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Carrier A, Desjobert C, Ponger L, Lamant L, Bustos M, Torres-Ferreira J, Henrique R, Jeronimo C, Lanfrancone L, Delmas A, Favre G, Delaunay A, Busato F, Hoon DSB, Tost J, Etievant C, Riond J, Arimondo PB. DNA methylome combined with chromosome cluster-oriented analysis provides an early signature for cutaneous melanoma aggressiveness. eLife 2022; 11:78587. [PMID: 36125262 PMCID: PMC9525058 DOI: 10.7554/elife.78587] [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: 03/11/2022] [Accepted: 09/18/2022] [Indexed: 11/24/2022] Open
Abstract
Aberrant DNA methylation is a well-known feature of tumours and has been associated with metastatic melanoma. However, since melanoma cells are highly heterogeneous, it has been challenging to use affected genes to predict tumour aggressiveness, metastatic evolution, and patients’ outcomes. We hypothesized that common aggressive hypermethylation signatures should emerge early in tumorigenesis and should be shared in aggressive cells, independent of the physiological context under which this trait arises. We compared paired melanoma cell lines with the following properties: (i) each pair comprises one aggressive counterpart and its parental cell line and (ii) the aggressive cell lines were each obtained from different host and their environment (human, rat, and mouse), though starting from the same parent cell line. Next, we developed a multi-step genomic pipeline that combines the DNA methylome profile with a chromosome cluster-oriented analysis. A total of 229 differentially hypermethylated genes was commonly found in the aggressive cell lines. Genome localization analysis revealed hypermethylation peaks and clusters, identifying eight hypermethylated gene promoters for validation in tissues from melanoma patients. Five Cytosine-phosphate-Guanine (CpGs) identified in primary melanoma tissues were transformed into a DNA methylation score that can predict survival (log-rank test, p=0.0008). This strategy is potentially universally applicable to other diseases involving DNA methylation alterations.
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Affiliation(s)
- Arnaud Carrier
- Unité de Service et de Recherche USR 3388, CNRS-Pierre Fabre, Toulouse, France
| | - Cécile Desjobert
- Unité de Service et de Recherche USR 3388, CNRS-Pierre Fabre, Toulouse, France
| | | | - Laurence Lamant
- Cancer Research Center of Toulouse, UMR 1037, INSERM, Université Toulouse III Paul Sabatier, Toulouse, France
| | - Matias Bustos
- Department of Translational Molecular Medicine, Providence Saint John's Health Center, Santa Monica, United States
| | - Jorge Torres-Ferreira
- Cancer Biology and Epigenetics Group, Portuguese Oncology Institute, Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, Portuguese Oncology Institute, Porto, Portugal
| | - Carmen Jeronimo
- Cancer Biology and Epigenetics Group, Portuguese Oncology Institute, Porto, Portugal
| | - Luisa Lanfrancone
- Department of Experimental Oncology, Instituto Europeo di Oncologia, Milan, Italy
| | - Audrey Delmas
- Cancer Research Center of Toulouse, UMR 1037, INSERM, Université Toulouse III Paul Sabatier, Toulouse, France
| | - Gilles Favre
- Cancer Research Center of Toulouse, UMR 1037, INSERM, Université Toulouse III Paul Sabatier, Toulouse, France
| | - Antoine Delaunay
- Laboratory for Functional Genomics, Fondation Jean Dausset-CEPH, Paris, France
| | - Florence Busato
- Laboratory for Epigenetics and Environment, CNRS, CEA-Institut de Biologie François Jacob, Evry, France
| | - Dave S B Hoon
- Department of Translational Molecular Medicine, Providence Saint John's Health Center, Santa Monica, United States
| | - Jorg Tost
- Laboratory for Epigenetics and Environment, CNRS, CEA-Institut de Biologie François Jacob, Evry, France
| | - Chantal Etievant
- Unité de Service et de Recherche USR 3388, CNRS-Pierre Fabre, Toulouse, France
| | - Joëlle Riond
- Unité de Service et de Recherche USR 3388, CNRS-Pierre Fabre, Toulouse, France
| | - Paola B Arimondo
- Department Structural Biology and Chemistry, Institut Pasteur, CNRS UMR 3523, Paris, France
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Liu YJ, Lin YF, Chen YF, Luo EC, Sher YP, Tsai MH, Chuang EY, Lai LC. MicroRNA-449a enhances radiosensitivity in CL1-0 lung adenocarcinoma cells. PLoS One 2013; 8:e62383. [PMID: 23614048 PMCID: PMC3629161 DOI: 10.1371/journal.pone.0062383] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 03/21/2013] [Indexed: 12/15/2022] Open
Abstract
Lung cancer is the leading cause of cancer-related mortality worldwide. Radiotherapy is often applied for treating lung cancer, but it often fails because of the relative non-susceptibility of lung cancer cells to radiation. MicroRNAs (miRNAs) have been reported to modulate the radiosensitivity of lung cancer cells and have the potential to improve the efficacy of radiotherapy. The purpose of this study was to identify a miRNA that can adjust radiosensitivity in lung adenocarcinoma cells. Two lung adenocarcinoma cell lines (CL1-0 and CL1-5) with different metastatic ability and radiosensitivity were used. In order to understand the regulatory mechanisms of differential radiosensitivity in these isogenic tumor cells, both CL1-0 and CL1-5 were treated with 10 Gy radiation, and were harvested respectively at 0, 1, 4, and 24 h after radiation exposure. The changes in expression of miRNA upon irradiation were examined using Illumina Human microRNA BeadChips. Twenty-six miRNAs were identified as having differential expression post-irradiation in CL1-0 or CL1-5 cells. Among these miRNAs, miR-449a, which was down-regulated in CL1-0 cells at 24 h after irradiation, was chosen for further investigation. Overexpression of miR-449a in CL1-0 cells effectively increased irradiation-induced DNA damage and apoptosis, altered the cell cycle distribution and eventually led to sensitization of CL1-0 to irradiation.
