica G, Petrescu SM. New panel of biomarkers to discriminate between amelanotic and melanotic metastatic melanoma. Front Oncol 2023; 12:1061832. [PMID: 36776379 PMCID: PMC9909407 DOI: 10.3389/fonc.2022.1061832] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/28/2022] [Indexed: 01/27/2023] Open
Abstract
Melanoma is a form of skin cancer that can rapidly invade distant organs. A distinctive feature of melanomas is their pigmentation status, as melanin is present in most skin melanomas, whilst many metastatic tumors could become amelanotic. Besides the obvious malfunction of the key genes of the melanin pathway, the amelanotic tumors could bear a characteristic molecular signature accounting for their aggressivity. Using mass spectrometry-based proteomics we report here a distinctive panel of biomarkers for amelanotic aggressive melanoma that differ from the less invasive pigmented cells. The developed method allows the label-free quantification of proteins identified by LC-MS/MS analysis. We found a set of proteins comprising AHNAK, MYOF, ANXA1, CAPN2, ASPH, EPHA2, THBS1, TGM2, ACTN4 along with proteins involved in cell adhesion/migration (integrins, PLEC, FSCN1, FN1) that are highly expressed in amelanotic melanoma. Accompanying the down regulation of pigmentation specific proteins such as tyrosinase and TYRP1, these biomarkers are highly specific for a type of highly invasive melanoma. Interestingly, the LC-MS/MS proteomics analysis in hypoxia revealed that the abundance of this specific set of proteins found in normoxia was rather unaltered in these conditions. These biomarkers could therefore predict a metastatic behaviour for the amelanotic cells in the early stages of the tumor development and thus serve in melanoma prognostic. Applying this algorithm to related databases including melanoma samples published by independent laboratories/public databases we confirm the specificity of the newly found signatures. Overall, we begin to unravel the molecular alterations in the amelanotic melanoma and how basic proteomics offers insights into how to assess the clinical, pathological and misdiagnosis differences between the main subtypes of melanoma.
Collapse
Affiliation(s)
- Ioana V. Militaru
- Department of Molecular Cell Biology, Institute of Biochemistry, Bucharest, Romania
| | - Alina Adriana Rus
- Department of Molecular Cell Biology, Institute of Biochemistry, Bucharest, Romania
| | - Cristian V.A. Munteanu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry, Bucharest, Romania
| | - Georgiana Manica
- Department of Molecular Cell Biology, Institute of Biochemistry, Bucharest, Romania
| | - Stefana M. Petrescu
- Department of Molecular Cell Biology, Institute of Biochemistry, Bucharest, Romania,*Correspondence: Stefana M. Petrescu,
| |
Collapse
|
43
|
Hossain SM, Eccles MR. Phenotype Switching and the Melanoma Microenvironment; Impact on Immunotherapy and Drug Resistance. Int J Mol Sci 2023; 24:ijms24021601. [PMID: 36675114 PMCID: PMC9864717 DOI: 10.3390/ijms24021601] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
Melanoma, a highly heterogeneous tumor, is comprised of a functionally diverse spectrum of cell phenotypes and subpopulations, including stromal cells in the tumor microenvironment (TME). Melanoma has been shown to dynamically shift between different transcriptional states or phenotypes. This is referred to as phenotype switching in melanoma, and it involves switching between quiescent and proliferative cell cycle states, and dramatic shifts in invasiveness, as well as changes in signaling pathways in the melanoma cells, and immune cell composition in the TME. Melanoma cell plasticity is associated with altered gene expression in immune cells and cancer-associated fibroblasts, as well as changes in extracellular matrix, which drive the metastatic cascade and therapeutic resistance. Therefore, resistance to therapy in melanoma is not only dependent on genetic evolution, but it has also been suggested to be driven by gene expression changes and adaptive phenotypic cell plasticity. This review discusses recent findings in melanoma phenotype switching, immunotherapy resistance, and the balancing of the homeostatic TME between the different melanoma cell subpopulations. We also discuss future perspectives of the biology of neural crest-like state(s) in melanoma.
