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Ma W, Wu Z, Maghsoudloo M, Ijaz I, Dehghan Shasaltaneh M, Zhang Y, Weng Q, Fu J, Imani S, Wen QL. Dermokine mutations contribute to epithelial-mesenchymal transition and advanced melanoma through ERK/MAPK pathways. PLoS One 2023; 18:e0285806. [PMID: 37432950 PMCID: PMC10335698 DOI: 10.1371/journal.pone.0285806] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/29/2023] [Indexed: 07/13/2023] Open
Abstract
To discover vulnerabilities associated with dermokine (DMKN) as a new trigger of the epithelial-mesenchymal transition (EMT) -driven melanoma, we undertook a genome-wide genetic screening using transgenic. Here, we showed that DMKN expression could be constitutively increased in human malignant melanoma (MM) and that this correlates with poor overall survival in melanoma patients, especially in BRAF-mutated MM samples. Furthermore, in vitro, knockdown of DMKN inhibited the cell proliferation, migration, invasion, and apoptosis of MM cancer cells by the activation of ERK/MAPK signaling pathways and regulator of STAT3 in downstream molecular. By interrogating the in vitro melanoma dataset and characterization of advanced melanoma samples, we found that DMKN downregulated the EMT-like transcriptional program by disrupting EMT cortical actin, increasing the expression of epithelial markers, and decreasing the expression of mesenchymal markers. In addition, whole exome sequencing was presented with p.E69D and p.V91A DMKN mutations as a novel somatic loss of function mutations in those patients. Moreover, our purposeful proof-of-principle modeled the interaction of ERK with p.E69D and p.V91A DMKN mutations in the ERK-MAPK kinas signaling that may be naturally associated with triggering the EMT during melanomagenesis. Altogether, these findings provide preclinical evidence for the role of DMKN in shaping the EMT-like melanoma phenotype and introduced DMKN as a new exceptional responder for personalized MM therapy.
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Affiliation(s)
- Wenqiong Ma
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Zexiu Wu
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Mazaher Maghsoudloo
- Faculty of Advanced Science and Technology, Department of Genetics, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- The Center of Research and Training for Occupational Technical Safety and Health, Tehran, Iran
| | - Iqra Ijaz
- Sichuan Provincial Center for Gynecological and Breast Diseases, Southwest Medical University, Luzhou, Sichuan, China
| | | | - Yuqin Zhang
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Qiao Weng
- Department of Obstetrics & Gynecology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Junjiang Fu
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Saber Imani
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang, China
| | - Qing Lian Wen
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
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Ariano C, Costanza F, Akman M, Riganti C, Corà D, Casanova E, Astanina E, Comunanza V, Bussolino F, Doronzo G. TFEB inhibition induces melanoma shut-down by blocking the cell cycle and rewiring metabolism. Cell Death Dis 2023; 14:314. [PMID: 37160873 PMCID: PMC10170071 DOI: 10.1038/s41419-023-05828-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 04/19/2023] [Accepted: 04/21/2023] [Indexed: 05/11/2023]
Abstract
Melanomas are characterised by accelerated cell proliferation and metabolic reprogramming resulting from the contemporary dysregulation of the MAPK pathway, glycolysis and the tricarboxylic acid (TCA) cycle. Here, we suggest that the oncogenic transcription factor EB (TFEB), a key regulator of lysosomal biogenesis and function, controls melanoma tumour growth through a transcriptional programme targeting ERK1/2 activity and glucose, glutamine and cholesterol metabolism. Mechanistically, TFEB binds and negatively regulates the promoter of DUSP-1, which dephosphorylates ERK1/2. In melanoma cells, TFEB silencing correlates with ERK1/2 dephosphorylation at the activation-related p-Thr185 and p-Tyr187 residues. The decreased ERK1/2 activity synergises with TFEB control of CDK4 expression, resulting in cell proliferation blockade. Simultaneously, TFEB rewires metabolism, influencing glycolysis, glucose and glutamine uptake, and cholesterol synthesis. In TFEB-silenced melanoma cells, cholesterol synthesis is impaired, and the uptake of glucose and glutamine is inhibited, leading to a reduction in glycolysis, glutaminolysis and oxidative phosphorylation. Moreover, the reduction in TFEB level induces reverses TCA cycle, leading to fatty acid production. A syngeneic BRAFV600E melanoma model recapitulated the in vitro study results, showing that TFEB silencing sustains the reduction in tumour growth, increase in DUSP-1 level and inhibition of ERK1/2 action, suggesting a pivotal role for TFEB in maintaining proliferative melanoma cell behaviour and the operational metabolic pathways necessary for meeting the high energy demands of melanoma cells.
