1
|
Wang J, Gilani SF, Noor N, Ahmed MR, Munazir M, Zubair A, Sultan R, Abdel-Maksoud MA, Saleh IA, Zomot N, Kodous AS, Ibrahim SS, El-Tayeb MA, Aufy M, Zaky MY, Hassan SS, Hameed Y. Decoding the DSCC1 gene as a pan-cancer biomarker in human cancers via comprehensive multi-omics analyses. Am J Transl Res 2024; 16:738-754. [PMID: 38586115 PMCID: PMC10994803 DOI: 10.62347/yorr3755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 03/06/2024] [Indexed: 04/09/2024]
Abstract
OBJECTIVES While dysregulation of DSCC1 (DNA Replication And Sister Chromatid Cohesion 1) has been established in breast cancer and colorectal cancer, its associations with other tumors remain unclear. Therefore, this study was launched to explore the role of DSCC1 in pan-cancer. METHODOLOGY In this study, we investigate the biological functions of DSCC1 across 33 solid tumors, elucidating its role in promoting oncogenesis and progression in various cancers through comprehensive analysis of multi-omics data. RESULTS We conducted a comprehensive analysis of DSCC1 expression using RNA-seq data from TCGA and GTEx databases across 30 cancer types. Striking variations were observed, with significant overexpression of DSCC1 identified in numerous cancers. Elevated DSCC1 level was strongly associated with poorer prognosis, shorter survival, and advanced tumor stages in kidney renal papillary cell carcinoma (KIRP), liver hepatocellular carcinoma (LIHC), lung adenocarcinoma (LUAD), as indicated by Kaplan-Meier curves and GEPIA2 analysis. Further investigation into the molecular mechanisms revealed reduced DNA methylation in the DSCC1 promoter region in KIRP, LIHC, and LUAD, supporting enhanced RNA transcription. Protein expression analysis via the Human Protein Atlas (HPA) corroborated mRNA expression findings, showcasing elevated DSCC1 protein in KIRP, LIHC, and LUAD tissues. Mutational analysis using cBioPortal revealed alterations in 0.4% of KIRP, 17% of LIHC, and 5% of LUAD samples, predominantly characterized by amplification. Immune cell infiltration analysis demonstrated robust positive correlations between DSCC1 expression and CD8+ T cells, CD4+ T cells, and B cells, influencing the tumor microenvironment. STRING and gene enrichment analyses unveiled DSCC1's involvement in critical pathways, emphasizing its multifaceted impact. Notably, drug sensitivity analysis highlighted a significant correlation between DSCC1 mRNA expression and responses to 78 anticancer treatments, suggesting its potential as a predictive biomarker and therapeutic target for KIRP, LIHC, and LUAD. Finally, immunohistochemistry staining of clinical samples validated computational results, confirming elevated DSCC1 protein expression. CONCLUSION Overall, this study provides comprehensive insights into the pivotal role of DSCC1 in KIRP, LIHC, and LUAD initiation, progression, and therapeutic responsiveness, laying the foundation for further investigations and personalized treatment strategies.
