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Mogal MR, Jame JA, Sohel M, Mozibullah M, Mahmod MR, Junayed A, Kar N, Arbia L, Al Mamun A, Sikder MA. Integrated bioinformatics analysis reveals upregulated extracellular matrix hub genes in pancreatic cancer: Implications for diagnosis, prognosis, immune infiltration, and therapeutic strategies. Cancer Rep (Hoboken) 2024; 7:e2059. [PMID: 38639039 PMCID: PMC11027013 DOI: 10.1002/cnr2.2059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 02/20/2024] [Accepted: 03/24/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Pancreatic cancer (PC) stands out as one of the most formidable malignancies and exhibits an exceptionally unfavorable clinical prognosis due to the absence of well-defined diagnostic indicators and its tendency to develop resistance to therapeutic interventions. The primary objective of this present study was to identify extracellular matrix (ECM)-related hub genes (HGs) and their corresponding molecular signatures, with the intent of potentially utilizing them as biomarkers for diagnostic, prognostic, and therapeutic applications. METHODS Three microarray datasets were sourced from the NCBI database to acquire upregulated differentially expressed genes (DEGs), while MatrisomeDB was employed for filtering ECM-related genes. Subsequently, a protein-protein interaction (PPI) network was established using the STRING database. The created network was visually inspected through Cytoscape, and HGs were identified using the CytoHubba plugin tool. Furthermore, enrichment analysis, expression pattern analysis, clinicopathological correlation, survival analysis, immune cell infiltration analysis, and examination of chemical compounds were carried out using Enrichr, GEPIA2, ULCAN, Kaplan Meier plotter, TIMER2.0, and CTD web platforms, respectively. The diagnostic and prognostic significance of HGs was evaluated through the ROC curve analysis. RESULTS Ten genes associated with ECM functions were identified as HGs among 131 DEGs obtained from microarray datasets. Notably, the expression of these HGs exhibited significantly (p < 0.05) higher in PC, demonstrating a clear association with tumor advancement. Remarkably, higher expression levels of these HGs were inversely correlated with the likelihood of patient survival. Moreover, ROC curve analysis revealed that identified HGs are promising biomarkers for both diagnostic (AUC > 0.75) and prognostic (AUC > 0.64) purposes. Furthermore, we observed a positive correlation between immune cell infiltration and the expression of most HGs. Lastly, our study identified nine compounds with significant interaction profiles that could potentially act as effective chemical agents targeting the identified HGs. CONCLUSION Taken together, our findings suggest that COL1A1, KRT19, MMP1, COL11A1, SDC1, ITGA2, COL1A2, POSTN, FN1, and COL5A1 hold promise as innovative biomarkers for both the diagnosis and prognosis of PC, and they present as prospective targets for therapeutic interventions aimed at impeding the progression PC.
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Affiliation(s)
- Md Roman Mogal
- Department of Biochemistry and Molecular BiologyMawlana Bhashani Science and Technology UniversityTangailBangladesh
| | - Jasmin Akter Jame
- Department of Biochemistry and Molecular BiologyMawlana Bhashani Science and Technology UniversityTangailBangladesh
| | - Md Sohel
- Department of Biochemistry and Molecular BiologyPrimeasia UniversityDhakaBangladesh
| | - Md Mozibullah
- Department of Biochemistry and Molecular BiologyMawlana Bhashani Science and Technology UniversityTangailBangladesh
| | - Md Rashel Mahmod
- Department of Biochemistry and Molecular BiologyMawlana Bhashani Science and Technology UniversityTangailBangladesh
| | - Asadullah Junayed
- Department of Biochemistry and Molecular BiologyMawlana Bhashani Science and Technology UniversityTangailBangladesh
| | - Newton Kar
- Department of Biochemistry and Molecular BiologyMawlana Bhashani Science and Technology UniversityTangailBangladesh
| | - Lubatul Arbia
- Department of Biochemistry and Molecular BiologyPrimeasia UniversityDhakaBangladesh
| | - Abdullah Al Mamun
- Department of Biochemistry and Molecular BiologyMawlana Bhashani Science and Technology UniversityTangailBangladesh
| | - Md Asaduzzaman Sikder
- Department of Biochemistry and Molecular BiologyMawlana Bhashani Science and Technology UniversityTangailBangladesh
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2
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Liu Y, Zhao M, Qu H. Identification of cytokine-induced cell communications by pan-cancer meta-analysis. PeerJ 2023; 11:e16221. [PMID: 38054018 PMCID: PMC10695116 DOI: 10.7717/peerj.16221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 09/11/2023] [Indexed: 12/07/2023] Open
Abstract
Cancer immune responses are complex cellular processes in which cytokine-receptor interactions play central roles in cancer development and response to therapy; dysregulated cytokine-receptor communication may lead to pathological processes, including cancer, autoimmune diseases, and cytokine storm; however, our knowledge regarding cytokine-mediated cell-cell communication (CCI) in different cancers remains limited. The present study presents a single-cell and pan-cancer-level transcriptomics integration of 41,900 cells across 25 cancer types. We developed a single-cell method to actively express 62 cytokine-receptor pairs to reveal stable cytokine-mediated cell communications involving 84 cytokines and receptors. The correlation between the sample-based CCI profile and the interactome analysis indicates multiple cytokine-receptor modules including TGFB1, IL16ST, IL15, and the PDGF family. Some isolated cytokine interactions, such as FN1-IL17RC, displayed diverse functions within over ten single-cell transcriptomics datasets. Further functional enrichment analysis revealed that the constructed cytokine-receptor interaction map is associated with the positive regulation of multiple immune response pathways. Using public TCGA pan-cancer mutational data, co-mutational analysis of the cytokines and receptors provided significant co-occurrence features, implying the existence of cooperative mechanisms. Analysis of 10,967 samples from 32 TCGA cancer types revealed that the 84 cytokine and receptor genes are significantly associated with clinical survival time. Interestingly, the tumor samples with mutations in any of the 84 cytokines and receptors have a substantially higher mutational burden, offering insights into antitumor immune regulation and response. Clinical cancer stage information revealed that tumor samples with mutations in any of the 84 cytokines and receptors stratify into earlier tumor stages, with unique cellular compositions and clinical outcomes. This study provides a comprehensive cytokine-receptor atlas of the cellular architecture in multiple cancers at the single-cell level.
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Affiliation(s)
- Yining Liu
- The School of Public Health, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, China
| | - Min Zhao
- School of Science and Engineering, University of the Sunshine Coast, Maroochydore DC, Australia
| | - Hong Qu
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
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3
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Mahdian S, Moini A, Esfandiari F, Shahhoseini M. Drug repurposing for targeting fibronectin in treatment of endometriosis and cancers. J Biomol Struct Dyn 2023:1-17. [PMID: 37948310 DOI: 10.1080/07391102.2023.2280677] [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: 11/03/2022] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
Increased concentrations of the fibronectin glycoprotein can cause ectopic tissue growth patients with endometriosis and the formation of various cancerous tumors. Furthermore, fibronectin binding to its receptors from the EDA (Extra Domain A) region contributes to promote tumorigenesis, metastasis and vasculogenesis. Thus, the EDA region can be considered a unique target for therapeutic intervention. Therefore, the present study used computational methods to identify the best fibronectin inhibitor(s) among FDA-approved drugs. First, docking-based virtual screening was performed using PyRx 0.8. Next, FDA-approved drugs that obtained favorable results in the docking phase were selected for further studies and analysis using molecular dynamics (MD) simulation. The preliminary findings of the virtual screening showed that 17 FDA-approved drugs (from 2471) had more favorable energy with their binding energy less than -9 kcal/mol. The MD simulation results of these 17 drugs showed that Avapritinib had a lower RMSD value and higher binding energy and hydrogen bonding than the other complexes in the EDA domain. Also, analyses related to the second structure changes displayed that Avapritinib in the EDA domain led to more changes in the second structure. According to the results, the anticancer drug Avapritinib forms a more stable complex with fibronectin than other FDA-approved drugs. Furthermore, this drug leads to more changes in the second EDA structure, which may have more serious potential for inhibiting EDA fibronectin.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Soodeh Mahdian
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Ashraf Moini
- Reproductive Epidemiology Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
- Breast Disease Research Center (BDRC), Tehran University of Medical Sciences, Tehran, Iran
- Department of Obstetrics and Gynecology, Arash Women's Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Fereshteh Esfandiari
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Maryam Shahhoseini
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
- Reproductive Epidemiology Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
- Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran
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Chen C, Ye L, Yi J, Liu T, Li Z. FN1 mediated activation of aspartate metabolism promotes the progression of triple-negative and luminal a breast cancer. Breast Cancer Res Treat 2023; 201:515-533. [PMID: 37458908 DOI: 10.1007/s10549-023-07032-9] [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: 03/16/2023] [Accepted: 06/28/2023] [Indexed: 08/29/2023]
Abstract
BACKGROUND Breast cancer (BC) is regarded as one of the most common cancers diagnosed among the female population and has an extremely high mortality rate. It is known that Fibronectin 1 (FN1) drives the occurrence and development of a variety of cancers through metabolic reprogramming. Aspartic acid is considered to be an important substrate for nucleotide synthesis. However, the regulatory mechanism between FN1 and aspartate metabolism is currently unclear. METHODS We used RNA sequencing (RNA seq) and liquid chromatography-mass spectrometry to analyze the tumor tissues and paracancerous tissues of patients. MCF7 and MDA-MB-231 cells were used to explore the effects of FN1-regulated aspartic acid metabolism on cell survival, invasion, migration and tumor growth. We used PCR, Western blot, immunocytochemistry and immunofluorescence techniques to study it. RESULTS We found that FN1 was highly expressed in tumor tissues, especially in Lumina A and TNBC subtypes, and was associated with poor prognosis. In vivo and in vitro experiments showed that silencing FN1 inhibits the activation of the YAP1/Hippo pathway by enhancing YAP1 phosphorylation, down-regulates SLC1A3-mediated aspartate uptake and utilization by tumor cells, inhibits BC cell proliferation, invasion and migration, and promotes apoptosis. In addition, inhibition of FN1 combined with the YAP1 inhibitor or SLC1A3 inhibitor can effectively inhibit tumor growth, of which inhibition of FN1 combined with the YAP1 inhibitor is more effective. CONCLUSION Targeting the "FN1/YAP1/SLC1A3/Aspartate metabolism" regulatory axis provides a new target for BC diagnosis and treatment. This study also revealed that intratumoral metabolic heterogeneity plays an important role in the progression of different subtypes of breast cancer.
