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Lins FV, Bispo ECI, Rodrigues NS, Silva MVS, Carvalho JL, Gelfuso GM, Saldanha-Araujo F. Ibrutinib Modulates Proliferation, Migration, Mitochondrial Homeostasis, and Apoptosis in Melanoma Cells. Biomedicines 2024; 12:1012. [PMID: 38790974 PMCID: PMC11117653 DOI: 10.3390/biomedicines12051012] [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: 04/07/2024] [Revised: 04/23/2024] [Accepted: 05/01/2024] [Indexed: 05/26/2024] Open
Abstract
Ibrutinib, a tyrosine kinase inhibitor with a broad spectrum of action, has been successfully explored to treat hematological and solid cancers. Herein, we investigated the anti-cancer effect of Ibrutinib on melanoma cell lines. Cytotoxicity was evaluated using the MTT assay. Apoptosis, mitochondrial membrane potential, reactive oxygen species (ROS) production, cell proliferation, and cell cycle stages were determined by flow cytometry. LDH release and Caspase 3/7 activity were determined by colorimetric and luminescent assays, respectively. Cell migration was evaluated by wound scratch assay. Gene expression was determined by real-time PCR. Gene Ontology (GO) enrichment analysis of melanoma clinical samples was performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID). MTT assays showed that Ibrutinib is toxic for MeWo, SK-MEL-28, and WM164 cells. The annexin V/PI staining, Caspase 3/7 activity, and LDH release in MeWo cells revealed that apoptosis is the primary mechanism of death caused by Ibrutinib. Corroborating such observation, we identified that Ibrutinib treatment impairs the mitochondrial membrane potential of such cells and significantly increases the transcriptional levels of the pro-apoptotic factors ATM, HRK, BAX, BAK, CASP3, and CASP8. Furthermore, Ibrutinib showed antimetastatic potential by inhibiting the migration of MeWo cells. Finally, we performed a functional enrichment analysis and identified that the differential expression of Ibrutinib-target molecules is associated with enrichment of apoptosis and necrosis pathways in melanoma samples. Taken together, our results clearly suggest that Ibrutinib can be successfully explored as an effective therapeutic approach for melanomas.
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Affiliation(s)
- Fernanda Vitelli Lins
- Laboratório de Hematologia e Células-Tronco, Faculdade de Ciências da Saúde, Universidade de Brasília, Brasília 70910-900, DF, Brazil; (F.V.L.); (E.C.I.B.); (N.S.R.)
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Elizabete Cristina Iseke Bispo
- Laboratório de Hematologia e Células-Tronco, Faculdade de Ciências da Saúde, Universidade de Brasília, Brasília 70910-900, DF, Brazil; (F.V.L.); (E.C.I.B.); (N.S.R.)
| | - Naomí Souza Rodrigues
- Laboratório de Hematologia e Células-Tronco, Faculdade de Ciências da Saúde, Universidade de Brasília, Brasília 70910-900, DF, Brazil; (F.V.L.); (E.C.I.B.); (N.S.R.)
| | - Maria Victória Souto Silva
- Laboratório Interdisciplinar de Biociências, Faculdade de Medicina, Universidade de Brasília, Brasília 70910-900, DF, Brazil; (M.V.S.S.); (J.L.C.)
| | - Juliana Lott Carvalho
- Laboratório Interdisciplinar de Biociências, Faculdade de Medicina, Universidade de Brasília, Brasília 70910-900, DF, Brazil; (M.V.S.S.); (J.L.C.)
| | - Guilherme Martins Gelfuso
- Laboratório de Medicamentos, Alimentos e Cosméticos, Universidade de Brasília, Brasília 70910-900, DF, Brazil;
| | - Felipe Saldanha-Araujo
- Laboratório de Hematologia e Células-Tronco, Faculdade de Ciências da Saúde, Universidade de Brasília, Brasília 70910-900, DF, Brazil; (F.V.L.); (E.C.I.B.); (N.S.R.)
