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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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Zhao Y, Zhao J, Zhong M, Zhang Q, Yan F, Feng Y, Guo Y. The expression and methylation of PITX genes is associated with the prognosis of head and neck squamous cell carcinoma. Front Genet 2022; 13:982241. [PMID: 36204311 PMCID: PMC9530742 DOI: 10.3389/fgene.2022.982241] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/07/2022] [Indexed: 12/24/2022] Open
Abstract
Background: The PITX gene family, comprising PITX1, PITX2, and PITX3, is critical in organogenesis and has been evolutionary conserved in animals. PITX genes are associated with the advanced progression and poor prognosis of multiple cancers. However, the relationship between the PITX genes and head and neck squamous cell carcinoma (HNSC) has not been reported. Methods: We used data from The Cancer Genome Atlas (TCGA) to analyze the association between PITX mRNA expression and clinicopathological parameters of patients with HNSC. The prognostic value of PITX genes was evaluated using the Kaplan-Meier plotter. Multivariate Cox analysis was used to screen out prognosis-associated genes to identify better prognostic indicators. The potential roles of PITX1 and PITX2 in HNSC prognosis were investigated using the protein-protein interaction (PPI) network, Gene Ontology (GO) analysis, and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. The correlation between PITX1 and PITX2 expression or methylation and immune cell infiltration was evaluated using the tumor-immune system interaction database (TISIDB). MethSurv was used to identify DNA methylation and its effect on HNSC prognosis. Results:PITX genes expression was correlated with different cancers. PITX1 and PITX2 expression was lower in the patients with HNSC. In HNSC, PITX1 expression was significantly related to the clinical stage, histologic grade, and N stage, while PITX2 expression was only significantly related to the histologic grade. The high expression of PITX3 was significantly related to the histologic grade, T stage, and N stage. Survival analysis revealed that PITX genes had prognostic value in HNSC, which was supported by multivariate Cox analysis. PPI network and enrichment analysis showed that the genes interacting with PITX1 and PITX2 belonged predominantly to signaling pathways associated with DNA binding and transcription. Of the CpG DNA methylation sites in PITX1 and PITX2, 28 and 22 were related to the prognosis of HNSC, respectively. Additionally, PITX1 and PITX2 expression and methylation was associated with tumor-infiltrating lymphocytes (TILs). Conclusion: The PITX genes were differentially expressed in patients with HNSC, highlighting their essential role in DNA methylation and tumor-infiltrating immune cell regulation, as well as overall prognostic value in HNSC.
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Affiliation(s)
- Yaqiong Zhao
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Jie Zhao
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Mengmei Zhong
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Qian Zhang
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Fei Yan
- Hunan Key Laboratory of Oral Health Research and Hunan 3D Printing Engineering Research Center of Oral Care and Hunan Clinical Research Center of Oral Major Diseases and Oral Health and Xiangya Stomatological Hospital and Xiangya School of Stomatology, Central South University, Changsha, China
| | - Yunzhi Feng
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yue Guo
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Yue Guo,
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Li Z, Wang W, Wu J, Ye X. Identification of N7-methylguanosine related signature for prognosis and immunotherapy efficacy prediction in lung adenocarcinoma. Front Med (Lausanne) 2022; 9:962972. [PMID: 36091687 PMCID: PMC9449120 DOI: 10.3389/fmed.2022.962972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundLung adenocarcinoma (LUAD) is one of the most frequent causes of tumor-related mortality worldwide. Recently, the role of N7-methylguanosine (m7G) in tumors has begun to receive attention, but no investigation on the impact of m7G on LUAD. This study aims to elucidate the significance of m7G on the prognosis and immunotherapy in LUAD.MethodsConsensus clustering was employed to determine the molecular subtype according to m7G-related regulators extracted from The Cancer Genome Atlas (TCGA) database. Survival, clinicopathological features and tumor mutational burden (TMB) analysis were applied to research molecular characteristics of each subtype. Subsequently, “limma” package was used to screen differentially expressed genes (DEGs) between subtypes. In the TCGA train cohort (n = 245), a prognostic signature was established by univariate Cox regression, lasso regression and multivariate Cox regression analysis according to DEGs and survival analysis was employed to assess the prognosis. Then the prognostic value of the signature was verified by TCGA test cohort (n = 245), TCGA entire cohort (n = 490) and GSE31210 cohort (n = 226). Moreover, the association among immune infiltration, clinical features and the signature was investigated. The immune checkpoints, TMB and tumor immune dysfunction and exclusion (TIDE) were applied to predict the immunotherapy response.ResultsTwo novel molecular subtypes (C1 and C2) of LUAD were identified. Compared to C2 subtype, C1 subtype had poorer prognosis and higher TMB. Subsequently, the signature (called the “m7G score”) was constructed according to four key genes (E2F7, FAM83A, PITX3, and HOXA13). The distribution of m7G score were significantly different between two molecular subtypes. The patients with lower m7G score had better prognosis in TCGA train cohort and three verification cohort. The m7G score was intensively related to immune infiltration. Compared with the lower score, the higher m7G score was related to remarkable upregulation of the PD-1 and PD-L1, the higher TMB and the lower TIDE score.ConclusionThis study established a m7G-related signature for predicting prognosis and immunotherapy in LUAD, which may contribute to the development of new therapeutic strategies for LUAD.