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Affiliation(s)
- C Ariano
- Department of Oncology, University of Torino, Torino, Italy
- Candiolo Cancer Institute- FPO-IRCCS, Candiolo, Italy
| | - F Costanza
- Department of Oncology, University of Torino, Torino, Italy
- Candiolo Cancer Institute- FPO-IRCCS, Candiolo, Italy
| | - M Akman
- Department of Oncology, University of Torino, Torino, Italy
| | - C Riganti
- Department of Oncology, University of Torino, Torino, Italy
| | - D Corà
- Department of Translational Medicine, Piemonte Orientale University, Novara, Italy
- Center for Translational Research on Autoimmune and Allergic Diseases - CAAD, Novara, Italy
| | - E Casanova
- Candiolo Cancer Institute- FPO-IRCCS, Candiolo, Italy
| | - E Astanina
- Department of Oncology, University of Torino, Torino, Italy
- Candiolo Cancer Institute- FPO-IRCCS, Candiolo, Italy
| | - V Comunanza
- Department of Oncology, University of Torino, Torino, Italy
- Candiolo Cancer Institute- FPO-IRCCS, Candiolo, Italy
| | - F Bussolino
- Department of Oncology, University of Torino, Torino, Italy.
- Candiolo Cancer Institute- FPO-IRCCS, Candiolo, Italy.
| | - G Doronzo
- Department of Oncology, University of Torino, Torino, Italy.
- Candiolo Cancer Institute- FPO-IRCCS, Candiolo, Italy.
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He W, Yang G, Liu S, Maghsoudloo M, Shasaltaneh MD, Kaboli PJ, Zhang C, Zhang J, Entezari M, Imani S, Wen Q. Comparative mRNA/micro-RNA co-expression network drives melanomagenesis by promoting epithelial-mesenchymal transition and vasculogenic mimicry signaling. Transl Oncol 2021; 14:101237. [PMID: 34626953 PMCID: PMC8512639 DOI: 10.1016/j.tranon.2021.101237] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 09/30/2021] [Indexed: 12/17/2022] Open
Abstract
This study aimed to identify a novel disease-associated differentially co-expressed mRNA-microRNA (miRNA) that is associated with vasculogenic mimicry (VM) and epithelial-to-mesenchymal transition (EMT) network at different stages of melanoma. By applying weighted gene co-expression network analysis, we constructed a VM+EMT biological network with the available microarray dataset downloaded from a public database. Quantitative real-time PCR, immunohistochemical staining, and CD31-periodic acid solution dual staining were performed to confirm the expression of genes associated with EMT and VM formation in subjects with malignant melanoma (n = 18) and primary melanoma (n = 13) and in healthy subjects (n = 10). Our findings suggested that phosphatidylserine-specific phospholipase A1-alpha (PLA1A) and dermokine (DMKN) genes function as oncogenes that trigger VM and EMT processes during melanomagenesis on interaction with miR-370, miR-563, and miR-770-5p. PLA1A and DMKN genes can be considered potential VM+EMT network-based diagnostic biomarkers for distinguishing between melanoma patients. We postulate that a network with altered PLA1A/miR-563 and DMNK/miR-770-5p/miR-370 may contribute to melanomagenesis by triggering the EMT signaling pathway and VM formation. This study provides a potentially valuable approach for the early diagnosis and prognosis of melanoma progression.
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Affiliation(s)
- WenFeng He
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Gang Yang
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China; Department of Oncology, Anyue Hospital of Traditional Chinese Medicine, Second Ziyang Hospital of Traditional Chinese Medicine, Ziyang, Sichuan, China
| | - Shuya Liu
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China; Department of Oncology, Chengdu Jinniu District People's Hospital, Chengdu, Sichuan, China
| | - Mazaher Maghsoudloo
- Laboratory of Systems Biology and Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | | | - Parham Jabbarzadeh Kaboli
- Graduate Institute of Biomedical Sciences, Research Center for Cancer Biology, and Center for Molecular Medicine, China Medical University, Taichung, Taiwan
| | - Cuiwei Zhang
- Department of Pathology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - JingHeng Zhang
- Oncology Department, Luzhou People's Hospital, Luzhou, Sichuan, China
| | - Maliheh Entezari
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Farhikhtegan Medical Convergence sciences Research Center, Farhikhtegan Hospital Tehran Medical sciences, Islamic Azad University, Tehran, Iran
| | - Saber Imani
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China.
| | - QingLian Wen
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China.