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2
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Yuan T, Edelmann D, Fan Z, Alwers E, Kather JN, Brenner H, Hoffmeister M. Machine learning in the identification of prognostic DNA methylation biomarkers among patients with cancer: A systematic review of epigenome-wide studies. Artif Intell Med 2023; 143:102589. [PMID: 37673571 DOI: 10.1016/j.artmed.2023.102589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 04/19/2023] [Accepted: 04/30/2023] [Indexed: 09/08/2023]
Abstract
BACKGROUND DNA methylation biomarkers have great potential in improving prognostic classification systems for patients with cancer. Machine learning (ML)-based analytic techniques might help overcome the challenges of analyzing high-dimensional data in relatively small sample sizes. This systematic review summarizes the current use of ML-based methods in epigenome-wide studies for the identification of DNA methylation signatures associated with cancer prognosis. METHODS We searched three electronic databases including PubMed, EMBASE, and Web of Science for articles published until 2 January 2023. ML-based methods and workflows used to identify DNA methylation signatures associated with cancer prognosis were extracted and summarized. Two authors independently assessed the methodological quality of included studies by a seven-item checklist adapted from 'A Tool to Assess Risk of Bias and Applicability of Prediction Model Studies (PROBAST)' and from the 'Reporting Recommendations for Tumor Marker Prognostic Studies (REMARK). Different ML methods and workflows used in included studies were summarized and visualized by a sunburst chart, a bubble chart, and Sankey diagrams, respectively. RESULTS Eighty-three studies were included in this review. Three major types of ML-based workflows were identified. 1) unsupervised clustering, 2) supervised feature selection, and 3) deep learning-based feature transformation. For the three workflows, the most frequently used ML techniques were consensus clustering, least absolute shrinkage and selection operator (LASSO), and autoencoder, respectively. The systematic review revealed that the performance of these approaches has not been adequately evaluated yet and that methodological and reporting flaws were common in the identified studies using ML techniques. CONCLUSIONS There is great heterogeneity in ML-based methodological strategies used by epigenome-wide studies to identify DNA methylation markers associated with cancer prognosis. In theory, most existing workflows could not handle the high multi-collinearity and potentially non-linearity interactions in epigenome-wide DNA methylation data. Benchmarking studies are needed to compare the relative performance of various approaches for specific cancer types. Adherence to relevant methodological and reporting guidelines are urgently needed.
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Affiliation(s)
- Tanwei Yuan
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany; Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Dominic Edelmann
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ziwen Fan
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Elizabeth Alwers
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jakob Nikolas Kather
- Else Kroener Fresenius Center for Digital Health, Technical University Dresden, Dresden, Germany; Medical Oncology, National Center of Tumour Diseases (NCT), University Hospital Heidelberg, Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany; Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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3
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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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4
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Zhou S, Han Y, Li J, Pi X, Lyu J, Xiang S, Zhou X, Chen X, Wang Z, Yang R. New Prognostic Biomarkers and Drug Targets for Skin Cutaneous Melanoma via Comprehensive Bioinformatic Analysis and Validation. Front Oncol 2021; 11:745384. [PMID: 34722301 PMCID: PMC8548670 DOI: 10.3389/fonc.2021.745384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 09/21/2021] [Indexed: 11/23/2022] Open
Abstract
Skin cutaneous melanoma (SKCM) is the most aggressive and fatal type of skin cancer. Its highly heterogeneous features make personalized treatments difficult, so there is an urgent need to identify markers for early diagnosis and therapy. Detailed profiles are useful for assessing malignancy potential and treatment in various cancers. In this study, we constructed a co-expression module using expression data for cutaneous melanoma. A weighted gene co-expression network analysis was used to discover a co-expression gene module for the pathogenesis of this disease, followed by a comprehensive bioinformatics analysis of selected hub genes. A connectivity map (CMap) was used to predict drugs for the treatment of SKCM based on hub genes, and immunohistochemical (IHC) staining was performed to validate the protein levels. After discovering a co-expression gene module for the pathogenesis of this disease, we combined GWAS validation and DEG analysis to identify 10 hub genes in the most relevant module. Survival curves indicated that eight hub genes were significantly and negatively associated with overall survival. A total of eight hub genes were positively correlated with SKCM tumor purity, and 10 hub genes were negatively correlated with the infiltration level of CD4+ T cells and B cells. Methylation levels of seven hub genes in stage 2 SKCM were significantly lower than those in stage 3. We also analyzed the isomer expression levels of 10 hub genes to explore the therapeutic target value of 10 hub genes in terms of alternative splicing (AS). All 10 hub genes had mutations in skin tissue. Furthermore, CMap analysis identified cefamandole, ursolic acid, podophyllotoxin, and Gly-His-Lys as four targeted therapy drugs that may be effective treatments for SKCM. Finally, IHC staining results showed that all 10 molecules were highly expressed in melanoma specimens compared to normal samples. These findings provide new insights into SKCM pathogenesis based on multi-omics profiles of key prognostic biomarkers and drug targets. GPR143 and SLC45A2 may serve as drug targets for immunotherapy and prognostic biomarkers for SKCM. This study identified four drugs with significant potential in treating SKCM patients.
