101
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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.
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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
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102
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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.
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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
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103
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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.
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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.
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104
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Delbart W, Marin G, Stamatopoulos B, de Wind R, Sirtaine N, Demetter P, Vercruyssen M, Woff E, Karfis I, Ghanem GE, Flamen P, Wimana Z. Disturbing the Redox Balance Using Buthionine Sulfoximine Radiosensitized Somatostatin Receptor-2 Expressing Pre-Clinical Models to Peptide Receptor Radionuclide Therapy with 177Lu-DOTATATE. Cancers (Basel) 2023; 15:cancers15082332. [PMID: 37190261 DOI: 10.3390/cancers15082332] [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: 03/03/2023] [Revised: 04/14/2023] [Accepted: 04/15/2023] [Indexed: 05/17/2023] Open
Abstract
Peptide receptor radionuclide therapy with 177Lu-DOTATATE improves the outcome of patients with somatostatin receptor (SSTR)-expressing neuroendocrine tumours. Nevertheless, stable disease has been the main response pattern observed, with some rare complete responses. Lu-177 exerts about two-thirds of its biological effects via the indirect effects of ionizing radiation that generate reactive oxygen species, eventually leading to oxidative damage and cell death. This provides a rationale for targeting the antioxidant defence system in combination with 177Lu-DOTATATE. In the present study, the radiosensitizing potential and the safety of depleting glutathione (GSH) levels using buthionine sulfoximine (BSO) during 177Lu-DOTATATE therapy were assessed in vitro and in vivo using a xenograft mouse model. In vitro, the combination resulted in a synergistic effect in cell lines exhibiting a BSO-mediated GSH decrease. In vivo, BSO neither influenced 177Lu-DOTATATE biodistribution nor induced liver, kidney or bone marrow toxicity. In terms of efficacy, the combination resulted in reduced tumour growth and metabolic activity. Our results showed that disturbing the cell redox balance using a GSH synthesis inhibitor increased 177Lu-DOTATATE efficacy without additional toxicity. Targeting the antioxidant defence system opens new safe treatment combination opportunities with 177Lu-DOTATATE.
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Affiliation(s)
- Wendy Delbart
- Nuclear Medicine Department, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (H.U.B), Université Libre de Bruxelles (ULB), 1000 Brussels, Belgium
- Laboratory of Oncology and Experimental Surgery, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (H.U.B), Université Libre de Bruxelles (ULB), 1000 Brussels, Belgium
| | - Gwennaëlle Marin
- Medical Physics Department, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (H.U.B), Université Libre de Bruxelles (ULB), 1000 Brussels, Belgium
| | - Basile Stamatopoulos
- Laboratory of Clinical Cell Therapy, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (H.U.B), Université Libre de Bruxelles (ULB), 1000 Brussels, Belgium
| | - Roland de Wind
- Pathology Department, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (H.U.B), Université Libre de Bruxelles (ULB), 1000 Brussels, Belgium
| | - Nicolas Sirtaine
- Pathology Department, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (H.U.B), Université Libre de Bruxelles (ULB), 1000 Brussels, Belgium
| | - Pieter Demetter
- Pathology Department, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (H.U.B), Université Libre de Bruxelles (ULB), 1000 Brussels, Belgium
| | - Marie Vercruyssen
- Haematology Department, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (H.U.B), Université Libre de Bruxelles (ULB), 1000 Brussels, Belgium
| | - Erwin Woff
- Nuclear Medicine Department, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (H.U.B), Université Libre de Bruxelles (ULB), 1000 Brussels, Belgium
| | - Ioannis Karfis
- Nuclear Medicine Department, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (H.U.B), Université Libre de Bruxelles (ULB), 1000 Brussels, Belgium
| | - Ghanem E Ghanem
- Laboratory of Oncology and Experimental Surgery, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (H.U.B), Université Libre de Bruxelles (ULB), 1000 Brussels, Belgium
| | - Patrick Flamen
- Nuclear Medicine Department, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (H.U.B), Université Libre de Bruxelles (ULB), 1000 Brussels, Belgium
| | - Zéna Wimana
- Nuclear Medicine Department, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (H.U.B), Université Libre de Bruxelles (ULB), 1000 Brussels, Belgium
- Laboratory of Oncology and Experimental Surgery, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (H.U.B), Université Libre de Bruxelles (ULB), 1000 Brussels, Belgium
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105
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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.
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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
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106
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Gruen C, Yang HH, Sassano A, Wu E, Gopalan V, Marie KL, Castro A, Mehrabadi FR, Wu CH, Church I, Needle GA, Smith C, Chin S, Ebersole J, Marcelus C, Fon A, Liu H, Malikic S, Sahinalp C, Carter H, Hannenhalli S, Day CP, Lee MP, Merlino G, Pérez-Guijarro E. Melanoma clonal subline analysis uncovers heterogeneity-driven immunotherapy resistance mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.03.535074. [PMID: 37333132 PMCID: PMC10274874 DOI: 10.1101/2023.04.03.535074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Intratumoral heterogeneity (ITH) can promote cancer progression and treatment failure, but the complexity of the regulatory programs and contextual factors involved complicates its study. To understand the specific contribution of ITH to immune checkpoint blockade (ICB) response, we generated single cell-derived clonal sublines from an ICB-sensitive and genetically and phenotypically heterogeneous mouse melanoma model, M4. Genomic and single cell transcriptomic analyses uncovered the diversity of the sublines and evidenced their plasticity. Moreover, a wide range of tumor growth kinetics were observed in vivo , in part associated with mutational profiles and dependent on T cell-response. Further inquiry into melanoma differentiation states and tumor microenvironment (TME) subtypes of untreated tumors from the clonal sublines demonstrated correlations between highly inflamed and differentiated phenotypes with the response to anti-CTLA-4 treatment. Our results demonstrate that M4 sublines generate intratumoral heterogeneity at both levels of intrinsic differentiation status and extrinsic TME profiles, thereby impacting tumor evolution during therapeutic treatment. These clonal sublines proved to be a valuable resource to study the complex determinants of response to ICB, and specifically the role of melanoma plasticity in immune evasion mechanisms.
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107
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Davalos V, Lovell CD, Von Itter R, Dolgalev I, Agrawal P, Baptiste G, Kahler DJ, Sokolova E, Moran S, Piqué L, Vega-Saenz de Miera E, Fontanals-Cirera B, Karz A, Tsirigos A, Yun C, Darvishian F, Etchevers HC, Osman I, Esteller M, Schober M, Hernando E. An epigenetic switch controls an alternative NR2F2 isoform that unleashes a metastatic program in melanoma. Nat Commun 2023; 14:1867. [PMID: 37015919 PMCID: PMC10073109 DOI: 10.1038/s41467-023-36967-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 02/24/2023] [Indexed: 04/06/2023] Open
Abstract
Metastatic melanoma develops once transformed melanocytic cells begin to de-differentiate into migratory and invasive melanoma cells with neural crest cell (NCC)-like and epithelial-to-mesenchymal transition (EMT)-like features. However, it is still unclear how transformed melanocytes assume a metastatic melanoma cell state. Here, we define DNA methylation changes that accompany metastatic progression in melanoma patients and discover Nuclear Receptor Subfamily 2 Group F, Member 2 - isoform 2 (NR2F2-Iso2) as an epigenetically regulated metastasis driver. NR2F2-Iso2 is transcribed from an alternative transcriptional start site (TSS) and it is truncated at the N-terminal end which encodes the NR2F2 DNA-binding domain. We find that NR2F2-Iso2 expression is turned off by DNA methylation when NCCs differentiate into melanocytes. Conversely, this process is reversed during metastatic melanoma progression, when NR2F2-Iso2 becomes increasingly hypomethylated and re-expressed. Our functional and molecular studies suggest that NR2F2-Iso2 drives metastatic melanoma progression by modulating the activity of full-length NR2F2 (Isoform 1) over EMT- and NCC-associated target genes. Our findings indicate that DNA methylation changes play a crucial role during metastatic melanoma progression, and their control of NR2F2 activity allows transformed melanocytes to acquire NCC-like and EMT-like features. This epigenetically regulated transcriptional plasticity facilitates cell state transitions and metastatic spread.
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Affiliation(s)
- Veronica Davalos
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA.
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA.
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain.
| | - Claudia D Lovell
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | - Richard Von Itter
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | - Igor Dolgalev
- Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Praveen Agrawal
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine/ Montefiore, Bronx, NY, 10461, USA
| | - Gillian Baptiste
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | - David J Kahler
- High Throughput Biology Core, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Elena Sokolova
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | - Sebastian Moran
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Laia Piqué
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Eleazar Vega-Saenz de Miera
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
- The Ronald O. Perelman Department of Dermatology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Barbara Fontanals-Cirera
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | - Alcida Karz
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Chi Yun
- High Throughput Biology Core, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Farbod Darvishian
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | | | - Iman Osman
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
- The Ronald O. Perelman Department of Dermatology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Centro de Investigacion Biomedica en Red, Cancer (CIBERONC), Madrid, Spain
| | - Markus Schober
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA.
- The Ronald O. Perelman Department of Dermatology, New York University Grossman School of Medicine, New York, NY, 10016, USA.
- Department of Cell Biology, New York Grossman University School of Medicine, New York, NY, 10016, USA.
| | - Eva Hernando
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA.
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA.
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108
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Pillai M, Hojel E, Jolly MK, Goyal Y. Unraveling non-genetic heterogeneity in cancer with dynamical models and computational tools. NATURE COMPUTATIONAL SCIENCE 2023; 3:301-313. [PMID: 38177938 DOI: 10.1038/s43588-023-00427-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 03/03/2023] [Indexed: 01/06/2024]
Abstract
Individual cells within an otherwise genetically homogenous population constantly undergo fluctuations in their molecular state, giving rise to non-genetic heterogeneity. Such diversity is being increasingly implicated in cancer therapy resistance and metastasis. Identifying the origins of non-genetic heterogeneity is therefore crucial for making clinical breakthroughs. We discuss with examples how dynamical models and computational tools have provided critical multiscale insights into the nature and consequences of non-genetic heterogeneity in cancer. We demonstrate how mechanistic modeling has been pivotal in establishing key concepts underlying non-genetic diversity at various biological scales, from population dynamics to gene regulatory networks. We discuss advances in single-cell longitudinal profiling techniques to reveal patterns of non-genetic heterogeneity, highlighting the ongoing efforts and challenges in statistical frameworks to robustly interpret such multimodal datasets. Moving forward, we stress the need for data-driven statistical and mechanistically motivated dynamical frameworks to come together to develop predictive cancer models and inform therapeutic strategies.
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Affiliation(s)
- Maalavika Pillai
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Emilia Hojel
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Department of Biomedical Engineering, Northwestern University McCormick School of Engineering, Evanston, IL, USA
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India.
| | - Yogesh Goyal
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- Department of Biomedical Engineering, Northwestern University McCormick School of Engineering, Evanston, IL, USA.
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109
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Patel RP, Somasundram PM, Smith LK, Sheppard KE, McArthur GA. The therapeutic potential of targeting minimal residual disease in melanoma. Clin Transl Med 2023; 13:e1197. [PMID: 36967556 PMCID: PMC10040726 DOI: 10.1002/ctm2.1197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/18/2023] [Accepted: 01/29/2023] [Indexed: 03/28/2023] Open
Abstract
Background Cutaneous melanoma is a lethal form of skin cancer with morbidity and mortality rates highest amongst European, North American and Australasian populations. The developments of targeted therapies (TTs) directed at the oncogene BRAF and its downstream mediator MEK, and immune checkpoint inhibitors (ICI), have revolutionized the treatment of metastatic melanoma, improving patient outcomes. However, both TT and ICI have their limitations. Although TTs are associated with high initial response rates, these are typically short‐lived due to resistance. Conversely, although ICIs provide more durable responses, they have lower initial response rates. Due to these distinct yet complementary response profiles, it has been proposed that sequencing ICI with TT could lead to a high frequency of durable responses whilst circumventing the toxicity associated with combined ICI + TT treatment. However, several questions remain unanswered, including the mechanisms underpinning this synergy and the optimal sequencing strategy. The key to determining this is to uncover the biology of each phase of the therapeutic response. Aims and methods In this review, we show that melanoma responds to TT and ICI in three phases: early response, minimal residual disease (MRD) and disease progression. We explore the effects of ICI and TT on melanoma cells and the tumour immune microenvironment, with a particular focus on MRD which is predicted to underpin the development of acquired resistance in the third phase of response. Conclusion In doing so, we provide a new framework which may inform novel therapeutic approaches for melanoma, including optimal sequencing strategies and agents that target MRD, thereby ultimately improving clinical outcomes for patients.
