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Silva MP, Ferreira LT, Brás NF, Torres L, Brandão A, Pinheiro M, Cardoso M, Resende A, Vieira J, Palmeira C, Martins G, Silva M, Pinto C, Peixoto A, Silva J, Henrique R, Maia S, Maiato H, Teixeira MR, Paulo P. BUB1B monoallelic germline variants contribute to prostate cancer predisposition by triggering chromosomal instability. J Biomed Sci 2024; 31:74. [PMID: 39014450 PMCID: PMC11251299 DOI: 10.1186/s12929-024-01056-z] [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: 08/03/2023] [Accepted: 06/21/2024] [Indexed: 07/18/2024] Open
Abstract
BACKGROUND Prostate cancer (PrCa) is the most frequently diagnosed cancer in men. Variants in known moderate- to high-penetrance genes explain less than 5% of the cases arising at early-onset (< 56 years) and/or with familial aggregation of the disease. Considering that BubR1 is an essential component of the mitotic spindle assembly checkpoint, we hypothesized that monoallelic BUB1B variants could be sufficient to fuel chromosomal instability (CIN), potentially triggering (prostate) carcinogenesis. METHODS To unveil BUB1B as a new PrCa predisposing gene, we performed targeted next-generation sequencing in germline DNA from 462 early-onset/familial PrCa patients and 1,416 cancer patients fulfilling criteria for genetic testing for other hereditary cancer syndromes. To explore the pan-cancer role of BUB1B, we used in silico BubR1 molecular modeling, in vitro gene-editing, and ex vivo patients' tumors and peripheral blood lymphocytes. RESULTS Rare BUB1B variants were found in ~ 1.9% of the early-onset/familial PrCa cases and in ~ 0.6% of other cancer patients fulfilling criteria for hereditary disease. We further show that BUB1B variants lead to decreased BubR1 expression and/or stability, which promotes increased premature chromatid separation and, consequently, triggers CIN, driving resistance to Taxol-based therapies. CONCLUSIONS Our study shows that different BUB1B variants may uncover a trigger for CIN-driven carcinogenesis, supporting the role of BUB1B as a (pan)-cancer predisposing gene with potential impact on genetic counseling and treatment decision-making.
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Affiliation(s)
- Maria P Silva
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
| | - Luísa T Ferreira
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
| | - Natércia F Brás
- LAQV, REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Lurdes Torres
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
| | - Andreia Brandão
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
| | - Manuela Pinheiro
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
| | - Marta Cardoso
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
| | - Adriana Resende
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
| | - Joana Vieira
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
| | - Carlos Palmeira
- Department of Immunology, Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
| | - Gabriela Martins
- Department of Immunology, Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
| | - Miguel Silva
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
| | - Carla Pinto
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
| | - Ana Peixoto
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
| | - João Silva
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
| | - Rui Henrique
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
| | - Sofia Maia
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
| | - Helder Maiato
- Chromosome Instability & Dynamics Group, Instituto de Investigação e Inovação em Saúde, University of Porto / Porto Comprehensive Cancer Center, Porto, i3S, Portugal
- Cell Division Group, Experimental Biology Unit, Department of Biomedicine, Faculty of Medicine, University of Porto, Porto, Portugal
- Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
| | - Manuel R Teixeira
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
| | - Paula Paulo
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal.
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Wang M, Liu C, Wang Y, Jamil M, Alhomrani M, Alamri AS, Alsanie WF, Alsharif A, Ali M, Jabeen N. Bone morphogenetic protein 1: a prognostic indicator and potential biomarker in three cancer types. Am J Transl Res 2024; 16:400-414. [PMID: 38463598 PMCID: PMC10918118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/10/2024] [Indexed: 03/12/2024]
Abstract
BACKGROUND Bone morphogenetic protein 1 (BMP1) is a metalloprotease that plays a role in activating both transforming growth factor-β (TGF-β) and BMP signaling pathways. TGF-β has been identified as a factor initiating and facilitating cancer development. Consequently, we propose the hypothesis that dysregulation of BMP1 could potentially contribute to the onset and advancement of human cancers. METHODS In this research, we aimed to analyze BMP1 expression level and the associated clinical outcomes across various cancers using online cancer OMICS databases, advanced Bioinformatics tools, and molecular analyses. RESULTS The outcomes of our web server-based expression analysis indicated an up-regulation of BMP1 in a majority of the human cancers examined. External validation using clinical samples also showed higher expression of BMP1. Moreover, heightened BMP1 expression exhibited a noteworthy correlation with reduced overall survival (OS) duration in Bladder Cancer (BLCA), Kidney Renal Clear Cell Carcinoma (KIRC), and Lung Adenocarcinoma (LUAD) patients. This suggests a substantial involvement of the BMP1 gene in the development and progression of these three types of cancers. The major signaling pathways related with BMP1 enriched genes were "ECM-receptor interaction, Amoebiasis, Focal adhesion, Protein digestion and absorption, progesterone-mediated, PI3K-Akt signaling pathway, and platelet activation". Moreover, we also explored some interesting correlations among BMP1 expression and its DNA promoter methylation level, CD8+ T immune cells level, and genetic variations. CONCLUSION In conclusion, our study has provided some solid basis for BMP1 to be used as a reliable common biomarker for BLCA, KIRC, and LUAD patients.
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Affiliation(s)
- Ming Wang
- Department of Oncology, Hebei Yanda HospitalLangfang 065200, Hebei, China
| | - Chunmei Liu
- Department of Oncology, Hebei Yanda HospitalLangfang 065200, Hebei, China
| | - Yingjie Wang
- Department of Oncology, Hebei Yanda HospitalLangfang 065200, Hebei, China
| | - Muhammad Jamil
- PARC Arid Zone Research CentreDera Ismail Khan 29050, Pakistan
| | - Majid Alhomrani
- College of Applied Medical Sciences, Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif UniversityP.O. Box 11099, Taif 21944, Saudi Arabia
- Research Centre for Health Sciences, Taif UniversityTaif 26571, Saudi Arabia
| | - Abdulhakeem S Alamri
- College of Applied Medical Sciences, Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif UniversityP.O. Box 11099, Taif 21944, Saudi Arabia
- Research Centre for Health Sciences, Taif UniversityTaif 26571, Saudi Arabia
| | - Walaa F Alsanie
- College of Applied Medical Sciences, Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif UniversityP.O. Box 11099, Taif 21944, Saudi Arabia
- Research Centre for Health Sciences, Taif UniversityTaif 26571, Saudi Arabia
| | - Abdulaziz Alsharif
- College of Applied Medical Sciences, Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif UniversityP.O. Box 11099, Taif 21944, Saudi Arabia
- Research Centre for Health Sciences, Taif UniversityTaif 26571, Saudi Arabia
| | - Mubarik Ali
- Animal Science Institute, National Agricultural Research CenterIslamabad 54000, Pakistan
| | - Norina Jabeen
- Department of Rural Sociology, University of Agriculture FaisalabadFaisalabad 38040, Punjab, Pakistan
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Zhang L, Sahar AM, Li C, Chaudhary A, Yousaf I, Saeedah MA, Mubarak A, Haris M, Nawaz M, Reem MA, Ramadan FA, Mostafa AAM, Feng W, Hameed Y. A detailed multi-omics analysis of GNB2 gene in human cancers. BRAZ J BIOL 2024; 84:e260169. [DOI: 10.1590/1519-6984.260169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/07/2022] [Indexed: 11/22/2022] Open
Abstract
Abstract The Guanine-nucleotide binding protein 2 (GNB2) encodes for β2 subunit (Gβ2) of the G-protein complex. Keeping in view the increased demand of reliable biomarkers in cancer, the current study was planned to extensively explored GNB2 expression variation and its roles in different cancers using online available databases and diverse methodology. In view of our results, the GNB2 was notably up-regulated relative to corresponding controls in twenty three cancer types. As well, the elevated expression of GNB2 was found to be associated with the reduced overall survival (OS) of the Liver Hepatocellular Carcinoma (LIHC) and Rectum Adenocarcinoma (READ) only out of all analyzed cancer types. This implies GNB2 plays vital role in the tumorigenesis of LIHC and READ. Several additional analysis also explored six critical pathways and few important correlations related to GNB2 expression and different other parameters such as promoter methylation, tumor purity, CD8+ T immune cells infiltration, and genetic alteration, and chemotherapeutic drugs. In conclusion, GNB2 gene has been identified in this study as a shared potential biomarker (diagnostic and prognostic) of LIHC and READ.