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Affiliation(s)
- Sitong Zhou
- Department of Dermatology, The First People's Hospital of Foshan, Foshan, China
| | - Yuanyuan Han
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, China
| | - Jiehua Li
- Department of Dermatology, The First People's Hospital of Foshan, Foshan, China
| | - Xiaobing Pi
- Department of Dermatology, The First People's Hospital of Foshan, Foshan, China
| | - Jin Lyu
- Department of Pathology, The First People's Hospital of Foshan, Foshan, China
| | - Shijian Xiang
- Department of Pharmacy, Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Xinzhu Zhou
- The Second School of Medicine, Wenzhou Medical University, Wenzhou, China
| | - Xiaodong Chen
- Department of Burn Surgery and Skin Regeneration, The First People's Hospital of Foshan, Foshan, China
| | - Zhengguang Wang
- Department of Orthopedics, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Ronghua Yang
- Department of Burn Surgery and Skin Regeneration, The First People's Hospital of Foshan, Foshan, China
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5
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Deng J, Zeng W, Kong W, Shi Y, Mou X. The Study of Sarcoma Microenvironment Heterogeneity Associated With Prognosis Based on an Immunogenomic Landscape Analysis. Front Bioeng Biotechnol 2020; 8:1003. [PMID: 32974322 PMCID: PMC7471631 DOI: 10.3389/fbioe.2020.01003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/31/2020] [Indexed: 12/14/2022] Open
Abstract
Microenvironment-driven tumor heterogeneity causes the limitation of immunotherapy of sarcomas. Nonetheless, systematical studies of various molecular levels can enhance the understanding of tumor microenvironment (TME) related to prognosis and provide novel insights of precision immunotherapy. Three prognostic-related TME phenotypes were identified by consensus clustering of the relative infiltration of 22 immune cells from 869 samples of sarcomas. Additionally, integrative immunogenomic analysis is applied to explore the characteristics of different TME groups. The results revealed that most of the immune cell infiltration is higher in the better prognostic group, which are more affected by lower DNA methylation levels and fewer copy number variations in the worse prognostic group. The signaling pathway crosstalk analysis suggested that the changes in the TME will cause considerable variation in the flow of information between pathways, especially when the degree of relative infiltration of immune cells is low, patient’s endocrine system may also be significantly affected. Also, the endogenous competitive network analysis indicated that several differentially expressed long non-coding RNAs (lncRNAs) associated with the prognosis or tumor recurrence of sarcoma patients affected the regulatory relationship between miRNAs and different genes when the sarcoma microenvironment changes. In summary, the significant relationship between genetic alterations and prognostic-related TME characteristics in sarcomas were determined in this study. These findings may provide new clues for the treatment of sarcomas.
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Affiliation(s)
- Jin Deng
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - Weiming Zeng
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - Wei Kong
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - Yuhu Shi
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - Xiaoyang Mou
- Department of Biochemistry, Rowan University and Guava Medicine, Glassboro, NJ, United States
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6
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Liao M, Zeng F, Li Y, Gao Q, Yin M, Deng G, Chen X. A novel predictive model incorporating immune-related gene signatures for overall survival in melanoma patients. Sci Rep 2020; 10:12462. [PMID: 32719391 PMCID: PMC7385638 DOI: 10.1038/s41598-020-69330-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/09/2020] [Indexed: 12/15/2022] Open
Abstract
Melanoma is the most invasive type of skin cancer, in which the immune system plays a vital role. In this study, we aimed to establish a prognostic prediction nomogram for melanoma patients that incorporates immune-related genes (IRGs). Ninety-seven differentially expressed IRGs between melanoma and normal skin were screened using gene expression omnibus database (GEO). Among these IRGs, a two-gene signature consisting of CCL8 and DEFB1 was found to be closely associated with patient prognosis using the cancer genome atlas (TCGA) database. Survival analysis verified that the IRGs score based on the signature gene expressions efficiently distinguished between high- and low-risk patients, and was identified to be an independent prognostic factor. A nomogram integrating the IRGs score, age and TNM stage was established to predict individual prognosis for melanoma. The prognostic performance was validated by the TCGA/GEO-based concordance indices and calibration plots. The area under the curve demonstrated that the nomogram was superior than the conventional staging system, which was confirmed by the decision curve analysis. Overall, we developed and validated a nomogram for prognosis prediction in melanoma based on IRGs signatures and clinical parameters, which could be valuable for decision making in the clinic.