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Affiliation(s)
- Riyaben P Patel
- Cancer Research DivisionPeter MacCallum Cancer CentreMelbourneVictoriaAustralia
- Sir Peter MacCallum Department of OncologyUniversity of MelbourneParkvilleVictoriaAustralia
| | - Pretashini M Somasundram
- Faculty of MedicineDentistry and Health Sciences, University of MelbourneParkvilleVictoriaAustralia
| | - Lorey K. Smith
- Cancer Research DivisionPeter MacCallum Cancer CentreMelbourneVictoriaAustralia
- Sir Peter MacCallum Department of OncologyUniversity of MelbourneParkvilleVictoriaAustralia
| | - Karen E. Sheppard
- Cancer Research DivisionPeter MacCallum Cancer CentreMelbourneVictoriaAustralia
- Sir Peter MacCallum Department of OncologyUniversity of MelbourneParkvilleVictoriaAustralia
| | - Grant A. McArthur
- Cancer Research DivisionPeter MacCallum Cancer CentreMelbourneVictoriaAustralia
- Sir Peter MacCallum Department of OncologyUniversity of MelbourneParkvilleVictoriaAustralia
- Department of Medical OncologyPeter MacCallum Cancer CentreMelbourneVictoriaAustralia
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110
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Danzi F, Pacchiana R, Mafficini A, Scupoli MT, Scarpa A, Donadelli M, Fiore A. To metabolomics and beyond: a technological portfolio to investigate cancer metabolism. Signal Transduct Target Ther 2023; 8:137. [PMID: 36949046 PMCID: PMC10033890 DOI: 10.1038/s41392-023-01380-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/08/2023] [Accepted: 02/15/2023] [Indexed: 03/24/2023] Open
Abstract
Tumour cells have exquisite flexibility in reprogramming their metabolism in order to support tumour initiation, progression, metastasis and resistance to therapies. These reprogrammed activities include a complete rewiring of the bioenergetic, biosynthetic and redox status to sustain the increased energetic demand of the cells. Over the last decades, the cancer metabolism field has seen an explosion of new biochemical technologies giving more tools than ever before to navigate this complexity. Within a cell or a tissue, the metabolites constitute the direct signature of the molecular phenotype and thus their profiling has concrete clinical applications in oncology. Metabolomics and fluxomics, are key technological approaches that mainly revolutionized the field enabling researchers to have both a qualitative and mechanistic model of the biochemical activities in cancer. Furthermore, the upgrade from bulk to single-cell analysis technologies provided unprecedented opportunity to investigate cancer biology at cellular resolution allowing an in depth quantitative analysis of complex and heterogenous diseases. More recently, the advent of functional genomic screening allowed the identification of molecular pathways, cellular processes, biomarkers and novel therapeutic targets that in concert with other technologies allow patient stratification and identification of new treatment regimens. This review is intended to be a guide for researchers to cancer metabolism, highlighting current and emerging technologies, emphasizing advantages, disadvantages and applications with the potential of leading the development of innovative anti-cancer therapies.
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Affiliation(s)
- Federica Danzi
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Verona, Italy
| | - Raffaella Pacchiana
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Verona, Italy
| | - Andrea Mafficini
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Maria T Scupoli
- Department of Neurosciences, Biomedicine and Movement Sciences, Biology and Genetics Section, University of Verona, Verona, Italy
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
- ARC-NET Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Massimo Donadelli
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Verona, Italy.
| | - Alessandra Fiore
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Verona, Italy
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111
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Ascolani G, Angaroni F, Maspero D, Craighero F, Bhavesh NLS, Piazza R, Damiani C, Ramazzotti D, Antoniotti M, Graudenzi A. LACE 2.0: an interactive R tool for the inference and visualization of longitudinal cancer evolution. BMC Bioinformatics 2023; 24:99. [PMID: 36932333 PMCID: PMC10022199 DOI: 10.1186/s12859-023-05221-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/03/2023] [Indexed: 03/19/2023] Open
Abstract
BACKGROUND Longitudinal single-cell sequencing experiments of patient-derived models are increasingly employed to investigate cancer evolution. In this context, robust computational methods are needed to properly exploit the mutational profiles of single cells generated via variant calling, in order to reconstruct the evolutionary history of a tumor and characterize the impact of therapeutic strategies, such as the administration of drugs. To this end, we have recently developed the LACE framework for the Longitudinal Analysis of Cancer Evolution. RESULTS The LACE 2.0 release aimed at inferring longitudinal clonal trees enhances the original framework with new key functionalities: an improved data management for preprocessing of standard variant calling data, a reworked inference engine, and direct connection to public databases. CONCLUSIONS All of this is accessible through a new and interactive Shiny R graphical interface offering the possibility to apply filters helpful in discriminating relevant or potential driver mutations, set up inferential parameters, and visualize the results. The software is available at: github.com/BIMIB-DISCo/LACE.
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Affiliation(s)
- Gianluca Ascolani
- Department of Informatics, Systems and Communication, University of Milan-Bicocca, Milan, Italy.
| | - Fabrizio Angaroni
- Department of Informatics, Systems and Communication, University of Milan-Bicocca, Milan, Italy
| | - Davide Maspero
- Department of Informatics, Systems and Communication, University of Milan-Bicocca, Milan, Italy
| | - Francesco Craighero
- Department of Informatics, Systems and Communication, University of Milan-Bicocca, Milan, Italy
| | - Narra Lakshmi Sai Bhavesh
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Rocco Piazza
- Department of Medicine and Surgery, University of Milan-Bicocca, University of Milan-Bicocca, Milan, Italy
- Bicocca Bioinformatics Biostatistics and Bioimaging Centre - B4, University of Milan-Bicocca, Vedano al Lambro, Monza, Italy
| | - Chiara Damiani
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan, Italy
| | - Daniele Ramazzotti
- Department of Medicine and Surgery, University of Milan-Bicocca, University of Milan-Bicocca, Milan, Italy
| | - Marco Antoniotti
- Department of Informatics, Systems and Communication, University of Milan-Bicocca, Milan, Italy
- Bicocca Bioinformatics Biostatistics and Bioimaging Centre - B4, University of Milan-Bicocca, Vedano al Lambro, Monza, Italy
| | - Alex Graudenzi
- Department of Informatics, Systems and Communication, University of Milan-Bicocca, Milan, Italy
- Bicocca Bioinformatics Biostatistics and Bioimaging Centre - B4, University of Milan-Bicocca, Vedano al Lambro, Monza, Italy
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112
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Shi ZD, Pang K, Wu ZX, Dong Y, Hao L, Qin JX, Wang W, Chen ZS, Han CH. Tumor cell plasticity in targeted therapy-induced resistance: mechanisms and new strategies. Signal Transduct Target Ther 2023; 8:113. [PMID: 36906600 PMCID: PMC10008648 DOI: 10.1038/s41392-023-01383-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 12/07/2022] [Accepted: 02/20/2023] [Indexed: 03/13/2023] Open
Abstract
Despite the success of targeted therapies in cancer treatment, therapy-induced resistance remains a major obstacle to a complete cure. Tumor cells evade treatments and relapse via phenotypic switching driven by intrinsic or induced cell plasticity. Several reversible mechanisms have been proposed to circumvent tumor cell plasticity, including epigenetic modifications, regulation of transcription factors, activation or suppression of key signaling pathways, as well as modification of the tumor environment. Epithelial-to-mesenchymal transition, tumor cell and cancer stem cell formation also serve as roads towards tumor cell plasticity. Corresponding treatment strategies have recently been developed that either target plasticity-related mechanisms or employ combination treatments. In this review, we delineate the formation of tumor cell plasticity and its manipulation of tumor evasion from targeted therapy. We discuss the non-genetic mechanisms of targeted drug-induced tumor cell plasticity in various types of tumors and provide insights into the contribution of tumor cell plasticity to acquired drug resistance. New therapeutic strategies such as inhibition or reversal of tumor cell plasticity are also presented. We also discuss the multitude of clinical trials that are ongoing worldwide with the intention of improving clinical outcomes. These advances provide a direction for developing novel therapeutic strategies and combination therapy regimens that target tumor cell plasticity.
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Affiliation(s)
- Zhen-Duo Shi
- Department of Urology, Xuzhou Clinical School of Xuzhou Medical University, Jiangsu, China.,Department of Urology, Xuzhou Central Hospital, Xuzhou, Jiangsu, China.,School of Life Sciences, Jiangsu Normal University, Jiangsu, China.,Department of Urology, Heilongjiang Provincial Hospital, Heilongjiang, China
| | - Kun Pang
- Department of Urology, Xuzhou Clinical School of Xuzhou Medical University, Jiangsu, China.,Department of Urology, Xuzhou Central Hospital, Xuzhou, Jiangsu, China
| | - Zhuo-Xun Wu
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, 11439, USA
| | - Yang Dong
- Department of Urology, Xuzhou Clinical School of Xuzhou Medical University, Jiangsu, China.,Department of Urology, Xuzhou Central Hospital, Xuzhou, Jiangsu, China
| | - Lin Hao
- Department of Urology, Xuzhou Clinical School of Xuzhou Medical University, Jiangsu, China.,Department of Urology, Xuzhou Central Hospital, Xuzhou, Jiangsu, China
| | - Jia-Xin Qin
- Department of Urology, Xuzhou Clinical School of Xuzhou Medical University, Jiangsu, China.,Department of Urology, Xuzhou Central Hospital, Xuzhou, Jiangsu, China
| | - Wei Wang
- Department of Medical College, Southeast University, Nanjing, China
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, 11439, USA.
| | - Cong-Hui Han
- Department of Urology, Xuzhou Clinical School of Xuzhou Medical University, Jiangsu, China. .,Department of Urology, Xuzhou Central Hospital, Xuzhou, Jiangsu, China. .,School of Life Sciences, Jiangsu Normal University, Jiangsu, China. .,Department of Urology, Heilongjiang Provincial Hospital, Heilongjiang, China.
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113
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Jarrosson L, Dalle S, Costechareyre C, Tang Y, Grimont M, Plaschka M, Lacourrège M, Teinturier R, Le Bouar M, Maucort‐Boulch D, Eberhardt A, Castellani V, Caramel J, Delloye‐Bourgeois C. An in vivo avian model of human melanoma to perform rapid and robust preclinical studies. EMBO Mol Med 2023; 15:e16629. [PMID: 36692026 PMCID: PMC9994476 DOI: 10.15252/emmm.202216629] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 12/20/2022] [Accepted: 12/23/2022] [Indexed: 01/25/2023] Open
Abstract
Metastatic melanoma patients carrying a BRAFV600 mutation can be treated with a combination of BRAF and MEK inhibitors (BRAFi/MEKi), but innate and acquired resistance invariably occurs. Predicting patient response to targeted therapies is crucial to guide clinical decision. We describe here the development of a highly efficient patient-derived xenograft model adapted to patient melanoma biopsies, using the avian embryo as a host (AVI-PDXTM ). In this in vivo paradigm, we depict a fast and reproducible tumor engraftment of patient samples within the embryonic skin, preserving key molecular and phenotypic features. We show that sensitivity and resistance to BRAFi/MEKi can be reliably modeled in these AVI-PDXTM , as well as synergies with other drugs. We further provide proof-of-concept that the AVI-PDXTM models the diversity of responses of melanoma patients to BRAFi/MEKi, within days, hence positioning it as a valuable tool for the design of personalized medicine assays and for the evaluation of novel combination strategies.