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Affiliation(s)
| | | | - C. Li
- Sichuan University, PR China
| | | | - I. Yousaf
- Government College University Faisalabad, Pakistan
| | | | | | - M. Haris
- Nowshera Medical College, Pakistan
| | | | | | | | | | - W. Feng
- Sichuan University, PR China
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Mi J, Luo J, Zeng H, Zhang H, Jamil M, Abdel-Maksoud MA, Zakri AM, Alfuraydi AA, Zhang N, Xiao M. Elucidating cuproptosis-related gene SLC31A1 diagnostic and prognostic values in cancer. Am J Transl Res 2023; 15:6026-6041. [PMID: 37969191 PMCID: PMC10641336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 09/28/2023] [Indexed: 11/17/2023]
Abstract
OBJECTIVES Cancer remains a global health challenge, necessitating the identification of novel biomarkers and therapeutic targets. Cuproptosis, a recently recognized form of cell death linked to copper metabolism, presents a promising avenue for anticancer strategies. We investigated the clinical significance of SLC31A1, a key regulator of cuproptosis, in multiple cancer types, aiming to elucidate its potential as a diagnostic biomarker, prognostic, indicator and therapeutic target. METHODS We conducted a pan-cancer analysis through TIMER2.0, evaluating SLC31A1 expression across multiple cancer types. Survival analysis was performed using KM plotter. Expression validation was carried out using UALCAN and Human Protein Atlas (HPA) databases. Methylation analysis was conducted with the help of ULACAN and OncoDB. Mutational analysis was performed using cBioPortal database. Immune infiltration analysis via the TIMER2.0 and gene enrichment analysis via the Metascape were performed to gain insights into the potential mechanisms underlying SLC31A1's role in cancer. Finally, Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was employed to confirm SLC31A1 expression in clinical samples. RESULTS Out of analyzed cancer, SLC31A1 exhibited significant up-regulation and correlation with worse overall survival (OS) across Breast Cancer (BRCA), Cervical Squamous Cell Carcinoma (CESC), Head and Neck Squamous Cell Carcinoma (HNSC), and Esophageal Carcinoma (ESCA). Mutational and promoter methylation analyses further revealed that hypomethylation is the major cause of SLC31A1 overexpression among BRCA, CESC, HNSC, and ESCA. Immune infiltration analysis showed significant associations between SLC31A1 expression and the presence of CD8+ T cells, CD4+ T cells, and macrophages in the tumor microenvironment. Gene enrichment analysis provided valuable insights into potential molecular pathways in context to BRCA, CESC, HNSC, and ESCA. Furthermore, when SLC31A1 was analyzed using clinical samples through RT-qPCR, this gene showed promising diagnostic potential, reflected by high Area Under the Curve (AUC) values. CONCLUSION Our pan-cancer study highlights the up-regulation of SLC31A1 and its correlation with worse OS in BRCA, CESC, HNSC, and ESCA. In sum, outcomes of this study showed that SLC31A1 could be a potential biomarker and novel therapeutic target of BRCA, CESC, HNSC, and ESCA.
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Affiliation(s)
- Jiaoping Mi
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital, Sun Yat-sen UniversityGuangzhou 510080, Guangdong, PR China
- Department of Otolaryngology Head and Neck Surgery, The Fifth Affiliated Hospital of Sun Yat-sen UniversityZhuhai 519000, Guangdong, PR China
| | - Juncong Luo
- Department of Oncology, The Fifth Affiliated Hospital of Sun Yat-sen UniversityZhuhai 519000, Guangdong, PR China
| | - Huanwen Zeng
- Department of Oncology, The Fifth Affiliated Hospital of Sun Yat-sen UniversityZhuhai 519000, Guangdong, PR China
| | - Hongyu Zhang
- Department of Oncology, The Fifth Affiliated Hospital of Sun Yat-sen UniversityZhuhai 519000, Guangdong, PR China
| | - Muhammad Jamil
- PARC Arid Zone Research CenterDera Ismail Khan 29050, Pakistan
| | - Mostafa A Abdel-Maksoud
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Adel M Zakri
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Akram A Alfuraydi
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ning Zhang
- Internal Medicine Oncology, Minhang Brunch Fudan University Shanghai Cancer CenterShanghai 200240, PR China
| | - Mei Xiao
- Department of Oncology, The Fifth Affiliated Hospital of Sun Yat-sen UniversityZhuhai 519000, Guangdong, PR China
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Hameed Y. Decoding the significant diagnostic and prognostic importance of maternal embryonic leucine zipper kinase in human cancers through deep integrative analyses. J Cancer Res Ther 2023; 19:1852-1864. [PMID: 38376289 DOI: 10.4103/jcrt.jcrt_1902_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/11/2022] [Indexed: 02/21/2024]
Abstract
BACKGROUND Cancer is a multifactorial disease and the second leading cause of human deaths worldwide. So far, the underlying mechanisms of cancer have not been yet fully elucidated. METHODS By using TCGA expression data, we determine the pathogenic roles of the maternal embryonic leucine zipper kinase (MELK) gene in various human cancers in this study. For this purpose, different online databases and tools (UALCAN, Kaplan-Meier (KM) plotter, TNMplot, GENT2, GEPIA, HPA, cBioPortal, STRING, Enrichr, TIMER, Cytoscape, DAVID, MuTarget, and CTD) were used. RESULTS MELK gene expression was analyzed in a total of 24 human cancers and was found notably up-regulated in all the 24 analyzed tumor tissues relative to controls. Moreover, across a few specific cancers, including kidney renal clear cell carcinoma (KIRC), stomach adenocarcinoma (STAD), lung adenocarcinoma (LUAD), and liver hepatocellular carcinoma (LIHC) patients, MELK up-regulation was observed to be correlated with the shorter survival duration and metastasis. This valuable information highlighted that MELK plays a significant role in the development and progression of these four cancers. Based on clinical variables, MELK higher expression was also found in KIRC, STAD, LUAD, and LIHC patients with different clinical variables. Gene ontology and pathway analysis outcomes showed that MELK-associated genes notably co-expressed with MELK and belongs to a variety of diverse biological processes, molecular functions, and pathways. MELK expression was also correlated with promoter methylation levels, genetic alterations, other mutant genes, tumor purity, CD8+ T, and CD+4 T immune cells infiltrations in KIRC, STAD, LUAD, and LIHC. CONCLUSION This pan-cancer study revealed the diagnostic and prognostic roles of MELK across four different cancers.
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Affiliation(s)
- Yasir Hameed
- Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
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Uqaili AA, Usman G, Bhatti U, Nasir H, Zia R, Akram MA, Jawad FA, Farid A, AbdelGawwad MR, Almutairi SM, Elshikh MS, Hussain S, Rasheed RA. Bioinformatics, RNA sequencing, and targeted bisulfite sequencing analyses identify the role of PROM2 as a diagnostic and prognostic biomarker. Am J Transl Res 2023; 15:5389-5407. [PMID: 37692961 PMCID: PMC10492044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 08/14/2023] [Indexed: 09/12/2023]
Abstract
OBJECTIVES Prominin 2 (PROM2) gene has been reported as a molecular biomarker of human cancers; however, its role is still controversial. This study was therefore arranged to seek the role of PROM2 in different cancers with Bioinformatics and in vitro analyses. METHODS A combination of bioinformatics and molecular experiments. RESULTS Through the utilization of Bioinformatics analysis, it was observed that in 19 out of the 24 human cancers studied, there was a significant increase in the expression of PROM2 compared to the respective control samples. Additionally, the overexpression of PROM2 was linked specifically to a decrease in overall survival (OS) among breast cancer (BRCA), lung adenocarcinoma (LUAD), and uterine corpus endometrial carcinoma (UCEC) patients. Furthermore, advanced molecular investigations were conducted, encompassing RNA sequencing (RNA-seq) as well as targeted bisulfite sequencing (bisulfite-seq) assessments of PROM2. These analyses were performed across an array of lung cancer cell lines (A549, ABC-1, EBC-1, and LK-2) and a normal control lung cell line (MRC-9). Results of these analysis revealed overexpression and reduced methylation of PROM2 within lung cancer cell lines, relative to the corresponding control cell line. This suggests that PROM2 assumes a substantial function in the advancement and course of BRCA, LUAD, and UCEC cancers. Subsequent pathway analysis revealed that genes enriched by PROM2 are actively engaged in four pivotal pathways. Additionally, intriguing associations were observed between PROM2 expression, tumor purity, infiltration of CD8+ T immune cells, and genetic modifications. Moreover, we also predicted a few MicroRNAs (miRNAs), transcription factors (TFs), and potential drugs that could help to understand and better manage these cancers via designing appropriate therapies targeting PROM2. CONCLUSION Via this study, we effectively revealed PROM2 overexpression as a potential diagnostic and prognostic biomarker of survival in BRCA, LUAD, and UCEC.
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Affiliation(s)
- Arsalan Ahmed Uqaili
- Department of Physiology, Liaquat University of Medical and Health SciencesJamshoro 76090, Pakistan
| | - Gulzar Usman
- Department of Community Medicine, LUMHSJamshoro 76090, Pakistan
| | - Urooj Bhatti
- Department of Physiology, LUMHSJamshoro 76090, Pakistan
| | - Hilal Nasir
- Clinical and Translational Oncology, Scuola Superiore Meridionale, Naples Federico II UniversityNaples 80131, Italy
| | - Rabeea Zia
- Pakistan Kidney and Liver Institute and Research CenterLahore 54000, Pakistan
| | - Muhammad Aitzaz Akram
- Institute of Biochemistry and Biotechnology, PMAS-Arid Agriculture UniversityRawalpindi 46000, Pakistan
| | - Fahim Ali Jawad
- Centre of Agricultural Biochemistry and Biotechnology-University of Agriculture FaisalabadFaisalabad 38040, Pakistan
| | - Afshan Farid
- Department of Botany, PMAS Arid Agriculture UniversityRawalpindi 46000, Pakistan
| | - Mohamed Ragab AbdelGawwad
- Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, International University of SarajevoSarajevo 71210, Bosnia and Herzegovina
| | - Saeedah Musaed Almutairi
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. 2455, Riyadh 11451, Saudi Arabia
| | - Mohamed S Elshikh
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. 2455, Riyadh 11451, Saudi Arabia
| | - Sajid Hussain
- Department of Botany, PMAS Arid Agriculture UniversityRawalpindi 46000, Pakistan
| | - Rabab Ahmed Rasheed
- Histology & Cell Biology Department, Faculty of Medicine, King Salman International UniversitySouth Sinai, Egypt
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Li J, Shaikh SN, Uqaili AA, Nasir H, Zia R, Akram MA, Jawad FA, Sohail S, AbdelGawwad MR, Almutairi SM, Elshikh MS, Jamil M, Rasheed RA. A pan-cancer analysis of pituitary tumor-transforming 3, pseudogene. Am J Transl Res 2023; 15:5408-5424. [PMID: 37692950 PMCID: PMC10492052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 08/14/2023] [Indexed: 09/12/2023]
Abstract
BACKGROUND Although evidence regarding pituitary tumor-transforming 3, pseudogene (PTTG3P) involvement in human cancers has been acquired via human and animal model-based molecular studies, there is a lack of pan-cancer analysis of this gene in human tumors. METHODS Tumor-causing effects of PTTG3P in 24 human tumors were explored using The Cancer Genome Atlas (TCGA) datasets from different bioinformatics databases and applying in silico tools such as The University of ALabama at Birmingham CANcer (UALCAN), Human Protein Atlas (HPA), Kaplan Meier (KM) plotter, cBioPortal, Search Tool for the Retrieval of Interacting Genes/Proteins (STRING), Cytoscape, Database for Annotation, Visualization, and Integrated Discovery (DAVID), Tumor IMmune Estimation Resource (TIMER), and Comparative Toxicogenomics Database (CTD). Then, via in vitro experiments, including RNA sequencing (RNA-seq) and targeted bisulfite sequencing (bisulfite-seq), expression and promoter methylation levels of PTTG3P were verified in cell lines. RESULTS The PTTG3P expression was overexpressed across 23 malignancies and its overexpression was further found significantly effecting the overall survival (OS) durations of the esophageal carcinoma (ESCA) and head and neck cancer (HNSC) patients. This important information helps us to understand that PTTG3P plays a significant role in the development and progression of ESCA and HNSC. As for PTTG3P functional mechanisms, this gene along with its other binding partners was significantly concentrated in "Oocyte meiosis", "Cell cycle", "Ubiquitin mediated proteolysis", and "Progesterone-mediated oocyte maturation". Moreover, ESCA and HNSC tissues having the higher expression of PTTG3P were found to have lower promoter methylation levels of PTTG3P and higher CD8+ T immune cells level. Additionally, PTTG3P expression-regulatory drugs were also explored in the current manuscript for designing appropriate treatment strategies for ESCA and HNSC with respect to PTTG3P expression. CONCLUSION Our pan-cancer based findings provided a comprehensive account of the oncogenic role and utilization of PTTG3P as a novel molecular biomarker of ESCA and HNSC.