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Zhang Y, Peng J, Du H, Zhang N, Fang X. Identification and Validation of Immune- and Stemness-Related Prognostic Signature of Melanoma. Front Cell Dev Biol 2021; 9:755284. [PMID: 34805163 PMCID: PMC8602573 DOI: 10.3389/fcell.2021.755284] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 10/11/2021] [Indexed: 12/13/2022] Open
Abstract
Purpose: Our aim was to construct a signature that accurately predicted the prognostic and immune response of melanoma. Methods: First, the weighted co-expression network analysis (WGCNA) algorithm was used to identify the hub genes related to clinical phenotypes of melanoma in the cancer genome atlas (TCGA) database. Nest, the least absolute shrinkage and selection operator (LASSO) analysis was used to dimensionality reduction of these hub genes and constructed a prognostic signature to predict the prognosis and immunosuppressive response of melanoma. Result: Through in-depth analysis, we constructed a 5-mRNA prognostic signature and verified its prognostic value in internal (TCGA-SKCM, n = 452) and external independent datasets (GSE53118, n = 79). Based on this signature, the tumor immune microenvironment (TME) of melanoma was characterized, and the result was found that patients in the high-risk group had lower CD8 T cell infiltration and immune checkpoint expression (PD-1, PD-L1, CTLA4), as well as higher M0/M2 macrophage infiltration. Our results also found the risk score based on a 5-mRNA signature was significantly associated with tumor mutational burden (TMB) and tumor stem cell markers (CD20, CD38, ABCB5, CD44, etc.). Lastly, we built a nomogram for clinician prediction for the prognosis of patients with melanoma. Conclusion: Our findings indicated that the 5-mRNA signature has an important predictive value for the overall survival of melanoma. By analyzing the tumor immune microenvironment and tumor stem cell marker between different groups, a new method is provided for the stratified diagnosis and treatment of melanoma.
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Affiliation(s)
- Yan Zhang
- Department of Dermatology, The First College of Clinical Medical Sciences, China Three Gorges University, Yichang, China.,Department of Dermatology, Yichang Central People's Hospital, Yichang, China
| | - Jing Peng
- Department of Dermatology, The First College of Clinical Medical Sciences, China Three Gorges University, Yichang, China.,Department of Dermatology, Yichang Central People's Hospital, Yichang, China
| | - Heng Du
- Department of Dermatology, The First College of Clinical Medical Sciences, China Three Gorges University, Yichang, China.,Department of Dermatology, Yichang Central People's Hospital, Yichang, China
| | - Niannian Zhang
- Department of Dermatology, The First College of Clinical Medical Sciences, China Three Gorges University, Yichang, China.,Department of Dermatology, Yichang Central People's Hospital, Yichang, China
| | - Xianfeng Fang
- Department of Dermatology, The First College of Clinical Medical Sciences, China Three Gorges University, Yichang, China.,Department of Dermatology, Yichang Central People's Hospital, Yichang, China
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5
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Cui W, Xue H, Wei L, Jin J, Tian X, Wang Q. High heterogeneity undermines generalization of differential expression results in RNA-Seq analysis. Hum Genomics 2021; 15:7. [PMID: 33509298 PMCID: PMC7845028 DOI: 10.1186/s40246-021-00308-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 01/19/2021] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND RNA sequencing (RNA-Seq) has been widely applied in oncology for monitoring transcriptome changes. However, the emerging problem that high variation of gene expression levels caused by tumor heterogeneity may affect the reproducibility of differential expression (DE) results has rarely been studied. Here, we investigated the reproducibility of DE results for any given number of biological replicates between 3 and 24 and explored why a great many differentially expressed genes (DEGs) were not reproducible. RESULTS Our findings demonstrate that poor reproducibility of DE results exists not only for small sample sizes, but also for relatively large sample sizes. Quite a few of the DEGs detected are specific to the samples in use, rather than genuinely differentially expressed under different conditions. Poor reproducibility of DE results is mainly caused by high variation of gene expression levels for the same gene in different samples. Even though biological variation may account for much of the high variation of gene expression levels, the effect of outlier count data also needs to be treated seriously, as outlier data severely interfere with DE analysis. CONCLUSIONS High heterogeneity exists not only in tumor tissue samples of each cancer type studied, but also in normal samples. High heterogeneity leads to poor reproducibility of DEGs, undermining generalization of differential expression results. Therefore, it is necessary to use large sample sizes (at least 10 if possible) in RNA-Seq experimental designs to reduce the impact of biological variability and DE results should be interpreted cautiously unless soundly validated.