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Affiliation(s)
- Chen Chen
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Leiguang Ye
- Department of Respiratory Medicine, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Jinfeng Yi
- Department of Pathology, Harbin Medical University, Harbin, 150081, China
| | - Tang Liu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China.
| | - Zhigao Li
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China.
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5
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Shen X, Liu H, Zhou H, Cheng Z, Liu G, Huang C, Dou R, Liu F, You X. Galectin-1 promotes gastric cancer peritoneal metastasis through peritoneal fibrosis. BMC Cancer 2023; 23:559. [PMID: 37328752 DOI: 10.1186/s12885-023-11047-2] [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: 04/04/2023] [Accepted: 06/07/2023] [Indexed: 06/18/2023] Open
Abstract
BACKGROUND Peritoneal metastasis is one of the main causes of death in patients with gastric cancer (GC). Galectin-1 regulates various undesirable biological behaviors in GC and may be key in GC peritoneal metastasis. METHODS In this study, we elucidated the regulatory role of galectin-1 in GC cell peritoneal metastasis. GC and peritoneal tissues underwent hematoxylin-eosin (HE), immunohistochemical (IHC), and Masson trichrome staining to analyze the difference in galectin-1 expression and peritoneal collagen deposition in different GC clinical stages. The regulatory role of galectin-1 in GC cell adhesion to mesenchymal cells and in collagen expression was determined using HMrSV5 human peritoneal mesothelial cells (HPMCs). Collagen and corresponding mRNA expression were detected with western blotting and reverse transcription PCR, respectively. The promoting effect of galectin-1 on GC peritoneal metastasis was verified in vivo. Collagen deposition and collagen I, collagen III, and fibronectin 1 (FN1) expression in the peritoneum of the animal models were detected by Masson trichrome and IHC staining. RESULTS Galectin-1 and collagen deposition in the peritoneal tissues was correlated with GC clinical staging and were positively correlated. Galectin-1 enhanced the ability of GC cells to adhere to the HMrSV5 cells by promoting collagen I, collagen III, and FN1 expression. The in vivo experiments confirmed that galectin-1 promoted GC peritoneal metastasis by promoting peritoneal collagen deposition. CONCLUSION Galectin-1-induced peritoneal fibrosis may create a favorable environment for GC cell peritoneal metastasis.
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Affiliation(s)
- Xianhe Shen
- Department of Gastrointestinal Surgery, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, Jiangsu, China
| | - Huilan Liu
- Oncology department, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, Jiangsu, China
| | - Haihua Zhou
- Department of Gastrointestinal Surgery, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, Jiangsu, China
| | - Zhiyi Cheng
- Department of Gastrointestinal Surgery, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, Jiangsu, China
| | - Guiyuan Liu
- Department of Gastrointestinal Surgery, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, Jiangsu, China
| | - Chuanjiang Huang
- Department of Gastrointestinal Surgery, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, Jiangsu, China
| | - Rongrong Dou
- Department of the Pathology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, Jiangsu, China
| | - Fuxing Liu
- Department of the Pathology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, Jiangsu, China
| | - Xiaolan You
- Department of Gastrointestinal Surgery, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, Jiangsu, China.
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6
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Darang E, Pezeshkian Z, Mirhoseini SZ, Ghovvati S. Bioinformatics and pathway enrichment analysis identified hub genes and potential biomarker for gastric cancer prognosis. Front Oncol 2023; 13:1187521. [PMID: 37361568 PMCID: PMC10288990 DOI: 10.3389/fonc.2023.1187521] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/23/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction Gastric cancer is one of the most common cancers in the world. This study aimed to identify genes, biomarkers, and metabolic pathways affecting gastric cancer using bioinformatic analysis and meta-analysis. Methods Datasets containing gene expression profiles of tumor lesions and adjacent non-tumor mucosa samples were downloaded. Common differentially expressed genes between data sets were selected to identify hub genes and further analysis. Gene Expression Profiling and Interactive Analyses (GEPIA) and the Kaplan-Meier method were used to further validate the expression level of genes and plot the overall survivalcurve, respectively. Results and disscussion KEGG pathway analysis showed that the most important pathway was enriched in ECM-receptor interaction. Hub genes includingCOL1A2, FN1, BGN, THBS2, COL5A2, COL6A3, SPARC and COL12A1 wereidentified. The top interactive miRNAs including miR-29a-3p, miR-101-3p,miR-183-5p, and miR-15a-5p targeted the most hub genes. The survival chart showed an increase in mortality in patients with gastric cancer, which shows the importance of the role of these genes in the development of the disease and can be considered candidate genes in the prevention and early diagnosis of gastric cancer.
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Affiliation(s)
- Elham Darang
- Department of Animal Sciences, Faculty of Agriculture, University of Guilan, Rasht, Guilan, Iran
| | - Zahra Pezeshkian
- Department of Animal Sciences, Faculty of Agriculture, University of Guilan, Rasht, Guilan, Iran
- Research and Development Center (R&D), BioGenTAC Inc., Rasht, Guilan, Iran
| | | | - Shahrokh Ghovvati
- Department of Animal Sciences, Faculty of Agriculture, University of Guilan, Rasht, Guilan, Iran
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7
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Pagadala M, Sears TJ, Wu VH, Pérez-Guijarro E, Kim H, Castro A, Talwar JV, Gonzalez-Colin C, Cao S, Schmiedel BJ, Goudarzi S, Kirani D, Au J, Zhang T, Landi T, Salem RM, Morris GP, Harismendy O, Patel SP, Alexandrov LB, Mesirov JP, Zanetti M, Day CP, Fan CC, Thompson WK, Merlino G, Gutkind JS, Vijayanand P, Carter H. Germline modifiers of the tumor immune microenvironment implicate drivers of cancer risk and immunotherapy response. Nat Commun 2023; 14:2744. [PMID: 37173324 PMCID: PMC10182072 DOI: 10.1038/s41467-023-38271-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
With the continued promise of immunotherapy for treating cancer, understanding how host genetics contributes to the tumor immune microenvironment (TIME) is essential to tailoring cancer screening and treatment strategies. Here, we study 1084 eQTLs affecting the TIME found through analysis of The Cancer Genome Atlas and literature curation. These TIME eQTLs are enriched in areas of active transcription, and associate with gene expression in specific immune cell subsets, such as macrophages and dendritic cells. Polygenic score models built with TIME eQTLs reproducibly stratify cancer risk, survival and immune checkpoint blockade (ICB) response across independent cohorts. To assess whether an eQTL-informed approach could reveal potential cancer immunotherapy targets, we inhibit CTSS, a gene implicated by cancer risk and ICB response-associated polygenic models; CTSS inhibition results in slowed tumor growth and extended survival in vivo. These results validate the potential of integrating germline variation and TIME characteristics for uncovering potential targets for immunotherapy.
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Affiliation(s)
- Meghana Pagadala
- Biomedical Sciences Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Timothy J Sears
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Victoria H Wu
- Department of Pharmacology, UCSD Moores Cancer Center, La Jolla, CA, 92093, USA
| | - Eva Pérez-Guijarro
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Hyo Kim
- Undergraduate Bioengineering Program, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Andrea Castro
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - James V Talwar
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | | | - Steven Cao
- Division of Epidemiology, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, 92093, USA
| | | | | | - Divya Kirani
- Undergraduate Biology and Bioinformatics Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jessica Au
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Rany M Salem
- Division of Epidemiology, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, 92093, USA
| | - Gerald P Morris
- Department of Pathology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Olivier Harismendy
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Sandip Pravin Patel
- Center for Personalized Cancer Therapy, Division of Hematology and Oncology, UC San Diego Moores Cancer Center, San Diego, CA, 92037, USA
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jill P Mesirov
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Maurizio Zanetti
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
- The Laboratory of Immunology and Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Chi-Ping Day
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Chun Chieh Fan
- Center for Population Neuroscience and Genetics, Laureate Institute for Brain Research, Tulsa, OK, 74136, USA
- Department of Radiology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Wesley K Thompson
- Division of Biostatistics, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, 92093, USA
| | - Glenn Merlino
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - J Silvio Gutkind
- Department of Pharmacology, UCSD Moores Cancer Center, La Jolla, CA, 92093, USA
| | | | - Hannah Carter
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA.