Collapse
Affiliation(s)
- Sultana Mehbuba Hossain
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland 1010, New Zealand
| | - Michael R. Eccles
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland 1010, New Zealand
- Correspondence:
| |
Collapse
|
44
|
Murphy RJ, Gunasingh G, Haass NK, Simpson MJ. Growth and adaptation mechanisms of tumour spheroids with time-dependent oxygen availability. PLoS Comput Biol 2023; 19:e1010833. [PMID: 36634128 PMCID: PMC9876349 DOI: 10.1371/journal.pcbi.1010833] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 01/25/2023] [Accepted: 12/21/2022] [Indexed: 01/13/2023] Open
Abstract
Tumours are subject to external environmental variability. However, in vitro tumour spheroid experiments, used to understand cancer progression and develop cancer therapies, have been routinely performed for the past fifty years in constant external environments. Furthermore, spheroids are typically grown in ambient atmospheric oxygen (normoxia), whereas most in vivo tumours exist in hypoxic environments. Therefore, there are clear discrepancies between in vitro and in vivo conditions. We explore these discrepancies by combining tools from experimental biology, mathematical modelling, and statistical uncertainty quantification. Focusing on oxygen variability to develop our framework, we reveal key biological mechanisms governing tumour spheroid growth. Growing spheroids in time-dependent conditions, we identify and quantify novel biological adaptation mechanisms, including unexpected necrotic core removal, and transient reversal of the tumour spheroid growth phases.
Collapse
Affiliation(s)
- Ryan J. Murphy
- Mathematical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- * E-mail:
| | - Gency Gunasingh
- Frazer Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Nikolas K. Haass
- Frazer Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Matthew J. Simpson
- Mathematical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| |
Collapse
|
45
|
Jung-Garcia Y, Maiques O, Monger J, Rodriguez-Hernandez I, Fanshawe B, Domart MC, Renshaw MJ, Marti RM, Matias-Guiu X, Collinson LM, Sanz-Moreno V, Carlton JG. LAP1 supports nuclear adaptability during constrained melanoma cell migration and invasion. Nat Cell Biol 2023; 25:108-119. [PMID: 36624187 PMCID: PMC9859759 DOI: 10.1038/s41556-022-01042-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/04/2022] [Indexed: 01/11/2023]
Abstract
Metastasis involves dissemination of cancer cells away from a primary tumour and colonization at distal sites. During this process, the mechanical properties of the nucleus must be tuned since they pose a challenge to the negotiation of physical constraints imposed by the microenvironment and tissue structure. We discovered increased expression of the inner nuclear membrane protein LAP1 in metastatic melanoma cells, at the invasive front of human primary melanoma tumours and in metastases. Human cells express two LAP1 isoforms (LAP1B and LAP1C), which differ in their amino terminus. Here, using in vitro and in vivo models that recapitulate human melanoma progression, we found that expression of the shorter isoform, LAP1C, supports nuclear envelope blebbing, constrained migration and invasion by allowing a weaker coupling between the nuclear envelope and the nuclear lamina. We propose that LAP1 renders the nucleus highly adaptable and contributes to melanoma aggressiveness.
Collapse
Affiliation(s)
- Yaiza Jung-Garcia
- Organelle Dynamics Laboratory, The Francis Crick Institute, London, UK.,Sanz-Moreno Group, Centre for the Tumour Microenvironment, Barts Cancer Institute, Queen Mary University of London, John Vane Science Building, Charterhouse Square, London, UK.,Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, King's College London, London, UK.,Randall Division of Cell and Molecular Biophysics, King's College London, London, UK
| | - Oscar Maiques
- Sanz-Moreno Group, Centre for the Tumour Microenvironment, Barts Cancer Institute, Queen Mary University of London, John Vane Science Building, Charterhouse Square, London, UK.,Randall Division of Cell and Molecular Biophysics, King's College London, London, UK
| | - Joanne Monger
- Sanz-Moreno Group, Centre for the Tumour Microenvironment, Barts Cancer Institute, Queen Mary University of London, John Vane Science Building, Charterhouse Square, London, UK
| | - Irene Rodriguez-Hernandez
- Sanz-Moreno Group, Centre for the Tumour Microenvironment, Barts Cancer Institute, Queen Mary University of London, John Vane Science Building, Charterhouse Square, London, UK.,Randall Division of Cell and Molecular Biophysics, King's College London, London, UK
| | - Bruce Fanshawe
- Randall Division of Cell and Molecular Biophysics, King's College London, London, UK
| | - Marie-Charlotte Domart
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
| | - Matthew J Renshaw
- Advanced Light Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
| | - Rosa M Marti
- Department of Dermatology, Hospital Universitari Arnau de Vilanova, University of Lleida, IRB Lleida, CIBERONC, Lleida, Spain
| | - Xavier Matias-Guiu
- Department of Pathology and Molecular Genetics, Hospital Universitari Arnau de Vilanova, University of Lleida, IRB Lleida, CIBERONC, Lleida, Spain
| | - Lucy M Collinson
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
| | - Victoria Sanz-Moreno
- Sanz-Moreno Group, Centre for the Tumour Microenvironment, Barts Cancer Institute, Queen Mary University of London, John Vane Science Building, Charterhouse Square, London, UK. .,Randall Division of Cell and Molecular Biophysics, King's College London, London, UK.