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Affiliation(s)
- Jie Li
- The Second Affiliated Hospital of Hainan Medical University Health Management CenterHaikou 570311, Hainan, China
| | - Saima Naz Shaikh
- Department of Physiology, Liaquat University of Medical and Health SciencesJamshoro, Sindh 76090, Pakistan
| | - Arsalan Ahmed Uqaili
- Department of Physiology, Liaquat University of Medical and Health SciencesJamshoro, Sindh 76090, Pakistan
| | - Hilal Nasir
- Clinical and Translational Oncology, Scuola Superiore Meridionale, Naples Federico II UniversityNapoli 80138, Italy
| | - Rabeea Zia
- Pakistan Kidney and Liver Institute and ResearchLahore, Punjab 54000, Pakistan
| | - Muhammad Aitzaz Akram
- University Institute of Biochemistry and Biotechnology, PMAS-Arid Agriculture UniversityRawalpindi 46000, Pakistan
| | - Fahim Ali Jawad
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture FaisalabadFaisalabad 38000, Pakistan
| | - Salman Sohail
- Registrar Ophthalmology, Al Shifa Trust Eye HospitalRawalpindi 46000, Pakistan
| | - Mohamed Ragab AbdelGawwad
- Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, International University of SarajevoSarajevo 71210, Bosnia and Herzegovina
| | - Saeedah Musaed Almutairi
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. 2455, Riyadh 11451, Saudi Arabia
| | - Mohamed S Elshikh
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. 2455, Riyadh 11451, Saudi Arabia
| | - Muhammad Jamil
- PARC Arid Zone Research CenterDera Ismail Khan 29050, Pakistan
| | - Rabab Ahmed Rasheed
- Histology & Cell Biology Department, Faculty of Medicine, King Salman International UniversitySouth Sinai, Egypt
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Usman M, Hameed Y, Ahmad M, Iqbal MJ, Maryam A, Mazhar A, Naz S, Tanveer R, Saeed H, Bint-E-Fatima, Ashraf A, Hadi A, Hameed Z, Tariq E, Aslam AS. SHMT2 is Associated with Tumor Purity, CD8+ T Immune Cells Infiltration, and a Novel Therapeutic Target in Four Different Human Cancers. Curr Mol Med 2023; 23:161-176. [PMID: 35023455 DOI: 10.2174/1566524022666220112142409] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 11/15/2021] [Accepted: 11/25/2021] [Indexed: 12/16/2022]
Abstract
AIMS This study was launched to identify the SHMT2 associated Human Cancer subtypes. BACKGROUND Cancer is the 2nd leading cause of death worldwide. Previous reports revealed the limited involvement of SHMT2 in human cancer. In the current study, we comprehensively analyzed the role of SHMT2 in 24 major subtypes of human cancers using in silico approach and identified a few subtypes that are mainly associated with SHMT2. OBJECTIVE We aim to comprehensively analyze the role of SHMT2 in 24 major subtypes of human cancers using in silico approach and identified a few subtypes that are mainly associated with SHMT2. Earlier, limited knowledge exists in the medical literature regarding the involvement of Serine Hydroxymethyltransferase 2 (SHMT2) in human cancer. METHODS In the current study, we comprehensively analyzed the role of SHMT2 in 24 major subtypes of human cancers using in silico approach and identified a few subtypes that are mainly associated with SHMT2. Pan-cancer transcriptional expression profiling of SHMT2 was done using UALCAN while further validation was performed using GENT2. For translational profiling of SHMT2, we utilized Human Protein Atlas (HPA) platform. Promoter methylation, genetic alteration, and copy number variations (CNVs) profiles were analyzed through MEXPRESS and cBioPortal. Survival analysis was carried out through Kaplan-Meier (KM) plotter platform. Pathway enrichment analysis of SHMT2 was performed using DAVID, while the gene-drug network was drawn through CTD and Cytoscape. Furthermore, in the tumor microenvironment, a correlation between tumor purity, CD8+ T immune cells infiltration, and SHMT2 expression was accessed using TIMER. RESULTS SHMT2 was found overexpressed in 24 different subtypes of human cancers and its overexpression was significantly associated with the reduced Overall survival (OS) and Relapse-free survival durations of Breast cancer (BRCA), Kidney renal papillary cell carcinoma (KIRP), Liver hepatocellular carcinoma (LIHC), and Lung adenocarcinoma (LUAD) patients. This implies that SHMT2 plays a significant role in the development and progression of these cancers. We further noticed that SHMT2 was also up-regulated in BRCA, KIRP, LIHC, and LUAD patients of different clinicopathological features. Pathways enrichment analysis revealed the involvement of SHMT2 enriched genes in five diverse pathways. Furthermore, we also explored some interesting correlations between SHMT2 expression and promoter methylation, genetic alterations, CNVs, tumor purity, and CD8+ T immune cell infiltrates. CONCLUSION Our results suggested that overexpressed SHMT2 is correlated with the reduced OS and RFS of the BRCA, KIRP, LIHC, and LUAD patients and can be a potential diagnostic and prognostic biomarker for these cancers.
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Affiliation(s)
- Muhammad Usman
- Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Yasir Hameed
- Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Mukhtiar Ahmad
- Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | | | - Aghna Maryam
- Department of Biochemistry, Quaid-i-Azam University Islamabad, Pakistan
| | - Afshan Mazhar
- Department of Biochemistry, Quaid-i-Azam University Islamabad, Pakistan
| | - Saima Naz
- Department of zoology, Government Sadiq College Women University Bahawalpur, Bahawalpur, Pakistan
| | - Rida Tanveer
- University College of Conventional Medicine, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Hina Saeed
- Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Bint-E-Fatima
- Department of Biotechnology, University of Gujrat, Gujrat, Pakistan
| | - Aneela Ashraf
- Department of Biochemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Alishba Hadi
- Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Zahid Hameed
- Department of Bioinformatics and Biotechnology, International Islamic University Islamabad, Islamabad, Pakistan
| | - Eman Tariq
- Department of Chemistry, The University of Swabi, Swabi, Pakistan
| | - Alia Sumyya Aslam
- Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
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9
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Angiotensinogen, a promising gene signature for rectum and stomach adenocarcinoma patients. Am J Transl Res 2022; 14:8879-8892. [PMID: 36628228 PMCID: PMC9827296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 10/24/2022] [Indexed: 01/12/2023]
Abstract
OBJECTIVES Angiotensinogen (AGT), as a component of the renin-angiotensin system (RAS), is one of the major risk factors for cancer development. To date, there has not been a systematic pan-cancer analysis of AGT. METHODS This pan-cancer study comprehensively investigated AGT in 24 different cancers based on the UALCAN, KM plotter, GENT2, HPA, MEXPRESS, cBioportal, STRING, TIMER, and CTD databases. RESULTS The results showed that AGT was highly expressed in most tumors, and AGT overexpression may be related to the worst survival of Rectum adenocarcinoma (READ) and Stomach Adenocarcinoma (STAD) patients only. Furthermore, pathway analysis indicated that AGT-associated genes are involved in six critical pathways. Moreover, the higher expression of AGT was found to be detrimental to the promoter methylation level (P<0.05), immune cells infiltration (P<0.05), and genetic alterations. We have also predicted various chemotherapeutic drugs contributing to the expression regulation of AGT. CONCLUSION Our results together support that AGT is a possible biomarker for READ and STAD.