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, USA.
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Ghosh N, Saha I, Plewczynski D. Unveiling the Biomarkers of Cancer and COVID-19 and Their Regulations in Different Organs by Integrating RNA-Seq Expression and Protein-Protein Interactions. ACS OMEGA 2022; 7:43589-43602. [PMID: 36506181 PMCID: PMC9730762 DOI: 10.1021/acsomega.2c04389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/13/2022] [Indexed: 06/17/2023]
Abstract
Cancer and COVID-19 have killed millions of people worldwide. COVID-19 is even more dangerous to people with comorbidities such as cancer. Thus, it is imperative to identify the key human genes or biomarkers that can be targeted to develop novel prognosis and therapeutic strategies. The transcriptomic data provided by the next-generation sequencing technique makes this identification very convenient. Hence, mRNA (messenger ribonucleic acid) expression data of 2265 cancer and 282 normal patients were considered, while for COVID-19 assessment, 784 and 425 COVID-19 and normal patients were taken, respectively. Initially, volcano plots were used to identify the up- and down-regulated genes for both cancer and COVID-19. Thereafter, protein-protein interaction (PPI) networks were prepared by combining all the up- and down-regulated genes for each of cancer and COVID-19. Subsequently, such networks were analyzed to identify the top 10 genes with the highest degree of connection to provide the biomarkers. Interestingly, these genes were all up-regulated for cancer, while they were down-regulated for COVID-19. This study had also identified common genes between cancer and COVID-19, all of which were up-regulated in both the diseases. This analysis revealed that FN1 was highly up-regulated in different organs for cancer, while EEF2 was dysregulated in most organs affected by COVID-19. Then, functional enrichment analysis was performed to identify significant biological processes. Finally, the drugs for cancer and COVID-19 biomarkers and the common genes between them were identified using the Enrichr online web tool. These drugs include lucanthone, etoposide, and methotrexate, targeting the biomarkers for cancer, while paclitaxel is an important drug for COVID-19.
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Affiliation(s)
- Nimisha Ghosh
- Faculty
of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw 02-097, Poland
- Department
of Computer Science and Information Technology, Institute of Technical
Education and Research, Siksha ‘O’
Anusandhan (Deemed to Be University), Bhubaneswar 751030 Odisha, India
| | - Indrajit Saha
- Department
of Computer Science and Engineering, National
Institute of Technical Teachers’ Training and Research, Kolkata 700106 West Bengal, India
| | - Dariusz Plewczynski
- Laboratory
of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Warsaw 02-097, Poland
- Laboratory
of Bioinformatics and Computational Genomics, Faculty of Mathematics
and Information Science, Warsaw University
of Technology, Warsaw 00-662, Poland
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9
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Tang X, Tang Q, Yang X, Xiao ZA, Zhu G, Yang T, Yang Q, Zhang Y, Li S. FN1 promotes prognosis and radioresistance in head and neck squamous cell carcinoma: From radioresistant HNSCC cell line to integrated bioinformatics methods. Front Genet 2022; 13:1017762. [PMID: 36212151 PMCID: PMC9533212 DOI: 10.3389/fgene.2022.1017762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 08/29/2022] [Indexed: 11/17/2022] Open
Abstract
Background: Radioresistance in head and neck squamous cell carcinoma (HNSCC) patients means response failure to current treatment. In order to screen radioresistant biomarkers and mechanisms associated with HNSCC, differentially expressed genes (DEGs) associated with radioresistance in HNSCC were investigated. Methods: The HNSCC cell line with radioresistance, Hep2-R, was established and detected the radiosensitivity using MTT, colony formation assay and flow cytometry analysis. Clariom™ D chip was applied to compare DEGs between Hep2 and Hep2-R groups and build the differential gene expression profiles associated with radioresistance in HNSCC. Bioinformatic analysis were used to find biological functions and pathways that related to radioresistance in HNSCC, including cell adhesion, cytochrome P450 and drug metabolism. Gene Expression Omnibus (GEO) datasets were selected to verify DEGs between HNSCC radioresistant cells and tissues. The representation of DEGs were validated between HNSCC patients with complete response and post-operative radiation therapy failure. In addition, we evaluated the clinical prognosis of DEGs using The Cancer Genome Atlas (TCGA) database. Results: 2,360 DEGs (|Fold Change|>1.5, p < 0.05) were identified between Hep2 and Hep2-R, including 1,144 upregulated DEGs and 1,216 downregulated DEGs. They were further verified by HNSCC radioresistant cells and tissues in GEO. 13 radioresistant DEGs showed same difference in expression level between cells and tissues. By comparing 13 DEGs with HNSCC patients, upregulations of FN1, SOX4 and ETV5 were found identical with above results. Only FN1 was a prognostic indicator of HNSCC in TCGA. Conclusion: FN1 is the potential novel biomarker for predicting poor prognosis and radioresistance in HNSCC patients. Overexpression of FN1 plays an important role in the tumorigenesis, prognosis and radioresistance of HNSCC.
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Affiliation(s)
| | | | | | | | | | | | | | - Ying Zhang
- *Correspondence: Ying Zhang, ; Shisheng Li,
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10
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Wang H, Zhang J, Li H, Yu H, Chen S, Liu S, Zhang C, He Y. FN1 is a prognostic biomarker and correlated with immune infiltrates in gastric cancers. Front Oncol 2022; 12:918719. [PMID: 36081567 PMCID: PMC9445423 DOI: 10.3389/fonc.2022.918719] [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: 04/12/2022] [Accepted: 07/25/2022] [Indexed: 01/13/2023] Open
Abstract
Fibronectin 1 (FN1) is a glycoprotein found throughout the extracellular matrix that has a role in the onset and progression of cancer. However, its immune relationship with gastric cancer is still unclear. FN1 was systematically reviewed by Gene Expression Profiling Interactive Analysis (GEPIA), Linked Omics, Tumor IMmune Estimation Resource (TIMER), and Kaplan–Meier (KM) plotter analysis. The TIMER, GEPIA, TISIDB, and cBioPortal databases investigated the association of FN1 with tumor immune infiltration and validated using immunohistochemistry. We discovered that tumor tissue expresses FN1 at a higher level than neighboring tissue, and those genes coexpressed with FN1 have a poor prognosis. At the same time, we discovered that increased FN1 expression was related to immunological infiltration, particularly macrophage infiltration. Using immunohistochemistry, we discovered that FN1 expression was tightly connected to M2 macrophages. It can be concluded that FN1 can affect the immunological microenvironment and is a prognostic marker in gastric cancer.
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Affiliation(s)
- Han Wang
- Department of Center for Digestive Disease, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Junchang Zhang
- Department of Center for Digestive Disease, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Huan Li
- Department of Center for Digestive Disease, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Hong Yu
- Department of Center for Digestive Disease, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Songyao Chen
- Department of Center for Digestive Disease, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shuhao Liu
- Department of Center for Digestive Disease, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Changhua Zhang
- Department of Center for Digestive Disease, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
- *Correspondence: Changhua Zhang, ; Yulong He,
| | - Yulong He
- Department of Center for Digestive Disease, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- *Correspondence: Changhua Zhang, ; Yulong He,
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11
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Ding C, Zhang Q, Jiang X, Wei D, Xu S, Li Q, Wu M, Wang H. The Analysis of Potential Diagnostic and Therapeutic Targets for the Occurrence and Development of Gastric Cancer Based on Bioinformatics. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:4321466. [PMID: 35756405 PMCID: PMC9232307 DOI: 10.1155/2022/4321466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/09/2022] [Accepted: 05/23/2022] [Indexed: 11/17/2022]
Abstract
Objective Gastric cancer is among the most common malignant tumors of the digestive system. This study explored the molecular mechanisms and potential therapeutic targets for gastric cancer occurrence and progression using bioinformatics. Methods The gastric cancer microarray dataset was downloaded from the Gene Expression Omnibus (GEO) database. The R package was used for data mining and screening differentially expressed genes (DEGs). Gene Ontology (GO) analysis and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway analysis were performed using the Database for Annotation, Visualization, and Integrated Discovery (DAVID). Based on the protein-protein interaction (PPI) network analysis, core targets and core subsets were screened. Then, the relationship between the expression level of the core genes and the prognosis of gastric cancer patients was analyzed using the Gene Expression Profiling Interactive Analysis (GEPIA) database. Results Using the GSE19826 and GSE54129 datasets, a total of 550 DEGs were identified, including 248 upregulated and 302 downregulated genes. GO and KEGG analyses showed that the upregulated DEGs were mainly enriched in the extracellular matrix (ECM) organization of the biological process (BP), the collagen-containing ECM of cellular component (CC), and the ECM structural constituent of molecular function (MF). DEGs were also enriched in human papillomavirus infections, the focal adhesion pathway, PI3K-Akt signaling pathway, and among others. The downregulated DEGs were mainly enriched in digestion, basal part of the cell, and aldo-keto reductase (NADP) activity. And the above pathways were enriched primarily in the metabolism of xenobiotics by cytochrome P450, drug metabolism-cytochrome P450, and retinol metabolism. Five core genes, including COL1A2, COL3A1, BGN, FN1, and VCAN, were significantly highly expressed in gastric cancer patients and were associated with poor prognosis. Conclusion This study identified new potential molecular targets closely related to gastric cancer occurrence and development via mining public data using bioinformatics analysis methods.