| | - Jeremy G Carlton
- Organelle Dynamics Laboratory, The Francis Crick Institute, London, UK. .,Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, King's College London, London, UK.
| |
Collapse
|
46
|
Liu Z, Chen K, Dai J, Xu P, Sun W, Liu W, Zhao Z, Bennett SP, Li P, Ma T, Lin Y, Kawakami A, Yu J, Wang F, Wang C, Li M, Chase P, Hodder P, Spicer TP, Scampavia L, Cao C, Pan L, Dong J, Chen Y, Yu B, Guo M, Fang P, Fisher DE, Wang J. A unique hyperdynamic dimer interface permits small molecule perturbation of the melanoma oncoprotein MITF for melanoma therapy. Cell Res 2023; 33:55-70. [PMID: 36588115 PMCID: PMC9810709 DOI: 10.1038/s41422-022-00744-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/17/2022] [Indexed: 01/03/2023] Open
Abstract
Microphthalmia transcription factor (MITF) regulates melanocyte development and is the "lineage-specific survival" oncogene of melanoma. MITF is essential for melanoma initiation, progression, and relapse and has been considered an important therapeutic target; however, direct inhibition of MITF through small molecules is considered impossible, due to the absence of a ligand-binding pocket for drug design. Here, our structural analyses show that the structure of MITF is hyperdynamic because of its out-of-register leucine zipper with a 3-residue insertion. The dynamic MITF is highly vulnerable to dimer-disrupting mutations, as we observed that MITF loss-of-function mutations in human Waardenburg syndrome type 2 A are frequently located on the dimer interface and disrupt the dimer forming ability accordingly. These observations suggest a unique opportunity to inhibit MITF with small molecules capable of disrupting the MITF dimer. From a high throughput screening against 654,650 compounds, we discovered compound TT-012, which specifically binds to dynamic MITF and destroys the latter's dimer formation and DNA-binding ability. Using chromatin immunoprecipitation assay and RNA sequencing, we showed that TT-012 inhibits the transcriptional activity of MITF in B16F10 melanoma cells. In addition, TT-012 inhibits the growth of high-MITF melanoma cells, and inhibits the tumor growth and metastasis with tolerable toxicity to liver and immune cells in animal models. Together, this study demonstrates a unique hyperdynamic dimer interface in melanoma oncoprotein MITF, and reveals a novel approach to therapeutically suppress MITF activity.
Collapse
Affiliation(s)
- Zaizhou Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Kaige Chen
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, Guangdong, China
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Jun Dai
- Department of Dermatology, Cutaneous Biology Research Center, Mass. General Hospital, Harvard Medical School, Boston, MA, USA
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | - Peng Xu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Wei Sun
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wanlin Liu
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhixin Zhao
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | | | - Peifeng Li
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Tiancheng Ma
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yuqi Lin
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Akinori Kawakami
- Department of Dermatology, Cutaneous Biology Research Center, Mass. General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jing Yu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Fei Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chunxi Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Miao Li
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Peter Chase
- Scripps Research, Jupiter, FL, USA
- BMS Inc., Lawrenceville, NJ, USA
| | - Peter Hodder
- Scripps Research, Jupiter, FL, USA
- Amgen Inc., Thousand Oaks, CA, USA
| | | | | | - Chunyang Cao
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lifeng Pan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Jiajia Dong
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yong Chen
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Biao Yu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, China.
| | - Min Guo
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- Kangma-Healthcode Biotech Co., Ltd., Shanghai, China.
| | - Pengfei Fang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, China.
| | - David E Fisher
- Department of Dermatology, Cutaneous Biology Research Center, Mass. General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Jing Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, China.
