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Wang J, Zhang W, Hou W, Zhao E, Li X. Molecular Characterization, Tumor Microenvironment Association, and Drug Susceptibility of DNA Methylation-Driven Genes in Renal Cell Carcinoma. Front Cell Dev Biol 2022; 10:837919. [PMID: 35386197 PMCID: PMC8978676 DOI: 10.3389/fcell.2022.837919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Accumulating evidence suggests that DNA methylation has essential roles in the development of renal cell carcinoma (RCC). Aberrant DNA methylation acts as a vital role in RCC progression through regulating the gene expression, yet little is known about the role of methylation and its association with prognosis in RCC. The purpose of this study is to explore the DNA methylation-driven genes for establishing prognostic-related molecular clusters and providing a basis for survival prediction. In this study, 5,198 differentially expressed genes (DEGs) and 270 DNA methylation-driven genes were selected to obtain 146 differentially expressed DNA methylation-driven genes (DEMDGs). Two clusters were distinguished by consensus clustering using 146 DEMDGs. We further evaluated the immune status of two clusters and selected 106 DEGs in cluster 1. Cluster-based immune status analysis and functional enrichment analysis of 106 DEGs provide new insights for the development of RCC. To predict the prognosis of patients with RCC, a prognostic model based on eight DEMDGs was constructed. The patients were divided into high-risk groups and low-risk groups based on their risk scores. The predictive nomogram and the web-based survival rate calculator (http://127.0.0.1:3496) were built to validate the predictive accuracy of the prognostic model. Gene set enrichment analysis was performed to annotate the signaling pathways in which the genes are enriched. The correlation of the risk score with clinical features, immune status, and drug susceptibility was also evaluated. These results suggested that the prognostic model might be a promising prognostic tool for RCC and might facilitate the management of patients with RCC.
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Affiliation(s)
- Jinpeng Wang
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Wei Zhang
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Wenbin Hou
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Enyang Zhao
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xuedong Li
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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DNA Methylation Malleability and Dysregulation in Cancer Progression: Understanding the Role of PARP1. Biomolecules 2022; 12:biom12030417. [PMID: 35327610 PMCID: PMC8946700 DOI: 10.3390/biom12030417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/28/2022] [Accepted: 03/04/2022] [Indexed: 02/05/2023] Open
Abstract
Mammalian genomic DNA methylation represents a key epigenetic modification and its dynamic regulation that fine-tunes the gene expression of multiple pathways during development. It maintains the gene expression of one generation of cells; particularly, the mitotic inheritance of gene-expression patterns makes it the key governing mechanism of epigenetic change to the next generation of cells. Convincing evidence from recent discoveries suggests that the dynamic regulation of DNA methylation is accomplished by the enzymatic action of TET dioxygenase, which oxidizes the methyl group of cytosine and activates transcription. As a result of aberrant DNA modifications, genes are improperly activated or inhibited in the inappropriate cellular context, contributing to a plethora of inheritable diseases, including cancer. We outline recent advancements in understanding how DNA modifications contribute to tumor suppressor gene silencing or oncogenic-gene stimulation, as well as dysregulation of DNA methylation in cancer progression. In addition, we emphasize the function of PARP1 enzymatic activity or inhibition in the maintenance of DNA methylation dysregulation. In the context of cancer remediation, the impact of DNA methylation and PARP1 pharmacological inhibitors, and their relevance as a combination therapy are highlighted.
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Biswas P, Dey D, Rahman A, Islam MA, Susmi TF, Kaium MA, Hasan MN, Rahman MDH, Mahmud S, Saleh MA, Paul P, Rahman MR, Saber MA, Song H, Rahman MA, Kim B. Analysis of SYK Gene as a Prognostic Biomarker and Suggested Potential Bioactive Phytochemicals as an Alternative Therapeutic Option for Colorectal Cancer: An In-Silico Pharmaco-Informatics Investigation. J Pers Med 2021; 11:888. [PMID: 34575665 PMCID: PMC8470848 DOI: 10.3390/jpm11090888] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 09/02/2021] [Accepted: 09/02/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND SYK gene regulates the expression of SYK kinase (Spleen tyrosine kinase), an important non-receptor protein-tyrosine kinase for immunological receptor-mediated signaling, which is also considered a tumor growth metastasis initiator. An onco-informatics analysis was adopted to evaluate the expression and prognostic value of the SYK gene in colorectal cancer (CRC), the third most fatal cancer type; of late, it may be a biomarker as another targeted site for CRC. In addition, identify the potential phytochemicals that may inhibit the overexpression of the SYK kinase protein and minimize the human CRC. MATERIALS & METHODS The differential expression of the SYK gene was analyzed using several transcriptomic databases, including Oncomine, UALCAN, GENT2, and GEPIA2. The server cBioPortal was used to analyze the mutations and copy number alterations, whereas GENT2, Gene Expression Profiling Interactive Analysis (GEPIA), Onco-Lnc, and PrognoScan were used to examine the survival rate. The protein-protein interaction network of SYK kinase and its co-expressed genes was conducted via Gene-MANIA. Considering the SYK kinase may be the targeted site, the selected phytochemicals were assessed by molecular docking using PyRx 0.8 packages. Molecular interactions were also observed by following the Ligplot+ version 2.2. YASARA molecular dynamics simulator was applied for the post-validation of the selected phytochemicals. RESULTS Our result reveals an increased level of mRNA expression of the SYK gene in colorectal adenocarcinoma (COAD) samples compared to those in normal tissues. A significant methylation level and various genetic alterations recurrence of the SYK gene were analyzed where the fluctuation of the SYK alteration frequency was detected across different CRC studies. As a result, a lower level of SYK expression was related to higher chances of survival. This was evidenced by multiple bioinformatics platforms and web resources, which demonstrated that the SYK gene can be a potential biomarker for CRC. In this study, aromatic phytochemicals, such as kaempferol and glabridin that target the macromolecule (SYK kinase), showed higher stability than the controls, and we have estimated that these bioactive potential phytochemicals might be a useful option for CRC patients after the clinical trial. CONCLUSIONS Our onco-informatics investigation suggests that the SYK gene can be a potential prognostic biomarker of CRC. On the contrary, SYK kinase would be a major target, and all selected compounds were validated against the protein using in-silico drug design approaches. Here, more in vitro and in vivo analysis is required for targeting SYK protein in CRC.