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Affiliation(s)
- Chuan Ding
- Department of Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221000, China
| | - Qiqi Zhang
- Department of Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221000, China
| | - Xinying Jiang
- Department of Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221000, China
| | - Diandian Wei
- Department of Laboratory, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221000, China
| | - Shu Xu
- Department of Oncology, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226000, China
| | - Qingdai Li
- Department of Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221000, China
| | - Meng Wu
- Department of Oncology, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226000, China
| | - Hongbin Wang
- Department of Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221000, China
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12
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Tracking the Molecular Scenarios for Tumorigenic Remodeling of Extracellular Matrix Based on Gene Expression Profiling in Equine Skin Neoplasia Models. Int J Mol Sci 2022; 23:ijms23126506. [PMID: 35742950 PMCID: PMC9223705 DOI: 10.3390/ijms23126506] [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: 05/24/2022] [Revised: 06/05/2022] [Accepted: 06/09/2022] [Indexed: 11/17/2022] Open
Abstract
An important component of tissues is the extracellular matrix (ECM), which not only forms a tissue scaffold, but also provides the environment for numerous biochemical reactions. Its composition is strictly regulated, and any irregularities can result in the development of many diseases, including cancer. Sarcoid is the most common skin cancer in equids. Its formation results from the presence of the genetic material of the bovine papillomavirus (BPV). In addition, it is assumed that sarcoid-dependent oncogenic transformation arises from a disturbed wound healing process, which may be due to the incorrect functioning of the ECM. Moreover, sarcoid is characterized by a failure to metastasize. Therefore, in this study we decided to investigate the differences in the expression profiles of genes related not only to ECM remodeling, but also to the cell adhesion pathway, in order to estimate the influence of disturbances within the ECM on the sarcoid formation process. Furthermore, we conducted comparative research not only between equine sarcoid tissue bioptates and healthy skin-derived explants, but also between dermal fibroblast cell lines transfected and non-transfected with a construct encoding the E4 protein of the BP virus, in order to determine its effect on ECM disorders. The obtained results strongly support the hypothesis that ECM-related genes are correlated with sarcoid formation. The deregulated expression of selected genes was shown in both equine sarcoid tissue bioptates and adult cutaneous fibroblast cell (ACFC) lines neoplastically transformed by nucleofection with gene constructs encoding BPV1-E1^E4 protein. The identified genes (CD99, ITGB1, JAM3 and CADM1) were up- or down-regulated, which pinpointed the phenotypic differences from the backgrounds noticed for adequate expression profiles in other cancerous or noncancerous tumors as reported in the available literature data. Unravelling the molecular pathways of ECM remodeling and cell adhesion in the in vivo and ex vivo models of epidermal/dermal sarcoid-related cancerogenesis might provide powerful tools for further investigations of genetic and epigenetic biomarkers for both silencing and re-initiating the processes of sarcoid-dependent neoplasia. Recognizing those biomarkers might insightfully explain the relatively high capacity of sarcoid-descended cancerous cell derivatives to epigenomically reprogram their nonmalignant neoplastic status in domestic horse cloned embryos produced by somatic cell nuclear transfer (SCNT).
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13
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Wang X, Tan M, Huang H, Zou Y, Wang M. Hsa_circ_0000285 contributes to gastric cancer progression by upregulating FN1 through the inhibition of miR-1278. J Clin Lab Anal 2022; 36:e24475. [PMID: 35535385 PMCID: PMC9169205 DOI: 10.1002/jcla.24475] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/23/2022] [Accepted: 04/25/2022] [Indexed: 12/16/2022] Open
Abstract
Background Gastric cancer (GC) is one of the most severe cancers worldwide, particularly in China. Circular RNA (circRNA) plays an essential role in GC. Hsa_circ_0000285 regulates the progression of several cancers. However, its role in GC has not been reported. This study elucidated the molecular mechanism and role of hsa_circ_0000285 in GC progression. Methods GC cells were transfected with silencers of hsa_circ_0000285 and fibronectin 1 (FN1), an inhibitor of miR‐1278, and their negative controls (NC). Mice were injected with short hairpin (sh) RNAs targeting hsa_circ_0000285 or NC. The expression levels of hsa_circ_0000285, miR‐1278, and FN1 were assessed using western blotting and reverse transcription quantitative real‐time polymerase chain reaction (qRT‐PCR). Several assays were used to evaluate cell proliferation, invasion, and apoptosis. Tumor burden was also analyzed. The interactions between miR‐1278, hsa_circ_0000285, and FN1 were ascertained using dual‐luciferase reporter assays. An RNA immunoprecipitation (RIP) assay was used to assess the enrichment of hsa_circ_0000285 and miR‐1278 in GC. Results Hsa_circ_0000285 was significantly overexpressed in the GC tissues. Silencing hsa_circ_0000285 inhibited cell proliferation and invasion, promoted apoptosis, and inhibited tumor development. Hsa_circ_0000285 sponged miR‐1278. Inhibition of miR‐1278 in vitro reversed the effects of hsa_circ_0000285 silencing on GC progression. MiR‐1278 targeted FN1, and silencing FN1 neutralized the effects of miR‐1278 inhibitors on GC progression. Conclusions The hsa_circ_0000285/miR‐1278/FN1 axis regulated GC progression. In addition, it may serve as a potential therapeutic biomarker for GC.
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Affiliation(s)
- Xue Wang
- Department of General Surgery, Chengdu Fifth People's Hospital, Chengdu, China
| | - Mao Tan
- Department of General Surgery, Chengdu Fifth People's Hospital, Chengdu, China
| | - He Huang
- Department of General Surgery, Chengdu Fifth People's Hospital, Chengdu, China
| | - Yanlei Zou
- Department of General Surgery, Chengdu Fifth People's Hospital, Chengdu, China
| | - Mengqiao Wang
- Department of General Surgery, Chengdu Fifth People's Hospital, Chengdu, China
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14
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Zhou WH, Du WD, Li YF, Al-Aroomi MA, Yan C, Wang Y, Zhang ZY, Liu FY, Sun CF. The Overexpression of Fibronectin 1 Promotes Cancer Progression and Associated with M2 Macrophages Polarization in Head and Neck Squamous Cell Carcinoma Patients. Int J Gen Med 2022; 15:5027-5042. [PMID: 35607361 PMCID: PMC9123938 DOI: 10.2147/ijgm.s364708] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/10/2022] [Indexed: 12/24/2022] Open
Abstract
Purpose This study aimed to investigate the biological roles of fibronectin 1 (FN1) in head and neck squamous cell carcinoma (HNSCC) and its effects on macrophage M2 polarization. Methods We analyzed FN1 expression pattern and examined its clinical relevance in HNSCC progression by bioinformatic analysis. Small interfering RNA (siRNA) was utilized to silence FN1 in HNSCC cells. Cell counting kit-8 (CCK-8) assay, colony formation assay, Transwell assay and wound healing assay were performed to reveal the effect of FN1 on malignant behaviors of HNSCC cells. Moreover, a co-culture model of macrophages and HNSCC cells was established to investigate whether FN1 induce macrophage M2 polarization. Finally, we used bioinformatic methods to explore the possible FN1-related pathways in HNSCC. Results FN1 is significantly overexpressed in HNSCC patients and has been obviously correlated with higher pathological stage and poor prognosis. Downregulation of FN1 suppressed the proliferation, migration and invasion of HNSCC cells, and inhibited macrophage M2 polarization in vitro. In addition, “PI3K-Akt” and “MAPK” signaling pathways may be involved in the malignant process of FN1 in HNSCC. Conclusion The overexpression of FN1 promotes HNSCC progression and induces macrophages M2 polarization. FN1 may serve as a promising prognostic biomarker and therapeutic target in HNSCC.