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Affiliation(s)
- Weitong Cui
- Key Laboratory of Biomedical Engineering & Technology of Shandong High School, Qilu Medical University, Zibo, 255300, China
| | - Huaru Xue
- Key Laboratory of Biomedical Engineering & Technology of Shandong High School, Qilu Medical University, Zibo, 255300, China
| | - Lei Wei
- Key Laboratory of Biomedical Engineering & Technology of Shandong High School, Qilu Medical University, Zibo, 255300, China
| | - Jinghua Jin
- Environmental Protection Research Institute of Light Industry, Beijing, 100089, China
| | - Xuewen Tian
- Shandong Sport University, Jinan, 250102, China
| | - Qinglu Wang
- Key Laboratory of Biomedical Engineering & Technology of Shandong High School, Qilu Medical University, Zibo, 255300, China.
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6
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Iacobas DA. Powerful quantifiers for cancer transcriptomics. World J Clin Oncol 2020; 11:679-704. [PMID: 33033692 PMCID: PMC7522543 DOI: 10.5306/wjco.v11.i9.679] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 06/06/2020] [Accepted: 07/01/2020] [Indexed: 02/06/2023] Open
Abstract
Every day, investigators find a new link between a form of cancer and a particular alteration in the sequence or/and expression level of a key gene, awarding this gene the title of “biomarker”. The clinician may choose from numerous available panels to assess the type of cancer based on the mutation or expression regulation (“transcriptomic signature”) of “driver” genes. However, cancer is not a “one-gene show” and, together with the alleged biomarker, hundreds other genes are found as mutated or/and regulated in cancer samples. Regardless of the platform, a well-designed transcriptomic study produces three independent features for each gene: Average expression level, expression variability and coordination with expression of each other gene. While the average expression level is used in all studies to identify what genes were up-/down-regulated or turn on/off, the other two features are unfairly ignored. We use all three features to quantify the transcriptomic change during the progression of the disease and recovery in response to a treatment. Data from our published microarray experiments on cancer nodules and surrounding normal tissue from surgically removed tumors prove that the transcriptomic topologies are not only different in histopathologically distinct regions of a tumor but also dynamic and unique for each human being. We show also that the most influential genes in cancer nodules [the Gene Master Regulators (GMRs)] are significantly less influential in the normal tissue. As such, “smart” manipulation of the cancer GMRs expression may selectively kill cancer cells with little consequences on the normal ones. Therefore, we strongly recommend a really personalized approach of cancer medicine and present the experimental procedure and the mathematical algorithm to identify the most legitimate targets (GMRs) for gene therapy.
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Affiliation(s)
- Dumitru Andrei Iacobas
- Personalized Genomics Laboratory, CRI Center for Computational Systems Biology, Roy G Perry College of Engineering, Prairie View A&M University, Prairie View, TX 77446, United States
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7
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Yan X, Fu X, Guo ZX, Liu XP, Liu TZ, Li S. Construction and validation of an eight-gene signature with great prognostic value in bladder cancer. J Cancer 2020; 11:1768-1779. [PMID: 32194788 PMCID: PMC7052873 DOI: 10.7150/jca.38741] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/30/2019] [Indexed: 12/24/2022] Open
Abstract
Bladder cancer (BC) is one of the most common malignancies in urinary system with a common malignancy in urinary system with a high mortality and recurrence rate, so we attempt to construct a gene signature to predict the prognosis of BCs. We initially established a co-expression network by performing WGCNA analysis and further identified magenta module as key module (P = 8e-05, R2 = 0.4). Subsequently, we screened 12 genes associated with survival from the key module, which were selected to construct an eight-gene signature by establishing a LASSO Cox model. Moreover, we reckoned the risk score (RS) of each sample, through which we could divide samples into two groups (the high-risk and low-risk groups) and verify the signature, in the training set and 3 validation sets (internal test set, GSE13507and E-MTAB-4321). This signature could distinguish between the high- and low- risk patients well (survival analysis: P = 0.015; AUC: 0.61 at 1 year, 0.61 at 3 years and 0.61 at 5 years). In the validation sets, this signature also showed good performance, which was consistent with the training test. Furthermore, we plotted a nomogram to predict the possibility of the overall survival (OS) and three calibration curves to predict the effectiveness of the nomogram, which suggested good value and clinical utility of the nomogram. In conclusion, we established an eight-gene signature, which was probably effective in the prediction of prognosis of patients with BC.
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Affiliation(s)
- Xin Yan
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China.,Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Xun Fu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Zi-Xin Guo
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Xiao-Ping Liu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Tong-Zu Liu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Sheng Li
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China.,Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan 430071, China.,Human Genetics Resource Preservation Center of Hubei Province, Wuhan 430071, China
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