Collapse
Affiliation(s)
- Jingru Wang
- Mengcheng County Hospital of Chinese MedicineChina
- Bozhou Second Chinese Medicine HospitalChina
| | | | - Nazia Noor
- Department of Pathology, Continental Medical CollegeLahore, Pakistan
| | | | - Mehmooda Munazir
- Department of Botany, Government College Women UniversitySialkot, Pakistan
| | - Ayesha Zubair
- Department of Biochemistry, CMH Lahore Medical College and Institute of DentistryLahore 54000, Punjab, Pakistan
| | - Rizwana Sultan
- Department of Pathology, Faculty of Veterinary and Animal Sciences, Cholistan University of Veterinary and Animal SciencesBahawalpur 63100, Punjab, Pakistan
| | - Mostafa A Abdel-Maksoud
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | | | - Naser Zomot
- Faculty of Science, Zarqa UniversityZarqa 13110, Jordan
| | - Ahmad S Kodous
- Department of Molecular Oncology, Cancer Institute (WIA)38, Sardar Patel Road, P.O. Box 600036, Chennai, Tamilnadu, India
- Department of Radiation Biology, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA)P.O. Box 13759, Cairo, Egypt
| | - Shebl Salah Ibrahim
- Department of Biochemistry, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Mohamed A El-Tayeb
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Mohammed Aufy
- Department of Pharmaceutical Sciences, Division of Pharmacology and Toxicology, University of ViennaVienna 1090, Austria
| | - Mohamed Y Zaky
- UPMC Hillman Cancer Center, Division of Hematology and Oncology, Department of Medicine, University of PittsburghPittsburgh, PA 15213, USA
| | - Syed Sairum Hassan
- Department of Medicine, Bilawal Medical College, Liaquat University of Medical and Health Sciences (LUMHS)Jamshoro 76090, Sindh, Pakistan
| | - Yasir Hameed
- Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, The Islamia University of BahawalpurBahawalpur 63100, Punjab, Pakistan
| |
Collapse
|
2
|
Sultan G, Zubair S. An ensemble of bioinformatics and machine learning approaches to identify shared breast cancer biomarkers among diverse populations. Comput Biol Chem 2024; 108:107999. [PMID: 38070457 DOI: 10.1016/j.compbiolchem.2023.107999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 11/27/2023] [Accepted: 12/03/2023] [Indexed: 01/22/2024]
Abstract
Breast cancer continues to be a prominent cause for substantial loss of life among women globally. Despite established treatment approaches, the rising prevalence of breast cancer is a concerning trend regardless of geographical location. This highlights the need to identify common key genes and explore their biological significance across diverse populations. Our research centered on establishing a correlation between common key genes identified in breast cancer patients. While previous studies have reported many of the genes independently, our study delved into the unexplored realm of their mutual interactions, that may establish a foundational network contributing to breast cancer development. Machine learning algorithms were employed for sample classification and key gene selection. The best performance model further selected the candidate genes through expression pattern recognition. Subsequently, the genes common in all the breast cancer patients from India, China, Czech Republic, Germany, Malaysia and Saudi Arabia were selected for further study. We found that among ten classifiers, Catboost exhibited superior performance with an average accuracy of 92%. Functional enrichment analysis and pathway analysis revealed that calcium signaling pathway, regulation of actin cytoskeleton pathway and other cancer-associated pathways were highly enriched with our identified genes. Notably, we observed that these genes regulate each other, forming a complex network. Additionally, we identified PALMD gene as a novel potential biomarker for breast cancer progression. Our study revealed key gene modules forming a complex network that were consistently expressed in different populations, affirming their critical role and biological significance in breast cancer. The identified genes hold promise as prospective biomarkers of breast cancer prognosis irrespective of country of origin or ethnicity. Future investigations will expand upon these genes in a larger population and validate their biological functions through in vivo analysis.
Collapse
Affiliation(s)
- Ghazala Sultan
- Department of Computer Science, Aligarh Muslim University, Aligarh 202002, India
| | - Swaleha Zubair
- Department of Computer Science, Aligarh Muslim University, Aligarh 202002, India.