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Affiliation(s)
- Wan-Hang Zhou
- Department of Oral Maxillofacial-Head and Neck Surgery, School of Stomatology, China Medical University; Oral Diseases Laboratory of Liaoning, Shenyang, 110000, People’s Republic of China
| | - Wei-Dong Du
- Department of Oral Maxillofacial-Head and Neck Surgery, School of Stomatology, China Medical University; Oral Diseases Laboratory of Liaoning, Shenyang, 110000, People’s Republic of China
| | - Yan-Fei Li
- Department of Prosthodontics, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University; Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, 510055, People’s Republic of China
| | - Maged Ali Al-Aroomi
- Department of Oral Maxillofacial-Head and Neck Surgery, School of Stomatology, China Medical University; Oral Diseases Laboratory of Liaoning, Shenyang, 110000, People’s Republic of China
| | - Cong Yan
- Department of Oral Maxillofacial-Head and Neck Surgery, School of Stomatology, China Medical University; Oral Diseases Laboratory of Liaoning, Shenyang, 110000, People’s Republic of China
| | - Yao Wang
- Department of Oral Maxillofacial-Head and Neck Surgery, School of Stomatology, China Medical University; Oral Diseases Laboratory of Liaoning, Shenyang, 110000, People’s Republic of China
| | - Ze-Ying Zhang
- Department of Oral Maxillofacial-Head and Neck Surgery, School of Stomatology, China Medical University; Oral Diseases Laboratory of Liaoning, Shenyang, 110000, People’s Republic of China
| | - Fa-Yu Liu
- Department of Oral Maxillofacial-Head and Neck Surgery, School of Stomatology, China Medical University; Oral Diseases Laboratory of Liaoning, Shenyang, 110000, People’s Republic of China
- Correspondence: Fa-Yu Liu; Chang-Fu Sun, Department of Oral Maxillofacial-Head and Neck Surgery, School of Stomatology, China Medical University; Oral Diseases Laboratory of Liaoning, 117 Nanjing North Road, Heping District, Shenyang, Liaoning, 110000, People’s Republic of China, Tel +86 24 22894773, Fax +86 24 86602310, Email ;
| | - Chang-Fu Sun
- Department of Oral Maxillofacial-Head and Neck Surgery, School of Stomatology, China Medical University; Oral Diseases Laboratory of Liaoning, Shenyang, 110000, People’s Republic of China
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15
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Kosik K, Sowińska A, Seremak-Mrozikiewicz A, Abu-Amara JA, Al-Saad SR, Karbowski LM, Gryczka K, Kurzawińska G, Szymankiewicz-Bręborowicz M, Drews K, Szpecht D. Polymorphisms of fibronectin-1 (rs3796123; rs1968510; rs10202709; rs6725958; and rs35343655) are not associated with bronchopulmonary dysplasia in preterm infants. Mol Cell Biochem 2022; 477:1645-1652. [PMID: 35230604 DOI: 10.1007/s11010-022-04397-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 02/16/2022] [Indexed: 11/27/2022]
Abstract
Bronchopulmonary dysplasia (BPD) is a chronic lung disease that mainly affects premature newborns. Many different factors, increasingly genetic, are involved in the pathogenesis of BPD. The aim of the study is to investigate the possible influence of fibronectin SNP on the occurrence of BPD. The study included 108 infants born between 24 and 32 weeks of gestation. BPD was diagnosed based on the National Institutes of Health Consensus definition. The 5 FN1 gene polymorphisms assessed in the study were the following: rs3796123; rs1968510; rs10202709; rs6725958; and rs35343655. BPD developed in 30 (27.8%) out of the 108 preterm infants. Incidence of BPD was higher in infants with lower APGAR scores and low birthweight. Investigation did not confirm any significant prevalence for BPD development in any genotypes and alleles of FN1. Further studies should be performed to confirm the role of genetic factors in etiology and pathogenesis of BPD.
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Affiliation(s)
- Katarzyna Kosik
- Department of Neonatology, Poznan University of Medical Sciences, Poznan, Poland.
| | - Anna Sowińska
- Department of Computer Science and Statistics, Poznan University of Medical Sciences, Poznan, Poland
| | | | | | | | | | - Katarzyna Gryczka
- Department of Neonatology, Poznan University of Medical Sciences, Poznan, Poland
| | - Grażyna Kurzawińska
- Department of Perinatology and Women's Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Krzysztof Drews
- Department of Perinatology and Women's Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Dawid Szpecht
- Department of Neonatology, Poznan University of Medical Sciences, Poznan, Poland
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16
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Dietrichs D, Grimm D, Sahana J, Melnik D, Corydon TJ, Wehland M, Krüger M, Vermeesen R, Baselet B, Baatout S, Hybel TE, Kahlert S, Schulz H, Infanger M, Kopp S. Three-Dimensional Growth of Prostate Cancer Cells Exposed to Simulated Microgravity. Front Cell Dev Biol 2022; 10:841017. [PMID: 35252204 PMCID: PMC8893349 DOI: 10.3389/fcell.2022.841017] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 01/25/2022] [Indexed: 12/12/2022] Open
Abstract
Prostate cancer metastasis has an enormous impact on the mortality of cancer patients. Factors involved in cancer progression and metastasis are known to be key players in microgravity (µg)-driven three-dimensional (3D) cancer spheroid formation. We investigated PC-3 prostate cancer cells for 30 min, 2, 4 and 24 h on the random positioning machine (RPM), a device simulating µg on Earth. After a 24 h RPM-exposure, the cells could be divided into two groups: one grew as 3D multicellular spheroids (MCS), the other one as adherent monolayer (AD). No signs of apoptosis were visible. Among others, we focused on cytokines involved in the events of metastasis and MCS formation. After 24 h of exposure, in the MCS group we measured an increase in ACTB, MSN, COL1A1, LAMA3, FN1, TIMP1, FLT1, EGFR1, IL1A, IL6, CXCL8, and HIF1A mRNA expression, and in the AD group an elevation of LAMA3, COL1A1, FN1, MMP9, VEGFA, IL6, and CXCL8 mRNAs compared to samples subjected to 1 g conditions. Significant downregulations in AD cells were detected in the mRNA levels of TUBB, KRT8, IL1B, IL7, PIK3CB, AKT1 and MTOR after 24 h. The release of collagen-1α1 and fibronectin protein in the supernatant was decreased, whereas the secretion of IL-6 was elevated in 24 h RPM samples. The secretion of IL-1α, IL-1β, IL-7, IL-2, IL-8, IL-17, TNF-α, laminin, MMP-2, TIMP-1, osteopontin and EGF was not significantly altered after 24 h compared to 1 g conditions. The release of soluble factors was significantly reduced after 2 h (IL-1α, IL-2, IL-7, IL-8, IL-17, TNF-α, collagen-1α1, MMP-2, osteopontin) and elevated after 4 h (IL-1β, IL-2, IL-6, IL-7, IL-8, TNF-α, laminin) in RPM samples. Taken together, simulated µg induced 3D growth of PC-3 cancer cells combined with a differential expression of the cytokines IL-1α, IL-1β, IL-6 and IL-8, supporting their involvement in growth and progression of prostate cancer cells.
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Affiliation(s)
- Dorothea Dietrichs
- Department of Microgravity and Translational Regenerative Medicine, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Daniela Grimm
- Department of Microgravity and Translational Regenerative Medicine, Otto von Guericke University Magdeburg, Magdeburg, Germany
- Research Group “Magdeburger Arbeitsgemeinschaft für Forschung unter Raumfahrt- und Schwerelosigkeitsbedingungen” (MARS), Otto von Guericke University Magdeburg, Magdeburg, Germany
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- *Correspondence: Daniela Grimm,
| | | | - Daniela Melnik
- Department of Microgravity and Translational Regenerative Medicine, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Thomas J. Corydon
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Ophthalmology, Aarhus University Hospital, Aarhus, Denmark
| | - Markus Wehland
- Department of Microgravity and Translational Regenerative Medicine, Otto von Guericke University Magdeburg, Magdeburg, Germany
- Research Group “Magdeburger Arbeitsgemeinschaft für Forschung unter Raumfahrt- und Schwerelosigkeitsbedingungen” (MARS), Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Marcus Krüger
- Department of Microgravity and Translational Regenerative Medicine, Otto von Guericke University Magdeburg, Magdeburg, Germany
- Research Group “Magdeburger Arbeitsgemeinschaft für Forschung unter Raumfahrt- und Schwerelosigkeitsbedingungen” (MARS), Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Randy Vermeesen
- Radiobiology Unit, SCK CEN, Belgian Nuclear Research Centre, Mol, Belgium
| | - Bjorn Baselet
- Radiobiology Unit, SCK CEN, Belgian Nuclear Research Centre, Mol, Belgium
| | - Sarah Baatout
- Radiobiology Unit, SCK CEN, Belgian Nuclear Research Centre, Mol, Belgium
- Department of Molecular Biotechnology, Ghent University, Ghent, Belgium
| | | | - Stefan Kahlert
- Institute of Anatomy, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Herbert Schulz
- Department of Microgravity and Translational Regenerative Medicine, Otto von Guericke University Magdeburg, Magdeburg, Germany
- Research Group “Magdeburger Arbeitsgemeinschaft für Forschung unter Raumfahrt- und Schwerelosigkeitsbedingungen” (MARS), Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Manfred Infanger
- Department of Microgravity and Translational Regenerative Medicine, Otto von Guericke University Magdeburg, Magdeburg, Germany
- Research Group “Magdeburger Arbeitsgemeinschaft für Forschung unter Raumfahrt- und Schwerelosigkeitsbedingungen” (MARS), Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Sascha Kopp
- Department of Microgravity and Translational Regenerative Medicine, Otto von Guericke University Magdeburg, Magdeburg, Germany
- Research Group “Magdeburger Arbeitsgemeinschaft für Forschung unter Raumfahrt- und Schwerelosigkeitsbedingungen” (MARS), Otto von Guericke University Magdeburg, Magdeburg, Germany
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17
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Zhai J, Luo G. GATA6‑induced FN1 activation promotes the proliferation, invasion and migration of oral squamous cell carcinoma cells. Mol Med Rep 2022; 25:102. [PMID: 35088888 PMCID: PMC8822886 DOI: 10.3892/mmr.2022.12618] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/12/2021] [Indexed: 12/28/2022] Open
Abstract
GATA binding protein 6 (GATA6) is a transcription factor involved in cell fate decision making and tissue morphogenesis and serves a significant role in the progression of a number of types of cancer. The present study aimed to investigate the role and mechanisms underlying the effects of GATA6 in oral squamous cell carcinoma (OSCC). The expression levels of GATA6 were determined in a number of OSCC cell lines and the expression of GATA6 was knocked down to evaluate its role in the proliferation, invasion and migration of OSCC cells. Subsequently, the association between GATA6 and fibronectin 1 (FN1) was investigated using bioinformatics and further verified using dual‑luciferase reporter and chromosomal immunoprecipitation assays. Following the overexpression of FN1 in OSCC cells with GATA6 silencing, functional assays were performed to assess the mechanisms underlying GATA6 in OSCC progression. The results of the present study indicated that OSCC cells exhibited markedly upregulated expression levels of GATA6, while knockdown of GATA6 inhibited the proliferation, colony formation, invasion and migration of OSCC cells. In addition, GATA6 regulated FN1 expression levels by binding to the FN1 promoter. The suppressive effects of GATA6 knockdown on the proliferation, colony formation, invasion and migration of OSCC cells were abolished following FN1 overexpression. In conclusion, the findings of the present study demonstrated that GATA6 promoted the malignant development of OSCC cells by binding to the FN1 promotor. These results may contribute to further understanding the pathogenesis of OSCC and provide potential therapeutic targets for the clinical treatment of OSCC.