| |
Collapse
|
47
|
Umar SA, Dong B, Nihal M, Chang H. Frizzled receptors in melanomagenesis: From molecular interactions to target identification. Front Oncol 2022; 12:1096134. [PMID: 36620565 PMCID: PMC9816865 DOI: 10.3389/fonc.2022.1096134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Frizzled (FZD) proteins are receptors for the WNT family ligands. Inherited human diseases and genetic experiments using knockout mice have revealed a central role of FZDs in multiple aspects of embryonic development and tissue homeostasis. Misregulated FZD signaling has also been found in many cancers. Recent studies on three out of the ten mammalian FZDs in melanoma have shown that they promote tumor cell proliferation and invasion, via the activation of the canonical WNT/β-catenin or non-canonical PCP signaling pathway. In this concise review, we summarize our current knowledge of individual FZDs in melanoma, discuss the involvement of both the canonical and non-canonical pathways, and describe ongoing efforts to target the FZD receptors for melanoma treatment.
Collapse
Affiliation(s)
- Sheikh A. Umar
- Department of Dermatology, University of Wisconsin-Madison, Madison, WI, United States
| | - Bo Dong
- Department of Dermatology, University of Wisconsin-Madison, Madison, WI, United States
| | - Minakshi Nihal
- William S. Middleton Memorial Veterans Hospital, Madison, WI, United States
| | - Hao Chang
- Department of Dermatology, University of Wisconsin-Madison, Madison, WI, United States,William S. Middleton Memorial Veterans Hospital, Madison, WI, United States,*Correspondence: Hao Chang,
| |
Collapse
|
48
|
Corrales E, Levit-Zerdoun E, Metzger P, Mertes R, Lehmann A, Münch J, Lemke S, Kowar S, Boerries M. PI3K/AKT signaling allows for MAPK/ERK pathway independency mediating dedifferentiation-driven treatment resistance in melanoma. Cell Commun Signal 2022; 20:187. [PMID: 36434616 PMCID: PMC9700886 DOI: 10.1186/s12964-022-00989-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/08/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Current therapeutic management of advanced melanoma patients largely depends on their BRAF mutation status. However, the vast heterogeneity of the tumors hampers the success of therapies targeting the MAPK/ERK pathway alone. Dissecting this heterogeneity will contribute to identifying key players in the oncogenic progression to tailor more effective therapies. METHODS We performed a comprehensive molecular and phenotypic characterization of a panel of patient-derived BRAFV600E-positive melanoma cell lines. Transcriptional profiling was used to identify groups of coregulated genes whose expression relates to an increased migratory potential and a higher resistance. RESULTS A decrease in sensitivity to MAPK/ERK pathway inhibition with vemurafenib or trametinib corresponded with an increasing quiescence and migratory properties of the cells. This was accompanied by the loss of transcriptional signatures of melanocytic differentiation, and the gain of stem cell features that conferred highly-resistant/mesenchymal-like cells with increased xenobiotic efflux capacity. Nevertheless, targeting of the implicated ABC transporters did not improve the response to vemurafenib, indicating that incomplete BRAF inhibition due to reduced drug uptake is not a main driver of resistance. Rather, indifference to MAPK/ERK pathway inhibition arose from the activation of compensatory signaling cascades. The PI3K/AKT pathway in particular showed a higher activity in mesenchymal-like cells, conferring a lower dependency on MAPK/ERK signaling and supporting stem-like properties that could be reverted by dual PI3K/mTOR inhibition with dactolisib. CONCLUSIONS In case of MAPK/ERK independency, therapeutic focus may be shifted to the PI3K/AKT pathway to overcome late-stage resistance in melanoma tumors that have acquired a mesenchymal phenotype. Video Abstract.