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Affiliation(s)
| | - Stéphane Dalle
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of LyonLyonFrance
- Centre Hospitalier Lyon SudHospices Civils de LyonPierre BéniteFrance
| | | | - Yaqi Tang
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of LyonLyonFrance
| | - Maxime Grimont
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of LyonLyonFrance
| | - Maud Plaschka
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of LyonLyonFrance
| | | | | | - Myrtille Le Bouar
- Centre Hospitalier Lyon SudHospices Civils de LyonPierre BéniteFrance
| | | | - Anaïs Eberhardt
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of LyonLyonFrance
- Centre Hospitalier Lyon SudHospices Civils de LyonPierre BéniteFrance
| | - Valérie Castellani
- University of Lyon, University of Lyon 1 Claude Bernard Lyon 1, MeLiS, CNRS UMR5284, INSERM U1314, NeuroMyoGene InstituteLyonFrance
| | - Julie Caramel
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of LyonLyonFrance
| | - Céline Delloye‐Bourgeois
- University of Lyon, University of Lyon 1 Claude Bernard Lyon 1, MeLiS, CNRS UMR5284, INSERM U1314, NeuroMyoGene InstituteLyonFrance
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114
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Kato S, Maeda Y, Sugiyama D, Watanabe K, Nishikawa H, Hinohara K. The cancer epigenome: Non-cell autonomous player in tumor immunity. Cancer Sci 2023; 114:730-740. [PMID: 36468774 PMCID: PMC9986067 DOI: 10.1111/cas.15681] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/28/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Dysregulation of the tumor-intrinsic epigenetic circuit is a key driver event for the development of cancer. Accumulating evidence suggests that epigenetic and/or genetic drivers stimulate intrinsic oncogenic pathways as well as extrinsic factors that modulate the immune system. These modulations indeed shape the tumor microenvironment (TME), allowing pro-oncogenic factors to become oncogenic, thereby contributing to cancer development and progression. Here we review the epigenetic dysregulation arising in cancer cells that disseminates throughout the TME and beyond. Recent CRISPR screening has elucidated key epigenetic drivers that play important roles in the proliferation of cancer cells (intrinsic) and inhibition of antitumor immunity (extrinsic), which lead to the development and progression of cancer. These epigenetic players can serve as promising targets for cancer therapy as a dual (two-in-one)-targeted approach. Considering the interplay between cancer and the immune system as a key determinant of immunotherapy, we discuss a novel lineage-tracing technology that enables longitudinal monitoring of cancer and immune phenotypic heterogeneity and fate paths during cancer development, progression, and therapeutic interventions.
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Affiliation(s)
- Shinichiro Kato
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Center for 5D Cell Dynamics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuka Maeda
- Division of Cancer Immunology, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Research Institute, Tokyo, Japan
| | - Daisuke Sugiyama
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Keisuke Watanabe
- Division of Cancer Immunology, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Research Institute, Tokyo, Japan
| | - Hiroyoshi Nishikawa
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Center for 5D Cell Dynamics, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Division of Cancer Immunology, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Research Institute, Tokyo, Japan.,Institute for Advanced Study, Nagoya University, Nagoya, Japan
| | - Kunihiko Hinohara
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Center for 5D Cell Dynamics, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Institute for Advanced Study, Nagoya University, Nagoya, Japan
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115
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Zhang Z, Tan Y, Huang C, Wei X. Redox signaling in drug-tolerant persister cells as an emerging therapeutic target. EBioMedicine 2023; 89:104483. [PMID: 36827719 PMCID: PMC9982619 DOI: 10.1016/j.ebiom.2023.104483] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 01/20/2023] [Accepted: 02/03/2023] [Indexed: 02/25/2023] Open
Abstract
Drug-tolerant persister (DTP) cells have attracted significant interest, given their predominant role in treatment failure. In this respect, DTP cells reportedly survive after anticancer drug exposure, and their DNA repair mechanisms are altered to enhance adaptive mutation, accounting for the emergence of drug-resistant mutations. DTP cells resume proliferation upon treatment withdrawal and are responsible for cancer relapse. Current evidence suggests that DTP cells mediate redox signaling-mediated cellular homeostasis by developing various adaptive mechanisms, especially metabolic reprogramming that promotes mitochondrial oxidative respiration and a robust antioxidant process. There is an increasing consensus that disrupting redox homeostasis by intervening with redox signaling is theoretically a promising therapeutic strategy for targeting these sinister cells. In this review, we provide a comprehensive overview of the characteristics of DTP cells and the underlying mechanisms involved in redox signaling, aiming to provide a unique perspective on potential therapeutic applications based on their vulnerabilities to redox regulation.
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Affiliation(s)
- Zhe Zhang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, PR China; State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Yunhan Tan
- West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China.
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, PR China.
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116
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Tong X, Burks HE, Ren Z, Koetsier JL, Roth-Carter QR, Green KJ. Crosstalk in skin: Loss of desmoglein 1 in keratinocytes inhibits BRAF V600E-induced cellular senescence in human melanocytes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.16.528886. [PMID: 36824910 PMCID: PMC9949056 DOI: 10.1101/2023.02.16.528886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Melanoma arises from transformation of melanocytes in the basal layer of the epidermis where they are surrounded by keratinocytes, with which they interact through cell contact and paracrine communication. Considerable effort has been devoted to determining how the accumulation of oncogene and tumor suppressor gene mutations in melanocytes drive melanoma development. However, the extent to which alterations in keratinocytes that occur in the developing tumor niche serve as extrinsic drivers of melanoma initiation and progression is poorly understood. We recently identified the keratinocyte-specific cadherin, desmoglein 1 (Dsg1), as an important mediator of keratinocyte:melanoma cell crosstalk, demonstrating that its chronic loss, which can occur through melanoma cell-dependent paracrine signaling, promotes behaviors that mimic a malignant phenotype. Here we address the extent to which Dsg1 loss affects early steps in melanomagenesis. RNA-Seq analysis revealed that paracrine signals from Dsg1-deficient keratinocytes mediate a transcriptional switch from a differentiated to undifferentiated cell state in melanocytes expressing BRAFV600E, a driver mutation commonly present in both melanoma and benign nevi and reported to cause growth arrest and oncogene-induced senescence (OIS). Of ~220 differentially expressed genes in BRAFV600E cells treated with Dsg1-deficient conditioned media (CM), the laminin superfamily member NTN4/Netrin-4, which inhibits senescence in endothelial cells, stood out. Indeed, while BRAFV600E melanocytes treated with Dsg1-deficient CM showed signs of senescence bypass as assessed by increased senescence-associated β-galactosidase activity and decreased p16, knockdown of NTN4 reversed these effects. These results suggest that Dsg1 loss in keratinocytes provides an extrinsic signal to push melanocytes towards oncogenic transformation once an initial mutation has been introduced.
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Affiliation(s)
- Xin Tong
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois
| | - Hope E. Burks
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Ziyou Ren
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Jennifer L. Koetsier
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Quinn R. Roth-Carter
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Kathleen J. Green
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
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117
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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: 12] [Impact Index Per Article: 12.0] [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.
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118
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Li Y, Chen H, Xie X, Yang B, Wang X, Zhang J, Qiao T, Guan J, Qiu Y, Huang YX, Tian D, Yao X, Lu D, Koeffler HP, Zhang Y, Yin D. PINK1-Mediated Mitophagy Promotes Oxidative Phosphorylation and Redox Homeostasis to Induce Drug-Tolerant Persister Cancer Cells. Cancer Res 2023; 83:398-413. [PMID: 36480196 DOI: 10.1158/0008-5472.can-22-2370] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 11/03/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022]
Abstract
The drug-tolerant persister (DTP) state enables cancer cells to evade cytotoxic stress from anticancer therapy. However, the mechanisms governing DTP generation remain poorly understood. Here, we observed that lung adenocarcinoma (LUAD) cells and organoids entered a quiescent DTP state to survive MAPK inhibitor treatment. DTP cells following MAPK inhibition underwent a metabolic switch from glycolysis to oxidative phosphorylation (OXPHOS). PTEN-induced kinase 1 (PINK1), a serine/threonine kinase that initiates mitophagy, was upregulated to maintain mitochondrial homeostasis during DTP generation. PINK1-mediated mitophagy supported DTP cell survival and contributed to poor prognosis. Mechanistically, MAPK pathway inhibition resulted in MYC-dependent transcriptional upregulation of PINK1, leading to mitophagy activation. Mitophagy inhibition using either clinically applicable chloroquine or depletion of PINK1 eradicated drug tolerance and allowed complete response to MAPK inhibitors. This study uncovers PINK1-mediated mitophagy as a novel tumor protective mechanism for DTP generation, providing a therapeutic opportunity to eradicate DTP and achieve complete responses. SIGNIFICANCE DTP cancer cells that cause relapse after anticancer therapy critically depend on PINK1-mediated mitophagy and metabolic reprogramming, providing a therapeutic opportunity to eradicate persister cells to prolong treatment efficacy.
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Affiliation(s)
- Yun Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Hengxing Chen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, P. R. China.,Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-Sen University, Guangdong, P. R. China
| | - Xuan Xie
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, P. R. China.,Department of Thoracic Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Bing Yang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Xiaojuan Wang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Jingyuan Zhang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Tian Qiao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Jiao Guan
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Yuntan Qiu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Yong-Xin Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Duanqing Tian
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Xinyi Yao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Daning Lu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, P. R. China
| | - H Phillip Koeffler
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, University of California Los Angeles School of Medicine, Los Angeles, California.,Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Yin Zhang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Dong Yin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, P. R. China
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119
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Khozyainova AA, Valyaeva AA, Arbatsky MS, Isaev SV, Iamshchikov PS, Volchkov EV, Sabirov MS, Zainullina VR, Chechekhin VI, Vorobev RS, Menyailo ME, Tyurin-Kuzmin PA, Denisov EV. Complex Analysis of Single-Cell RNA Sequencing Data. BIOCHEMISTRY (MOSCOW) 2023; 88:231-252. [PMID: 37072324 PMCID: PMC10000364 DOI: 10.1134/s0006297923020074] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) is a revolutionary tool for studying the physiology of normal and pathologically altered tissues. This approach provides information about molecular features (gene expression, mutations, chromatin accessibility, etc.) of cells, opens up the possibility to analyze the trajectories/phylogeny of cell differentiation and cell-cell interactions, and helps in discovery of new cell types and previously unexplored processes. From a clinical point of view, scRNA-seq facilitates deeper and more detailed analysis of molecular mechanisms of diseases and serves as a basis for the development of new preventive, diagnostic, and therapeutic strategies. The review describes different approaches to the analysis of scRNA-seq data, discusses the advantages and disadvantages of bioinformatics tools, provides recommendations and examples of their successful use, and suggests potential directions for improvement. We also emphasize the need for creating new protocols, including multiomics ones, for the preparation of DNA/RNA libraries of single cells with the purpose of more complete understanding of individual cells.
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Affiliation(s)
- Anna A Khozyainova
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634050, Russia.
| | - Anna A Valyaeva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Mikhail S Arbatsky
- Laboratory of Artificial Intelligence and Bioinformatics, The Russian Clinical Research Center for Gerontology, Pirogov Russian National Medical University, Moscow, 129226, Russia
- School of Public Administration, Lomonosov Moscow State University, Moscow, 119991, Russia
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Sergey V Isaev
- Research Institute of Personalized Medicine, National Center for Personalized Medicine of Endocrine Diseases, National Medical Research Center for Endocrinology, Moscow, 117036, Russia
| | - Pavel S Iamshchikov
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634050, Russia
- Laboratory of Complex Analysis of Big Bioimage Data, National Research Tomsk State University, Tomsk, 634050, Russia
| | - Egor V Volchkov
- Department of Oncohematology, Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117198, Russia
| | - Marat S Sabirov
- Laboratory of Bioinformatics and Molecular Genetics, Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, 119334, Russia
| | - Viktoria R Zainullina
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634050, Russia
| | - Vadim I Chechekhin
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Rostislav S Vorobev
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634050, Russia
| | - Maxim E Menyailo
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634050, Russia
| | - Pyotr A Tyurin-Kuzmin
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Evgeny V Denisov
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634050, Russia
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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.
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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.