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Affiliation(s)
- Partha Biswas
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology (JUST), Jashore 7408, Bangladesh; (P.B.); (A.R.); (M.A.I.); (T.F.S.); (M.A.K.)
- ABEx Bio-Research Center, East Azampur, Dhaka 1230, Bangladesh;
- Laboratory of Pharmaceutical Biotechnology and Bioinformatics, Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology (JUST), Jashore 7408, Bangladesh;
| | - Dipta Dey
- Department of Biochemistry and Molecular Biology, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalgonj 8100, Bangladesh; (D.D.); (P.P.)
| | - Atikur Rahman
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology (JUST), Jashore 7408, Bangladesh; (P.B.); (A.R.); (M.A.I.); (T.F.S.); (M.A.K.)
- Fermentation Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Md. Aminul Islam
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology (JUST), Jashore 7408, Bangladesh; (P.B.); (A.R.); (M.A.I.); (T.F.S.); (M.A.K.)
- Department of Biochemistry and Molecular Biology, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalgonj 8100, Bangladesh; (D.D.); (P.P.)
| | - Tasmina Ferdous Susmi
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology (JUST), Jashore 7408, Bangladesh; (P.B.); (A.R.); (M.A.I.); (T.F.S.); (M.A.K.)
| | - Md. Abu Kaium
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology (JUST), Jashore 7408, Bangladesh; (P.B.); (A.R.); (M.A.I.); (T.F.S.); (M.A.K.)
| | - Md. Nazmul Hasan
- Laboratory of Pharmaceutical Biotechnology and Bioinformatics, Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology (JUST), Jashore 7408, Bangladesh;
| | - MD. Hasanur Rahman
- ABEx Bio-Research Center, East Azampur, Dhaka 1230, Bangladesh;
- Department of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Shafi Mahmud
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.M.); (M.A.S.)
| | - Md. Abu Saleh
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.M.); (M.A.S.)
| | - Priyanka Paul
- Department of Biochemistry and Molecular Biology, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalgonj 8100, Bangladesh; (D.D.); (P.P.)
| | - Md Rezanur Rahman
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Md. Al Saber
- Biotechnology, University of Pécs, Medical School, 7624 Pécs, Hungary;
| | - Hangyeul Song
- Department of Pathology, College of Korean Medicine, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Korea;
| | - Md. Ataur Rahman
- Department of Pathology, College of Korean Medicine, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Korea;
- Korean Medicine-Based Drug Repositioning Cancer Research Center, College of Korean Medicine, Kyung Hee University, Seoul 02447, Korea
- Global Biotechnology & Biomedical Research Network (GBBRN), Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh
| | - Bonglee Kim
- Department of Pathology, College of Korean Medicine, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Korea;
- Korean Medicine-Based Drug Repositioning Cancer Research Center, College of Korean Medicine, Kyung Hee University, Seoul 02447, Korea
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Bu F, Zhu X, Liu S, Lin K, Zhu J, Huang J. Comprehensive analysis of Syk gene methylation in colorectal cancer. IMMUNITY INFLAMMATION AND DISEASE 2021; 9:923-931. [PMID: 33979042 PMCID: PMC8342196 DOI: 10.1002/iid3.449] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/25/2021] [Accepted: 04/27/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND Metastasis of colorectal cancer (CRC) extremely affects the prognosis of CRC patients. Recently, the genetic methylation has been shown to associate with tumor metastasis. This research aimed to explore the Syk gene, which is frequently hypermethylated in different cancers, and its impact on the metastasis of CRC cells. METHODS We employed the UALCAN database for the detection of the methylation levels of Syk in different cancers. CIBERSORT, TIMER and TISIDB tools were employed to analyze the association of Syk expression with immune features of CRC. Treatment with decitabine has been noted to restore the expression of Syk in CRC cells. The invasion and migration abilities of CRC cell lines were determined using transwell and wound healing assays. The correlation between Syk and c-Myc was established using the GEPIA2 database and Western blot assays. Results: Our results, based on UALCAN, revealed that the methylation level of Syk was altered in diverse cancers including colon adenocarcinoma. We found that expression profile and methylation level of Syk was correlated with immune features of colon adenocarcinoma. Decitabine can restore the expression of Syk in HCT116 and SW480 cells, hence affecting their migration and invasion. Results from GEPIA2 showed that Syk expression was correlated with c-Myc, while Western blotting analysis revealed a negative association between the expression level of Syk and c-Myc. Conclusions: This study demonstrates that the expression of Syk could be restored by decitabine in colorectal cancer, thus affecting the migration and invasion abilities of CRC cells.
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Affiliation(s)
- Fanqin Bu
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China
| | - Xiaojian Zhu
- Department of Research Center, Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Sicheng Liu
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China
| | - Kang Lin
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China
| | - Jinfeng Zhu
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China
| | - Jun Huang
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China
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