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Verma VM, Puri S, Puri V. Bioinformatics-driven identification of prognostic biomarkers in kidney renal clear cell carcinoma. FRONTIERS IN NEPHROLOGY 2024; 4:1349859. [PMID: 38638111 PMCID: PMC11024385 DOI: 10.3389/fneph.2024.1349859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/06/2024] [Indexed: 04/20/2024]
Abstract
Renal cell carcinoma (RCC), particularly the clear cell subtype (ccRCC), poses a significant global health concern due to its increasing prevalence and resistance to conventional therapies. Early detection of ccRCC remains challenging, resulting in poor patient survival rates. In this study, we employed a bioinformatic approach to identify potential prognostic biomarkers for kidney renal clear cell carcinoma (KIRC). By analyzing RNA sequencing data from the TCGA-KIRC project, differentially expressed genes (DEGs) associated with ccRCC were identified. Pathway analysis utilizing the Qiagen Ingenuity Pathway Analysis (IPA) tool elucidated key pathways and genes involved in ccRCC dysregulation. Prognostic value assessment was conducted through survival analysis, including Cox univariate proportional hazards (PH) modeling and Kaplan-Meier plotting. This analysis unveiled several promising biomarkers, such as MMP9, PIK3R6, IFNG, and PGF, exhibiting significant associations with overall survival and relapse-free survival in ccRCC patients. Cox multivariate PH analysis, considering gene expression and age at diagnosis, further confirmed the prognostic potential of MMP9, IFNG, and PGF genes. These findings enhance our understanding of ccRCC and provide valuable insights into potential prognostic biomarkers that can aid healthcare professionals in risk stratification and treatment decision-making. The study also establishes a foundation for future research, validation, and clinical translation of the identified prognostic biomarkers, paving the way for personalized approaches in the management of KIRC.
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Affiliation(s)
| | - Sanjeev Puri
- Biotechnology University Institute of Engineering and Technology (UIET), Panjab University, Chandigarh, India
| | - Veena Puri
- Centre for Systems Biology and Bioinformatics, Panjab University, Chandigarh, India
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Deng Z, Ji Y, Han B, Tan Z, Ren Y, Gao J, Chen N, Ma C, Zhang Y, Yao Y, Lu H, Huang H, Xu M, Chen L, Zheng L, Gu J, Xiong D, Zhao J, Gu J, Chen Z, Wang K. Early detection of hepatocellular carcinoma via no end-repair enzymatic methylation sequencing of cell-free DNA and pre-trained neural network. Genome Med 2023; 15:93. [PMID: 37936230 PMCID: PMC10631027 DOI: 10.1186/s13073-023-01238-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 09/26/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND Early detection of hepatocellular carcinoma (HCC) is important in order to improve patient prognosis and survival rate. Methylation sequencing combined with neural networks to identify cell-free DNA (cfDNA) carrying aberrant methylation offers an appealing and non-invasive approach for HCC detection. However, some limitations exist in traditional methylation detection technologies and models, which may impede their performance in the read-level detection of HCC. METHODS We developed a low DNA damage and high-fidelity methylation detection method called No End-repair Enzymatic Methyl-seq (NEEM-seq). We further developed a read-level neural detection model called DeepTrace that can better identify HCC-derived sequencing reads through a pre-trained and fine-tuned neural network. After pre-training on 11 million reads from NEEM-seq, DeepTrace was fine-tuned using 1.2 million HCC-derived reads from tumor tissue DNA after noise reduction, and 2.7 million non-tumor reads from non-tumor cfDNA. We validated the model using data from 130 individuals with cfDNA whole-genome NEEM-seq at around 1.6X depth. RESULTS NEEM-seq overcomes the drawbacks of traditional enzymatic methylation sequencing methods by avoiding the introduction of unmethylation errors in cfDNA. DeepTrace outperformed other models in identifying HCC-derived reads and detecting HCC individuals. Based on the whole-genome NEEM-seq data of cfDNA, our model showed high accuracy of 96.2%, sensitivity of 93.6%, and specificity of 98.5% in the validation cohort consisting of 62 HCC patients, 48 liver disease patients, and 20 healthy individuals. In the early stage of HCC (BCLC 0/A and TNM I), the sensitivity of DeepTrace was 89.6 and 89.5% respectively, outperforming Alpha Fetoprotein (AFP) which showed much lower sensitivity in both BCLC 0/A (50.5%) and TNM I (44.7%). CONCLUSIONS By combining high-fidelity methylation data from NEEM-seq with the DeepTrace model, our method has great potential for HCC early detection with high sensitivity and specificity, making it potentially suitable for clinical applications. DeepTrace: https://github.com/Bamrock/DeepTrace.