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A Network of MicroRNAs and mRNAs Involved in Melanosome Maturation and Trafficking Defines the Lower Response of Pigmentable Melanoma Cells to Targeted Therapy. Cancers (Basel) 2023; 15:cancers15030894. [PMID: 36765859 PMCID: PMC9913661 DOI: 10.3390/cancers15030894] [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: 11/01/2022] [Revised: 01/16/2023] [Accepted: 01/23/2023] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The ability to increase their degree of pigmentation is an adaptive response that confers pigmentable melanoma cells higher resistance to BRAF inhibitors (BRAFi) compared to non-pigmentable melanoma cells. METHODS Here, we compared the miRNome and the transcriptome profile of pigmentable 501Mel and SK-Mel-5 melanoma cells vs. non-pigmentable A375 melanoma cells, following treatment with the BRAFi vemurafenib (vem). In depth bioinformatic analyses (clusterProfiler, WGCNA and SWIMmeR) allowed us to identify the miRNAs, mRNAs and biological processes (BPs) that specifically characterize the response of pigmentable melanoma cells to the drug. Such BPs were studied using appropriate assays in vitro and in vivo (xenograft in zebrafish embryos). RESULTS Upon vem treatment, miR-192-5p, miR-211-5p, miR-374a-5p, miR-486-5p, miR-582-5p, miR-1260a and miR-7977, as well as GPR143, OCA2, RAB27A, RAB32 and TYRP1 mRNAs, are differentially expressed only in pigmentable cells. These miRNAs and mRNAs belong to BPs related to pigmentation, specifically melanosome maturation and trafficking. In fact, an increase in the number of intracellular melanosomes-due to increased maturation and/or trafficking-confers resistance to vem. CONCLUSION We demonstrated that the ability of pigmentable cells to increase the number of intracellular melanosomes fully accounts for their higher resistance to vem compared to non-pigmentable cells. In addition, we identified a network of miRNAs and mRNAs that are involved in melanosome maturation and/or trafficking. Finally, we provide the rationale for testing BRAFi in combination with inhibitors of these biological processes, so that pigmentable melanoma cells can be turned into more sensitive non-pigmentable cells.
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Rebecca VW, Xiao M, Kossenkov A, Godok T, Brown GS, Fingerman D, Alicea GM, Wei M, Ji H, Bravo J, Chen Y, Fane ME, Villanueva J, Nathanson K, Liu Q, Gopal YNV, Davies MA, Herlyn M. Dasatinib Resensitizes MAPK Inhibitor Efficacy in Standard-of-Care Relapsed Melanomas. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.20.524923. [PMID: 36711814 PMCID: PMC9882271 DOI: 10.1101/2023.01.20.524923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Resistance to combination BRAF/MEK inhibitor (BRAFi/MEKi) therapy arises in nearly every patient with BRAFV600E/K melanoma, despite promising initial responses. Achieving cures in this expanding BRAFi/MEKi-resistant cohort represents one of the greatest challenges to the field; few experience additional durable benefit from immunotherapy and no alternative therapies exist. To better personalize therapy in cancer patients to address therapy relapse, umbrella trials have been initiated whereby genomic sequencing of a panel of potentially actionable targets guide therapy selection for patients; however, the superior efficacy of such approaches remains to be seen. We here test the robustness of the umbrella trial rationale by analyzing relationships between genomic status of a gene and the downstream consequences at the protein level of related pathway, which find poor relationships between mutations, copy number amplification, and protein level. To profile candidate therapeutic strategies that may offer clinical benefit in the context of acquired BRAFi/MEKi resistance, we established a repository of patient-derived xenograft models from heavily pretreated patients with resistance to BRAFi/MEKi and/or immunotherapy (R-PDX). With these R-PDXs, we executed in vivo compound repurposing screens using 11 FDA-approved agents from an NCI-portfolio with pan-RTK, non-RTK and/or PI3K-mTOR specificity. We identify dasatinib as capable of restoring BRAFi/MEKi antitumor efficacy in ~70% of R-PDX tested. A systems-biology analysis indicates elevated baseline protein expression of canonical drivers of therapy resistance (e.g., AXL, YAP, HSP70, phospho-AKT) as predictive of MAPKi/dasatinib sensitivity. We therefore propose that dasatinib-based MAPKi therapy may restore antitumor efficacy in patients that have relapsed to standard-of-care therapy by broadly targeting proteins critical in melanoma therapy escape. Further, we submit that this experimental PDX paradigm could potentially improve preclinical evaluation of therapeutic modalities and augment our ability to identify biomarker-defined patient subsets that may respond to a given clinical trial.
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Affiliation(s)
- Vito W Rebecca
- The Wistar Institute, Philadelphia, PA, USA
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Min Xiao
- The Wistar Institute, Philadelphia, PA, USA
| | | | | | | | | | - Gretchen M Alicea
- The Wistar Institute, Philadelphia, PA, USA
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Meihan Wei
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Hongkai Ji
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jeremy Bravo
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Mitchell E Fane
- The Wistar Institute, Philadelphia, PA, USA
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | | | | | - Qin Liu
- The Wistar Institute, Philadelphia, PA, USA
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123
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Chhouri H, Alexandre D, Grumolato L. Mechanisms of Acquired Resistance and Tolerance to EGFR Targeted Therapy in Non-Small Cell Lung Cancer. Cancers (Basel) 2023; 15:cancers15020504. [PMID: 36672453 PMCID: PMC9856371 DOI: 10.3390/cancers15020504] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/09/2023] [Accepted: 01/09/2023] [Indexed: 01/17/2023] Open
Abstract
Non-small cell lung cancers (NSCLC) harboring activating mutations of the epidermal growth factor receptor (EGFR) are treated with specific tyrosine kinase inhibitors (EGFR-TKIs) of this receptor, resulting in clinically responses that can generally last several months. Unfortunately, EGFR-targeted therapy also favors the emergence of drug tolerant or resistant cells, ultimately resulting in tumor relapse. Recently, cellular barcoding strategies have arisen as a powerful tool to investigate the clonal evolution of these subpopulations in response to anti-cancer drugs. In this review, we provide an overview of the currently available treatment options for NSCLC, focusing on EGFR targeted therapy, and discuss the common mechanisms of resistance to EGFR-TKIs. We also review the characteristics of drug-tolerant persister (DTP) cells and the mechanistic basis of drug tolerance in EGFR-mutant NSCLC. Lastly, we address how cellular barcoding can be applied to investigate the response and the behavior of DTP cells upon EGFR-TKI treatment.
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124
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Lehmann J, Caduff N, Krzywińska E, Stierli S, Salas-Bastos A, Loos B, Levesque MP, Dummer R, Stockmann C, Münz C, Diener J, Sommer L. Escape from NK cell tumor surveillance by NGFR-induced lipid remodeling in melanoma. SCIENCE ADVANCES 2023; 9:eadc8825. [PMID: 36638181 PMCID: PMC9839334 DOI: 10.1126/sciadv.adc8825] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 12/09/2022] [Indexed: 05/27/2023]
Abstract
Metastatic disease is a major cause of death for patients with melanoma. Melanoma cells can become metastatic not only due to cell-intrinsic plasticity but also due to cancer-induced protumorigenic remodeling of the immune microenvironment. Here, we report that innate immune surveillance by natural killer (NK) cells is bypassed by human melanoma cells expressing the stem cell marker NGFR. Using in vitro and in vivo cytotoxic assays, we show that NGFR protects melanoma cells from NK cell-mediated killing and, furthermore, boosts metastasis formation in a mouse model with adoptively transferred human NK cells. Mechanistically, NGFR leads to down-regulation of NK cell activating ligands and simultaneous up-regulation of the fatty acid stearoyl-coenzyme A desaturase (SCD) in melanoma cells. Notably, pharmacological and small interfering RNA-mediated inhibition of SCD reverted NGFR-induced NK cell evasion in vitro and in vivo. Hence, NGFR orchestrates immune control antagonizing pathways to protect melanoma cells from NK cell clearance, which ultimately favors metastatic disease.
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Affiliation(s)
- Julia Lehmann
- University of Zurich, Institute of Anatomy, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Nicole Caduff
- University of Zurich, Institute of Experimental Immunology, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Ewelina Krzywińska
- University of Zurich, Institute of Anatomy, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Salome Stierli
- University of Zurich, Institute of Anatomy, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Adrian Salas-Bastos
- University of Zurich, Institute of Anatomy, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Benjamin Loos
- University of Zurich, Institute of Anatomy, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Mitchell P. Levesque
- University of Zurich Hospital, Department of Dermatology, Gloriastrasse 31, 8091 Zürich, Switzerland
| | - Reinhard Dummer
- University of Zurich Hospital, Department of Dermatology, Gloriastrasse 31, 8091 Zürich, Switzerland
| | - Christian Stockmann
- University of Zurich, Institute of Anatomy, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Christian Münz
- University of Zurich, Institute of Experimental Immunology, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Johanna Diener
- University of Zurich, Institute of Anatomy, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Lukas Sommer
- University of Zurich, Institute of Anatomy, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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125
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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: 13] [Impact Index Per Article: 13.0] [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.
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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:
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CHRNA1 and its correlated-myogenesis/cell cycle genes are prognosis-related markers of metastatic melanoma. Biochem Biophys Rep 2023; 33:101425. [PMID: 36654921 PMCID: PMC9841360 DOI: 10.1016/j.bbrep.2023.101425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Nicotinic acetylcholine receptors (CHRNs) expression and their critical role in various types of cancer have been reported. However, it is still unclear which CHRNs and their associated genes play essential roles in metastasis in melanoma patients. Here, we performed bioinformatics analyses on publicly available bulk RNA sequencing (RNA-seq) data of patients with melanoma to identify the CHRNs highly expressed in metastatic melanoma. We found that CHRNA1 was highly expressed in metastatic melanoma samples compared to primary melanoma samples and was strongly associated with CHRNB1 and CHRNG. These muscle-type CHRNs (CHRNA1, CHRNB1, and CHRNG) were correlated with the ZEB1 and Rho/ROCK pathway-related genes in metastatic melanoma samples. Pairwise correlations and enrichment analyses revealed that CHRNA1 was significantly associated with myogenesis/muscle contraction and cell cycle genes. Kaplan-Meier curves illustrated the involvement of CHRNA1, four of its correlated genes (DES, FLNC, CDK1, and CDC20), and the myogenesis gene signature in the prognosis of melanoma patients. Following the bulk RNA-seq analysis, single-cell RNA-seq (scRNA-seq) analysis showed that the CHRNA1-expressing melanoma cells are primarily metastatic and had high expression levels of CHRNB1, CHRNG, and myogenesis/cell cycle-related genes. Our bioinformatics analyses of the bulk RNA-seq and scRNA-seq data of patients with melanoma revealed that CHRNA1 and its correlated myogenesis/cell-related cycle genes are critical prognosis-related markers of metastatic melanoma.
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127
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Hattori T, Maso L, Araki KY, Koide A, Hayman J, Akkapeddi P, Bang I, Neel BG, Koide S. Creating MHC-Restricted Neoantigens with Covalent Inhibitors That Can Be Targeted by Immune Therapy. Cancer Discov 2023; 13:132-145. [PMID: 36250888 PMCID: PMC9827112 DOI: 10.1158/2159-8290.cd-22-1074] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 01/16/2023]
Abstract
Intracellular oncoproteins can be inhibited with targeted therapy, but responses are not durable. Immune therapies can be curative, but most oncogene-driven tumors are unresponsive to these agents. Fragments of intracellular oncoproteins can act as neoantigens presented by the major histocompatibility complex (MHC), but recognizing minimal differences between oncoproteins and their normal counterparts is challenging. We have established a platform technology that exploits hapten-peptide conjugates generated by covalent inhibitors to create distinct neoantigens that selectively mark cancer cells. Using the FDA-approved covalent inhibitors sotorasib and osimertinib, we developed "HapImmune" antibodies that bind to drug-peptide conjugate/MHC complexes but not to the free drugs. A HapImmune-based bispecific T-cell engager selectively and potently kills sotorasib-resistant lung cancer cells upon sotorasib treatment. Notably, it is effective against KRASG12C-mutant cells with different HLA supertypes, HLA-A*02 and A*03/11, suggesting loosening of MHC restriction. Our strategy creates targetable neoantigens by design, unifying targeted and immune therapies. SIGNIFICANCE Targeted therapies against oncoproteins often have dramatic initial efficacy but lack durability. Immunotherapies can be curative, yet most tumors fail to respond. We developed a generalizable technology platform that exploits hapten-peptides generated by covalent inhibitors as neoantigens presented on MHC to enable engineered antibodies to selectively kill drug-resistant cancer cells. See related commentary by Cox et al., p. 19. This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- Takamitsu Hattori
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, New York.,Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York
| | - Lorenzo Maso
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, New York
| | - Kiyomi Y. Araki
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, New York
| | - Akiko Koide
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, New York.,Division of Hematology Oncology, Department of Medicine, New York University Grossman School of Medicine, New York, New York
| | - James Hayman
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, New York
| | - Padma Akkapeddi
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, New York
| | - Injin Bang
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, New York
| | - Benjamin G. Neel
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, New York.,Division of Hematology Oncology, Department of Medicine, New York University Grossman School of Medicine, New York, New York.,Corresponding Authors: Shohei Koide, Smilow Research Center, Room 1105, 522 First Avenue, New York, NY 10016. Phone: 646-501-4601; E-mail: ; and Benjamin G. Neel, Smilow Research Center, Suite 1201, 522 First Avenue, New York, NY 10016. Phone: 212-263-3019; E-mail:
| | - Shohei Koide
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, New York.,Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York.,Corresponding Authors: Shohei Koide, Smilow Research Center, Room 1105, 522 First Avenue, New York, NY 10016. Phone: 646-501-4601; E-mail: ; and Benjamin G. Neel, Smilow Research Center, Suite 1201, 522 First Avenue, New York, NY 10016. Phone: 212-263-3019; E-mail:
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Smalley KSM. Too Much Fuel on the Fire? Linking Obesity, Metabolism, and Melanoma Outcomes. Clin Cancer Res 2023; 29:5-7. [PMID: 36315002 DOI: 10.1158/1078-0432.ccr-22-3028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 10/23/2022] [Accepted: 10/27/2022] [Indexed: 11/07/2022]
Abstract
Patients with metastatic melanoma who are overweight or obese have improved outcomes when treated with immunotherapies or targeted therapies. A recent study provides the first evidence that the host metabolic state influences the tumor metabolic phenotype, with implications for tumor progression and therapeutic response. See related article by Hahn et al., p. 154.