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Cai W, Jing M, Wen J, Guo H, Xue Z. Epigenetic Alterations of DNA Methylation and miRNA Contribution to Lung Adenocarcinoma. Front Genet 2022; 13:817552. [PMID: 35711943 PMCID: PMC9194831 DOI: 10.3389/fgene.2022.817552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/26/2022] [Indexed: 12/24/2022] Open
Abstract
This study focused on the epigenetic alterations of DNA methylation and miRNAs for lung adenocarcinoma (LUAD) diagnosis and treatment using bioinformatics analyses. DNA methylation data and mRNA and miRNA expression microarray data were obtained from The Cancer Genome Atlas (TCGA) database. The differentially methylated genes (DMGs), differentially expressed genes (DEGs), and differentially expressed miRNAs were analyzed by using the limma package. The DAVID database performed GO and KEGG pathway enrichment analyses. Using STRING and Cytoscape, we constructed the protein-protein interaction (PPI) network and achieved visualization. The online analysis tool CMap was used to identify potential small-molecule drugs for LUAD. In LUAD, 607 high miRNA-targeting downregulated genes and 925 low miRNA-targeting upregulated genes, as well as 284 hypermethylated low-expression genes and 315 hypomethylated high-expression genes, were obtained. They were mainly enriched in terms of pathways in cancer, neuroactive ligand-receptor interaction, cAMP signaling pathway, and cytosolic DNA-sensing pathway. In addition, 40 upregulated and 84 downregulated genes were regulated by both aberrant alternations of DNA methylation and miRNAs. Five small-molecule drugs were identified as a potential treatment for LUAD, and five hub genes (SLC2A1, PAX6, LEP, KLF4, and FGF10) were found in PPI, and two of them (SLC2A1 and KLF4) may be related to the prognosis of LUAD. In summary, our study identified a series of differentially expressed genes associated with epigenetic alterations of DNA methylation and miRNA in LUAD. Five small-molecule drugs and five hub genes may be promising drugs and targets for LUAD treatment.