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Affiliation(s)
- Jianbo Zhai
- Welle Dental, Jingan, Shanghai 200040, P.R. China
| | - Gang Luo
- Welle Dental, Jingan, Shanghai 200040, P.R. China
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18
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Sun B, Hou L, Sun B, Han Y, Zou Y, Huang J, Zhang Y, Feng C, Dou X, Xu F. Use of Electrospun Phenylalanine/Poly-ε-Caprolactone Chiral Hybrid Scaffolds to Promote Endothelial Remodeling. Front Bioeng Biotechnol 2021; 9:773635. [PMID: 34900965 PMCID: PMC8656108 DOI: 10.3389/fbioe.2021.773635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/27/2021] [Indexed: 02/02/2023] Open
Abstract
The fabrication of tissue-engineered vascular grafts to replace damaged vessels is a promising therapy for cardiovascular diseases. Endothelial remodeling in the lumen of TEVGs is critical for successful revascularization. However, the construction of well-functioning TEVGs remains a fundamental challenge. Herein, chiral hybrid scaffolds were prepared by electrospinning using D/L-phenylalanine based gelators [D(L)PHEG] and poly-ε-caprolactone (PCL). The chirality of scaffolds significantly affected the endothelial remodeling progress of TEVGs. Compared with L-phenylalanine based gelators/poly-ε-caprolactone (L/PCL) and PCL, D-phenylalanine based gelators/poly-ε-caprolactone (D/PCL) scaffolds enhanced cell adhesion, and proliferation and upregulated the expression of fibronectin-1, and vinculin. These results suggests that chiral hybrid scaffolds can promote endothelial remodeling of TEVGs by upregulating adhesion-associated protein levels. This study offers an innovative strategy for endothelial remodeling of TEVGs by fabricating chiral hybrid scaffolds, and provides new insight for the treatment of cardiovascular diseases.
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Affiliation(s)
- Benlin Sun
- Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, China
| | - Lei Hou
- Department of Cardiology, Tongren Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Binbin Sun
- Department of Orthopaedic Surgery, Shanghai Key Laboratory of Orthopaedic Implants, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Clinical and Translational Research Center for 3D Printing Technology, Medical 3D Printing Innovation Research Center, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Han
- Department of Orthopaedic Surgery, Shanghai Key Laboratory of Orthopaedic Implants, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Clinical and Translational Research Center for 3D Printing Technology, Medical 3D Printing Innovation Research Center, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yunqing Zou
- State Key Lab of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Juexin Huang
- State Key Lab of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yanan Zhang
- Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, China
| | - Chuanliang Feng
- State Key Lab of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoqiu Dou
- State Key Lab of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Feng Xu
- Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, China.,Department of Subject Planning Shanghai, Ninth People's Hospital Shanghai, Jiao Tong University School of Medicine, Shanghai, China
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19
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Park Y, Jeong J, Seong S, Kim W. In Silico Evaluation of Natural Compounds for an Acidic Extracellular Environment in Human Breast Cancer. Cells 2021; 10:2673. [PMID: 34685653 PMCID: PMC8534855 DOI: 10.3390/cells10102673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/01/2021] [Accepted: 10/03/2021] [Indexed: 12/11/2022] Open
Abstract
The survival rates for breast cancer (BC) have improved in recent years, but resistance, metastasis, and recurrence still remain major therapeutic challenges for BC. The acidic tumor microenvironment (TME) has attracted attention because of its association with tumorigenesis, metastasis, drug resistance, and immune surveillance. In this study, we evaluated natural compounds from traditional herbal medicine used to treat cancer that selectively target genes regulated by extracellular acidosis. We integrated four transcriptomic data including BC prognostic data from The Cancer Genome Atlas database, gene expression profiles of MCF-7 cells treated with 102 natural compounds, patterns of gene profiles by acidic condition, and single-cell RNA-sequencing from BC patient samples. Bruceine D (BD) was predicted as having the highest therapeutic potential, having an information gain (IG) score of 0.24, to regulate reprogrammed genes driven by acidosis affecting the survival of BC patients. BD showed the highest IG on EMT (IG score: 0.11) and invasion (IG score: 0.1) compared to the other phenotypes with the CancerSEA database. BD also demonstrated therapeutic potential by interfering with the tumor cell-TME interactions by reducing the amyloid beta precursor protein and CD44 expression. Therefore, BD is a potential candidate to target the acidic TME induced metastatic process in BC.
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Affiliation(s)
- YoungJoon Park
- Cnh Center for Cancer Research, Cnh Corporation, Gangnam-gu, Seoul 06154, Korea;
| | - Jaekwang Jeong
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06519, USA;
| | - Shin Seong
- Soram Korean Medicine Hospital, Gangnam-gu, Seoul 06154, Korea;
| | - Wonnam Kim
- Cnh Center for Cancer Research, Cnh Corporation, Gangnam-gu, Seoul 06154, Korea;
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20
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Downregulation of fibronectin 1 attenuates ATRA-induced inhibition of cell migration and invasion in neuroblastoma cells. Mol Cell Biochem 2021; 476:3601-3612. [PMID: 34024029 DOI: 10.1007/s11010-021-04113-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/12/2021] [Indexed: 10/21/2022]
Abstract
Neuroblastoma (NB) is the most common malignant extra cranial solid tumors in children. It has been well established that retinoic acid (RA) inhibits proliferation of neuroblastoma (NB) by blocking cells at G1 phase of the cell cycle. Clinically, RA has been successfully used to treat NB patients. However, the precise mechanism underlying the potent action of RA-treated NB is not fully explored. In this work, we carried out a gene expression profiling by RNA sequencing on all-trans retinoic acid (ATRA)-treated NB cells. Cancer-related pathway enrichment and subsequent protein-protein interaction (PPI) network analysis identified fibronectin 1 (FN1) as one of the central molecules in the network, which was significantly upregulated during ATRA treatment. In addition, we found that although downregulation of FN1 had no significant effects on either cell proliferation or cell cycle distributions in the presence or absence of ATRA, it increased cell migration and invasion in NB cells and partially blocked ATRA-induced inhibition of cell migration and invasion in SY5Y NB cells. Consistent with this finding, FN1 expression levels in NB patients positively correlate with their overall survivals. Taken together, our data suggest that FN1 is a potential target for effective ATRA treatment on NB patients, likely by facilitating ATRA-induced inhibition of cell migration and invasion.
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21
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Kuijpers TJM, Kleinjans JCS, Jennen DGJ. From multi-omics integration towards novel genomic interaction networks to identify key cancer cell line characteristics. Sci Rep 2021; 11:10542. [PMID: 34006939 PMCID: PMC8131752 DOI: 10.1038/s41598-021-90047-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 04/26/2021] [Indexed: 11/09/2022] Open
Abstract
Cancer is a complex disease where cancer cells express epigenetic and transcriptomic mechanisms to promote tumor initiation, progression, and survival. To extract relevant features from the 2019 Cancer Cell Line Encyclopedia (CCLE), a multi-layer nonnegative matrix factorization approach is used. We used relevant feature genes and DNA promoter regions to construct genomic interaction network to study gene-gene and gene-DNA promoter methylation relationships. Here, we identified a set of gene transcripts and methylated DNA promoter regions for different clusters, including one homogeneous lymphoid neoplasms cluster. In this cluster, we found different methylated transcription factors that affect transcriptional activation of EGFR and downstream interactions. Furthermore, the hippo-signaling pathway might not function properly because of DNA hypermethylation and low gene expression of both LATS2 and YAP1. Finally, we could identify a potential dysregulation of the CD28-CD86-CTLA4 axis. Characterizing the interaction of the epigenome and the transcriptome is vital for our understanding of cancer cell line behavior, not only for deepening insights into cancer-related processes but also for future disease treatment and drug development. Here we have identified potential candidates that characterize cancer cell lines, which give insight into the development and progression of cancers.