Collapse
Affiliation(s)
- Eyleen Corrales
- grid.5963.9Institute of Molecular Medicine and Cell Research (IMMZ), University of Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany ,grid.5963.9Faculty of Medicine, Medical Center-University of Freiburg, Institute of Medical Bioinformatics and Systems Medicine (IBSM), University of Freiburg, Breisacherstr. 153, 79110 Freiburg, Germany ,grid.5963.9Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Ella Levit-Zerdoun
- grid.5963.9Institute of Molecular Medicine and Cell Research (IMMZ), University of Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany ,grid.5963.9Faculty of Medicine, Medical Center-University of Freiburg, Institute of Medical Bioinformatics and Systems Medicine (IBSM), University of Freiburg, Breisacherstr. 153, 79110 Freiburg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), Freiburg, Germany
| | - Patrick Metzger
- grid.5963.9Institute of Molecular Medicine and Cell Research (IMMZ), University of Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany ,grid.5963.9Faculty of Medicine, Medical Center-University of Freiburg, Institute of Medical Bioinformatics and Systems Medicine (IBSM), University of Freiburg, Breisacherstr. 153, 79110 Freiburg, Germany
| | - Ralf Mertes
- grid.5963.9Institute of Molecular Medicine and Cell Research (IMMZ), University of Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany ,grid.5963.9Faculty of Medicine, Medical Center-University of Freiburg, Institute of Medical Bioinformatics and Systems Medicine (IBSM), University of Freiburg, Breisacherstr. 153, 79110 Freiburg, Germany
| | - Ariane Lehmann
- grid.5963.9Institute of Molecular Medicine and Cell Research (IMMZ), University of Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany ,grid.5963.9Faculty of Medicine, Medical Center-University of Freiburg, Institute of Medical Bioinformatics and Systems Medicine (IBSM), University of Freiburg, Breisacherstr. 153, 79110 Freiburg, Germany
| | - Julia Münch
- grid.5963.9Institute of Molecular Medicine and Cell Research (IMMZ), University of Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany
| | - Steffen Lemke
- grid.5963.9Institute of Molecular Medicine and Cell Research (IMMZ), University of Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany
| | - Silke Kowar
- grid.5963.9Institute of Molecular Medicine and Cell Research (IMMZ), University of Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany ,grid.5963.9Faculty of Medicine, Medical Center-University of Freiburg, Institute of Medical Bioinformatics and Systems Medicine (IBSM), University of Freiburg, Breisacherstr. 153, 79110 Freiburg, Germany
| | - Melanie Boerries
- grid.5963.9Institute of Molecular Medicine and Cell Research (IMMZ), University of Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany ,grid.5963.9Faculty of Medicine, Medical Center-University of Freiburg, Institute of Medical Bioinformatics and Systems Medicine (IBSM), University of Freiburg, Breisacherstr. 153, 79110 Freiburg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), Freiburg, Germany
| |
Collapse
|
49
|
Helweg LP, Storm J, Witte KE, Schulten W, Wrachtrup L, Janotte T, Kitke A, Greiner JFW, Knabbe C, Kaltschmidt B, Simon M, Kaltschmidt C. Targeting Key Signaling Pathways in Glioblastoma Stem Cells for the Development of Efficient Chemo- and Immunotherapy. Int J Mol Sci 2022; 23:12919. [PMID: 36361720 PMCID: PMC9659205 DOI: 10.3390/ijms232112919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/23/2022] [Accepted: 10/21/2022] [Indexed: 01/12/2024] Open
Abstract
Glioblastoma multiforme (GBM) is the most aggressive and most common malignant brain tumor with poor patient survival despite therapeutic intervention. On the cellular level, GBM comprises a rare population of glioblastoma stem cells (GSCs), driving therapeutic resistance, invasion, and recurrence. GSCs have thus come into the focus of therapeutic strategies, although their targeting remains challenging. In the present study, we took advantage of three GSCs-populations recently established in our lab to investigate key signaling pathways and subsequent therapeutic strategies targeting GSCs. We observed that NF-κB, a crucial transcription factor in GBM progression, was expressed in all CD44+/CD133+/Nestin+-GSC-populations. Exposure to TNFα led to activation of NF-κB-RELA and/or NF-κB-c-REL, depending on the GBM type. GSCs further expressed the proto-oncogene MYC family, with MYChigh GSCs being predominantly located in the tumor spheres ("GROW"-state) while NF-κB-RELAhigh GSCs were migrating out of the sphere ("GO"-state). We efficiently targeted GSCs by the pharmacologic inhibition of NF-κB using PTDC/Bortezomib or inhibition of MYC by KJ-Pyr-9, which significantly reduced GSC-viability, even in comparison to the standard chemotherapeutic drug temozolomide. As an additional cell-therapeutic strategy, we showed that NK cells could kill GSCs. Our findings offer new perspectives for developing efficient patient-specific chemo- and immunotherapy against GBM.