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Affiliation(s)
- Yi-Jyun Liu
- Graduate Institute of Physiology, National Taiwan University, Taipei, Taiwan
| | - Yu-Fen Lin
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Yi-Fan Chen
- YongLin Biomedical Engineering Center, National Taiwan University, Taipei, Taiwan
| | - En-Ching Luo
- Graduate Institute of Physiology, National Taiwan University, Taipei, Taiwan
| | - Yuh-Ping Sher
- Graduate Institute of Clinical Medical Science, China Medical University, Taichung, Taiwan
| | - Mong-Hsun Tsai
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
- Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan
| | - Eric Y. Chuang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
- Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan
- YongLin Biomedical Engineering Center, National Taiwan University, Taipei, Taiwan
| | - Liang-Chuan Lai
- Graduate Institute of Physiology, National Taiwan University, Taipei, Taiwan
- Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan
- * E-mail:
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Thomas-Pfaab M, Annereau JP, Munsch C, Guilbaud N, Garrido I, Paul C, Brousset P, Lamant L, Meyer N. CD10 expression by melanoma cells is associated with aggressive behavior in vitro and predicts rapid metastatic progression in humans. J Dermatol Sci 2012; 69:105-13. [PMID: 23219141 DOI: 10.1016/j.jdermsci.2012.11.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 10/05/2012] [Accepted: 11/03/2012] [Indexed: 11/30/2022]
Abstract
BACKGROUND No biological or molecular marker of primary melanoma tumor cells has been shown to predict clinical outcome in melanoma. OBJECTIVE To determine whether CD10, CD133, nestin and CD20 may evaluate the prognosis of melanoma. METHODS The differential expression of these molecules was assessed in pairs of cell lines. We evaluated, by both immunohistochemical staining and RT-qPCR, their expression in a cohort of 32 patients (68 samples) with a history of metastatic melanoma, divided into two groups according to their clinical outcome profile. RESULTS CD10 over expression in cancer cell lines was associated with more aggressive behavior in vitro. A CD10-positive staining was more frequent in patients in the "rapidly progressive" group than those in the "long survivor" group (23/35 versus 2/18, p<10(-4)). CD10 expression was associated with a lower median overall survival (1.15 year - IQR: [0.50-2.58] versus 4.27 - IQR: [1.66-6.33]; p=10(-4)). The Odds Ratio of displaying a "rapidly progressive" melanoma when tumor cells expressed CD10 was 15 (95% confidence interval: [3-78]). After adjusting for confounding factors, CD10 expression in melanoma tumor cells remained associated with an increased risk of death and more rapid disease progression (p=6×10(-4); HR=3.71). CONCLUSION CD10 may predict clinical outcome in melanoma patients.
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Thomas C, Fertil B, Foray N. Hyperradiosensibilité aux très faibles doses: impact en radiothérapie des micrométastases. Cancer Radiother 2007; 11:260-5. [PMID: 17683966 DOI: 10.1016/j.canrad.2007.06.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2007] [Revised: 06/06/2007] [Accepted: 06/26/2007] [Indexed: 11/26/2022]
Abstract
Radiobiologists have pointed out a novel radiobiological phenomenon observed in many tumor and normal cell lines: hyper-radiosensitivity to very low-dose (HRS) followed by induced radioresistance (IRR) after a threshold dose of 0.1-0.3 Gy that depends on the cell line. Radioresistance at high dose (i.e. higher than 0.5 Gy) and metastatic potential of tumor cells are likely major factors of failure in radiotherapy. A careful review of literature suggests that: 1) radiotherapy does not increase the metastatic potential of tumor cells; 2) radioresistance at high dose and metastatic potential are not related. However, inside a given tumor cell line, highly metastatic clones may elicit more cells showing HRS or are more radiosensitive at high dose than poorly metastatic ones. Recent data obtained from molecular techniques (comet and immunofluorescence assays) applied to single cells irradiated at very low radiation doses (1-100 mGy) suggest that DNA single-strand breaks (SSB) and double-strand breaks (DSB) may be the key-lesions responsible for the HRS phenomenon. These data suggest that the HRS phenomenon may find application in radiotherapy for micrometastasis. These early disseminated and probably unvascularised cells may escape the influence of high-dose chemotherapy after excision of the primary tumor. Considering the link between metastatic potential and HRS, we have previously proposed to apply very low-dose total body irradiation (TBI) at M(0) stage that may prevent the development of micrometastases. Literature data suggest that the smallest radiation dose that can produce HRS without increasing the risk of cancer may be in the milliGrays range.