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Affiliation(s)
- T J M Kuijpers
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, the Netherlands.
| | - J C S Kleinjans
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, the Netherlands
| | - D G J Jennen
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, the Netherlands
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22
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Mohanty V, Subbannayya Y, Patil S, Puttamallesh VN, Najar MA, Datta KK, Pinto SM, Begum S, Mohanty N, Routray S, Abdulla R, Ray JG, Sidransky D, Gowda H, Prasad TSK, Chatterjee A. Molecular alterations in oral cancer using high-throughput proteomic analysis of formalin-fixed paraffin-embedded tissue. J Cell Commun Signal 2021; 15:447-459. [PMID: 33683571 DOI: 10.1007/s12079-021-00609-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 02/01/2021] [Indexed: 01/04/2023] Open
Abstract
Loss of cell differentiation is a hallmark for the progression of oral squamous cell carcinoma (OSCC). Archival Formalin-Fixed Paraffin-Embedded (FFPE) tissues constitute a valuable resource for studying the differentiation of OSCC and can offer valuable insights into the process of tumor progression. In the current study, we performed LC-MS/MS-based quantitative proteomics of FFPE specimens from pathologically-confirmed well-differentiated, moderately-differentiated, and poorly-differentiated OSCC cases. The data were analyzed in four technical replicates, resulting in the identification of 2376 proteins. Of these, 141 and 109 were differentially expressed in moderately-differentiated and poorly differentiated OSCC cases, respectively, compared to well-differentiated OSCC. The data revealed significant metabolic reprogramming with respect to lipid metabolism and glycolysis with proteins belonging to both these processes downregulated in moderately-differentiated OSCC when compared to well-differentiated OSCC. Signaling pathway analysis indicated the alteration of extracellular matrix organization, muscle contraction, and glucose metabolism pathways across tumor grades. The extracellular matrix organization pathway was upregulated in moderately-differentiated OSCC and downregulated in poorly differentiated OSCC, compared to well-differentiated OSCC. PADI4, an epigenetic enzyme transcriptional regulator, and its transcriptional target HIST1H1B were both found to be upregulated in moderately differentiated and poorly differentiated OSCC, indicating epigenetic events underlying tumor differentiation. In conclusion, the findings support the advantage of using high-resolution mass spectrometry-based FFPE archival blocks for clinical and translational research. The candidate signaling pathways identified in the study could be used to develop potential therapeutic targets for OSCC.
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Affiliation(s)
- Varshasnata Mohanty
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, Karnataka, 575018, India
| | - Yashwanth Subbannayya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, Karnataka, 575018, India.,Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, N-7491, Trondheim, Norway
| | - Shankargouda Patil
- Division of Oral Pathology, College of Dentistry, Department of Maxillofacial Surgery and Diagnostic Sciences, Jazan University, Jazan, 45142, Saudi Arabia
| | - Vinuth N Puttamallesh
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, 560066, India
| | - Mohd Altaf Najar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, Karnataka, 575018, India
| | - Keshava K Datta
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, Karnataka, 575018, India
| | - Sneha M Pinto
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, Karnataka, 575018, India.,Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, N-7491, Trondheim, Norway
| | - Sameera Begum
- Department of Oral Pathology, Yenepoya Dental College, Yenepoya (Deemed To Be University), Mangalore, Karnataka, 575018, India
| | - Neeta Mohanty
- Department of Oral Pathology & Microbiology, Institute of Dental Sciences, Siksha'O'Anusandhan University, Bhubaneswar, Odisha, 751003, India
| | - Samapika Routray
- Department of Oral Pathology & Microbiology, Institute of Dental Sciences, Siksha'O'Anusandhan University, Bhubaneswar, Odisha, 751003, India.,Department of Dental Surgery, All India Institute of Medical Sciences, Bhubaneswar, Odisha, 751019, India
| | - Riaz Abdulla
- Department of Oral Pathology, Yenepoya Dental College, Yenepoya (Deemed To Be University), Mangalore, Karnataka, 575018, India
| | - Jay Gopal Ray
- Department of Oral Pathology, Dr. R. Ahmed Dental College & Hospital, Kolkata, West Bengal, 700 014, India.,Department of Pathology, Burdwan Dental College and Hospital, Burdwan, West Bengal, 713101, India
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, Johns Hopkins University, Baltimore, MD, 21231, USA
| | - Harsha Gowda
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, Karnataka, 575018, India.,Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, 560066, India.,Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, Karnataka, 575018, India.
| | - Aditi Chatterjee
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, Karnataka, 575018, India. .,Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, 560066, India. .,Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
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23
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Stromal Protein-Mediated Immune Regulation in Digestive Cancers. Cancers (Basel) 2021; 13:cancers13010146. [PMID: 33466303 PMCID: PMC7795083 DOI: 10.3390/cancers13010146] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/21/2020] [Accepted: 12/24/2020] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Solid cancers are surrounded by a network of non-cancerous cells comprising different cell types, including fibroblasts, and acellular protein structures. This entire network is called the tumor microenvironment (TME) and it provides a physical barrier to the tumor shielding it from infiltrating immune cells, such as lymphocytes, or therapeutic agents. In addition, the TME has been shown to dampen efficient immune responses of infiltrated immune cells, which are key in eliminating cancer cells from the organism. In this review, we will discuss how TME proteins in particular are involved in this dampening effect, known as immunosuppression. We will focus on three different types of digestive cancers: pancreatic cancer, colorectal cancer, and gastric cancer. Moreover, we will discuss current therapeutic approaches using TME proteins as targets to reverse their immunosuppressive effects. Abstract The stromal tumor microenvironment (TME) consists of immune cells, vascular and neural structures, cancer-associated fibroblasts (CAFs), as well as extracellular matrix (ECM), and favors immune escape mechanisms promoting the initiation and progression of digestive cancers. Numerous ECM proteins released by stromal and tumor cells are crucial in providing physical rigidity to the TME, though they are also key regulators of the immune response against cancer cells by interacting directly with immune cells or engaging with immune regulatory molecules. Here, we discuss current knowledge of stromal proteins in digestive cancers including pancreatic cancer, colorectal cancer, and gastric cancer, focusing on their functions in inhibiting tumor immunity and enabling drug resistance. Moreover, we will discuss the implication of stromal proteins as therapeutic targets to unleash efficient immunotherapy-based treatments.
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24
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Jang B, Kim A, Hwang J, Song HK, Kim Y, Oh ES. Emerging Role of Syndecans in Extracellular Matrix Remodeling in Cancer. J Histochem Cytochem 2020; 68:863-870. [PMID: 32623937 PMCID: PMC7711240 DOI: 10.1369/0022155420930112] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 05/06/2020] [Indexed: 12/20/2022] Open
Abstract
The extracellular matrix (ECM) offers a structural basis for regulating cell functions while also acting as a collection point for bioactive molecules and connective tissue cells. To perform pathological functions under a pathological condition, the involved cells need to regulate the ECM to support their altered functions. This is particularly common in the development of cancer. The ECM has been recognized as a key driver of cancer development and progression, and ECM remodeling occurs at all stages of cancer progression. Thus, cancer cells need to change the ECM to support relevant cell surface adhesion receptor-mediated cell functions. In this context, it is interesting to examine how cancer cells regulate ECM remodeling, which is critical to tumor malignancy and metastatic progression. Here, we review how the cell surface adhesion receptor, syndecan, regulates ECM remodeling as cancer progresses, and explore how this can help us better understand ECM remodeling under these pathological conditions.
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Affiliation(s)
- Bohee Jang
- Department of Life Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Ayoung Kim
- Department of Life Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Jisun Hwang
- Department of Life Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Hyun-Kuk Song
- Department of Life Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Yunjeon Kim
- Department of Life Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Eok-Soo Oh
- Department of Life Sciences, Ewha Womans University, Seoul, Republic of Korea
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25
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Chang HY, Lee CH, Li YS, Huang JT, Lan SH, Wang YF, Lai WW, Wang YC, Lin YJ, Liu HS, Cheng HC. MicroRNA-146a suppresses tumor malignancy via targeting vimentin in esophageal squamous cell carcinoma cells with lower fibronectin membrane assembly. J Biomed Sci 2020; 27:102. [PMID: 33248456 PMCID: PMC7697386 DOI: 10.1186/s12929-020-00693-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022] Open
Abstract
Background Esophageal squamous cell carcinoma (ESCC) is widely prevalent in Taiwan, and high metastatic spread of ESCC leads to poor survival rate. Fibronectin (FN) assembly on the cell membrane may induce ESCC mobility. MicroRNAs (MiRNAs) are abundant in and participate in tumorigenesis in many cancers. However, the role of MiRNA in FN assembly-related ESCC mobility remains unexplored. Methods We divided ESCC CE81T cells into high-FN assembly (CE81FN+) and low-FN assembly (CE81FN−) groups by flow cytometry. MiRNA microarray analysis identified miR-146a expression as the most down-regulated miRNA in comparison of CE81FN+ and CE81FN− cells. Results Cell proliferation and migration were decreased when CE81FN+ cells overexpressed transgenic miR-146a compared to the parental cells, indicating an inverse correlation between low miR-146a expression and high proliferation as well as motility of FN assembly ESCC cells. Furthermore, vimentin is the target gene of miR-146a involved in ESCC tumorigenesis. MiR-146a suppressed cell proliferation, migration and invasion of CE81FN+ cells through the inhibition of vimentin expression, as confirmed by real-time PCR, Western blotting and Transwell™ assay. Analysis of one hundred and thirty-six paired ESCC patient specimens revealed that low miR-146a and high vimentin levels were frequently detected in tumor, and that the former was associated with late tumor stages (III and IV). Notably, either low miR-146a expression or high vimentin level was significantly associated with poor overall survival rate among ESCC patients. Conclusions This is the first report to link FN assembly in the cell membrane with miR-146a, vimentin and ESCC tumorigenesis both in vitro and in ESCC patients.