| |
Collapse
|
3
|
Honar YS, Javaher S, Soleimani M, Zarebkohan A, Farhadihosseinabadi B, Tohidfar M, Abdollahpour-Alitappeh M. Advanced stage, high-grade primary tumor ovarian cancer: a multi-omics dissection and biomarker prediction process. Sci Rep 2023; 13:17265. [PMID: 37828118 PMCID: PMC10570268 DOI: 10.1038/s41598-023-44246-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 10/05/2023] [Indexed: 10/14/2023] Open
Abstract
Ovarian cancer (OC) incidence and mortality rates continue to escalate globally. Early detection of OC is challenging due to extensive metastases and the ambiguity of biomarkers in advanced High-Grade Primary Tumors (HGPTs). In the present study, we conducted an in-depth in silico analysis in OC cell lines using the Gene Expression Omnibus (GEO) microarray dataset with 53 HGPT and 10 normal samples. Differentially-Expressed Genes (DEGs) were also identified by GEO2r. A variety of analyses, including gene set enrichment analysis (GSEA), ChIP enrichment analysis (ChEA), eXpression2Kinases (X2K) and Human Protein Atlas (HPA), elucidated signaling pathways, transcription factors (TFs), kinases, and proteome, respectively. Protein-Protein Interaction (PPI) networks were generated using STRING and Cytoscape, in which co-expression and hub genes were pinpointed by the cytoHubba plug-in. Validity of DEG analysis was achieved via Gene Expression Profiling Interactive Analysis (GEPIA). Of note, KIAA0101, RAD51AP1, FAM83D, CEP55, PRC1, CKS2, CDCA5, NUSAP1, ECT2, and TRIP13 were found as top 10 hub genes; SIN3A, VDR, TCF7L2, NFYA, and FOXM1 were detected as predominant TFs in HGPTs; CEP55, PRC1, CKS2, CDCA5, and NUSAP1 were identified as potential biomarkers from hub gene clustering. Further analysis indicated hsa-miR-215-5p, hsa-miR-193b-3p, and hsa-miR-192-5p as key miRNAs targeting HGPT genes. Collectively, our findings spotlighted HGPT-associated genes, TFs, miRNAs, and pathways as prospective biomarkers, offering new avenues for OC diagnostic and therapeutic approaches.
Collapse
Affiliation(s)
- Yousof Saeedi Honar
- Department of Plant Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, 1983963113, Iran
| | - Saleh Javaher
- Department of Plant Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, 1983963113, Iran
| | - Marziye Soleimani
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, 1983969411, Iran
| | - Amir Zarebkohan
- Department of Medical Nanotechnology, Drug Applied Research Center, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, 516661-4733, Iran
| | | | - Masoud Tohidfar
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, 1983969411, Iran.
| | | |
Collapse
|
4
|
ETNK2 Low-Expression Predicts Poor Prognosis in Renal Cell Carcinoma with Immunosuppressive Tumor Microenvironment. JOURNAL OF ONCOLOGY 2023; 2023:1743357. [PMID: 36866238 PMCID: PMC9974283 DOI: 10.1155/2023/1743357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/11/2022] [Accepted: 01/17/2023] [Indexed: 02/23/2023]
Abstract
Background The ethanolamine kinase 2 (ETNK2) gene is implicated in carcinogenesis, but its expression and involvement in kidney renal clear cell carcinoma (KIRC) remain unknown. Methods Initially, we conducted a pan-cancer study in which we searched the Gene Expression Profiling Interactive Analysis, the UALCAN, and the Human Protein Atlas databases to determine the expression level of the ETNK2 gene in KIRC. The Kaplan-Meier curve was then used to calculate the overall survival (OS) of KIRC patients. We then used the differentially expressed genes (DEGs) and enrichment analysis to explain the mechanism of the ETNK2 gene. Finally, the immune cell infiltration analysis was performed. Results Although the ETNK2 gene expression was lower in KIRC tissues, the findings illustrated a link between the ETNK2 gene expression and a shorter OS time for KIRC patients. DEGs and enrichment analysis revealed that the ETNK2 gene in KIRC involved multiple metabolic pathways. Finally, the ETNK2 gene expression has been linked to several immune cell infiltrations. Conclusions According to the findings, the ETNK2 gene plays a crucial role in tumor growth. It can potentially serve as a negative prognostic biological marker for KIRC by modifying immune infiltrating cells.