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10
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Munir H, Rana AT, Faheem M, Almutairi SM, Siddique T, Asghar S, Abdel-Maksoud MA, Mubarak A, Elkhamisy FAA, Studenik CR, Yaz H. Decoding signal transducer and activator of transcription 1 across various cancers through data mining and integrative analysis. Am J Transl Res 2022; 14:3638-3657. [PMID: 35836889 PMCID: PMC9274611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 01/25/2022] [Indexed: 06/15/2023]
Abstract
OBJECTIVES Using different online available databases and Bioinformatics tools, we extensively studied the role STAT1 across different cancers. METHODS STAT1 mRNA, protein expression, and promoter methylation were analyzed and validated using UALCAN, GENT2, Human Protein Atlas (HPA), and MEXPRESS. Furthermore, the potential prognostic values were evaluated through KM plotter. Then, cBioPortal was utilized to examine the STAT1-related genetic mutations, while pathway enrichment analysis was performed using DAVID. To identify STAT1 targeted microRNAs (miRNAs) and transcription factors (TFs) we used Enricher. Moreover, a correlational analysis between STAT1 expression tumor purity and CD8+ T immune cells and a gene-drug interaction network analysis was performed using TIMER, CTD, and Cytoscape. RESULTS In 23 major human cancers, STAT1 expression was notably up-regulated relative to corresponding controls. As well, the elevated expression of STAT1 was exclusively found to be associated with the reduced overall survival (OS) of Esophageal Carcinoma (ESCA), Kidney Renal Clear Cell Carcinoma (KIRC), and Lung adenocarcinoma (LUAD) patients. This implies that STAT1 plays a significant role in the development and progression of these three cancers. Further pathway analysis indicated that STAT1 enriched genes were involved in six critical pathways, while a few interesting correlations were also documented between STAT1 expression and promoter methylation level, tumor purity, CD8+ T immune cells infiltration, and genetic alteration. In addition, we have also predicted a few miRNAs, TFs, and chemotherapeutic drugs that could regulate the STAT1 expression. CONCLUSION The current study revealed the shared oncogenic, diagnostic, and prognostic role of STAT1 in ESCA, KIRC, and LUAD.
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Affiliation(s)
- Hadia Munir
- Akhtar Saeed Medical and Dental CollegePakistan
| | | | - Muhammad Faheem
- District Head Quarter Hospital FaisalabadFaisalabad, Pakistan
| | - Saeedah Musaed Almutairi
- Department of Botany and Microbiology, College of Science, King Saud UniversityRiyadh, P.O. 2455, Riyadh 11451, Saudi Arabia
| | - Tehmina Siddique
- Department of Biotechnology, Faculty of Life Sciences, University of OkaraOkara, Pakistan
| | - Samra Asghar
- Department of Medical Laboratory Technology, Faculty of Rehablitation and Allied Health Sciences, Riphah International UniversityFaisalabad, Pakistan
| | - Mostafa A Abdel-Maksoud
- Department of Botany and Microbiology, College of Science, King Saud UniversityRiyadh, P.O. 2455, Riyadh 11451, Saudi Arabia
| | - Ayman Mubarak
- Department of Botany and Microbiology, College of Science, King Saud UniversityRiyadh, P.O. 2455, Riyadh 11451, Saudi Arabia
| | - Fatma Alzahraa A Elkhamisy
- Pathology Department, Faculty of Medicine, Helwan UniversityCairo, Egypt
- Basic Medical Sciences Department, Faculty of Medicine, King Salman International UniversitySouth Sinai, Egypt
| | - Christian R Studenik
- Department of Pharmaceutical Sciences, Division of Pharmacology and Toxicology, University of ViennaVienna, Austria
| | - Hamid Yaz
- Department of Botany and Microbiology, College of Science, King Saud UniversityRiyadh, P.O. 2455, Riyadh 11451, Saudi Arabia
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11
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Ahmad M, Khan M, Asif R, Sial N, Abid U, Shamim T, Hameed Z, Iqbal MJ, Sarfraz U, Saeed H, Asghar Z, Akram M, Ullah Q, Younas QUA, Rauf L, Hadi A, Maryam S, Hameed Y, Khan MR, Tariq E, Saeed S. Expression Characteristics and Significant Diagnostic and Prognostic Values of ANLN in Human Cancers. Int J Gen Med 2022. [DOI: 10.2147/ijgm.s343975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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12
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Hameed Y, Usman M. GNB1, a novel diagnostic and prognostic potential biomarker of head and neck and liver hepatocellular carcinoma. J Cancer Res Ther 2022. [DOI: 10.4103/jcrt.jcrt_1901_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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13
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Ahmad M, Hameed Y, Khan M, Usman M, Rehman A, Abid U, Asif R, Ahmed H, Hussain MS, Rehman JU, Asif HM, Arshad R, Atif M, Hadi A, Sarfraz U, Khurshid U. Up-regulation of GINS1 highlighted a good diagnostic and prognostic potential of survival in three different subtypes of human cancer. BRAZ J BIOL 2021; 84:e250575. [PMID: 34852135 DOI: 10.1590/1519-6984.250575] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/30/2021] [Indexed: 12/13/2022] Open
Abstract
Cancer is a fatal malignancy and its increasing worldwide prevalence demands the discovery of more sensitive and reliable molecular biomarkers. To investigate the GINS1 expression level and its prognostic value in distinct human cancers using a series of multi-layered in silico approach may help to establish it as a potential shared diagnostic and prognostic biomarker of different cancer subtypes. The GINS1 mRNA, protein expression, and promoter methylation were analyzed using UALCAN and Human Protein Atlas (HPA), while mRNA expression was further validated via GENT2. The potential prognostic values of GINS1 were evaluated through KM plotter. Then, cBioPortal was utilized to examine the GINS1-related genetic mutations and copy number variations (CNVs), while pathway enrichment analysis was performed using DAVID. Moreover, a correlational analysis between GINS1 expression and CD8+ T immune cells and a the construction of gene-drug interaction network was performed using TIMER, CDT, and Cytoscape. The GINS1 was found down-regulated in a single subtypes of human cancer while commonly up-regulated in 23 different other subtypes. The up-regulation of GINS1 was significantly correlated with the poor overall survival (OS) of Liver Hepatocellular Carcinoma (LIHC), Lung Adenocarcinoma (LUAD), and Kidney renal clear cell carcinoma (KIRC). The GINS1 was also found up-regulated in LIHC, LUAD, and KIRC patients of different clinicopathological features. Pathways enrichment analysis revealed the involvement of GINS1 in two diverse pathways, while few interesting correlations were also documented between GINS1 expression and its promoter methylation level, CD8+ T immune cells level, and CNVs. Moreover, we also predicted few drugs that could be used in the treatment of LIHC, LUAD, and KIRC by regulating the GINS1 expression. The expression profiling of GINS1 in the current study has suggested it a novel shared diagnostic and prognostic biomarker of LIHC, LUAD, and KIRC.
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Affiliation(s)
- M Ahmad
- The Islamia University of Bahawalpur, Department of Biochemistry and Biotechnology, Bahawalpur, Pakistan
| | - Y Hameed
- The Islamia University of Bahawalpur, Department of Biochemistry and Biotechnology, Bahawalpur, Pakistan
| | - M Khan
- The Islamia University of Bahawalpur, Department of Pharmacy, Bahawalpur, Pakistan
| | - M Usman
- The Islamia University of Bahawalpur, Department of Biochemistry and Biotechnology, Bahawalpur, Pakistan
| | - A Rehman
- Qarshi University, Department of Eastern Medicine, Lahore, Pakistan
| | - U Abid
- Bahauddin Zakariya University, Department of Pharmaceutics, Multan, Pakistan
| | - R Asif
- Government College University Faisalabad, Department of Microbiology, Faisalabad, Pakistan
| | - H Ahmed
- Government College University Faisalabad, Department of Eastern Medicine, Faisalabad, Pakistan
| | - M S Hussain
- The Islamia University of Bahawalpur, Department of Biochemistry and Biotechnology, Bahawalpur, Pakistan
| | - J U Rehman
- The Islamia University of Bahawalpur, College of Conventional Medicine, Faculty of Pharmacy and Alternative Medicine, Bahawalpur, Pakistan
| | - H M Asif
- The Islamia University of Bahawalpur, College of Conventional Medicine, Faculty of Pharmacy and Alternative Medicine, Bahawalpur, Pakistan
| | - R Arshad
- The Islamia University of Bahawalpur, College of Conventional Medicine, Faculty of Pharmacy and Alternative Medicine, Bahawalpur, Pakistan
| | - M Atif
- The Islamia University of Bahawalpur, College of Conventional Medicine, Faculty of Pharmacy and Alternative Medicine, Bahawalpur, Pakistan
| | - A Hadi
- The Islamia University of Bahawalpur, Department of Biochemistry and Biotechnology, Bahawalpur, Pakistan
| | - U Sarfraz
- COMSATS University Islamabad, Department of Biosciences, Islamabad, Pakistan
| | - U Khurshid
- The Islamia University of Bahawalpur, Department of Pharmacy, Bahawalpur, Pakistan
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14
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Sial N, Ahmad M, Hussain MS, Iqbal MJ, Hameed Y, Khan M, Abbas M, Asif R, Rehman JU, Atif M, Khan MR, Hameed Z, Saeed H, Tanveer R, Saeed S, Sharif A, Asif HM. CTHRC1 expression is a novel shared diagnostic and prognostic biomarker of survival in six different human cancer subtypes. Sci Rep 2021; 11:19873. [PMID: 34615943 PMCID: PMC8494806 DOI: 10.1038/s41598-021-99321-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/14/2021] [Indexed: 02/08/2023] Open
Abstract
According to the previous reports, the collagen triple helix repeat containing 1 (CTHRC1) causes tumorigenesis by modulating the tumor microenvironment, however, the evidence is limited to a few human cancer subtypes. In the current study, we analyzed and validated the CTHRC1 expression variations in 24 different human cancer tissues paired with normal tissues using publically available databases. We observed that CTHRC1 was overexpressed in all the 24 major subtypes of human cancers and its overexpression was significantly associated with the reduced overall survival (OS) duration of head and neck squamous cell carcinoma (HNSC), kidney renal clear cell carcinoma (KIRC), liver hepatocellular carcinoma (LIHC), Lung adenocarcinoma (LUAD), stomach adenocarcinoma (STAD), and Uterine corpus endometrial carcinoma (UCEC). This implies that CTHRC1 plays a significant role in the development and progression of these cancers. We further noticed that CTHRC1 was also overexpressed in HNSC, KIRC, LIHC, LUAD, STAD, and UCEC patients of different clinicopathological features. Pathways enrichment analysis revealed the involvement of CTHRC1 associated genes in seven diverse pathways. We also explored few interesting correlations between CTHRC1 expression and promoter methylation, genetic alterations, CNVs, CD8+ T immune cells infiltration, and tumor purity. In conclusion, CTHRC1 can serve as a shared diagnostic and prognostic biomarker in HNSC, KIRC, LIHC, LUAD, STAD, and UCEC patients of different clinicopathological features.