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Affiliation(s)
- Zhenzhong Deng
- Department of Oncology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yongkun Ji
- BamRock Research Department, Suzhou BamRock Biotechnology Ltd., Suzhou, Jiangsu Province, China
| | - Bing Han
- Division of Hepatobiliary and Transplantation Surgery, Department of General Surgery, Nanjing Drum Tower Hospital, the Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
- Department of Transplantation, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhongming Tan
- Hepatobiliary Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Yuqi Ren
- College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Jinghan Gao
- Department of Software Engineering, Tsinghua University, Beijing, China
| | - Nan Chen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Cong Ma
- Suzhou Known Biotechnology Ltd, Suzhou, Jiangsu Province, China
| | - Yichi Zhang
- Department of Transplantation, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yunhai Yao
- Infectious Disease Department, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Hong Lu
- Infectious Disease Department, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Heqing Huang
- Infectious Disease Department, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Midie Xu
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lei Chen
- Department of Pathology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Leizhen Zheng
- Department of Oncology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianchun Gu
- Department of Oncology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Deyi Xiong
- College of Intelligence and Computing, Tianjin University, Tianjin, China.
| | - Jianxin Zhao
- Department of Interventional Medicine, the affiliated hospital of infectious diseases of Soochow University, Suzhou, 215131, Jiangsu Province, China.
| | - Jinyang Gu
- Department of Transplantation, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Liver Transplantation Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China.
| | - Zutao Chen
- Infectious Disease Department, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China.
- Suzhou Key Laboratory of Pathogen Bioscience and Anti-Infective Medicine, Suzhou, Jiangsu Province, China.
| | - Ke Wang
- Hepatobiliary Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China.
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Ephraim R, Fraser S, Devereaux J, Stavely R, Feehan J, Eri R, Nurgali K, Apostolopoulos V. Differential Gene Expression of Checkpoint Markers and Cancer Markers in Mouse Models of Spontaneous Chronic Colitis. Cancers (Basel) 2023; 15:4793. [PMID: 37835487 PMCID: PMC10571700 DOI: 10.3390/cancers15194793] [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: 09/04/2023] [Revised: 09/17/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
The presence of checkpoint markers in cancer cells aids in immune escape. The identification of checkpoint markers and early cancer markers is of utmost importance to gain clarity regarding the relationship between colitis and progressive inflammation leading to cancer. Herein, the gene expression levels of checkpoint makers, cancer-related pathways, and cancer genes in colon tissues of mouse models of chronic colitis (Winnie and Winnie-Prolapse mice) using next-generation sequencing are determined. Winnie mice are a result of a Muc2 missense mutation. The identification of such genes and their subsequent expression and role at the protein level would enable novel markers for the early diagnosis of cancer in IBD patients. The differentially expressed genes in the colonic transcriptome were analysed based on the Kyoto Encyclopedia of Genes and Genomes pathway. The expression of several oncogenes is associated with the severity of IBD, with Winnie-Prolapse mice expressing a large number of key genes associated with development of cancer. This research presents a number of new targets to evaluate for the development of biomarkers and therapeutics.
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Affiliation(s)
- Ramya Ephraim
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (R.E.); (S.F.); (J.D.); (J.F.); (K.N.)
| | - Sarah Fraser
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (R.E.); (S.F.); (J.D.); (J.F.); (K.N.)
| | - Jeannie Devereaux
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (R.E.); (S.F.); (J.D.); (J.F.); (K.N.)
| | - Rhian Stavely
- Pediatric Surgery Research Laboratories, Department of Pediatric Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA;
| | - Jack Feehan
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (R.E.); (S.F.); (J.D.); (J.F.); (K.N.)
- Immunology Program, Australian Institute of Musculoskeletal Science (AIMSS), Melbourne, VIC 3021, Australia
| | - Rajaraman Eri
- STEM/School of Science, RMIT University, Melbourne, VIC 3001, Australia;
| | - Kulmira Nurgali
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (R.E.); (S.F.); (J.D.); (J.F.); (K.N.)
- Department of Medicine Western Health, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia
- Regenerative Medicine and Stem Cells Program, Australian Institute of Musculoskeletal Science (AIMSS), Melbourne, VIC 3021, Australia
| | - Vasso Apostolopoulos
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (R.E.); (S.F.); (J.D.); (J.F.); (K.N.)