Collapse
|
5
|
Apoptotic Cell Death via Activation of DNA Degradation, Caspase-3 Activity, and Suppression of Bcl-2 Activity: An Evidence-Based Citrullus colocynthis Cytotoxicity Mechanism toward MCF-7 and A549 Cancer Cell Lines. SEPARATIONS 2022. [DOI: 10.3390/separations9120411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
Abstract
The objectives of this study are to investigate the cytotoxic effect of different Citrullus colocynthis extracts on breast and lung cancer cell lines using flow cytometry to gain mechanistic insights. C. colocynthis was extracted sequentially using the Soxhlet method. We first tested the plant extracts’ cytotoxicity on non-malignant L929 cells and cancerous breast (MCF-7) and lung (A549) cell lines. We observed that the IC50 of the methanol extract on the viability of MCF-7 and A549 cell lines was 81.08 µg/mL and 17.84 µg/mL, respectively, using the MTT assay. The aqueous and methanol extracts were less toxic when tested against the non-cancerous L929 cell line, with IC50 values of 235.48 µg/mL and 222.29 µg/mL, respectively. Then, using flow cytometry, we investigated the underlying molecular pathways with Annexin-V, Anti-Bcl-2, Caspase-3, and DNA fragmentation (TUNEL) assays. Flow cytometric and molecular marker analyses revealed that the methanol extract activated caspase-3 and inhibited Bcl-2 protein, causing early and late apoptosis, as well as cell death via DNA damage in breast and lung cancer cells. These findings indicate that the methanol extract of C. colocynthis is cytotoxic to breast and lung cancer cell lines. The total phenolic and flavonoid content analysis results showed the methanolic extract of C. colocynthis has a concentration of 326.25 μg GAE/g dwt and 274.61 μg QE/g dwt, respectively. GC-MS analysis of the methanol extract revealed phytochemicals relevant to its cytotoxicity.
Collapse
|
6
|
Deng Y, Huang H, Shi J, Jin H. Identification of Candidate Genes in Breast Cancer Induced by Estrogen Plus Progestogens Using Bioinformatic Analysis. Int J Mol Sci 2022; 23:ijms231911892. [PMID: 36233194 PMCID: PMC9569986 DOI: 10.3390/ijms231911892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/28/2022] [Accepted: 10/04/2022] [Indexed: 11/16/2022] Open
Abstract
Menopausal hormone therapy (MHT) was widely used to treat menopause-related symptoms in menopausal women. However, MHT therapies were controversial with the increased risk of breast cancer because of different estrogen and progestogen combinations, and the molecular basis behind this phenomenon is currently not understood. To address this issue, we identified differentially expressed genes (DEGs) between the estrogen plus progestogens treatment (EPT) and estrogen treatment (ET) using the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) data. As a result, a total of 96 upregulated DEGs were first identified. Seven DEGs related to the cell cycle (CCNE2, CDCA5, RAD51, TCF19, KNTC1, MCM10, and NEIL3) were validated by RT-qPCR. Specifically, these seven DEGs were increased in EPT compared to ET (p < 0.05) and had higher expression levels in breast cancer than adjacent normal tissues (p < 0.05). Next, we found that estrogen receptor (ER)-positive breast cancer patients with a higher CNNE2 expression have a shorter overall survival time (p < 0.05), while this effect was not observed in the other six DEGs (p > 0.05). Interestingly, the molecular docking results showed that CCNE2 might bind to 17β-estradiol (−6.791 kcal/mol), progesterone (−6.847 kcal/mol), and medroxyprogesterone acetate (−6.314 kcal/mol) with a relatively strong binding affinity, respectively. Importantly, CNNE2 protein level could be upregulated with EPT and attenuated by estrogen receptor antagonist, acolbifene and had interactions with cancer driver genes (AKT1 and KRAS) and high mutation frequency gene (TP53 and PTEN) in breast cancer patients. In conclusion, the current study showed that CCNE2, CDCA5, RAD51, TCF19, KNTC1, MCM10, and NEIL3 might contribute to EPT-related tumorigenesis in breast cancer, with CCNE2 might be a sensitive risk indicator of breast cancer risk in women using MHT.