Collapse
Affiliation(s)
- Laureen P. Helweg
- Department of Cell Biology, University of Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany
- Forschungsverbund BioMedizin Bielefeld, OWL (FBMB e.V.), Maraweg 21, 33617 Bielefeld, Germany
| | - Jonathan Storm
- Department of Cell Biology, University of Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany
- Forschungsverbund BioMedizin Bielefeld, OWL (FBMB e.V.), Maraweg 21, 33617 Bielefeld, Germany
| | - Kaya E. Witte
- Department of Cell Biology, University of Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany
- Forschungsverbund BioMedizin Bielefeld, OWL (FBMB e.V.), Maraweg 21, 33617 Bielefeld, Germany
| | - Wiebke Schulten
- Department of Cell Biology, University of Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Lennart Wrachtrup
- Department of Cell Biology, University of Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Till Janotte
- Department of Cell Biology, University of Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Angelika Kitke
- Department of Cell Biology, University of Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Johannes F. W. Greiner
- Department of Cell Biology, University of Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany
- Forschungsverbund BioMedizin Bielefeld, OWL (FBMB e.V.), Maraweg 21, 33617 Bielefeld, Germany
| | - Cornelius Knabbe
- Forschungsverbund BioMedizin Bielefeld, OWL (FBMB e.V.), Maraweg 21, 33617 Bielefeld, Germany
- Heart and Diabetes Centre NRW, Institute for Laboratory and Transfusion Medicine, Ruhr-University Bochum, 32545 Bad Oeynhausen, Germany
| | - Barbara Kaltschmidt
- Department of Cell Biology, University of Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany
- Forschungsverbund BioMedizin Bielefeld, OWL (FBMB e.V.), Maraweg 21, 33617 Bielefeld, Germany
- Molecular Neurobiology, Faculty of Biology, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Matthias Simon
- Forschungsverbund BioMedizin Bielefeld, OWL (FBMB e.V.), Maraweg 21, 33617 Bielefeld, Germany
- Department of Neurosurgery and Epilepsy Surgery, Protestant Hospital of Bethel Foundation, University Medical School OWL at Bielefeld, Bielefeld University, Campus Bielefeld-Bethel, Burgsteig 13, 33617 Bielefeld, Germany
| | - Christian Kaltschmidt
- Department of Cell Biology, University of Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany
- Forschungsverbund BioMedizin Bielefeld, OWL (FBMB e.V.), Maraweg 21, 33617 Bielefeld, Germany
| |
Collapse
|
50
|
Zhu EY, Riordan JD, Vanneste M, Henry MD, Stipp CS, Dupuy AJ. SRC-RAC1 signaling drives drug resistance to BRAF inhibition in de-differentiated cutaneous melanomas. NPJ Precis Oncol 2022; 6:74. [PMID: 36271142 PMCID: PMC9587254 DOI: 10.1038/s41698-022-00310-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 08/31/2022] [Indexed: 11/09/2022] Open
Abstract
Rare gain-of-function mutations in RAC1 drive drug resistance to targeted BRAF inhibition in cutaneous melanoma. Here, we show that wildtype RAC1 is a critical driver of growth and drug resistance, but only in a subset of melanomas with elevated markers of de-differentiation. Similarly, SRC inhibition also selectively sensitized de-differentiated melanomas to BRAF inhibition. One possible mechanism may be the suppression of the de-differentiated state, as SRC and RAC1 maintained markers of de-differentiation in human melanoma cells. The functional differences between melanoma subtypes suggest that the clinical management of cutaneous melanoma can be enhanced by the knowledge of differentiation status. To simplify the task of classification, we developed a binary classification strategy based on a small set of ten genes. Using this gene set, we reliably determined the differentiation status previously defined by hundreds of genes. Overall, our study informs strategies that enhance the precision of BRAFi by discovering unique vulnerabilities of the de-differentiated cutaneous melanoma subtype and creating a practical method to resolve differentiation status.
Collapse
Affiliation(s)
- Eliot Y Zhu
- Department of Anatomy and Cell Biology, The University of Iowa, Iowa City, IA, USA.,Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA, USA.,Cancer Biology Graduate Program, The University of Iowa, Iowa City, IA, USA.,The Medical Scientist Training Program, The University of Iowa, Iowa City, IA, USA
| | - Jesse D Riordan
- Department of Anatomy and Cell Biology, The University of Iowa, Iowa City, IA, USA.,Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA, USA
| | - Marion Vanneste
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA, USA.,Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, IA, USA
| | - Michael D Henry
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA, USA.,Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, IA, USA
| | - Christopher S Stipp
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA, USA.,Department of Biology, The University of Iowa, Iowa City, IA, USA
| | - Adam J Dupuy
- Department of Anatomy and Cell Biology, The University of Iowa, Iowa City, IA, USA. .,Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA, USA.
| |
Collapse
|