- Immunology Program, Australian Institute of Musculoskeletal Science (AIMSS), Melbourne, VIC 3021, Australia
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Allione A, Viberti C, Cotellessa I, Catalano C, Casalone E, Cugliari G, Russo A, Guarrera S, Mirabelli D, Sacerdote C, Gentile M, Eichelmann F, Schulze MB, Harlid S, Eriksen AK, Tjønneland A, Andersson M, Dollé MET, Van Puyvelde H, Weiderpass E, Rodriguez-Barranco M, Agudo A, Heath AK, Chirlaque MD, Truong T, Dragic D, Severi G, Sieri S, Sandanger TM, Ardanaz E, Vineis P, Matullo G. Blood cell DNA methylation biomarkers in preclinical malignant pleural mesothelioma: The EPIC prospective cohort. Int J Cancer 2023; 152:725-737. [PMID: 36305648 DOI: 10.1002/ijc.34339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 02/01/2023]
Abstract
Malignant pleural mesothelioma (MPM) is a rare and aggressive cancer mainly caused by asbestos exposure. Specific and sensitive noninvasive biomarkers may facilitate and enhance screening programs for the early detection of cancer. We investigated DNA methylation (DNAm) profiles in MPM prediagnostic blood samples in a case-control study nested in the European Prospective Investigation into Cancer and nutrition (EPIC) cohort, aiming to characterise DNAm biomarkers associated with MPM. From the EPIC cohort, we included samples from 135 participants who developed MPM during 20 years of follow-up and from 135 matched, cancer-free, controls. For the discovery phase we selected EPIC participants who developed MPM within 5 years from enrolment (n = 36) with matched controls. We identified nine differentially methylated CpGs, selected by 10-fold cross-validation and correlation analyses: cg25755428 (MRI1), cg20389709 (KLF11), cg23870316, cg13862711 (LHX6), cg06417478 (HOOK2), cg00667948, cg01879420 (AMD1), cg25317025 (RPL17) and cg06205333 (RAP1A). Receiver operating characteristic (ROC) analysis showed that the model including baseline characteristics (age, sex and PC1wbc) along with the nine MPM-related CpGs has a better predictive value for MPM occurrence than the baseline model alone, maintaining some performance also at more than 5 years before diagnosis (area under the curve [AUC] < 5 years = 0.89; AUC 5-10 years = 0.80; AUC >10 years = 0.75; baseline AUC range = 0.63-0.67). DNAm changes as noninvasive biomarkers in prediagnostic blood samples of MPM cases were investigated for the first time. Their application can improve the identification of asbestos-exposed individuals at higher MPM risk to possibly adopt more intensive monitoring for early disease identification.
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Affiliation(s)
| | - Clara Viberti
- Department of Medical Sciences, University of Turin, Turin, Italy
| | | | - Chiara Catalano
- Department of Medical Sciences, University of Turin, Turin, Italy
| | | | | | - Alessia Russo
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Simonetta Guarrera
- IIGM-Italian Institute for Genomic Medicine, c/o IRCCS, Turin, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Dario Mirabelli
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
- Interdepartmental Center for Studies on Asbestos and Other Toxic Particulates "G. Scansetti", University of Turin, Turin, Italy
| | - Carlotta Sacerdote
- Unit of Cancer Epidemiology, Città Della Salute e Della Scienza University-Hospital and Center for Cancer Prevention (CPO), Turin, Italy
| | | | - Fabian Eichelmann
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Matthias B Schulze
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
- University of Potsdam, Institute of Nutritional Science, Nuthetal, Germany
| | - Sophia Harlid
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
| | - Anne Kirstine Eriksen
- Danish Cancer Society Research Center, Diet, Genes and Environment, Copenhagen, Denmark
| | - Anne Tjønneland
- Danish Cancer Society Research Center, Diet, Genes and Environment, Copenhagen, Denmark
- Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Martin Andersson
- Department of Public Health and Clinical Medicine, Sustainable Health, Umeå University, Umeå, Sweden
| | - Martijn E T Dollé
- Centre for Health Protection National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Heleen Van Puyvelde
- International Agency for Research on Cancer, World Health Organisation, Lyon, France
| | - Elisabete Weiderpass
- International Agency for Research on Cancer, World Health Organisation, Lyon, France
| | - Miguel Rodriguez-Barranco
- Escuela Andaluza de Salud Pública (EASP), Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Antonio Agudo
- Unit of Nutrition and Cancer, Catalan Institute of Oncology-ICO, L'Hospitalet de Llobregat, Barcelona, Spain
- Nutrition and Cancer Group, Epidemiology, Public Health, Cancer Prevention and Palliative Care Program, Bellvitge Biomedical Research Institute-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Alicia K Heath
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - María-Dolores Chirlaque
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Department of Epidemiology, Regional Health Council, IMIB-Arrixaca, Murcia University, Murcia, Spain
| | - Thérèse Truong
- Université Paris-Saclay, UVSQ, Inserm, CESP U1018, "Exposome, Heredity, Cancer and Health" Team, Paris, France
| | - Dzevka Dragic
- Université Paris-Saclay, UVSQ, Inserm, CESP U1018, "Exposome, Heredity, Cancer and Health" Team, Paris, France
- Centre de Recherche sur le Cancer de l'Université Laval, Département de Médecine Sociale et Préventive, Faculté de Médecine, Québec, Canada
- Axe Oncologie, Centre de Recherche du CHU de Québec-Université Laval, Québec, Canada
| | - Gianluca Severi
- Université Paris-Saclay, UVSQ, Inserm, CESP U1018, "Exposome, Heredity, Cancer and Health" Team, Paris, France
- Department of Statistics, Computer Science and Applications "G. Parenti" (DISIA), University of Florence, Florence, Italy
| | - Sabina Sieri
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano Via Venezian, Milan, Italy
| | - Torkjel M Sandanger
- Department of Community Medicine, UiT The Arctic University of Norway, Tromsø, Norway
| | - Eva Ardanaz
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Navarra Public Health Institute, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Paolo Vineis
- MRC Centre for Environment and Health, Imperial College London, London, UK
| | - Giuseppe Matullo
- Department of Medical Sciences, University of Turin, Turin, Italy
- Interdepartmental Center for Studies on Asbestos and Other Toxic Particulates "G. Scansetti", University of Turin, Turin, Italy
- Medical Genetics Unit, AOU Città della Salute e Della Scienza, Turin, Italy
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Xie Q, Zhang P, Wang Y, Mei W, Zeng C. Overcoming resistance to immune checkpoint inhibitors in hepatocellular carcinoma: Challenges and opportunities. Front Oncol 2022; 12:958720. [PMID: 36119533 PMCID: PMC9478417 DOI: 10.3389/fonc.2022.958720] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 08/15/2022] [Indexed: 11/23/2022] Open
Abstract
Hepatocellular carcinoma is one of the leading causes of cancer mortality globally, and its incidence is increasing. Immune checkpoint therapy has revolutionized the treatment of hepatocellular carcinoma over the past few years. However, only a limited proportion of patients with hepatocellular carcinoma respond to immunotherapy. Despite the significant breakthroughs, the molecular mechanisms that drive immune responses and evasion are largely unresolved. Predicting tumor response and resistance to immune checkpoint inhibitors is a significant challenge. In this review, we focus on the current research progress of immune checkpoint inhibitors in hepatocellular carcinoma. Importantly, this review highlights the underlying mechanisms of resistance to immune checkpoint inhibitors and summarizes potential strategies to overcome the resistance to immune checkpoint inhibitors in hepatocellular carcinoma.