Collapse
Affiliation(s)
- Yu Deng
- Department of Obstetrics and Gynecology, Peking University First Hospital, No. 8 Xishiku Street, Beijing 100034, China
| | - He Huang
- Department of Obstetrics and Gynecology, Peking University First Hospital, No. 8 Xishiku Street, Beijing 100034, China
| | - Jiangcheng Shi
- School of Life Sciences, Tiangong University, Tianjin 300387, China
| | - Hongyan Jin
- Department of Obstetrics and Gynecology, Peking University First Hospital, No. 8 Xishiku Street, Beijing 100034, China
- Correspondence:
| |
Collapse
|
7
|
Suravajhala P, Goltsov A. Three Grand Challenges in High Throughput Omics Technologies. Biomolecules 2022; 12:biom12091238. [PMID: 36139077 PMCID: PMC9496467 DOI: 10.3390/biom12091238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
- Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwavidyapeetham, Amritapuri, Clappana, Kerala 690525, India
- Bioclues.org, Hyderabad 500072, India
- Correspondence:
| | - Alexey Goltsov
- Biocybernetics Systems and Technologies Division, Institute for Artificial intelligence, MIREA–Russian Technological University, 119454 Moscow, Russia
| |
Collapse
|
8
|
Liu L, Yang S, Lin K, Yu X, Meng J, Ma C, Wu Z, Hao Y, Chen N, Ge Q, Gao W, Wang X, Lam EWF, Zhang L, Li F, Jin B, Jin D. Sp1 induced gene TIMP1 is related to immune cell infiltration in glioblastoma. Sci Rep 2022; 12:11181. [PMID: 35778451 PMCID: PMC9249770 DOI: 10.1038/s41598-022-14751-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 06/13/2022] [Indexed: 11/29/2022] Open
Abstract
Tumor immune microenvironment exerts a profound effect on the population of infiltrating immune cells. Tissue inhibitor of matrix metalloproteinase 1 (TIMP1) is frequently overexpressed in a variety of cells, particularly during inflammation and tissue injury. However, its function in cancer and immunity remains enigmatic. In this study, we find that TIMP1 is substantially up-regulated during tumorigenesis through analyzing cancer bioinformatics databases, which is further confirmed by IHC tissue microarrays of clinical samples. The TIMP1 level is significantly increased in lymphocytes infiltrating the tumors and correlated with cancer progression, particularly in GBM. Notably, we find that the transcriptional factor Sp1 binds to the promoter of TIMP1 and triggers its expression in GBM. Together, our findings suggest that the Sp1-TIMP1 axis can be a potent biomarker for evaluating immune cell infiltration at the tumor sites and therefore, the malignant progression of GBM.
Collapse
Affiliation(s)
- Lu Liu
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Shuyao Yang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Kefeng Lin
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Xiaoman Yu
- Department of Neurosurgery, Guangzhou Women and Children's Medical Center, Guangzhou, 510623, Guangdong, People's Republic of China
| | - Jiaqi Meng
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Chao Ma
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Zheng Wu
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Yuchao Hao
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Ning Chen
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Qi Ge
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Wenli Gao
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Xiang Wang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Eric W-F Lam
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, Guangdong, People's Republic of China
| | - Lin Zhang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Fangcheng Li
- Department of Neurosurgery, Guangzhou Women and Children's Medical Center, Guangzhou, 510623, Guangdong, People's Republic of China.
| | - Bilian Jin
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China.
| | - Di Jin
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China.