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Affiliation(s)
- Hong-Yi Chang
- Department of Biotechnology and Food Technology, College of Engineering, Southern Taiwan University of Science and Technology, Tainan, Taiwan
| | - Chi-Hua Lee
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yi-Syuan Li
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Jing-Tong Huang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Sheng-Hui Lan
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Yi-Fang Wang
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wu-Wei Lai
- Division of Thoracic Surgery, Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yi-Ching Wang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yan-Ju Lin
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan
| | - Hsiao-Sheng Liu
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan. .,Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan. .,M. Sc. Program in Tropical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan. .,Center for Cancer Research, Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
| | - Hung-Chi Cheng
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan. .,Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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26
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Ha NT, Lee CH. Roles of Farnesyl-Diphosphate Farnesyltransferase 1 in Tumour and Tumour Microenvironments. Cells 2020; 9:cells9112352. [PMID: 33113804 PMCID: PMC7693003 DOI: 10.3390/cells9112352] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/23/2020] [Accepted: 10/24/2020] [Indexed: 12/14/2022] Open
Abstract
Farnesyl-diphosphate farnesyltransferase 1 (FDFT1, squalene synthase), a membrane-associated enzyme, synthesizes squalene via condensation of two molecules of farnesyl pyrophosphate. Accumulating evidence has noted that FDFT1 plays a critical role in cancer, particularly in metabolic reprogramming, cell proliferation, and invasion. Based on these advances in our knowledge, FDFT1 could be a potential target for cancer treatment. This review focuses on the contribution of FDFT1 to the hallmarks of cancer, and further, we discuss the applicability of FDFT1 as a cancer prognostic marker and target for anticancer therapy.
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27
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Yang B, Zhang M, Luo T. Identification of Potential Core Genes Associated With the Progression of Stomach Adenocarcinoma Using Bioinformatic Analysis. Front Genet 2020; 11:517362. [PMID: 33193601 PMCID: PMC7642829 DOI: 10.3389/fgene.2020.517362] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 09/28/2020] [Indexed: 12/24/2022] Open
Abstract
Purpose Stomach adenocarcinoma (STAD) is one of the most frequently diagnosed cancer in the world with both high mortality and high metastatic capacity. Therefore, the present study aimed to investigate novel therapeutic targets and prognostic biomarkers that can be used for STAD treatment. Materials and Methods We acquired four original gene chip profiles, namely GSE13911, GSE19826, GSE54129, and GSE65801 from the Gene Expression Omnibus (GEO). The datasets included a total of 114 STAD tissues and 110 adjacent normal tissues. The GEO2R online tool and Venn diagram software were used to discriminate differentially expressed genes (DEGs). Gene ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG) enriched pathways were also performed for annotation and visualization with DEGs. The STRING online database was used to identify the functional interactions of DEGs. Subsequently, we selected the most significant DEGs to construct the protein-protein interaction (PPI) network and to reveal the core genes involved. Finally, the Kaplan-Meier Plotter online database and Gene Expression Profiling Interactive Analysis (GEPIA) were used to analyze the prognostic information of the core DEGs. Results A total of 114 DEGs (35 upregulated and 79 downregulated) were identified, which were abnormally expressed in the GEO datasets. GO analysis demonstrated that the majority of the upregulated DEGs were significantly enriched in collagen trimer, cell adhesion, and identical protein binding. The downregulated DEGs were involved in extracellular space, digestion, and inward rectifier potassium channel activity. Signaling pathway analysis indicated that upregulated DEGs were mainly enriched in receptor interaction, whereas downregulated DEGs were involved in gastric acid secretion. A total of 80 DEGs were screened into the PPI network complex, and one of the most important modules with a high degree was detected. Furthermore, 10 core genes were identified, namely COL1A1, COL1A2, FN1, COL5A2, BGN, COL6A3, COL12A1, THBS2, CDH11, and SERPINH1. Finally, the results of the prognostic information further demonstrated that all 10 core genes exhibited significantly higher expression in STAD tissues compared with that noted in normal tissues. Conclusion The multiple molecular mechanisms of these novel core genes in STAD are worthy of further investigation and may reveal novel therapeutic targets and biomarkers for STAD treatment.
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Affiliation(s)
- Biao Yang
- Department of General Surgery, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Meijing Zhang
- Department of Oncology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Tianhang Luo
- Department of General Surgery, Changhai Hospital, Second Military Medical University, Shanghai, China
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28
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Integrated Analysis Identifies an Immune-Based Prognostic Signature for the Mesenchymal Identity in Gastric Cancer. BIOMED RESEARCH INTERNATIONAL 2020; 2020:9780981. [PMID: 32352015 PMCID: PMC7171688 DOI: 10.1155/2020/9780981] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 03/16/2020] [Indexed: 12/14/2022]
Abstract
Background Gastric cancer (GC) has been divided into four molecular subtypes, of which the mesenchymal subtype has the poorest survival. Our goal is to develop a prognostic signature by integrating the immune system and molecular modalities involved in the mesenchymal subtype. Methods The gene expression profiles collected from 6 public datasets were applied to this study, including 1,221 samples totally. Network analysis was applied to integrate the mesenchymal modalities and immune signature to establish an immune-based prognostic signature for GC (IPSGC). Results We identified six immune genes as key factors of the mesenchymal subtype and established the IPSGC. The IPSGC can significantly divide patients into high- and low-risk groups in terms of overall survival (OS) and relapse-free survival (RFS) in discovery (OS: P < 0.001) and 5 independent validation sets (OS range: P = 0.05 to P < 0.001; RFS range: P = 0.03 to P < 0.001). Further, in multivariate analysis, the IPSGC remained an independent predictor of prognosis and performed better efficiency compared to clinical characteristics. Moreover, macrophage M2 was significantly enriched in the high-risk group, while plasma cells were enriched in the low-risk group. Conclusions We propose an immune-based signature identified by network analysis, which is a promising prognostic biomarker and help for the selection of GC patients who might benefit from more rigorous therapies. Further prospective studies are warranted to test and validate its efficiency for clinical application.
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29
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Loss of 5'-Methylthioadenosine Phosphorylase (MTAP) is Frequent in High-Grade Gliomas; Nevertheless, it is Not Associated with Higher Tumor Aggressiveness. Cells 2020; 9:cells9020492. [PMID: 32093414 PMCID: PMC7072758 DOI: 10.3390/cells9020492] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/04/2020] [Accepted: 02/10/2020] [Indexed: 12/12/2022] Open
Abstract
The 5’-methylthioadenosine phosphorylase (MTAP) gene is located in the chromosomal region 9p21. MTAP deletion is a frequent event in a wide variety of human cancers; however, its biological role in tumorigenesis remains unclear. The purpose of this study was to characterize the MTAP expression profile in a series of gliomas and to associate it with patients’ clinicopathological features. Moreover, we sought to evaluate, through glioma gene-edited cell lines, the biological impact of MTAP in gliomas. MTAP expression was evaluated in 507 glioma patients by immunohistochemistry (IHC), and the expression levels were associated with patients’ clinicopathological features. Furthermore, an in silico study was undertaken using genomic databases totalizing 350 samples. In glioma cell lines, MTAP was edited, and following MTAP overexpression and knockout (KO), a transcriptome analysis was performed by NanoString Pan-Cancer Pathways panel. Moreover, MTAP’s role in glioma cell proliferation, migration, and invasion was evaluated. Homozygous deletion of 9p21 locus was associated with a reduction of MTAP mRNA expression in the TCGA (The Cancer Genome Atlas) - glioblastoma dataset (p < 0.01). In addition, the loss of MTAP expression was markedly high in high-grade gliomas (46.6% of cases) determined by IHC and Western blotting (40% of evaluated cell lines). Reduced MTAP expression was associated with a better prognostic in the adult glioblastoma dataset (p < 0.001). Nine genes associated with five pathways were differentially expressed in MTAP-knockout (KO) cells, with six upregulated and three downregulated in MTAP. Analysis of cell proliferation, migration, and invasion did not show any significant differences between MTAP gene-edited and control cells. Our results integrating data from patients as well as in silico and in vitro models provide evidence towards the lack of strong biological importance of MTAP in gliomas. Despite the frequent loss of MTAP, it seems not to have a clinical impact in survival and does not act as a canonic tumor suppressor gene in gliomas.
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