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Affiliation(s)
- Keiran S M Smalley
- Department of Tumor Biology, Moffitt Cancer Center, Tampa, Florida.,Department of Cutaneous Oncology, Moffitt Cancer Center, Tampa, Florida
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129
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Song Y, Wang Y, Guan A, Xue J, Li B, Huang Z, Zheng Z, Liang N, Yang Y, Li S. Footprints: Stamping hallmarks of lung cancer with patient-derived models, from molecular mechanisms to clinical translation. Front Bioeng Biotechnol 2023; 11:1132940. [PMID: 36911198 PMCID: PMC9993089 DOI: 10.3389/fbioe.2023.1132940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 02/13/2023] [Indexed: 02/24/2023] Open
Abstract
The conventional two-dimensional (2D) tumor cell lines in Petri dishes have played an important role in revealing the molecular biological mechanism of lung cancer. However, they cannot adequately recapitulate the complex biological systems and clinical outcomes of lung cancer. The three-dimensional (3D) cell culture enables the possible 3D cell interactions and the complex 3D systems with co-culture of different cells mimicking the tumor microenvironments (TME). In this regard, patient-derived models, mainly patient-derived tumor xenograft (PDX) and patient-derived organoids discussed hereby, are with higher biological fidelity of lung cancer, and regarded as more faithful preclinical models. The significant Hallmarks of Cancer is believed to be the most comprehensive coverage of current research on tumor biological characteristics. Therefore, this review aims to present and discuss the application of different patient-derived lung cancer models from molecular mechanisms to clinical translation with regards to the dimensions of different hallmarks, and to look to the prospects of these patient-derived lung cancer models.
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Affiliation(s)
- Yang Song
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Yadong Wang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Ai Guan
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Jianchao Xue
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Bowen Li
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhicheng Huang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhibo Zheng
- Department of International Medical Services, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Naixin Liang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Yanlian Yang
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China
| | - Shanqing Li
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
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130
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Oncosuppressive miRNAs loaded in lipid nanoparticles potentiate targeted therapies in BRAF-mutant melanoma by inhibiting core escape pathways of resistance. Oncogene 2023; 42:293-307. [PMID: 36418472 PMCID: PMC9684877 DOI: 10.1038/s41388-022-02547-9] [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: 06/11/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/27/2022]
Abstract
BRAF-mutated melanoma relapsing after targeted therapies is an aggressive disease with unmet clinical need. Hence the need to identify novel combination therapies able to overcome drug resistance. miRNAs have emerged as orchestrators of non-genetic mechanisms adopted by melanoma cells to challenge therapies. In this context we previously identified a subset of oncosuppressor miRNAs downregulated in drug-resistant melanomas. Here we demonstrate that lipid nanoparticles co-encapsulating two of them, miR-199-5p and miR-204-5p, inhibit tumor growth both in vitro and in vivo in combination with target therapy and block the development of drug resistance. Mechanistically they act by directly reducing melanoma cell growth and also indirectly by hampering the recruitment and reprogramming of pro-tumoral macrophages. Molecularly, we demonstrate that the effects on macrophages are mediated by the dysregulation of a newly identified miR-204-5p-miR-199b-5p/CCL5 axis. Finally, we unveiled that M2 macrophages programs are molecular signatures of resistance and predict response to therapy in patients. Overall, these findings have strong translational implications to propose new combination therapies making use of RNA therapeutics for metastatic melanoma patients.
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131
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Mani N, Daiya A, Chowdhury R, Mukherjee S, Chowdhury S. Epigenetic adaptations in drug-tolerant tumor cells. Adv Cancer Res 2023; 158:293-335. [PMID: 36990535 DOI: 10.1016/bs.acr.2022.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Traditional chemotherapy against cancer is often severely hampered by acquired resistance to the drug. Epigenetic alterations and other mechanisms like drug efflux, drug metabolism, and engagement of survival pathways are crucial in evading drug pressure. Herein, growing evidence suggests that a subpopulation of tumor cells can often tolerate drug onslaught by entering a "persister" state with minimal proliferation. The molecular features of these persister cells are gradually unraveling. Notably, the "persisters" act as a cache of cells that can eventually re-populate the tumor post-withdrawal drug pressure and contribute to acquiring stable drug-resistant features. This underlines the clinical significance of the tolerant cells. Accumulating evidence highlights the importance of modulation of the epigenome as a critical adaptive strategy for evading drug pressure. Chromatin remodeling, altered DNA methylation, and de-regulation of non-coding RNA expression and function contribute significantly to this persister state. No wonder targeting adaptive epigenetic modifications is increasingly recognized as an appropriate therapeutic strategy to sensitize them and restore drug sensitivity. Furthermore, manipulating the tumor microenvironment and "drug holiday" is also explored to maneuver the epigenome. However, heterogeneity in adaptive strategies and lack of targeted therapies have significantly hindered the translation of epigenetic therapy to the clinics. In this review, we comprehensively analyze the epigenetic alterations adapted by the drug-tolerant cells, the therapeutic strategies employed to date, and their limitations and future prospects.
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132
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Qi R, Zou Q. Trends and Potential of Machine Learning and Deep Learning in Drug Study at Single-Cell Level. RESEARCH (WASHINGTON, D.C.) 2023; 6:0050. [PMID: 36930772 PMCID: PMC10013796 DOI: 10.34133/research.0050] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/27/2022] [Indexed: 01/12/2023]
Abstract
Cancer treatments always face challenging problems, particularly drug resistance due to tumor cell heterogeneity. The existing datasets include the relationship between gene expression and drug sensitivities; however, the majority are based on tissue-level studies. Study drugs at the single-cell level are perspective to overcome minimal residual disease caused by subclonal resistant cancer cells retained after initial curative therapy. Fortunately, machine learning techniques can help us understand how different types of cells respond to different cancer drugs from the perspective of single-cell gene expression. Good modeling using single-cell data and drug response information will not only improve machine learning for cell-drug outcome prediction but also facilitate the discovery of drugs for specific cancer subgroups and specific cancer treatments. In this paper, we review machine learning and deep learning approaches in drug research. By analyzing the application of these methods on cancer cell lines and single-cell data and comparing the technical gap between single-cell sequencing data analysis and single-cell drug sensitivity analysis, we hope to explore the trends and potential of drug research at the single-cell data level and provide more inspiration for drug research at the single-cell level. We anticipate that this review will stimulate the innovative use of machine learning methods to address new challenges in precision medicine more broadly.
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Affiliation(s)
- Ren Qi
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324000, China.,School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Quan Zou
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324000, China.,Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
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133
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Criscione SW, Martin MJ, Oien DB, Gorthi A, Miragaia RJ, Zhang J, Chen H, Karl DL, Mendler K, Markovets A, Gagrica S, Delpuech O, Dry JR, Grondine M, Hattersley MM, Urosevic J, Floc’h N, Drew L, Yao Y, Smith PD. The landscape of therapeutic vulnerabilities in EGFR inhibitor osimertinib drug tolerant persister cells. NPJ Precis Oncol 2022; 6:95. [PMID: 36575215 PMCID: PMC9794691 DOI: 10.1038/s41698-022-00337-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 12/12/2022] [Indexed: 12/28/2022] Open
Abstract
Third-generation EGFR tyrosine kinase inhibitors (EGFR-TKIs), including osimertinib, an irreversible EGFR-TKI, are important treatments for non-small cell lung cancer with EGFR-TKI sensitizing or EGFR T790M resistance mutations. While patients treated with osimertinib show clinical benefit, disease progression and drug resistance are common. Emergence of de novo acquired resistance from a drug tolerant persister (DTP) cell population is one mechanism proposed to explain progression on osimertinib and other targeted cancer therapies. Here we profiled osimertinib DTPs using RNA-seq and ATAC-seq to characterize the features of these cells and performed drug screens to identify therapeutic vulnerabilities. We identified several vulnerabilities in osimertinib DTPs that were common across models, including sensitivity to MEK, AURKB, BRD4, and TEAD inhibition. We linked several of these vulnerabilities to gene regulatory changes, for example, TEAD vulnerability was consistent with evidence of Hippo pathway turning off in osimertinib DTPs. Last, we used genetic approaches using siRNA knockdown or CRISPR knockout to validate AURKB, BRD4, and TEAD as the direct targets responsible for the vulnerabilities observed in the drug screen.
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Affiliation(s)
- Steven W. Criscione
- grid.418152.b0000 0004 0543 9493Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA USA
| | - Matthew J. Martin
- grid.417815.e0000 0004 5929 4381Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Derek B. Oien
- grid.418152.b0000 0004 0543 9493Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA USA
| | - Aparna Gorthi
- grid.418152.b0000 0004 0543 9493Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA USA ,grid.267309.90000 0001 0629 5880Department of Cell Systems & Anatomy, Greehey Children’s Cancer Research Institute, University of Texas at Health San Antonio, San Antonio, TX USA
| | - Ricardo J. Miragaia
- grid.417815.e0000 0004 5929 4381Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Jingwen Zhang
- grid.418152.b0000 0004 0543 9493Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA USA
| | - Huawei Chen
- grid.418152.b0000 0004 0543 9493Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA USA
| | - Daniel L. Karl
- grid.418152.b0000 0004 0543 9493Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA USA
| | - Kerrin Mendler
- grid.418152.b0000 0004 0543 9493Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA USA
| | - Aleksandra Markovets
- grid.418152.b0000 0004 0543 9493Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA USA
| | - Sladjana Gagrica
- grid.417815.e0000 0004 5929 4381Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Oona Delpuech
- grid.417815.e0000 0004 5929 4381Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Jonathan R. Dry
- grid.418152.b0000 0004 0543 9493Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA USA
| | - Michael Grondine
- grid.418152.b0000 0004 0543 9493Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA USA
| | - Maureen M. Hattersley
- grid.418152.b0000 0004 0543 9493Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA USA
| | - Jelena Urosevic
- grid.417815.e0000 0004 5929 4381Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Nicolas Floc’h
- grid.417815.e0000 0004 5929 4381Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Lisa Drew
- grid.418152.b0000 0004 0543 9493Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA USA
| | - Yi Yao
- grid.418152.b0000 0004 0543 9493Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA USA
| | - Paul D. Smith
- grid.417815.e0000 0004 5929 4381Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
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134
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Vegliante R, Pastushenko I, Blanpain C. Deciphering functional tumor states at single-cell resolution. EMBO J 2022; 41:e109221. [PMID: 34918370 PMCID: PMC8762559 DOI: 10.15252/embj.2021109221] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/07/2021] [Accepted: 11/10/2021] [Indexed: 01/19/2023] Open
Abstract
Within a tumor, cancer cells exist in different states that are associated with distinct tumor functions, including proliferation, differentiation, invasion, metastasis, and resistance to anti-cancer therapy. The identification of the gene regulatory networks underpinning each state is essential for better understanding functional tumor heterogeneity and revealing tumor vulnerabilities. Here, we review the different studies identifying tumor states by single-cell sequencing approaches and the mechanisms that promote and sustain these functional states and regulate their transitions. We also describe how different tumor states are spatially distributed and interact with the specific stromal cells that compose the tumor microenvironment. Finally, we discuss how the understanding of tumor plasticity and transition states can be used to develop new strategies to improve cancer therapy.