| |
Collapse
|
9
|
Toolabi N, Daliri FS, Mokhlesi A, Talkhabi M. Identification of key regulators associated with colon cancer prognosis and pathogenesis. J Cell Commun Signal 2022; 16:115-127. [PMID: 33770351 PMCID: PMC8688655 DOI: 10.1007/s12079-021-00612-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 02/25/2021] [Indexed: 12/11/2022] Open
Abstract
Colon cancer (CC) is the fourth deadliest cancer in the world. New insights into prognostication might be helpful to define the optimal adjuvant treatments for patients in routine clinical practice. Here, a microarray dataset with 30 primary tumors and 30 normal samples was analyzed using GEO2R to find differentially expressed genes (DEGs). Then, DAVID, KEGG, ChEA and X2K were used to analyze DEGs-related Gene Ontology, pathways, transcription factors (TFs) and kinases, respectively. Protein-protein interaction (PPI) networks were constructed using the STRING database and Cytoscape. The modules and hub genes of DEGs was determined through MCODE and CytoHubba plugins, and the expression of hub genes was verified using GEPIA. To find microRNAs and metabolites associated with DEGs, miRTarBase and HMDB were used, respectively. It was found that 233 and 373 genes were upregulated and downregulated in CC, respectively. GO analysis showed that the upregulated DEGs were mainly involved in mitotic nuclear division and cell division. Top 10 hub genes were identified, including AURKB, CDK1, DLGAP5, AURKA, CCNB2, CCNB1, BUB1B, CCNA2, KIF20A and BUB1. Whereas, FOMX1, E2F7, E2F1, E2F4 and AR were identified as top 5 TFs in CC. Moreover, CDK1, CDC2, MAPK14, ATM and CK2ALPHA was identified as top 5 kinases in CC. miRNAs analysis showed that Hsa-miR-215-5p hsa-miR-193b-3p, hsa-miR-192-5p and hsa-miR-16-5p could target the largest number of CC genes. Taken together, CC-related genes, especially the hub genes, TFs, and metabolites might be used as novel biomarkers for CC, as well as for diagnosis and guiding therapeutic strategies for CC.
Collapse
Affiliation(s)
- Narges Toolabi
- Department of Animal Sciences and Marine Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Fattane Sam Daliri
- Department of Animal Sciences and Marine Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Amir Mokhlesi
- Department of Animal Sciences and Marine Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Mahmood Talkhabi
- Department of Animal Sciences and Marine Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran.
| |
Collapse
|
10
|
Integrative Molecular Analyses of an Individual Transcription Factor-Based Genomic Model for Lung Cancer Prognosis. DISEASE MARKERS 2021; 2021:5125643. [PMID: 34925645 PMCID: PMC8672105 DOI: 10.1155/2021/5125643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/12/2021] [Accepted: 11/17/2021] [Indexed: 12/24/2022]
Abstract
Objective Precision medicine with molecular profiles has revolutionized the management of lung cancer contributing to improved prognosis. Herein, we aimed to uncover the gene expression profiling of transcription factors (TFs) in lung cancer as well as to develop a TF-based genomic model. Methods We retrospectively curated lung cancer patients from public databases. Through comparing mRNA expression profiling between lung cancer and normal specimens, specific TFs were determined. Thereafter, a TF genomic model was developed with univariate Cox regression and stepwise multivariable Cox analyses, which was verified through the GSE72094 dataset. Gene set enrichment analyses (GSEA) were presented. Downstream targets of TFs were predicted with ChEA, JASPAR, and MotifMap projects, and their biological significance was investigated through the clusterProfiler algorithm. Results In the TCGA cohort, we proposed a TF-based genomic model, comprised of SATB2, HLF, and NPAS2. Lung cancer individuals were remarkably stratified into high- and low-risk groups. Survival analyses uncovered that high-risk populations presented unfavorable survival outcomes. ROCs confirmed the excellent predictive potency in patients' prognosis. Additionally, this model was an independent prognostic indicator in accordance with multivariate analyses. The clinical implication of the model was well verified in an independent dataset. High risk score was in relation to carcinogenic pathways. Downstream targets were characterized by immune and carcinogenic activation. Conclusion The proposed TF genomic model acts as a promising marker for estimation of lung cancer patients' outcomes. Prospective research is required for testing the clinical utility of the model in individualized management of lung cancer.