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Affiliation(s)
- Mengting Liao
- Health Management Center, Xiangya Hospital, Central South University, Changsha, 410008, China.,Department of Dermatology, Xiangya Hospital, Central South University, Xiangya Road 87, Changsha, 410008, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, 410008, China.,Hunan Engineering Research Center of Skin Health and Disease, Changsha, 410008, China
| | - Furong Zeng
- Department of Dermatology, Xiangya Hospital, Central South University, Xiangya Road 87, Changsha, 410008, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, 410008, China.,Hunan Engineering Research Center of Skin Health and Disease, Changsha, 410008, China
| | - Yao Li
- Department of Dermatology, Xiangya Hospital, Central South University, Xiangya Road 87, Changsha, 410008, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, 410008, China.,Hunan Engineering Research Center of Skin Health and Disease, Changsha, 410008, China
| | - Qian Gao
- Department of Dermatology, Xiangya Hospital, Central South University, Xiangya Road 87, Changsha, 410008, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, 410008, China.,Hunan Engineering Research Center of Skin Health and Disease, Changsha, 410008, China
| | - Mingzhu Yin
- Department of Dermatology, Xiangya Hospital, Central South University, Xiangya Road 87, Changsha, 410008, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, 410008, China.,Hunan Engineering Research Center of Skin Health and Disease, Changsha, 410008, China
| | - Guangtong Deng
- Department of Dermatology, Xiangya Hospital, Central South University, Xiangya Road 87, Changsha, 410008, China. .,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, 410008, China. .,Hunan Engineering Research Center of Skin Health and Disease, Changsha, 410008, China.
| | - Xiang Chen
- Department of Dermatology, Xiangya Hospital, Central South University, Xiangya Road 87, Changsha, 410008, China. .,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, 410008, China. .,Hunan Engineering Research Center of Skin Health and Disease, Changsha, 410008, China.
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7
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Gu HY, Lin LL, Zhang C, Yang M, Zhong HC, Wei RX. The Potential of Five Immune-Related Prognostic Genes to Predict Survival and Response to Immune Checkpoint Inhibitors for Soft Tissue Sarcomas Based on Multi-Omic Study. Front Oncol 2020; 10:1317. [PMID: 32850416 PMCID: PMC7396489 DOI: 10.3389/fonc.2020.01317] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/24/2020] [Indexed: 12/12/2022] Open
Abstract
Low response rates to immunotherapy have been reported in soft tissue sarcoma (STS). There are few predictive biomarkers of response, and the tumor immune microenvironment associated with progression and prognosis remains unclear in STS. Gene expression data from the Cancer Genome Atlas were used to identify the immune-related prognostic genes (IRPGs) and construct the immune gene-related prognostic model (IGRPM). The tumor immune microenvironment was characterized to reveal differences between patients with different prognoses. Furthermore, somatic mutation data and DNA methylation data were analyzed to understand the underlying mechanism leading to different prognoses. The IGRPM was constructed using five IRPGs (IFIH1, CTSG, STC2, SECTM1, and BIRC5). Two groups (high- and low-risk patients) were identified based on the risk score. Low-risk patients with higher overall survival time had higher immune scores, more immune cell infiltration (e.g., CD8 T cell and activated natural killer cells), higher expression of immune-stimulating molecules, higher stimulating cytokines and corresponding receptors, higher innate immunity molecules, and stronger antigen-presenting capacity. However, inhibition of immunity was observed in low-risk patients owing to the higher expression of immune checkpoint molecules and inhibiting cytokines. High-risk patients had high tumor mutation burden, which did not significantly influence survival. Gene set enrichment analysis further revealed that pathways of cell cycle and cancers were activated in high-risk patients. DNA methylation analysis indicated that relative high methylation was associated with better overall survival. Finally, the age, mitotic counts, and risk scores were independent prognostic factors for STS. Five IRPGs performed well in risk stratification of patients and are candidate biomarkers for predicting response to immunotherapy. Differences observed through the multi-omic study of patients with different prognoses may reveal the underlying mechanism of the development and progression of STS, and thereby improve treatment.