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Affiliation(s)
- Nuzhat Sial
- Department of Zoology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Mukhtiar Ahmad
- Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Muhammad Safdar Hussain
- Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | | | - Yasir Hameed
- Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan.
| | - Mehran Khan
- Department of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Mustansar Abbas
- Department of Eastern Medicine, Government College University Faisalabad, Faisalabad, Pakistan
| | - Rizwan Asif
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Jalil Ur Rehman
- University College of Conventional Medicine, Faculty of Pharmacy and Alternative Medicine, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Muhammad Atif
- University College of Conventional Medicine, Faculty of Pharmacy and Alternative Medicine, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Muhammad Rashid Khan
- University College of Eastern Medicine, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Zahid Hameed
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Hina Saeed
- Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Rida Tanveer
- University College of Conventional Medicine, Faculty of Pharmacy and Alternative Medicine, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Saba Saeed
- Department of Zoology, University of the Punjab, Lahore, Pakistan
| | - Aneeqa Sharif
- Department of Zoology, Mirpur University of Science and Technology, Mirpur, Pakistan
| | - Hafiz Muhammad Asif
- University College of Conventional Medicine, Faculty of Pharmacy and Alternative Medicine, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
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15
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Sakalli-Tecim E, Uyar-Arpaci P, Guray NT. Identification of Potential Therapeutic Genes and Pathways in Phytoestrogen Emodin Treated Breast Cancer Cell Lines via Network Biology Approaches. Nutr Cancer 2021; 74:592-604. [PMID: 33645356 DOI: 10.1080/01635581.2021.1889622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Phytoestrogens have been investigated for their potential anti-tumorigenic effects in various cancers including breast cancer. Emodin being a phytoestrogen shows anti-carcinogenic properties especially in estrogen receptor positive (ER+) breast cancers. The aim of this study is to identify the molecular mechanism and related biological pathways in both (ER+) MCF-7 and (ER-) MDA-MB-231 breast cancer cell lines upon Emodin treatment via microarray analysis in order to find out therapeutic biomarkers. In both cell lines, first differentially expressed genes were identified, then gene ontology and functional pathway enrichment analyses were performed. Genes regulated through multiple pathways were studied together with literature and a gene cluster was determined for each cell line. Further GeneMANIA and STRING databases were used to study the interactions within the related gene clusters. The results showed that, the genes which are related to cell cycle were significantly regulated in both cell lines. Also, Forkhead Box O1-related genes were found to be prominent in MCF-7 cells. In MDA-MB-231 cells, spindle attachment checkpoint mechanism-related genes were regulated, remarkably. As a result, novel gene regulations reported in this study in response to Emodin will give more information about its metabolism and antiproliferative effect, especially in ER + cells.
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Affiliation(s)
- Elif Sakalli-Tecim
- Department of Biotechnology, Middle East Technical University, Ankara, Turkey
| | | | - N Tulin Guray
- Department of Biotechnology, Middle East Technical University, Ankara, Turkey.,Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
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16
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Voutsadakis IA. Clinical Implications of Chromosomal Instability (CIN) and Kinetochore Abnormalities in Breast Cancers. Mol Diagn Ther 2020; 23:707-721. [PMID: 31372940 DOI: 10.1007/s40291-019-00420-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Genetic instability is a defining property of cancer cells and is the basis of various lesions including point mutations, copy number alterations and translocations. Chromosomal instability (CIN) is part of the genetic instability of cancer and consists of copy number alterations in whole or parts of cancer cell chromosomes. CIN is observed in differing degrees in most cancers. In breast cancer, CIN is commonly part of the genomic landscape of the disease and has a higher incidence in aggressive sub-types. Tumor suppressors that are commonly mutated or disabled in cancer, such as p53 and pRB, play roles in protection against CIN, and as a result, their dysfunction contributes to the establishment or tolerance of CIN. Several structural and regulatory proteins of the centromeres and kinetochore, the complex structure that is responsible for the correct distribution of genetic material in the daughter cells during mitosis, are direct or, mostly, indirect transcription targets of p53 and pRB. Thus, despite the absence of structural defects in genes encoding for centromere and kinetochore components, dysfunction of these tumor suppressors may have profound implications for the correct function of the mitotic apparatus contributing to CIN. CIN and its prognostic and therapeutic implications in breast cancer are discussed in this article.
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Affiliation(s)
- Ioannis A Voutsadakis
- Algoma District Cancer Program, Sault Area Hospital, 750 Great Northern Road, Sault Ste Marie, ON, P6B 0A8, Canada. .,Section of Internal Medicine, Division of Clinical Sciences, Northern Ontario School of Medicine, Sudbury, ON, Canada.
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17
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Wang J, Hu ZG, Li D, Xu JX, Zeng ZG. Gene expression and prognosis of insulin‑like growth factor‑binding protein family members in non‑small cell lung cancer. Oncol Rep 2019; 42:1981-1995. [PMID: 31545451 PMCID: PMC6787967 DOI: 10.3892/or.2019.7314] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 08/09/2019] [Indexed: 01/03/2023] Open
Abstract
Lung cancer is the leading cause of cancer mortality worldwide. Approximately 85% of all lung cancer cases are classified as non-small cell lung cancer (NSCLC). Currently, there is no standard method to predict the survival of patients with NSCLC. Insulin-like growth factor-binding proteins (IGFBPs) function as modulators of IGF signaling and are attracting increasing attention for their role in NSCLC. However, the prognostic values of individual IGFBPs in NSCLC, particularly at the mRNA level, remain unknown. In the present study, the distinct expression patterns and prognostic values of IGFBP family members in patients with NSCLC through bioinformatics analysis were reported using a series of databases, including Gene Expression Profiling Interactive Analysis, Kaplan-Meier Plotter, cBioPortal, GeneMANIA, and the Database for Annotation, Visualization and Integrated Discovery. In patients with NSCLC, IGFBP2 and IGFBP3 were significantly upregulated, while IGFBP6 was downregulated. High IGFBP1/2/4 expression was correlated with poor overall survival (OS) in all NSCLC types, especially adenocarcinoma; however, high IGFBP2/5 expression was significantly correlated with favorable OS only in patients with squamous cell carcinoma. In addition, aberrant IGFBP1/2/3/4/5 mRNA levels were associated with the prognosis of subsets of NSCLC with different clinicopathological features. These results indicated that various IGFBPs can serve as useful prognostic biomarkers and as potential targets for NSCLC therapies.
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Affiliation(s)
- Jiao Wang
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Zhi-Guo Hu
- Department of Critical Care Medicine, Inner Mongolia People's Hospital, Hohhot, Inner Mongolia 010017, P.R. China
| | - Dan Li
- Department of Respiratory Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Ji-Xion Xu
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Zhen-Guo Zeng
- Department of Critical Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
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18
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Simonetti G, Bruno S, Padella A, Tenti E, Martinelli G. Aneuploidy: Cancer strength or vulnerability? Int J Cancer 2018; 144:8-25. [PMID: 29981145 PMCID: PMC6587540 DOI: 10.1002/ijc.31718] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 06/05/2018] [Accepted: 06/14/2018] [Indexed: 12/12/2022]
Abstract
Aneuploidy is a very rare and tissue‐specific event in normal conditions, occurring in a low number of brain and liver cells. Its frequency increases in age‐related disorders and is one of the hallmarks of cancer. Aneuploidy has been associated with defects in the spindle assembly checkpoint (SAC). However, the relationship between chromosome number alterations, SAC genes and tumor susceptibility remains unclear. Here, we provide a comprehensive review of SAC gene alterations at genomic and transcriptional level across human cancers and discuss the oncogenic and tumor suppressor functions of aneuploidy. SAC genes are rarely mutated but frequently overexpressed, with a negative prognostic impact on different tumor types. Both increased and decreased SAC gene expression show oncogenic potential in mice. SAC gene upregulation may drive aneuploidization and tumorigenesis through mitotic delay, coupled with additional oncogenic functions outside mitosis. The genomic background and environmental conditions influence the fate of aneuploid cells. Aneuploidy reduces cellular fitness. It induces growth and contact inhibition, mitotic and proteotoxic stress, cell senescence and production of reactive oxygen species. However, aneuploidy confers an evolutionary flexibility by favoring genome and chromosome instability (CIN), cellular adaptation, stem cell‐like properties and immune escape. These properties represent the driving force of aneuploid cancers, especially under conditions of stress and pharmacological pressure, and are currently under investigation as potential therapeutic targets. Indeed, promising results have been obtained from synthetic lethal combinations exploiting CIN, mitotic defects, and aneuploidy‐tolerating mechanisms as cancer vulnerability.