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Affiliation(s)
- Wenhan Cai
- Medical School of Chinese PLA, Beijing, China
| | - Miao Jing
- Medical School of Chinese PLA, Beijing, China
| | - Jiaxin Wen
- Department of Thoracic Surgery, The First Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Hua Guo
- Medical School of Chinese PLA, Beijing, China
| | - Zhiqiang Xue
- Department of Thoracic Surgery, The First Medical Centre, Chinese PLA General Hospital, Beijing, China
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PITX1 Is a Regulator of TERT Expression in Prostate Cancer with Prognostic Power. Cancers (Basel) 2022; 14:cancers14051267. [PMID: 35267575 PMCID: PMC8909694 DOI: 10.3390/cancers14051267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Most prostate cancer is of an indolent form and is curable. However, some prostate cancer belongs to rather aggressive subtypes leading to metastasis and death, and immediate therapy is mandatory. However, for these, the therapeutic options are highly invasive, such as radical prostatectomy, radiation or brachytherapy. Hence, a precise diagnosis of these tumor subtypes is needed, and the thus far applied diagnostic means are insufficient for this. Besides this, for their endless cell divisions, prostate cancer cells need the enzyme telomerase to elongate their telomeres (chromatin endings). In this study, we developed a gene regulatory model based on large data from transcription profiles from prostate cancer and chromatin-immuno-precipitation studies. We identified the developmental regulator PITX1 regulating telomerase. Besides observing experimental evidence of PITX1′s functional role in telomerase regulation, we also found PITX1 serving as a prognostic marker, as concluded from an analysis of more than 15,000 prostate cancer samples. Abstract The current risk stratification in prostate cancer (PCa) is frequently insufficient to adequately predict disease development and outcome. One hallmark of cancer is telomere maintenance. For telomere maintenance, PCa cells exclusively employ telomerase, making it essential for this cancer entity. However, TERT, the catalytic protein component of the reverse transcriptase telomerase, itself does not suit as a prognostic marker for prostate cancer as it is rather low expressed. We investigated if, instead of TERT, transcription factors regulating TERT may suit as prognostic markers. To identify transcription factors regulating TERT, we developed and applied a new gene regulatory modeling strategy to a comprehensive transcriptome dataset of 445 primary PCa. Six transcription factors were predicted as TERT regulators, and most prominently, the developmental morphogenic factor PITX1. PITX1 expression positively correlated with telomere staining intensity in PCa tumor samples. Functional assays and chromatin immune-precipitation showed that PITX1 activates TERT expression in PCa cells. Clinically, we observed that PITX1 is an excellent prognostic marker, as concluded from an analysis of more than 15,000 PCa samples. PITX1 expression in tumor samples associated with (i) increased Ki67 expression indicating increased tumor growth, (ii) a worse prognosis, and (iii) correlated with telomere length.
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Liu L, He H, Peng Y, Yang Z, Gao S. A four-gene prognostic signature for predicting the overall survival of patients with lung adenocarcinoma. PeerJ 2021; 9:e11911. [PMID: 34631307 PMCID: PMC8465999 DOI: 10.7717/peerj.11911] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 07/14/2021] [Indexed: 01/12/2023] Open
Abstract
Background The prognosis of patients for lung adenocarcinoma (LUAD) is known to vary widely; the 5-year overall survival rate is just 63% even for the pathological IA stage. Thus, in order to identify high-risk patients and facilitate clinical decision making, it is vital that we identify new prognostic markers that can be used alongside TNM staging to facilitate risk stratification. Methods We used mRNA expression from The Cancer Genome Atlas (TCGA) cohort to identify a prognostic gene signature and combined this with clinical data to develop a predictive model for the prognosis of patients for lung adenocarcinoma. Kaplan-Meier curves, Lasso regression, and Cox regression, were used to identify specific prognostic genes. The model was assessed via the area under the receiver operating characteristic curve (AUC-ROC) and validated in an independent dataset (GSE50081) from the Gene Expression Omnibus (GEO). Results Our analyses identified a four-gene prognostic signature (CENPH, MYLIP, PITX3, and TRAF3IP3) that was associated with the overall survival of patients with T1-4N0-2M0 in the TCGA dataset. Multivariate regression suggested that the total risk score for the four genes represented an independent prognostic factor for the TCGA and GEO cohorts; the hazard ratio (HR) (high risk group vs low risk group) were 2.34 (p < 0.001) and 2.10 (p = 0.017). Immune infiltration estimations, as determined by an online tool (TIMER2.0) showed that CD4+ T cells were in relative abundance in the high risk group compared to the low risk group in both of the two cohorts (both p < 0.001). We established a composite prognostic model for predicting OS, combined with risk-grouping and clinical factors. The AUCs for 1-, 3-, 5- year OS in the training set were 0.750, 0.737, and 0.719; and were 0.645, 0.766, and 0.725 in the validation set. The calibration curves showed a good match between the predicted probabilities and the actual probabilities. Conclusions We identified a four-gene predictive signature which represents an independent prognostic factor and can be used to identify high-risk patients from different TNM stages of LUAD. A new prognostic model that combines a prognostic gene signature with clinical features exhibited better discriminatory ability for OS than traditional TNM staging.
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Affiliation(s)
- Lei Liu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Huayu He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yue Peng
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhenlin Yang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shugeng Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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