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Affiliation(s)
- Hui-Yun Gu
- Department of Spine and Orthopedic Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Lu-Lu Lin
- Department of Pathology and Pathophysiology, School of Basic Medicine, Wuhan University, Wuhan, China
| | - Chao Zhang
- Center for Evidence-Based Medicine and Clinical Research, Taihe Hospital, Hubei University of Medicine, Shiyan, China.,Department of Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Min Yang
- Department of Spine and Orthopedic Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hou-Cheng Zhong
- Department of Spine and Orthopedic Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ren-Xiong Wei
- Department of Spine and Orthopedic Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
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8
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Neagu M, Constantin C, Cretoiu SM, Zurac S. miRNAs in the Diagnosis and Prognosis of Skin Cancer. Front Cell Dev Biol 2020; 8:71. [PMID: 32185171 PMCID: PMC7058916 DOI: 10.3389/fcell.2020.00071] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 01/27/2020] [Indexed: 12/16/2022] Open
Abstract
Skin cancer is, at present, the most common type of malignancy in the Caucasian population. Its incidence has increased rapidly in the last decade for both melanoma and non-melanoma skin cancer. Differential expression profiles of microRNAs (miRNAs) have been reported for a variety of different cancers, including skin cancers. Since miRNAs’ discovery as regulators of gene expression, their importance grew in the field of oncology. miRNAs can post-transcriptionally regulate gene expression, tumor initiation, development progression, and aggressiveness. Nowadays, these short regulatory RNAs are perceived as one of the epigenetic markers for the identification of new diagnostic and/or prognostic molecular markers. Moreover, as miRNAs can drive tumorigenesis, they might eventually represent new therapy targets. Some miRNAs are pleiotropic, such as miR-214, which was found deregulated in several other tumors besides skin cancers. Some others are specific for one or more skin cancer types, like miR-21 and miR-221 for cutaneous melanoma and cutaneous squamous carcinoma or miR-155 for melanoma and cutaneous lymphoma. The goal of this review was to summarize some of the main miRNA detection technologies that are used to evaluate miRNAs in tissues and body fluids. Furthermore, their quantification limits, conformity, and robustness are discussed. Aberrant miRNA expression is analyzed for cutaneous melanoma, cutaneous squamous cell carcinoma (CSCC), skin lymphomas, cutaneous lymphoma, and Merkel cell carcinoma (MCC). In this type of disease, miRNAs are described as potential biomarkers to diagnose early lesion and/or early metastatic disease. In the future, whether in tissue or circulating in body fluids, miRNAs will gain their place in skin cancer diagnosis, prognosis, and future therapeutic targets.
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Affiliation(s)
- Monica Neagu
- Immunology Laboratory, "Victor Babeş" National Institute of Pathology, Bucharest, Romania.,Doctoral School, Faculty of Biology, University of Bucharest, Bucharest, Romania.,Department of Pathology, Colentina Clinical Hospital, Bucharest, Romania
| | - Carolina Constantin
- Immunology Laboratory, "Victor Babeş" National Institute of Pathology, Bucharest, Romania.,Department of Pathology, Colentina Clinical Hospital, Bucharest, Romania
| | - Sanda Maria Cretoiu
- Division of Cell and Molecular Biology and Histology, "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania
| | - Sabina Zurac
- Department of Pathology, Colentina Clinical Hospital, Bucharest, Romania.,Department of Pathology, Faculty of Dental Medicine, "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania
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9
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Detection of Gene Mutations in Liquid Biopsy of Melanoma Patients: Overview and Future Perspectives. Curr Treat Options Oncol 2020; 21:19. [PMID: 32048063 DOI: 10.1007/s11864-020-0708-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
OPINION STATEMENT Liquid biopsies are still far from widely implanted in the clinical arena. Issues related to the added sensitivity of this test beyond conventional methods have not been fully resolved. Additionally, issues related to the specificity of these results especially as many cancers may share common mutation need further investigations. One way to resolve this may include the development and testing of large gene panels to add higher specificity. On the other hand, further studies are needed to support the idea that ctDNA or circulating tumor cells may constitute a better representation of the tumor subpopulation that is capable of metastasizing, which will strongly support its clinical value. Finally, survival studies showing a positive impact of this technology will also justify its widespread implementation in clinical practice.
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