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Affiliation(s)
- Giorgia Simonetti
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna and Institute of Hematology "L. e A. Seràgnoli", Bologna, Italy
| | - Samantha Bruno
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna and Institute of Hematology "L. e A. Seràgnoli", Bologna, Italy
| | - Antonella Padella
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna and Institute of Hematology "L. e A. Seràgnoli", Bologna, Italy
| | - Elena Tenti
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna and Institute of Hematology "L. e A. Seràgnoli", Bologna, Italy
| | - Giovanni Martinelli
- Scientific Directorate, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
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19
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Liu K, Jin M, Xiao L, Liu H, Wei S. Distinct prognostic values of mRNA expression of glutathione peroxidases in non-small cell lung cancer. Cancer Manag Res 2018; 10:2997-3005. [PMID: 30214294 PMCID: PMC6118261 DOI: 10.2147/cmar.s163432] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Introduction Glutathione peroxidases (GPxs) constitutes an enzyme family which has the ability to reduce free hydrogen peroxide to water and lipid hydroperoxides to their corresponding alcohols, and its main biological roles are to protect organisms from oxidative stress-induced damage. GPxs include eight members in different tissues of the body, and they play essential roles in carcinogenesis. However, the prognostic value of individual GPx in non-small cell lung cancer (NSCLC) remains elusive. Materials and methods In the current study, we investigated the prognostic value of GPxs in NSCLC patients through the “Kaplan–Meier plotter” database, wherein updated gene expression data and survival information from a total of 1,926 NSCLC patients are included. Results High expression of GPx1 mRNA was correlated with worse overall survival (OS) in adenocarcinoma patients. High expression of GPx2 mRNA was correlated with worse OS for all NSCLC patients. In contrast, high expression of GPx3 mRNA was associated with better OS for all NSCLC patients. High expression of GPx4 mRNA was significantly correlated with worsening adenocarcinoma in these patients. GPx5 mRNA high expression correlated with worsening OS for all NSCLC patients. Discussion The current findings of prognostic values of individual mRNA expression of GPxs in NSCLC patients indicate some GPxs may have prognostic value in NSCLC patients, and this needs further study.
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Affiliation(s)
- Kui Liu
- Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China, ;
| | - Meng Jin
- Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China, ;
| | - Li Xiao
- Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China, ;
| | - Huiguo Liu
- Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China, ;
| | - Shuang Wei
- Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China, ;
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20
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Prognostic roles of Notch receptor mRNA expression in human ovarian cancer. Oncotarget 2018; 8:32731-32740. [PMID: 28415574 PMCID: PMC5464823 DOI: 10.18632/oncotarget.16387] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 03/09/2017] [Indexed: 12/30/2022] Open
Abstract
Aberrant activation of Notch signaling pathway has been correlated with high grade ovarian carcinoma and carcinogenesis. However, the predictive and prognostic values of Notch signaling pathway in ovarian cancer patients remains unclear. We utilize “The Kaplan-Meier plotter” (KM plotter) background database to access the prognostic values including overall survival (OS), progression-free survival (PFS), as well as post-progression survival (PPS) of four Notch receptor mRNA expression in ovarian cancer patients. Notch1 mRNA high expression was not correlated with OS, PFS and PPS for all ovarian cancer patients, but significantly correlated with poor PFS in TP53 wild type and favorite PFS in TP53 mutation type ovarian cancer patients. Notch2 mRNA high expression was significantly correlated with poor PFS for all ovarian cancer patients, especially in grade II patients. Notch3 mRNA high expression was significantly correlated with favorite PFS for all ovarian cancer patients. Notch4 mRNA high expression was significantly correlated with favorite OS, but not PFS and PPS for all ovarian cancer patients. The results strongly support that there are distinct prognostic values of four Notch receptor mRNA expression in ovarian cancer patients.
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21
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Zhao M, Li S, Zhou L, Shen Q, Zhu H, Zhu X. Prognostic values of excision repair cross-complementing genes mRNA expression in ovarian cancer patients. Life Sci 2017; 194:34-39. [PMID: 29247747 DOI: 10.1016/j.lfs.2017.12.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/02/2017] [Accepted: 12/12/2017] [Indexed: 12/12/2022]
Abstract
Excision repair cross-complementing (ERCC) genes, key components of the nucleotide excision repair pathway, are regarded as crucial factors for DNA repair capacity. Previous studies have investigated prognostic values of ERCC genes in a number of malignancies. However, the relationship between ERCC genes and prognosis of ovarian cancer patients remains controversial. Therefore, in the current study, we systematically analyze the prognostic values of ERCC genes in ovarian cancer by the Kaplan-Meier plotter, which includes updated gene expression data and survival information of 1656 ovarian cancer patients. Our results showed that high expression of ERCC1 and ERCC8 mRNA was related to a worse overall survival among ovarian cancer patients, especially in late stage and poor differentiation serous ovarian patients. Increased ERCC4 mRNA expression indicated a better overall survival among serous ovarian cancer patients. The other ERCC genes were uncorrelated with prognosis in ovarian cancer. These results indicate that some ERCC genes have critical prognostic values in ovarian cancer.
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Affiliation(s)
- Menghuang Zhao
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Saisai Li
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Lulu Zhou
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Qi Shen
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Haiyan Zhu
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
| | - Xueqiong Zhu
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
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22
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Xiong J, Zhang X, Chen X, Wei Y, Lu DG, Han YW, Xu J, Yu D. Prognostic roles of mRNA expression of notch receptors in non-small cell lung cancer. Oncotarget 2017; 8:13157-13165. [PMID: 28061457 PMCID: PMC5355084 DOI: 10.18632/oncotarget.14483] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 12/15/2016] [Indexed: 12/11/2022] Open
Abstract
Notch signalling is aberrantly activated in human non-small cell lung cancer (NSCLC). Nevertheless, the prognostic roles of mRNA expression of four Notch receptors in NSCLC patients remain elusive. In this report, we reported the prognostic roles of Notch receptors in a total of 1,926 NSCLC patients through “The Kaplan-Meier plotter” (KM plotter) database which is capable to assess the effect of 22,277 genes on survival of NSCLC patients. We found that mRNA high expression level of Notch1 was associated with better overall survival (OS) for all NSCLC patients, hazard ratio (HR) 0.78 (0.69-0.89), p=0.00019, better OS in adenocarcinoma (Ade) patients, HR 0.59 (0.46-0.75), p=1.5e-05, as well as in squamous cell carcinoma (SCC) patients, HR 0.78 (0.62-0.99), p=0.044. mRNA high expression levels of Notch2 and Notch3 were associated with worsen OS for all NSCLC patients, as well as in Ade, but not in SCC patients. mRNA high expression level of Notch4 was not found to be associated with to OS for all NSCLC patients. In addition, mRNA high expression levels of Notch2, Notch3, but Notch4 are significantly associated with the NSCLC patients who have different smoking status. Our results indicate that mRNA expression of Notch receptors may have distinct prognostic values in NSCLC patients. These results will benefit for developing tools to accurately predict the prognosis of NSCLC patients.
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Affiliation(s)
- Jianwen Xiong
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province 330006, P. R. China
| | - Xiaoqiang Zhang
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province 330006, P. R. China
| | - Xianglai Chen
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province 330006, P. R. China
| | - Yiping Wei
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province 330006, P. R. China
| | - De-Guo Lu
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Yun-Wei Han
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Jianjun Xu
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province 330006, P. R. China
| | - Dongliang Yu
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province 330006, P. R. China
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23
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Prognostic values of four Notch receptor mRNA expression in gastric cancer. Sci Rep 2016; 6:28044. [PMID: 27363496 PMCID: PMC4929462 DOI: 10.1038/srep28044] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 05/23/2016] [Indexed: 01/09/2023] Open
Abstract
Notch ligands and receptors are frequently deregulated in several human malignancies including gastric cancer. The activation of Notch signaling has been reported to contribute to gastric carcinogenesis and progression. However, the prognostic roles of individual Notch receptors in gastric cancer patients remain elusive. In the current study, we accessed the prognostic roles of four Notch receptors, Notch 1-4, in gastric cancer patients through "The Kaplan-Meier plotter" (KM plotter) database, in which updated gene expression data and survival information include a total of 876 gastric cancer patients. All four Notch receptors' high mRNA expression was found to be correlated to worsen overall survival (OS) for all gastric cancer patients followed for 20 years. We further accessed the prognostic roles of individual Notch receptors in different clinicopathological features using Lauren classification, pathological grades, clinical grades, HER2 status and different choices of treatments of gastric cancer patients. These results indicate that there are critical prognostic values of the four Notch receptors in gastric cancer. This information will be useful for better understanding of the heterogeneity and complexity in the molecular biology of gastric cancer and to develop tools to more accurately predict their prognosis.
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24
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Li K, Guo X, Wang Z, Li X, Bu Y, Bai X, Zheng L, Huang Y. The prognostic roles of ALDH1 isoenzymes in gastric cancer. Onco Targets Ther 2016; 9:3405-14. [PMID: 27354812 PMCID: PMC4907742 DOI: 10.2147/ott.s102314] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Increased aldehyde dehydrogenase 1 (ALDH1) activity has been determined to be present in the stem cells of several kinds of cancers including gastric cancer (GC). Nevertheless, which ones of ALDH1's isoenzymes are leading to ALDH1 activity remains elusive. In this study, we examined the prognostic value and hazard ratio (HR) of individual ALDH1 isoenzymes in patients with GC using "The Kaplan-Meier plotter" database. mRNA high expression level of ALDH1A1 was not found to be significantly correlated with the overall survival (OS) of all patients with GC followed for 20 years, HR =0.86 (95% confidence interval [CI]: 0.7-1.05), P=0.13. mRNA high expression level of ALDH1A2 was also not significantly correlated with OS for all patients with GC, HR =1.13 (95% CI: 0.91-1.41), P=0.25. mRNA high expression level of ALDH1A3 was found to be significantly correlated with worsened OS in either intestinal-type patients, HR =2.24 (95% CI: 1.44-3.49), P=0.00026, or diffuse-type patients, HR =1.91 (95% CI: 1.02-3.59), P=0.04. Interestingly, mRNA high expression level of ALDH1B1 was found to be significantly correlated with better OS for all patients with GC, HR =0.66 (95% CI: 0.53-0.81), P=7.8e-05, and mRNA high expression level of ALDH1L1 was found to be significantly correlated with worsened OS for all patients with GC, HR =1.23 (95% CI: 1-1.51), P=0.048. Furthermore, our results also indicate that ALDH1A3 and ALDH1L1 are potential major contributors to the ALDH1 activity in GC, since mRNA high expression levels of ALDH1A3 and ALDH1L1 were found to be significantly correlated with worsened OS for all patients with GC. Based on our study, ALDH1A3 and ALDH1L1 are potential prognostic markers and therapeutic targets for patients with GC.