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Affiliation(s)
- Rolando Vegliante
- Laboratory of Stem Cells and CancerUniversité Libre de BruxellesBrusselsBelgium
| | | | - Cédric Blanpain
- Laboratory of Stem Cells and CancerUniversité Libre de BruxellesBrusselsBelgium
- WELBIOUniversité Libre de BruxellesBrusselsBelgium
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135
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Gambi G, Mengus G, Davidson G, Demesmaeker E, Cuomo A, Bonaldi T, Katopodi V, Malouf GG, Leucci E, Davidson I. The LncRNA LENOX Interacts with RAP2C to Regulate Metabolism and Promote Resistance to MAPK Inhibition in Melanoma. Cancer Res 2022; 82:4555-4570. [PMID: 36214632 PMCID: PMC9755964 DOI: 10.1158/0008-5472.can-22-0959] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/27/2022] [Accepted: 09/21/2022] [Indexed: 01/24/2023]
Abstract
Tumor heterogeneity is a key feature of melanomas that hinders development of effective treatments. Aiming to overcome this, we identified LINC00518 (LENOX; lincRNA-enhancer of oxidative phosphorylation) as a melanoma-specific lncRNA expressed in all known melanoma cell states and essential for melanoma survival in vitro and in vivo. Mechanistically, LENOX promoted association of the RAP2C GTPase with mitochondrial fission regulator DRP1, increasing DRP1 S637 phosphorylation, mitochondrial fusion, and oxidative phosphorylation. LENOX expression was upregulated following treatment with MAPK inhibitors, facilitating a metabolic switch from glycolysis to oxidative phosphorylation and conferring resistance to MAPK inhibition. Consequently, combined silencing of LENOX and RAP2C synergized with MAPK inhibitors to eradicate melanoma cells. Melanomas are thus addicted to the lncRNA LENOX, which acts to optimize mitochondrial function during melanoma development and progression. SIGNIFICANCE The lncRNA LENOX is a novel regulator of melanoma metabolism, which can be targeted in conjunction with MAPK inhibitors to eradicate melanoma cells.
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Affiliation(s)
- Giovanni Gambi
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Gabrielle Mengus
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Guillaume Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | | | - Alessandro Cuomo
- Nuclear Proteomics Institute to Study Gene Expression, Milano, Italy
| | - Tiziana Bonaldi
- Nuclear Proteomics Institute to Study Gene Expression, Milano, Italy
| | - Vicky Katopodi
- Laboratory for RNA Cancer Biology, KU Leuven, Leuven, Belgium
| | - Gabriel G. Malouf
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Eleonora Leucci
- Laboratory for RNA Cancer Biology, KU Leuven, Leuven, Belgium.,Corresponding Authors: Irwin Davidson, Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1 Rue Laurent Fries, Illkirch, 67404, France. E-mail: ; and Eleonora Leucci, Laboratory for RNA Cancer Biology, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. E-mail:
| | - Irwin Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France.,Equipe Labélisée Ligue contre le Cancer.,Corresponding Authors: Irwin Davidson, Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1 Rue Laurent Fries, Illkirch, 67404, France. E-mail: ; and Eleonora Leucci, Laboratory for RNA Cancer Biology, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. E-mail:
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136
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Pagliuca C, Di Leo L, De Zio D. New Insights into the Phenotype Switching of Melanoma. Cancers (Basel) 2022; 14:cancers14246118. [PMID: 36551603 PMCID: PMC9776915 DOI: 10.3390/cancers14246118] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/02/2022] [Accepted: 12/10/2022] [Indexed: 12/14/2022] Open
Abstract
Melanoma is considered one of the deadliest skin cancers, partly because of acquired resistance to standard therapies. The most recognized driver of resistance relies on acquired melanoma cell plasticity, or the ability to dynamically switch among differentiation phenotypes. This confers the tumor noticeable advantages. During the last year, two new features have been included in the hallmarks of cancer, namely "Unlocking phenotypic plasticity" and "Non-mutational epigenetic reprogramming". Such are inextricably intertwined as, most of the time, plasticity is not discernable at the genetic level, as it rather consists of epigenetic reprogramming heavily influenced by external factors. By analyzing current literature, this review provides reasoning about the origin of plasticity and clarifies whether such features already exist among tumors or are acquired by selection. Moreover, markers of plasticity, molecular effectors, and related tumor advantages in melanoma will be explored. Ultimately, as this new branch of tumor biology opened a wide landscape of therapeutic possibilities, in the final paragraph of this review, we will focus on newly characterized drugs targeting melanoma plasticity.
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Affiliation(s)
- Chiara Pagliuca
- Melanoma Research Team, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Luca Di Leo
- Melanoma Research Team, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Daniela De Zio
- Melanoma Research Team, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Correspondence:
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137
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Wirth AK, Wange L, Vosberg S, Henrich KO, Rausch C, Özdemir E, Zeller CM, Richter D, Feuchtinger T, Kaller M, Hermeking H, Greif PA, Senft D, Jurinovic V, Bahrami E, Jayavelu AK, Westermann F, Mann M, Enard W, Herold T, Jeremias I. In vivo PDX CRISPR/Cas9 screens reveal mutual therapeutic targets to overcome heterogeneous acquired chemo-resistance. Leukemia 2022; 36:2863-2874. [PMID: 36333584 PMCID: PMC9712105 DOI: 10.1038/s41375-022-01726-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 08/30/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022]
Abstract
Resistance towards cancer treatment represents a major clinical obstacle, preventing cure of cancer patients. To gain mechanistic insights, we developed a model for acquired resistance to chemotherapy by treating mice carrying patient derived xenografts (PDX) of acute lymphoblastic leukemia with widely-used cytotoxic drugs for 18 consecutive weeks. In two distinct PDX samples, tumors initially responded to treatment, until stable disease and eventually tumor re-growth evolved under therapy, at highly similar kinetics between replicate mice. Notably, replicate tumors developed different mutations in TP53 and individual sets of chromosomal alterations, suggesting independent parallel clonal evolution rather than selection, driven by a combination of stochastic and deterministic processes. Transcriptome and proteome showed shared dysregulations between replicate tumors providing putative targets to overcome resistance. In vivo CRISPR/Cas9 dropout screens in PDX revealed broad dependency on BCL2, BRIP1 and COPS2. Accordingly, venetoclax re-sensitized derivative tumors towards chemotherapy, despite genomic heterogeneity, demonstrating direct translatability of the approach. Hence, despite the presence of multiple resistance-associated genomic alterations, effective rescue treatment for polychemotherapy-resistant tumors can be identified using functional testing in preclinical models.
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Affiliation(s)
- Anna-Katharina Wirth
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany
| | - Lucas Wange
- Anthropology and Human Genomics, Faculty of Biology, Ludwig Maximilian University (LMU), Martinsried, Germany
| | - Sebastian Vosberg
- Clinical Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Kai-Oliver Henrich
- Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
| | - Christian Rausch
- Department of Medicine III, and Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Erbey Özdemir
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany
| | - Christina M Zeller
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany
| | - Daniel Richter
- Anthropology and Human Genomics, Faculty of Biology, Ludwig Maximilian University (LMU), Martinsried, Germany
| | - Tobias Feuchtinger
- Department of Pediatrics, Dr. von Hauner Children´s Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Markus Kaller
- Experimental and Molecular Pathology, Institute of Pathology, Ludwig Maximilian University (LMU), Munich, Germany
| | - Heiko Hermeking
- Experimental and Molecular Pathology, Institute of Pathology, Ludwig Maximilian University (LMU), Munich, Germany
| | - Philipp A Greif
- Department of Medicine III, and Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partnering Site Munich, Munich, Germany
| | - Daniela Senft
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany
| | - Vindi Jurinovic
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany
- Department of Medicine III, and Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Ehsan Bahrami
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany
| | - Ashok Kumar Jayavelu
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Clinical Cooperation Unit Pediatric Leukemia, German Cancer Research Center, Heidelberg, Germany
| | - Frank Westermann
- Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Wolfgang Enard
- Anthropology and Human Genomics, Faculty of Biology, Ludwig Maximilian University (LMU), Martinsried, Germany
| | - Tobias Herold
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany
- Department of Medicine III, and Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Irmela Jeremias
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany.
- Department of Pediatrics, Dr. von Hauner Children´s Hospital, University Hospital, LMU Munich, Munich, Germany.
- German Cancer Consortium (DKTK), Partnering Site Munich, Munich, Germany.
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138
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Wang M, Wang Y, Liu R, Yu R, Gong T, Zhang Z, Fu Y. TLR4 Blockade Using Docosahexaenoic Acid Restores Vulnerability of Drug-Tolerant Tumor Cells and Prevents Breast Cancer Metastasis and Postsurgical Relapse. ACS BIO & MED CHEM AU 2022; 3:97-113. [PMID: 37101603 PMCID: PMC10125315 DOI: 10.1021/acsbiomedchemau.2c00061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/05/2022] [Accepted: 11/21/2022] [Indexed: 12/05/2022]
Abstract
Nonmutational mechanisms were recently discovered leading to reversible drug tolerance. Despite the rapid elimination of a majority of tumor cells, a small subpopulation of "'drug-tolerant"' cells remain viable with lethal drug exposure, which may further lead to resistance or tumor relapse. Several signaling pathways are involved in the local or systemic inflammatory responses contributing to drug-induced phenotypic switch. Here, we report that Toll-like receptor 4 (TLR4)-interacting lipid docosahexaenoic acid (DHA) restores the cytotoxic effect of doxorubicin (DOX) in the lipopolysaccharide-treated breast tumor cell line 4T1, preventing the phenotypic switch to drug-tolerant cells, which significantly reduces primary tumor growth and lung metastasis in both 4T1 orthotopic and experimental metastasis models. Importantly, DHA in combination with DOX delays and inhibits tumor recurrence following surgical removal of the primary tumor. Furthermore, the coencapsulation of DHA and DOX in a nanoemulsion significantly prolongs the survival of mice in the postsurgical 4T1 tumor relapse model with significantly reduced systemic toxicity. The synergistic antitumor, antimetastasis, and antirecurrence effects of DHA + DOX combination are likely mediated by attenuating TLR4 activation, thus sensitizing tumor cells to standard chemotherapy.
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Affiliation(s)
- Mou Wang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu610041, China
| | - Yuejing Wang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu610041, China
| | - Renhe Liu
- The Scripps Research Institute, 10550 North Torrey Pines Road,
La Jolla, San Diego, California92037, United States
| | - Ruilian Yu
- Department of Oncology, Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu610072, China
| | - Tao Gong
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu610041, China
| | - Zhirong Zhang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu610041, China
| | - Yao Fu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu610041, China
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139
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Rubanov A, Berico P, Hernando E. Epigenetic Mechanisms Underlying Melanoma Resistance to Immune and Targeted Therapies. Cancers (Basel) 2022; 14:cancers14235858. [PMID: 36497341 PMCID: PMC9738385 DOI: 10.3390/cancers14235858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 11/22/2022] [Indexed: 11/30/2022] Open
Abstract
Melanoma is an aggressive skin cancer reliant on early detection for high likelihood of successful treatment. Solar UV exposure transforms melanocytes into highly mutated tumor cells that metastasize to the liver, lungs, and brain. Even upon resection of the primary tumor, almost thirty percent of patients succumb to melanoma within twenty years. Identification of key melanoma genetic drivers led to the development of pharmacological BRAFV600E and MEK inhibitors, significantly improving metastatic patient outcomes over traditional cytotoxic chemotherapy or pioneering IFN-α and IL-2 immune therapies. Checkpoint blockade inhibitors releasing the immunosuppressive effects of CTLA-4 or PD-1 proved to be even more effective and are the standard first-line treatment. Despite these major improvements, durable responses to immunotherapy and targeted therapy have been hindered by intrinsic or acquired resistance. In addition to gained or selected genetic alterations, cellular plasticity conferred by epigenetic reprogramming is emerging as a driver of therapy resistance. Epigenetic regulation of chromatin accessibility drives gene expression and establishes distinct transcriptional cell states. Here we review how aberrant chromatin, transcriptional, and epigenetic regulation contribute to therapy resistance and discuss how targeting these programs sensitizes melanoma cells to immune and targeted therapies.