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Affiliation(s)
- Qingqing Xie
- Department of Medical Laboratory, Shenzhen Longhua District Central Hospital, Guangdong Medical University, Shenzhen, China
| | - Pengfei Zhang
- Department of Medical Laboratory, Shenzhen Longhua District Central Hospital, Guangdong Medical University, Shenzhen, China
| | - Yuanyuan Wang
- Xianning Medical College, Hubei University of Science and Technology, Xianning, China
| | - Wuxuan Mei
- Xianning Medical College, Hubei University of Science and Technology, Xianning, China
| | - Changchun Zeng
- Department of Medical Laboratory, Shenzhen Longhua District Central Hospital, Guangdong Medical University, Shenzhen, China
- *Correspondence: Changchun Zeng,
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Khan SA, Lee TKW. Investigations of nitazoxanide molecular targets and pathways for the treatment of hepatocellular carcinoma using network pharmacology and molecular docking. Front Pharmacol 2022; 13:968148. [PMID: 35959427 PMCID: PMC9358010 DOI: 10.3389/fphar.2022.968148] [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: 06/16/2022] [Accepted: 07/06/2022] [Indexed: 11/13/2022] Open
Abstract
Nitazoxanide has been investigated for colorectal cancer and breast cancer. However, its molecular targets and pathways have not yet been explored for hepatocellular carcinoma (HCC) treatment. Utilizing a network pharmacology approach, nitazoxanide’s potential targets and molecular pathways for HCC treatment were investigated. HCC targets were extracted from the GeneCards database. Potential targets of nitazoxanide were predicted using Swiss Target Prediction and Super Pred. Intersecting targets were analyzed with VENNY online tool. Using Cytoscape, a protein-protein interaction (PPI), cluster, and core targets-pathways networks were constructed. Using the Database for Annotation, Visualization and Integrated Discovery (DAVID), gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted. The nitazoxanide was molecularly docked with anti-HCC core targets by employing Auto Dock Vina. A total of 168 potential targets of nitazoxanide, 13,415 HCC-related targets, and 153 intersecting targets were identified. The top eight anti-HCC core targets were identified: SRC, EGFR, CASP3, MMP9, mTOR, HIF1A, ERBB2, and PPARG. GO enrichment analysis showed that nitazoxanide might have anti-HCC effects by affecting gene targets involved in multiple biological processes (BP) (protein phosphorylation, transmembrane receptor protein tyrosine kinase (RTKs) signaling pathway, positive regulation of MAP kinase activity, etc.). KEGG pathways and core targets-pathways network analysis indicated that pathways in cancer and proteoglycans in cancer are two key pathways that significantly contribute to the anti-HCC effects of nitazoxanide. Results of molecular docking demonstrated the potential for active interaction between the top eight anti-HCC core targets and nitazoxanide. Our research offers a theoretical basis for the notion that nitazoxanide may have distinct therapeutic effects in HCC, and the identified pharmacological targets and pathways might function as biomarkers for HCC therapy.
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Affiliation(s)
- Shakeel Ahmad Khan
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
- *Correspondence: Shakeel Ahmad Khan, ; Terence Kin Wah Lee,
| | - Terence Kin Wah Lee
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
- State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
- *Correspondence: Shakeel Ahmad Khan, ; Terence Kin Wah Lee,
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Wang X, Tang W, Lu Y, You J, Han Y, Zheng Y. Prognostic Significance of Alternative Splicing Genes in Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma. Int J Gen Med 2021; 14:7933-7949. [PMID: 34785939 PMCID: PMC8590485 DOI: 10.2147/ijgm.s335475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/20/2021] [Indexed: 01/16/2023] Open
Abstract
Background Alternative splicing (AS) acts on many tumors and its relationship with cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) needs to be researched. Methods RNA sequencing data and clinical information of CESC cohorts were obtained from the Cancer Genome Atlas (TCGA) and SpliceSeq was used to analyze the splicing profile of mRNA in CESC. UpSetR displayed the intersections among AS events and univariate analysis chose survival-associated AS and splicing factor (SF) genes. Functional analysis was operated on Enrichr, STRING database and MCODE analysis were used to evaluate protein-protein interaction (PPI) information. LASSO and multivariate analysis constructed prognostic model and risk analysis of tumor infiltrating immune cells was also conducted. Results A total of 402 AS-generated genes were found to be associated with CESC prognosis. Functional analysis showed that Golgi to lysosome transport was enriched. PPI network suggested that UBA52 was most functional. Dendritic cells activated, dendritic cells resting, macrophages M0, mast cells resting, T cells CD4 memory activated and T cells CD8 were most correlative with the risk score. Conclusion SFs and AS events can directly or indirectly affect the prognosis of CESC patients and this study identified SNRPA and CELF2 as two CESC-engaged SFs.
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Affiliation(s)
- Xiaoyu Wang
- Department of Obstetrics and Gynecology, Nantong First People's Hospital, Nantong, Jiangsu, 226001, People's Republic of China
| | - Weichun Tang
- Department of Obstetrics and Gynecology, Nantong First People's Hospital, Nantong, Jiangsu, 226001, People's Republic of China
| | - Yilin Lu
- Department of Obstetrics and Gynecology, Nantong First People's Hospital, Nantong, Jiangsu, 226001, People's Republic of China
| | - Jun You
- Department of Obstetrics and Gynecology, Nantong First People's Hospital, Nantong, Jiangsu, 226001, People's Republic of China
| | - Yun Han
- Department of Obstetrics and Gynecology, Nantong First People's Hospital, Nantong, Jiangsu, 226001, People's Republic of China
| | - Yanli Zheng
- Department of Obstetrics and Gynecology, Nantong First People's Hospital, Nantong, Jiangsu, 226001, People's Republic of China
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