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Affiliation(s)
- Kai Li
- Hepatobiliary Treatment Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China; Department of Medical Oncology, Baotou Cancer Hospital, Baotou, Inner Mongolia, People's Republic of China
| | - Xiaoguang Guo
- Surgical Department, Baotou Cancer Hospital, Baotou, Inner Mongolia, People's Republic of China
| | - Ziwei Wang
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Xiaofeng Li
- Department of Medical Oncology, Baotou Cancer Hospital, Baotou, Inner Mongolia, People's Republic of China
| | - Youquan Bu
- Department of Biology, Chongqing Medical University, Chongqing, People's Republic of China
| | - Xuefeng Bai
- Department of Pathology, Baotou Cancer Hospital, Baotou, Inner Mongolia, People's Republic of China
| | - Liansheng Zheng
- Surgical Oncology, Baotou Cancer Hospital, Baotou, Inner Mongolia, People's Republic of China
| | - Ying Huang
- Department of Medical Oncology, Baotou Cancer Hospital, Baotou, Inner Mongolia, People's Republic of China
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25
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Abstract
Aldehyde dehydrogenase 1 (ALDH1) activity has been used as a functional stem cell marker to isolate cancer stem cells in different cancer types, including ovarian cancer. However, which ALDH1’s isoenzymes are contributing to ALDH1 activity in ovarian cancer remains elusive. In addition, the prognostic value of an individual ALDH1 isoenzyme in ovarian cancer is not clear. Thus, we accessed the prognostic value of ALDH1 isoenzymes in ovarian cancer patients through the “Kaplan–Meier plotter” online database, which can be used to determine the effect of the genes on ovarian cancer prognosis. We found that high mRNA expression of five ALDH1 isoenzymes, such as ALDH1A1, ALDH1A2, ALDH1A3, ALDH1B1, and ALDH1L1, was not correlated with overall survival (OS) for all 1,306 ovarian cancer patients. In addition, all five of the ALDH1 isoenzymes’ high mRNA expression was found to be uncorrelated with OS in serous cancer or endometrioid cancer patients. However, ALDH1A3’s high mRNA expression is associated with worse OS in grade II ovarian cancer patients, hazard ratio (HR) 1.53 (1.14–2.07), P=0.005. ALDH1A2’s high mRNA expression is significantly associated with worse OS in TP53 wild-type ovarian cancer patients, HR 2.86 (1.56–5.08), P=0.00036. In addition, ALDH1A3’s high mRNA expression is significantly associated with better OS in TP53 wild-type ovarian cancer patients, HR 0.56 (0.32–1.00), P=0.04. Our results indicate that although ALDH1 isoenzyme mRNA might not be a prognostic marker for overall ovarian cancer patients, some isoenzymes, such as ALDH1A2 and ALDH1A3, might be a good prognostic marker for some types of ovarian cancer patients.
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Affiliation(s)
- Yu-Mei Ma
- Department of Pathology, The Second Hospital of Hebei Medical University, Shijiazhuang City, People's Republic of China
| | - Shan Zhao
- Department of Cancer Second Division, The Second Hospital of Hebei Medical University, Shijiazhuang City, People's Republic of China
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26
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Prognostic implications of securin expression and sub-cellular localization in human breast cancer. Cell Oncol (Dordr) 2016; 39:319-31. [DOI: 10.1007/s13402-016-0277-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2016] [Indexed: 02/06/2023] Open
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27
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Zhou X, Teng L, Wang M. Distinct prognostic values of four-Notch-receptor mRNA expression in ovarian cancer. Tumour Biol 2015; 37:6979-85. [PMID: 26662955 DOI: 10.1007/s13277-015-4594-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 12/03/2015] [Indexed: 12/18/2022] Open
Abstract
Notch signaling pathway includes ligands and Notch receptors, which are frequently deregulated in several human malignancies including ovarian cancer. Aberrant activation of Notch signaling has been linked to ovarian carcinogenesis and progression. In the current study, we used the "Kaplan-Meier plotter" (KM plotter) database, in which updated gene expression data and survival information from a total of 1306 ovarian cancer patients were used to access the prognostic value of four Notch receptors in ovarian cancer patients. Hazard ratio (HR), 95 % confidence intervals, and log-rank P were calculated. Notch1 messenger RNA (mRNA) high expression was not found to be correlated to overall survival (OS) for all ovarian cancer, as well as in serous and endometrioid cancer patients followed for 20 years. However, Notch1 mRNA high expression is significantly associated with worsen OS in TP53 wild-type ovarian cancer patients, while it is significantly associated with better OS in TP53 mutation-type ovarian cancer patients. Notch2 mRNA high expression was found to be significantly correlated to worsen OS for all ovarian cancer patients, as well as in grade II ovarian cancer patients. Notch3 mRNA high expression was found to be significantly correlated to better OS for all ovarian cancer patients, but not in serous cancer patients and endometrioid cancer patients. Notch4 mRNA high expression was not found to be significantly correlated to OS for all ovarian cancer patients, serous cancer patients, and endometrioid cancer patients. These results indicate that there are distinct prognostic values of four Notch receptors in ovarian cancer. This information will be useful for better understanding of the heterogeneity and complexity in the molecular biology of ovarian cancer and for developing tools to more accurately predict their prognosis. Based on our results, Notch1 could be a potential drug target of TP53 wild-type ovarian cancer and Notch2 could be a potential drug target of ovarian cancer.
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Affiliation(s)
- Xinling Zhou
- Department of Obstetrics and Gynecology, The Second People's Hospital of Liaocheng Affiliated to Taishan Medical College, No. 306 Jiankang Rd, Linqing, 252601, Shandong Province, People's Republic of China.
| | - Lingling Teng
- Department of Obstetrics and Gynecology, The Second People's Hospital of Liaocheng Affiliated to Taishan Medical College, No. 306 Jiankang Rd, Linqing, 252601, Shandong Province, People's Republic of China
| | - Min Wang
- Department of Pathology, The Second People's Hospital of Liaocheng Affiliated to Taishan Medical College, Linqing, 252601, Shandong Province, People's Republic of China
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28
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You Q, Guo H, Xu D. Distinct prognostic values and potential drug targets of ALDH1 isoenzymes in non-small-cell lung cancer. DRUG DESIGN DEVELOPMENT AND THERAPY 2015; 9:5087-97. [PMID: 26366059 PMCID: PMC4562757 DOI: 10.2147/dddt.s87197] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Increased aldehyde dehydrogenase 1 (ALDH1) activity has been found in the stem cell populations of leukemia and some solid tumors including non-small-cell lung cancer (NSCLC). However, which ALDH1’s isoenzymes are contributing to ALDH1 activity remains elusive. In addition, the prognostic value of individual ALDH1 isoenzyme is not clear. In the current study, we investigated the prognostic value of ALDH1 isoenzymes in NSCLC patients through the Kaplan–Meier plotter database, which contains updated gene expression data and survival information from a total of 1,926 NSCLC patients. High expression of ALDH1A1 mRNA was found to be correlated to a better overall survival (OS) in all NSCLC patients followed for 20 years (hazard ratio [HR] 0.88 [0.77–0.99], P=0.039). In addition, high expression of ALDH1A1 mRNA was also found to be correlated to better OS in adenocarcinoma (Ade) patients (HR 0.71 [0.57–0.9], P=0.0044) but not in squamous cell carcinoma (SCC) patients (HR 0.92 [0.72–1.16], P=0.48). High expression of ALDH1A2 and ALDH1B1 mRNA was found to be correlated to worser OS in all NSCLC patients, as well as in Ade, but not in SCC patients. High expression of both ALDH1A3 and ALDH1L1 mRNA was not found to be correlated to OS in all NSCLC patients. These results strongly support that ALDH1A1 mRNA in NSCLC is associated with better prognosis. In addition, our current study also supports that ALDH1A2 and ALDH1B1 might be major contributors to the ALDH1 activity in NSCLC, since high expression of ALDH1A2 and ALDH1B1 mRNA was found to be significantly correlated to worser OS in all NSCLC patients. Based on our study, ALDH1A2 and ALDH1B1 might be excellent potential drug targets for NSCLC patients.
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Affiliation(s)
- Qinghua You
- Department of Pathology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, People's Republic of China
| | - Huanchen Guo
- Department of Respiratory Medicine, Shouguang Hospital of Traditional Chinese Medicine, Shouguang, People's Republic of China
| | - Dongxiang Xu
- Department of Endocrinology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, People's Republic of China
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29
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Prognostic values of Notch receptors in breast cancer. Tumour Biol 2015; 37:1871-7. [PMID: 26323259 DOI: 10.1007/s13277-015-3961-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 08/19/2015] [Indexed: 12/19/2022] Open
Abstract
Notch receptors are frequently deregulated in several human malignancies including human breast cancer. Activation of Notch has been reported to cause mammary carcinomas in mice. However, the prognostic value of individual Notch receptors in breast cancer (BC) patients remains elusive. In the current study, we investigated the prognostic value of Notch receptors in human BC patients. More specifically, we investigated the prognostic value of four Notch receptors in breast cancer patients through "the Kaplan-Meier plotter" (KM plotter) database, in which updated gene expression data and survival information are from a total of 3554 breast cancer patients. Our results showed that Notch1 messenger RNA (mRNA) high expression was correlated to worsen overall survival (OS) in PgR-negative BC patients. Notch2, Notch3, and Notch4 mRNA high expressions were found to be correlated to better OS for all breast cancer patients. Notch2 was also found to be correlated to better OS in lymph node-negative breast cancer patients and HER2-positive breast cancer patients. These results will be useful for better understanding of the heterogeneity and complexity in the molecular biology of breast cancer and for developing tools to more accurately predict their prognosis and design their customized treatment strategies.