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Affiliation(s)
- Andrey Rubanov
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Pietro Berico
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Eva Hernando
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
- Correspondence:
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140
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Decoding molecular programs in melanoma brain metastases. Nat Commun 2022; 13:7304. [PMID: 36435874 PMCID: PMC9701224 DOI: 10.1038/s41467-022-34899-x] [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: 02/16/2022] [Accepted: 11/07/2022] [Indexed: 11/28/2022] Open
Abstract
Melanoma brain metastases (MBM) variably respond to therapeutic interventions; thus determining patient's prognosis. However, the mechanisms that govern therapy response are poorly understood. Here, we use a multi-OMICS approach and targeted sequencing (TargetSeq) to unravel the programs that potentially control the development of progressive intracranial disease. Molecularly, the expression of E-cadherin (Ecad) or NGFR, the BRAF mutation state and level of immune cell infiltration subdivides tumors into proliferative/pigmented and invasive/stem-like/therapy-resistant irrespective of the intracranial location. The analysis of MAPK inhibitor-naive and refractory MBM reveals switching from Ecad-associated into NGFR-associated programs during progression. NGFR-associated programs control cell migration and proliferation via downstream transcription factors such as SOX4. Moreover, global methylome profiling uncovers 46 differentially methylated regions that discriminate BRAFmut and wildtype MBM. In summary, we propose that the expression of Ecad and NGFR sub- classifies MBM and suggest that the Ecad-to-NGFR phenotype switch is a rate-limiting process which potentially indicates drug-response and intracranial progression states in melanoma patients.
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141
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Vera J, Lai X, Baur A, Erdmann M, Gupta S, Guttà C, Heinzerling L, Heppt MV, Kazmierczak PM, Kunz M, Lischer C, Pützer BM, Rehm M, Ostalecki C, Retzlaff J, Witt S, Wolkenhauer O, Berking C. Melanoma 2.0. Skin cancer as a paradigm for emerging diagnostic technologies, computational modelling and artificial intelligence. Brief Bioinform 2022; 23:6761961. [PMID: 36252807 DOI: 10.1093/bib/bbac433] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/28/2022] [Accepted: 09/08/2022] [Indexed: 12/19/2022] Open
Abstract
We live in an unprecedented time in oncology. We have accumulated samples and cases in cohorts larger and more complex than ever before. New technologies are available for quantifying solid or liquid samples at the molecular level. At the same time, we are now equipped with the computational power necessary to handle this enormous amount of quantitative data. Computational models are widely used helping us to substantiate and interpret data. Under the label of systems and precision medicine, we are putting all these developments together to improve and personalize the therapy of cancer. In this review, we use melanoma as a paradigm to present the successful application of these technologies but also to discuss possible future developments in patient care linked to them. Melanoma is a paradigmatic case for disruptive improvements in therapies, with a considerable number of metastatic melanoma patients benefiting from novel therapies. Nevertheless, a large proportion of patients does not respond to therapy or suffers from adverse events. Melanoma is an ideal case study to deploy advanced technologies not only due to the medical need but also to some intrinsic features of melanoma as a disease and the skin as an organ. From the perspective of data acquisition, the skin is the ideal organ due to its accessibility and suitability for many kinds of advanced imaging techniques. We put special emphasis on the necessity of computational strategies to integrate multiple sources of quantitative data describing the tumour at different scales and levels.
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Affiliation(s)
- Julio Vera
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
| | - Xin Lai
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
| | - Andreas Baur
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
| | - Michael Erdmann
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
| | - Shailendra Gupta
- Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, Rostock 18051, Germany
| | - Cristiano Guttà
- Institute of Cell Biology and Immunology, University of Stuttgart, 70569 Stuttgart, Germany
| | - Lucie Heinzerling
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany.,Department of Dermatology, LMU University Hospital, Munich, Germany
| | - Markus V Heppt
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
| | | | - Manfred Kunz
- Department of Dermatology, Venereology and Allergology, University of Leipzig, 04103 Leipzig, Germany
| | - Christopher Lischer
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
| | - Brigitte M Pützer
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, 18057 Rostock, Germany
| | - Markus Rehm
- Institute of Cell Biology and Immunology, University of Stuttgart, 70569 Stuttgart, Germany.,Stuttgart Research Center Systems Biology, University of Stuttgart, 70569 Stuttgart, Germany
| | - Christian Ostalecki
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
| | - Jimmy Retzlaff
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
| | | | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, Rostock 18051, Germany
| | - Carola Berking
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
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142
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Nyberg WA, Velasquez‐Pulgarin DA, He T, Sjöstrand M, Pellé L, Covacu R, Espinosa A. The bromodomain protein TRIM28 controls the balance between growth and invasiveness in melanoma. EMBO Rep 2022; 24:e54944. [PMID: 36341538 PMCID: PMC9827549 DOI: 10.15252/embr.202254944] [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: 02/28/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 11/09/2022] Open
Abstract
Melanoma tumors are highly metastatic partly due to the ability of melanoma cells to transition between invasive and proliferative states. However, the mechanisms underlying this plasticity are still not fully understood. To identify new epigenetic regulators of melanoma plasticity, we combined data mining, tumor models, proximity proteomics, and CUT&RUN sequencing. We focus on the druggable family of bromodomain epigenetic readers and identify TRIM28 as a new regulator of melanoma plasticity. We find that TRIM28 promotes the expression of pro-invasive genes and that TRIM28 controls the balance between invasiveness and growth of melanoma cells. We demonstrate that TRIM28 acts via the transcription factor JUNB that directly regulates the expression of pro-invasive and pro-growth genes. Mechanistically, TRIM28 controls the expression of JUNB by negatively regulating its transcriptional elongation by RNA polymerase II. In conclusion, our results demonstrate that a TRIM28-JUNB axis controls the balance between invasiveness and growth in melanoma tumors and suggest that the bromodomain protein TRIM28 could be targeted to reduce tumor spread.
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Affiliation(s)
- William A Nyberg
- Department of Medicine, Center for Molecular Medicine, Karolinska InstitutetKarolinska University HospitalStockholmSweden,Present address:
Department of MedicineUniversity of California San FranciscoSan FranciscoCAUSA
| | - Diego A Velasquez‐Pulgarin
- Department of Medicine, Center for Molecular Medicine, Karolinska InstitutetKarolinska University HospitalStockholmSweden,Department of Biomedical EngineeringUniversity of MemphisMemphisTNUSA
| | - Tianlin He
- Department of Medicine, Center for Molecular Medicine, Karolinska InstitutetKarolinska University HospitalStockholmSweden
| | - Maria Sjöstrand
- Department of Medicine, Center for Molecular Medicine, Karolinska InstitutetKarolinska University HospitalStockholmSweden,Present address:
Department of Medicine, Center for Cell EngineeringMemorial Sloan‐Kettering Cancer CenterNew YorkNYUSA
| | - Lucia Pellé
- Department of Medicine, Center for Molecular Medicine, Karolinska InstitutetKarolinska University HospitalStockholmSweden
| | - Ruxandra Covacu
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska InstitutetKarolinska University HospitalStockholmSweden
| | - Alexander Espinosa
- Department of Medicine, Center for Molecular Medicine, Karolinska InstitutetKarolinska University HospitalStockholmSweden
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143
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Caksa S, Baqai U, Aplin AE. The future of targeted kinase inhibitors in melanoma. Pharmacol Ther 2022; 239:108200. [PMID: 35513054 PMCID: PMC10187889 DOI: 10.1016/j.pharmthera.2022.108200] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/20/2022] [Accepted: 04/28/2022] [Indexed: 12/13/2022]
Abstract
Melanoma is a cancer of the pigment-producing cells of the body and its incidence is rising. Targeted inhibitors that act against kinases in the MAPK pathway are approved for BRAF-mutant metastatic cutaneous melanoma and increase patients' survival. Response to these therapies is limited by drug resistance and is less durable than with immune checkpoint inhibition. Conversely, rare melanoma subtypes have few therapeutic options for advanced disease and MAPK pathway targeting agents show minimal anti-tumor effects. Nevertheless, there is a future for targeted kinase inhibitors in melanoma: in new applications such as adjuvant or neoadjuvant therapy and in novel combinations with immunotherapies or other targeted therapies. Pre-clinical studies continue to identify tumor dependencies and their corresponding actionable drug targets, paving the way for rational targeted kinase inhibitor combinations as a personalized medicine approach for melanoma.
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Affiliation(s)
- Signe Caksa
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Usman Baqai
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Andrew E Aplin
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA; Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.
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144
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Martin-Perez M, Urdiroz-Urricelqui U, Bigas C, Benitah SA. The role of lipids in cancer progression and metastasis. Cell Metab 2022; 34:1675-1699. [PMID: 36261043 DOI: 10.1016/j.cmet.2022.09.023] [Citation(s) in RCA: 96] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Lipids have essential biological functions in the body (e.g., providing energy storage, acting as a signaling molecule, and being a structural component of membranes); however, an excess of lipids can promote tumorigenesis, colonization, and metastatic capacity of tumor cells. To metastasize, a tumor cell goes through different stages that require lipid-related metabolic and structural adaptations. These adaptations include altering the lipid membrane composition for invading other niches and overcoming cell death mechanisms and promoting lipid catabolism and anabolism for energy and oxidative stress protective purposes. Cancer cells also harness lipid metabolism to modulate the activity of stromal and immune cells to their advantage and to resist therapy and promote relapse. All this is especially worrying given the high fat intake in Western diets. Thus, metabolic interventions aiming to reduce lipid availability to cancer cells or to exacerbate their metabolic vulnerabilities provide promising therapeutic opportunities to prevent cancer progression and treat metastasis.
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Affiliation(s)
- Miguel Martin-Perez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain; Department of Cell Biology, Physiology and Immunology, University of Barcelona, 08028 Barcelona, Spain.
| | - Uxue Urdiroz-Urricelqui
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Claudia Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Salvador Aznar Benitah
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain.
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145
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Chen J, Wang X, Ma A, Wang QE, Liu B, Li L, Xu D, Ma Q. Deep transfer learning of cancer drug responses by integrating bulk and single-cell RNA-seq data. Nat Commun 2022; 13:6494. [PMID: 36310235 PMCID: PMC9618578 DOI: 10.1038/s41467-022-34277-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/19/2022] [Indexed: 12/25/2022] Open
Abstract
Drug screening data from massive bulk gene expression databases can be analyzed to determine the optimal clinical application of cancer drugs. The growing amount of single-cell RNA sequencing (scRNA-seq) data also provides insights into improving therapeutic effectiveness by helping to study the heterogeneity of drug responses for cancer cell subpopulations. Developing computational approaches to predict and interpret cancer drug response in single-cell data collected from clinical samples can be very useful. We propose scDEAL, a deep transfer learning framework for cancer drug response prediction at the single-cell level by integrating large-scale bulk cell-line data. The highlight in scDEAL involves harmonizing drug-related bulk RNA-seq data with scRNA-seq data and transferring the model trained on bulk RNA-seq data to predict drug responses in scRNA-seq. Another feature of scDEAL is the integrated gradient feature interpretation to infer the signature genes of drug resistance mechanisms. We benchmark scDEAL on six scRNA-seq datasets and demonstrate its model interpretability via three case studies focusing on drug response label prediction, gene signature identification, and pseudotime analysis. We believe that scDEAL could help study cell reprogramming, drug selection, and repurposing for improving therapeutic efficacy.
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Affiliation(s)
- Junyi Chen
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Xiaoying Wang
- Department of Mathematics, Shandong University, Shandong, 250100, China
| | - Anjun Ma
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA.
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA.
| | - Qi-En Wang
- Department of Radiation Oncology, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Bingqiang Liu
- Department of Mathematics, Shandong University, Shandong, 250100, China
| | - Lang Li
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Qin Ma
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA.
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA.