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Affiliation(s)
- C Thomas
- Inserm U647, ID17, European Synchrotron Research Facility (ESRF), rue Horowitz, 38043 Grenoble, France
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Thomas CP, Buronfosse A, Portoukalian J, Fertil B. The gangliosides as a possible molecular coupling factor between the proportion of radiosensitive cells in vitro and the metastatic potential in vivo within a human melanoma cell line. Br J Cancer 1997; 75:639-49. [PMID: 9043018 PMCID: PMC2063334 DOI: 10.1038/bjc.1997.115] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
With an experimental model of spontaneous lung metastases in immunosuppressed newborn rats, seven clones and variants with different metastatic potential and gangliosides expression were derived from a single parental human melanoma cell line M4Be. The cellular radiosensitivity of M4Be and its seven sublines was estimated using an in vitro colony assay. The total amount of gangliosides in M4Be and its seven sublines was determined by cell extraction and thin-layer chromatography, while the expression of GD3 gangliosides was estimated by flow cytometry with a monoclonal antibody. The radiation-cell survival curves of most clones and variants derived from M4Be showed a zero dose extrapolation clearly lower than 100%, suggesting that two populations of cells of very different radiosensitivity coexist within each of these clones and variants. Although the proportion of radiosensitive cells could be estimated from the shape of the survival curve, its radiosensitivity is too high to be properly evaluated by the colony assay. The eight survival curves differ essentially in the proportion of radiosensitive cells--which varied from 0% to 40% among M4Be and its seven sublines--whereas the cellular radiosensitivity of the radioresistant population was similar among them. The metastatic potential in vivo of M4Be and its seven sublines was not significantly related to the cellular radiosensitivity of their corresponding radioresistant population, but significantly increased with the fraction of radiosensitive cells. This relationship is valid only when the highly metastatic cells are cultured for no more than five passages in vitro as the fraction of radiosensitive cells is rapidly lost during subcultures. The relationship remains valid in vivo as metastatic melanoma-bearing newborn rats whole body irradiated with 20 cGy show no lung metastasis compared with controls. The radiosensitive cell fraction is inversely correlated with both the total ganglioside content (r = 0.84, P < 0.02) and the number of cells positively labelled with the monoclonal antibody directed to GD3 (r = 0.92, P < 0.001). The incubation of a radiosensitive clone with the exogenous bovine brain ganglioside GM1 significantly increases the proportion of radioresistant cells and suppresses its metastatic potential, while the inhibition of the endogenous gangliosides synthesis in the radioresistant cell line M4Be increases the proportion of radiosensitive cells. This study provides a possible explanation for the correlation between the metastatic potential and the proportion of radiosensitive cells within the seven sublines derived from a single parental human melanoma cell line.
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Affiliation(s)
- C P Thomas
- The Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire d'Immunologie et de Cancérologie Expérimentale (Unité INSERM ex218), Lyon, France
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Thomas CP, Buronfosse A, Combaret V, Pedron S, Fertil B, Portoukalian J. Gangliosides protect human melanoma cells from ionizing radiation-induced clonogenic cell death. Glycoconj J 1996; 13:377-84. [PMID: 8781968 DOI: 10.1007/bf00731470] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
With an experimental model of spontaneous lung metastases of melanoma developed in this laboratory, a range of sublines (variants and clones) with different metastatic potential and ganglioside expression was established from a single human melanoma cell line M4Be. Using an in vitro clonogenic assay and provided that cells were cultured for no more than five passages, variations in cellular radioresistance of M4Be and seven sublines derived from M4Be were detected. This study shows a positive correlation between the cell intrinsic radioresistance of M4Be and its seven sublines and their total ganglioside content. More precisely, the proportion of radioresistant cells in M4Be and the seven sublines correlated with the number of cells determined by flow cytometry that were positively labelled with a monoclonal antibody directed to GD3 disialoganglioside. Blocking the cellular biosynthesis of gangliosides with the inhibitor Fumonisin B1 or cleaving with Vibrio cholerae neuraminidase the cell surface ganglioside-bound sialic acid in a radioresistant poorly metastatic subline increased its radiosensitivity in vitro. In contrast, enrichment of a radiosensitive metastatic subline with exogenous bovine brain GM1 increased its radioresistance in vitro. These results suggest that, in the radiation dose range important for radioprotection (0-1 Gy), membrane gangliosides radioprotect human melanoma cells in vitro.
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Affiliation(s)
- C P Thomas
- Laboratoire de Cancérologie Expérimentale (INSERM ex U. 218) Centre Léon Bérard, Lyon, France
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