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30
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Chen H, Lee J, Kljavin NM, Haley B, Daemen A, Johnson L, Liang Y. Requirement for BUB1B/BUBR1 in tumor progression of lung adenocarcinoma. Genes Cancer 2015; 6:106-18. [PMID: 26000094 PMCID: PMC4426948 DOI: 10.18632/genesandcancer.53] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 03/04/2015] [Indexed: 01/09/2023] Open
Abstract
Lung adenocarcinoma is often discovered as metastatic disease with very poor prognosis. However, much remains unknown about the mechanisms of lung adenocarcinoma tumor progression. In this study we showed that knockdown of BUB1B/BUBR1, a critical mitotic checkpoint protein, significantly inhibited anchorage-independent growth of lung adenocarcinoma cell lines. In allograft and tail vein mouse model studies, BUB1B suppression inhibited primary tumor growth and reduced metastasis to the lung and lymph nodes, resulting in prolonged survival in both tumor prevention and tumor intervention settings. Mechanistic studies revealed that BUB1B knockdown sensitized cells to anoikis. The N-terminal region and GLEBS domain of BUB1B were required for its functions in both anchorage-independent growth and anoikis resistance, whereas the kinase domain was less critical. Overexpression of BUB1B is associated with disease progression and poor survival in human lung adenocarcinoma patients. Collectively, these data reveal a novel function for BUB1B in mediating anchorage-independent survival and growth, thereby facilitating lung adenocarcinoma dissemination during metastasis. Thus, targeting BUB1B could provide potential therapeutic benefit in suppressing metastasis and prolonging survival in lung adenocarcinoma patients.
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Affiliation(s)
- Honglin Chen
- Departments of Molecular Biology, Genentech Inc., South San Francisco, California, USA
| | - James Lee
- Discovery Oncology, Genentech Inc., South San Francisco, California, USA
| | - Noelyn M Kljavin
- Molecular Oncology, Genentech Inc., South San Francisco, California, USA
| | - Benjamin Haley
- Departments of Molecular Biology, Genentech Inc., South San Francisco, California, USA
| | - Anneleen Daemen
- Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, California, USA
| | - Leisa Johnson
- Discovery Oncology, Genentech Inc., South San Francisco, California, USA
| | - Yuxin Liang
- Departments of Molecular Biology, Genentech Inc., South San Francisco, California, USA
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31
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Cirak Y, Furuncuoglu Y, Yapicier O, Alici S, Argon A. Predictive and prognostic values of BubR1 and synuclein-gamma expression in breast cancer. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:5345-5353. [PMID: 26191236 PMCID: PMC4503107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 04/14/2015] [Indexed: 06/04/2023]
Abstract
The aim of this study is to determine the expression level of spindle assembly checkpoint (SAC) proteins-BubR1 and synuclein-gamma (SNCG) in human breast cancer tissues and to test whether there is a relationship between their expression levels and clinicopathologic parameters including respons to taxanes, tumor grade, estrogen receptor (ER) pozitivity, HER2 status, and overall survival (OS). We analyzed retrospectively paraffin-embedded tissue sections from 55 breast cancer patients whose clinical outcomes had been tracked after taxane treatment in neoadjuvan and metastatic setting. The expression status of BubR1 and SNCG was defined by immunohistochemistry (IHC) using the anti-BubR1 and anti-SNCG antibody. The BubR1 and SNCG was overexpressed in 38% and 62% of the study group, respectively. There was borderline significant correlation between low BubR1 expression and increased taxane sensitivity (P=0.05). In contrast, high SNCG expression was significantly associated with decreased taxane sensitivity (P=0.01). There was no association between the clinicopathologic parameters including histologic grade, ER positivity and HER2 status and the level of these proteins. However, triple negative tumors showed significantly more high BubR1 expression than those other molecular subtypes (P=0.04). Kaplan-Meier survival analysis failed to show a significant correlation between expression levels of BubR1 and SNCG and overall survival although patients with low levels of both proteins had a marginally longer survival time compared to those with high levels. In summary, our data suggest that both BubR1 and SNCG may be promising predictive marker rather than prognostic marker in patients with breast cancer.
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Affiliation(s)
- Yalcin Cirak
- Department of Medical Onkology, Bahcesehir University School of Medicine, Goztepe Medical Park HospitalIstanbul, Turkey
| | - Yavuz Furuncuoglu
- Department of Internal Medicine, Bahcesehir University School of Medicine, Goztepe Medical Park HospitalIstanbul, Turkey
| | - Ozlem Yapicier
- Department of Pathology, Bahcesehir University School of Medicine, Goztepe Medical Park HospitalIstanbul, Turkey
| | - Suleyman Alici
- Department of Medical Onkology, Bahcesehir University School of Medicine, Goztepe Medical Park HospitalIstanbul, Turkey
| | - Andac Argon
- Department of Medical Onkology, Bahcesehir University School of Medicine, Goztepe Medical Park HospitalIstanbul, Turkey
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32
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Singh CK, George J, Nihal M, Sabat G, Kumar R, Ahmad N. Novel downstream molecular targets of SIRT1 in melanoma: a quantitative proteomics approach. Oncotarget 2015; 5:1987-99. [PMID: 24743044 PMCID: PMC4039116 DOI: 10.18632/oncotarget.1898] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Melanoma is one of the most lethal forms of skin cancer and its incidence is continuing to rise in the United States. Therefore, novel mechanism and target-based strategies are needed for the management of this disease. SIRT1, a NAD(+)-dependent class III histone deacetylase, has been implicated in a variety of physiological processes and pathological conditions. We recently demonstrated that SIRT1 is upregulated in melanoma and its inhibition by a small-molecule, tenovin-1, inhibits cell proliferation and clonogenic survival of melanoma cells, possibly via activating p53. Here, we employed a gel free quantitative proteomics approach to identify the downstream effectors and targets of SIRT1 in melanoma. The human malignant melanoma, G361 cells were treated with tenovin-1 followed by protein extraction, in liquid trypsin digestion, and peptide analyses using nanoLC-MS/MS. A total of 1091 proteins were identified, of which 20 proteins showed significant differential expression with 95% confidence interval. These proteins were subjected to gene ontology and Ingenuity Pathway Analysis (IPA) to obtain the information regarding their biological and molecular functions. Real-Time qRT-PCR validation showed that five of these (PSAP, MYO1B, MOCOS, HIS1H4A and BUB3) were differentially expressed at mRNA levels. Based on their important role in cell cycle regulation, we selected to focus on BUB family proteins (BUB3, as well as BUB1 and BUBR1) for subsequent validation. The qRT-PCR and immunoblot analyses showed that tenovin-1 inhibition of SIRT1 resulted in a downregulation of BUB3, BUB1 and BUBR1 in multiple melanoma cell lines. Since tenovin-1 is an inhibitor of both SIRT1 and SIRT2, we employed lentivirus mediated silencing of SIRT1 and SIRT2 in G361 cells to determine if the observed effects on BUB family proteins are due to SIRT1- or SIRT2- inhibition. We found that only SIRT1 inhibition resulted in a decrease in BUB3, BUB1 and BUBR1. Our study identified the mitotic checkpoint regulator BUB family proteins as novel downstream targets of SIRT1. However, further validation is needed in appropriate models to confirm our findings and expand on our observations.
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Affiliation(s)
- Chandra K Singh
- Department of Dermatology, University of Wisconsin, Madison, WI
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Wu S, Xue W, Huang X, Yu X, Luo M, Huang Y, Liu Y, Bi Z, Qiu X, Bai S. Distinct prognostic values of ALDH1 isoenzymes in breast cancer. Tumour Biol 2015; 36:2421-6. [PMID: 25582316 DOI: 10.1007/s13277-014-2852-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 11/13/2014] [Indexed: 12/31/2022] Open
Abstract
Aldehyde dehydrogenase 1 (ALDH1), also known as aldehyde dehydrogenase 1 family, is composed of six enzymes that are expressed at high levels in stem cells and are involved in the regulation of stem cell function. Increased ALDH1 activity has been found in the stem cell populations of leukemia and some solid tumors including breast cancer (BC). However, which ALDH1's isoenzymes are contributing to ALDH1 activity has not been determined. In addition, the prognostic value of individual ALDH1 isoenzyme is not clear. In the current study, we investigated the prognostic value of ALDH1 isoenzymes in BC patients through "the Kaplan-Meier plotter" (KM plotter) database, in which updated gene expression data and survival information are from a total of 3455 BC patients. ALDH1A1 messenger RNA (mRNA) high expression was found to be correlated to worsen overall survival (OS) for all BC patients. ALDH1A2 and ALDH1L1 mRNA high expressions were found to be correlated to better OS for all BC patients. Both of ALDH1A3 and ALDH1B1 mRNA high expressions were not found to be correlated to OS for all BC patients. These results strongly support that ALDH1A1 was only a biomarker for predicting poor survival of BC patients among ALDH1 isoenzymes. ALDH1A1 might be a major contributor of ALDH1 activity in BC, since only ALDH1A1 mRNA high expression was found to be significantly correlated to worsen OS for all BC patients.
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Affiliation(s)
- Shaokun Wu
- Department of Oncology, SunYat-Sen Memorial Hospital, SunYat-Sen University, Guangzhou, 510120, People's Republic of China
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