Collapse
|
11
|
Alternative splicing acts as an independent prognosticator in ovarian carcinoma. Sci Rep 2021; 11:10413. [PMID: 34001978 PMCID: PMC8129203 DOI: 10.1038/s41598-021-89778-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 04/29/2021] [Indexed: 02/04/2023] Open
Abstract
Alternative splicing (AS) events associated with oncogenic processes present anomalous perturbations in many cancers, including ovarian carcinoma. There are no reliable features to predict survival outcomes for ovarian cancer patients. In this study, comprehensive profiling of AS events was conducted by integrating AS data and clinical information of ovarian serous cystadenocarcinoma (OV). Survival-related AS events were identified by Univariate Cox regression analysis. Then, least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression analysis were used to construct the prognostic signatures within each AS type. Furthermore, we established a splicing-related network to reveal the potential regulatory mechanisms between splicing factors and candidate AS events. A total of 730 AS events were identified as survival-associated splicing events, and the final prognostic signature based on all seven types of AS events could serve as an independent prognostic indicator and had powerful efficiency in distinguishing patient outcomes. In addition, survival-related AS events might be involved in tumor-related pathways including base excision repair and pyrimidine metabolism pathways, and some splicing factors might be correlated with prognosis-related AS events, including SPEN, SF3B5, RNPC3, LUC7L3, SRSF11 and PRPF38B. Our study constructs an independent prognostic signature for predicting ovarian cancer patients’ survival outcome and contributes to elucidating the underlying mechanism of AS in tumor development.
Collapse
|
12
|
Semenas J, Wang T, Sajid Syed Khaja A, Firoj Mahmud AKM, Simoulis A, Grundström T, Fällman M, Persson JL. Targeted inhibition of ERα signaling and PIP5K1α/Akt pathways in castration-resistant prostate cancer. Mol Oncol 2021; 15:968-986. [PMID: 33275817 PMCID: PMC8024724 DOI: 10.1002/1878-0261.12873] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/26/2020] [Accepted: 11/14/2020] [Indexed: 01/02/2023] Open
Abstract
Selective ERα modulator, tamoxifen, is well tolerated in a heavily pretreated castration-resistant prostate cancer (PCa) patient cohort. However, its targeted gene network and whether expression of intratumor ERα due to androgen deprivation therapy (ADT) may play a role in PCa progression is unknown. In this study, we examined the inhibitory effect of tamoxifen on castration-resistant PCa in vitro and in vivo. We found that tamoxifen is a potent compound that induced a high degree of apoptosis and significantly suppressed growth of xenograft tumors in mice, at a degree comparable to ISA-2011B, an inhibitor of PIP5K1α that acts upstream of PI3K/AKT survival signaling pathway. Moreover, depletion of tumor-associated macrophages using clodronate in combination with tamoxifen increased inhibitory effect of tamoxifen on aggressive prostate tumors. We showed that both tamoxifen and ISA-2011B exert their on-target effects on prostate cancer cells by targeting cyclin D1 and PIP5K1α/AKT network and the interlinked estrogen signaling. Combination treatment using tamoxifen together with ISA-2011B resulted in tumor regression and had superior inhibitory effect compared with that of tamoxifen or ISA-2011B alone. We have identified sets of genes that are specifically targeted by tamoxifen, ISA-2011B or combination of both agents by RNA-seq. We discovered that alterations in unique gene signatures, in particular estrogen-related marker genes are associated with poor patient disease-free survival. We further showed that ERα interacted with PIP5K1α through formation of protein complexes in the nucleus, suggesting a functional link. Our finding is the first to suggest a new therapeutic potential to inhibit or utilize the mechanisms related to ERα, PIP5K1α/AKT network, and MMP9/VEGF signaling axis, providing a strategy to treat castration-resistant ER-positive subtype of prostate cancer tumors with metastatic potential.
Collapse
Affiliation(s)
| | - Tianyan Wang
- Department of Molecular BiologyUmeå UniversitySweden
| | | | | | - Athanasios Simoulis
- Department of Clinical Pathology and CytologySkåne University HospitalMalmöSweden
| | | | - Maria Fällman
- Department of Molecular BiologyUmeå UniversitySweden
| | - Jenny L. Persson
- Department of Molecular BiologyUmeå UniversitySweden
- Division of Experimental Cancer ResearchDepartment of Translational MedicineLund UniversityClinical Research Centre in MalmöSweden
- Department of Biomedical ScienceMalmö UniversitySweden
| |
Collapse
|