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146
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Paris A, Tardif N, Baietti FM, Berra C, Leclair HM, Leucci E, Galibert M, Corre S. The AhR-SRC axis as a therapeutic vulnerability in BRAFi-resistant melanoma. EMBO Mol Med 2022; 14:e15677. [PMID: 36305167 PMCID: PMC9728058 DOI: 10.15252/emmm.202215677] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 09/30/2022] [Accepted: 09/30/2022] [Indexed: 12/14/2022] Open
Abstract
The nongenetic mechanisms required to control tumor phenotypic plasticity and shape drug-resistance remain unclear. We show here that the Aryl hydrocarbon Receptor (AhR) transcription factor directly regulates the gene expression program associated with the acquisition of resistance to BRAF inhibitor (BRAFi) in melanoma. In addition, we show in melanoma cells that canonical activation of AhR mediates the activation of the SRC pathway and promotes the acquisition of an invasive and aggressive resistant phenotype to front-line BRAFi treatment in melanoma. This nongenetic reprogramming identifies a clinically compatible approach to reverse BRAFi resistance in melanoma. Using a preclinical BRAFi-resistant PDX melanoma model, we demonstrate that SRC inhibition with dasatinib significantly re-sensitizes melanoma cells to BRAFi. Together we identify the AhR/SRC axis as a new therapeutic vulnerability to trigger resistance and warrant the introduction of SRC inhibitors during the course of the treatment in combination with front-line therapeutics to delay BRAFi resistance.
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Affiliation(s)
- Anaïs Paris
- Univ Rennes, CNRS, INSERM, IGDR (Institut de Génétique et Développement de Rennes) – UMR6290, ERL U1305RennesFrance
| | - Nina Tardif
- Univ Rennes, CNRS, INSERM, IGDR (Institut de Génétique et Développement de Rennes) – UMR6290, ERL U1305RennesFrance
| | - Francesca M Baietti
- Laboratory for RNA Cancer Biology, Department of OncologyLKI, KU LeuvenLeuvenBelgium,Trace PDX Platform, Department of OncologyLKI, KU LeuvenLeuvenBelgium
| | - Cyrille Berra
- Univ Rennes, CNRS, INSERM, IGDR (Institut de Génétique et Développement de Rennes) – UMR6290, ERL U1305RennesFrance,Department of Molecular Genetics and GenomicsHospital University of Rennes (CHU Rennes)RennesFrance
| | - Héloïse M Leclair
- Univ Rennes, CNRS, INSERM, IGDR (Institut de Génétique et Développement de Rennes) – UMR6290, ERL U1305RennesFrance
| | - Eleonora Leucci
- Laboratory for RNA Cancer Biology, Department of OncologyLKI, KU LeuvenLeuvenBelgium,Trace PDX Platform, Department of OncologyLKI, KU LeuvenLeuvenBelgium
| | - Marie‐Dominique Galibert
- Univ Rennes, CNRS, INSERM, IGDR (Institut de Génétique et Développement de Rennes) – UMR6290, ERL U1305RennesFrance,Department of Molecular Genetics and GenomicsHospital University of Rennes (CHU Rennes)RennesFrance
| | - Sébastien Corre
- Univ Rennes, CNRS, INSERM, IGDR (Institut de Génétique et Développement de Rennes) – UMR6290, ERL U1305RennesFrance
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147
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Delbart W, Karabet J, Marin G, Penninckx S, Derrien J, Ghanem GE, Flamen P, Wimana Z. Understanding the Radiobiological Mechanisms Induced by 177Lu-DOTATATE in Comparison to External Beam Radiation Therapy. Int J Mol Sci 2022; 23:ijms232012369. [PMID: 36293222 PMCID: PMC9604190 DOI: 10.3390/ijms232012369] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/07/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022] Open
Abstract
Radionuclide Therapy (RNT) with 177Lu-DOTATATE targeting somatostatin receptors (SSTRs) in neuroendocrine tumours (NET) has been successfully used in routine clinical practice, mainly leading to stable disease. Radiobiology holds promise for RNT improvement but is often extrapolated from external beam radiation therapy (EBRT) studies despite differences in these two radiation-based treatment modalities. In a panel of six human cancer cell lines expressing SSTRs, common radiobiological endpoints (i.e., cell survival, cell cycle, cell death, oxidative stress and DNA damage) were evaluated over time in 177Lu-DOTATATE- and EBRT-treated cells, as well as the radiosensitizing potential of poly (ADP-ribose) polymerase inhibition (PARPi). Our study showed that common radiobiological mechanisms were induced by both 177Lu-DOTATATE and EBRT, but to a different extent and/or with variable kinetics, including in the DNA damage response. A higher radiosensitizing potential of PARPi was observed for EBRT compared to 177Lu-DOTATATE. Our data reinforce the need for dedicated RNT radiobiology studies, in order to derive its maximum therapeutic benefit.
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Affiliation(s)
- Wendy Delbart
- Nuclear Medicine Department, Institut Jules Bordet, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
- Laboratory of Oncology and Experimental Surgery, Institut Jules Bordet, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
- Correspondence: ; Tel.: +32-2-541-30-05
| | - Jirair Karabet
- Medical Physics Department, Institut Jules Bordet, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Gwennaëlle Marin
- Medical Physics Department, Institut Jules Bordet, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Sébastien Penninckx
- Medical Physics Department, Institut Jules Bordet, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Jonathan Derrien
- Laboratoire de Physique Nucléaire et Des Radiations, Institut Supérieur Industriel de Bruxelles (ISIB), 1000 Brussels, Belgium
- NEMP Applied Research Lab, Institut de Recherche de l’Institut Supérieur Industriel de Bruxelles (IRISIB), 1000 Brussels, Belgium
| | - Ghanem E. Ghanem
- Nuclear Medicine Department, Institut Jules Bordet, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
- Laboratory of Oncology and Experimental Surgery, Institut Jules Bordet, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Patrick Flamen
- Nuclear Medicine Department, Institut Jules Bordet, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Zéna Wimana
- Nuclear Medicine Department, Institut Jules Bordet, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
- Laboratory of Oncology and Experimental Surgery, Institut Jules Bordet, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
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148
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Yamauchi T, Shangraw S, Zhai Z, Ravindran Menon D, Batta N, Dellavalle RP, Fujita M. Alcohol as a Non-UV Social-Environmental Risk Factor for Melanoma. Cancers (Basel) 2022; 14:5010. [PMID: 36291794 PMCID: PMC9599745 DOI: 10.3390/cancers14205010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 12/24/2022] Open
Abstract
Although cancer mortality has declined among the general population, the incidence of melanoma continues to rise. While identifying high-risk cohorts with genetic risk factors improves public health initiatives and clinical care management, recognizing modifiable risk factors such as social-environmental risk factors would also affect the methods of patient outreach and education. One major modifiable social-environmental risk factor associated with melanoma is ultraviolet (UV) radiation. However, not all forms of melanoma are correlated with sun exposure or occur in sun-exposed areas. Additionally, UV exposure is rarely associated with tumor progression. Another social-environmental factor, pregnancy, does not explain the sharply increased incidence of melanoma. Recent studies have demonstrated that alcohol consumption is positively linked with an increased risk of cancers, including melanoma. This perspective review paper summarizes epidemiological data correlating melanoma incidence with alcohol consumption, describes the biochemical mechanisms of ethanol metabolism, and discusses how ethanol and ethanol metabolites contribute to human cancer, including melanoma.
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Affiliation(s)
- Takeshi Yamauchi
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sarah Shangraw
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Zili Zhai
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Dinoop Ravindran Menon
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Nisha Batta
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Robert P Dellavalle
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Veterans Affairs Medical Center, VA Eastern Colorado Health Care System, Aurora, CO 80045, USA
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Mayumi Fujita
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Veterans Affairs Medical Center, VA Eastern Colorado Health Care System, Aurora, CO 80045, USA
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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149
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Krossa I, Strub T, Aplin AE, Ballotti R, Bertolotto C. Lysine Methyltransferase NSD1 and Cancers: Any Role in Melanoma? Cancers (Basel) 2022; 14:cancers14194865. [PMID: 36230787 PMCID: PMC9563040 DOI: 10.3390/cancers14194865] [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: 08/31/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 11/23/2022] Open
Abstract
Simple Summary Epigenetic events, which comprise post-translational modifications of histone tails or DNA methylation, control gene expression by altering chromatin structure without change in the DNA sequence. Histone tails modifications are driven by specific cellular enzymes such as histone methyltransferases or histone acetylases, which play a key role in regulating diverse biological processes. Their alteration may have consequences on growth and tumorigenesis. Abstract Epigenetic regulations, that comprise histone modifications and DNA methylation, are essential to processes as diverse as development and cancer. Among the histone post-translational modifications, lysine methylation represents one of the most important dynamic marks. Here, we focused on methyltransferases of the nuclear binding SET domain 1 (NSD) family, that catalyze the mono- and di-methylation of histone H3 lysine 36. We review the loss of function mutations of NSD1 in humans that are the main cause of SOTOS syndrome, a disease associated with an increased risk of developing cancer. We then report the role of NSD1 in triggering tumor suppressive or promoter functions according to the tissue context and we discuss the role of NSD1 in melanoma. Finally, we examine the ongoing efforts to target NSD1 signaling in cancers.
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Affiliation(s)
- Imène Krossa
- Université Côte d’Azur, 06100 Nice, France
- Team 1, Biology and Pathologies of melanocytes, Inserm, Equipe labellisée Ligue 2020 and Equipe labellisée ARC 2022, Centre Méditerranéen de Médecine Moléculaire, 06200 Nice, France
- Correspondence: (I.K.); (C.B.)
| | - Thomas Strub
- Université Côte d’Azur, 06100 Nice, France
- Team 1, Biology and Pathologies of melanocytes, Inserm, Equipe labellisée Ligue 2020 and Equipe labellisée ARC 2022, Centre Méditerranéen de Médecine Moléculaire, 06200 Nice, France
| | - Andrew E. Aplin
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Robert Ballotti
- Université Côte d’Azur, 06100 Nice, France
- Team 1, Biology and Pathologies of melanocytes, Inserm, Equipe labellisée Ligue 2020 and Equipe labellisée ARC 2022, Centre Méditerranéen de Médecine Moléculaire, 06200 Nice, France
| | - Corine Bertolotto
- Université Côte d’Azur, 06100 Nice, France
- Team 1, Biology and Pathologies of melanocytes, Inserm, Equipe labellisée Ligue 2020 and Equipe labellisée ARC 2022, Centre Méditerranéen de Médecine Moléculaire, 06200 Nice, France
- Correspondence: (I.K.); (C.B.)
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CaSee: A lightning transfer-learning model directly used to discriminate cancer/normal cells from scRNA-seq. Oncogene 2022; 41:4866-4876. [PMID: 36192479 DOI: 10.1038/s41388-022-02478-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 09/13/2022] [Accepted: 09/20/2022] [Indexed: 11/08/2022]
Abstract
Single-cell RNA sequencing (scRNA-seq) is one of the most efficient technologies for human tumor research. However, data analysis is still faced with technical challenges, especially the difficulty in efficiently and accurately discriminating cancer/normal cells in the scRNA-seq expression matrix. If we can address these challenges, we can have a deeper understanding of the intratumoral and intertumoral heterogeneity. In this study, we developed a cancer/normal cell discrimination pipeline called pan-Cancer Seeker (CaSee) devoted to scRNA-seq expression matrix, which is based on the traditional high-quality pan-cancer bulk sequencing data using transfer learning. CaSee is the first tool directly used to discriminate cancer/normal cells in the scRNA-seq expression matrix, with much wider application fields and higher efficiency than copy number variation (CNV) method which requires corresponding reference cells. CaSee is user-friendly and can adapt to a variety of data sources, including but not limited to scRNA tissue sequencing data, scRNA cell line sequencing data, scRNA xenograft cell sequencing data and scRNA circulating tumor cell sequencing data. It is compatible with mainstream sequencing technology platforms, 10× Genomics Chromium, Smart-seq2, and Microwell-seq. Here, CaSee pipeline exhibited excellent performance in the multicenter data evaluation of 11 retrospective cohorts and one independent dataset, with an average discrimination accuracy of 96.69%. In general, the development of a deep-learning based, pan-cancer cell discrimination model, CaSee, to distinguish cancer cells from normal cells will be compelling to researchers working in the genomics, cancer, and single-cell fields.
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