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Abi Zamer B, Rah B, Jayakumar MN, Abumustafa W, Hamad M, Muhammad JS. DNA methylation-mediated epigenetic regulation of oncogenic RPS2 as a novel therapeutic target and biomarker in hepatocellular carcinoma. Biochem Biophys Res Commun 2024; 696:149453. [PMID: 38181486 DOI: 10.1016/j.bbrc.2023.149453] [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: 11/19/2023] [Revised: 12/21/2023] [Accepted: 12/27/2023] [Indexed: 01/07/2024]
Abstract
Ribosomal Protein S2 (RPS2) has emerged as a potential prognostic biomarker due to its involvement in key cellular processes and its altered expression pattern in certain types of cancer. However, its role in hepatocellular carcinoma (HCC) has yet to be investigated. Herein, we analyzed RPS2 mRNA expression and promoter methylation in HCC patient samples and HepG2 cells. Subsequently, loss-of-function experiments were conducted to determine the function of RPS2 in HCC cells in vitro. Our results revealed that RPS2 mRNA expression is significantly elevated, and its promoter is hypomethylated in HCC patient samples compared to controls. In addition, 5-Azacytidine treatment in HepG2 cells decreased RPS2 promoter methylation level and increased its mRNA expression. RPS2 knockdown in HepG2 cells suppressed cell proliferation and promoted apoptosis. Functional pathway analysis of genes positively and negatively associated with RPS2 expression in HCC showed enrichment in ribosomal biogenesis, translation machinery, cell cycle regulation, and DNA processing. Furthermore, utilizing drug-protein 3D docking, we found that doxorubicin, sorafenib, and 5-Fluorouracil, showed high affinity to the active sites of RPS2, and in vitro treatment with these drugs reduced RPS2 expression. For the first time, we report on DNA methylation-mediated epigenetic regulation of RPS2 and its oncogenic role in HCC. Our findings suggest that RPS2 plays a significant role in the development and progression of HCC, hence its potential prognostic and therapeutic utility. Moreover, as epigenetic changes happen early in cancer development, RPS2 may serve as a potential biomarker for tumor progression.
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Affiliation(s)
- Batoul Abi Zamer
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates; Research Institute of Medical and Health Sciences, University of Sharjah, United Arab Emirates
| | - Bilal Rah
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Manju Nidagodu Jayakumar
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Wafaa Abumustafa
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates; Research Institute of Medical and Health Sciences, University of Sharjah, United Arab Emirates
| | - Mawieh Hamad
- Research Institute of Medical and Health Sciences, University of Sharjah, United Arab Emirates; Department of Medical Laboratory Sciences, College of Health Sciences, University of Sharjah, United Arab Emirates
| | - Jibran Sualeh Muhammad
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates; Research Institute of Medical and Health Sciences, University of Sharjah, United Arab Emirates.
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Pawaskar R, Huang KZ, Pham H, Nagrial A, Wong M, O’Neill S, Pleass H, Yuen L, Lam VWT, Richardson A, Pang T, Nahm CB. Systematic Review of Preoperative Prognostic Biomarkers in Perihilar Cholangiocarcinoma. Cancers (Basel) 2024; 16:698. [PMID: 38398089 PMCID: PMC10886549 DOI: 10.3390/cancers16040698] [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: 01/18/2024] [Revised: 02/03/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Perihilar cholangiocarcinoma (pCCA) is an uncommon malignancy with generally poor prognosis. Surgery is the primary curative treatment; however, the perioperative mortality and morbidity rates are high, with a low 5-year survival rate. Use of preoperative prognostic biomarkers to predict survival outcomes after surgery for pCCA are not well-established currently. This systematic review aimed to identify and summarise preoperative biomarkers associated with survival in pCCA, thereby potentially improving treatment decision-making. The Embase, Medline, and Cochrane databases were searched, and a systematic review was performed using the PRISMA guidelines. English-language studies examining the association between serum and/or tissue-derived biomarkers in pCCA and overall and/or disease-free survival were included. Our systematic review identified 64 biomarkers across 48 relevant studies. Raised serum CA19-9, bilirubin, CEA, neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR) and tumour MMP9, and low serum albumin were most associated with poorer survival; however, the cutoff values used widely varied. Several promising molecular markers with prognostic significance were also identified, including tumour HMGA2, MUC5AC/6, IDH1, PIWIL2, and DNA index. In conclusion, several biomarkers have been identified in serum and tumour specimens that prognosticate overall and disease-free survival after pCCA resection. These, however, require external validation in large cohort studies and/or in preoperatively obtained specimens, especially tissue biopsy, to recommend their use.
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Affiliation(s)
- Rishaan Pawaskar
- Department of Upper GI Surgery, Westmead Hospital, Sydney, NSW 2145, Australia; (R.P.); (H.P.); (H.P.); (L.Y.); (V.W.T.L.); (A.R.); (T.P.)
| | | | - Helen Pham
- Department of Upper GI Surgery, Westmead Hospital, Sydney, NSW 2145, Australia; (R.P.); (H.P.); (H.P.); (L.Y.); (V.W.T.L.); (A.R.); (T.P.)
- Westmead Hospital, Sydney, NSW 2145, Australia;
- Surgical Innovations Unit, Westmead Hospital, Sydney, NSW 2145, Australia
| | - Adnan Nagrial
- Westmead Clinical School, Faculty of Medicine and Health Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (A.N.); (M.W.)
- Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, NSW 2145, Australia;
| | - Mark Wong
- Westmead Clinical School, Faculty of Medicine and Health Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (A.N.); (M.W.)
- Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, NSW 2145, Australia;
| | - Siobhan O’Neill
- Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, NSW 2145, Australia;
| | - Henry Pleass
- Department of Upper GI Surgery, Westmead Hospital, Sydney, NSW 2145, Australia; (R.P.); (H.P.); (H.P.); (L.Y.); (V.W.T.L.); (A.R.); (T.P.)
- Westmead Hospital, Sydney, NSW 2145, Australia;
- Surgical Innovations Unit, Westmead Hospital, Sydney, NSW 2145, Australia
- Westmead Clinical School, Faculty of Medicine and Health Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (A.N.); (M.W.)
| | - Lawrence Yuen
- Department of Upper GI Surgery, Westmead Hospital, Sydney, NSW 2145, Australia; (R.P.); (H.P.); (H.P.); (L.Y.); (V.W.T.L.); (A.R.); (T.P.)
- Westmead Hospital, Sydney, NSW 2145, Australia;
- Surgical Innovations Unit, Westmead Hospital, Sydney, NSW 2145, Australia
- Westmead Clinical School, Faculty of Medicine and Health Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (A.N.); (M.W.)
| | - Vincent W. T. Lam
- Department of Upper GI Surgery, Westmead Hospital, Sydney, NSW 2145, Australia; (R.P.); (H.P.); (H.P.); (L.Y.); (V.W.T.L.); (A.R.); (T.P.)
- Westmead Hospital, Sydney, NSW 2145, Australia;
- Surgical Innovations Unit, Westmead Hospital, Sydney, NSW 2145, Australia
- Westmead Clinical School, Faculty of Medicine and Health Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (A.N.); (M.W.)
- Macquarie University Medical School, Macquarie University, Sydney, NSW 2145, Australia
| | - Arthur Richardson
- Department of Upper GI Surgery, Westmead Hospital, Sydney, NSW 2145, Australia; (R.P.); (H.P.); (H.P.); (L.Y.); (V.W.T.L.); (A.R.); (T.P.)
- Westmead Hospital, Sydney, NSW 2145, Australia;
- Surgical Innovations Unit, Westmead Hospital, Sydney, NSW 2145, Australia
| | - Tony Pang
- Department of Upper GI Surgery, Westmead Hospital, Sydney, NSW 2145, Australia; (R.P.); (H.P.); (H.P.); (L.Y.); (V.W.T.L.); (A.R.); (T.P.)
- Westmead Hospital, Sydney, NSW 2145, Australia;
- Surgical Innovations Unit, Westmead Hospital, Sydney, NSW 2145, Australia
- Westmead Clinical School, Faculty of Medicine and Health Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (A.N.); (M.W.)
| | - Christopher B. Nahm
- Department of Upper GI Surgery, Westmead Hospital, Sydney, NSW 2145, Australia; (R.P.); (H.P.); (H.P.); (L.Y.); (V.W.T.L.); (A.R.); (T.P.)
- Westmead Hospital, Sydney, NSW 2145, Australia;
- Surgical Innovations Unit, Westmead Hospital, Sydney, NSW 2145, Australia
- Westmead Clinical School, Faculty of Medicine and Health Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (A.N.); (M.W.)
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Hossain MB, Islam MK, Adhikary A, Rahaman A, Islam MZ. Bioinformatics Approach to Identify Significant Biomarkers, Drug Targets Shared Between Parkinson's Disease and Bipolar Disorder: A Pilot Study. Bioinform Biol Insights 2022; 16:11779322221079232. [PMID: 35221677 PMCID: PMC8874170 DOI: 10.1177/11779322221079232] [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: 07/20/2021] [Accepted: 02/01/2022] [Indexed: 11/17/2022] Open
Abstract
Parkinson’s disease (PD) is a neurodegenerative disorder responsible for shaking, rigidity, and trouble in walking and patients’ coordination ability and physical stability deteriorate day by day. Bipolar disorder (BD) is a psychiatric disorder which is the reason behind extreme shiftiness in mood, and frequent mood inversion may reach too high called mania. People with BD have a greater chance of developing PD during the follow-up period. A lot of work has been done to understand the key factors for developing these 2 diseases. But the molecular functionalities that trigger the development of PD in people with BD are not clear yet. In our study, we are intended to identify the molecular biomarkers and pathways shared between BD and PD. We have investigated the RNA-Seq gene expression data sets of PD and BD. A total of 45 common unique genes (32 up-regulated and 13 down-regulated) abnormally expressed in both PD and BD were identified by applying statistical methods on the GEO data sets. Gene ontology (GO) and BioCarta, KEGG, and Reactome pathways analysis of these 45 common dysregulated genes identified numerous altered molecular pathways such as mineral absorption, Epstein-Barr virus infection, HTLV-I infection, antigen processing, and presentation. Analysis of protein-protein interactions revealed 9 significant hub-proteins, namely RPL21, RPL34, CKS2, B2M, TNFRSF10A, DTX2, HLA-B, ATP2A3, and TAPBP. Significant transcription factors (IRF8, SPI1, RUNX1, and FOXA1) and posttranscriptional regulator microRNAs (hsa-miR-491-3p and hsa-miR-1246) are also found by analyzing gene-transcription factors and gene-miRNAs interactions, respectively. Protein-drug interaction analysis revealed hub-protein B2M’s interaction with molecular drug candidates like N-formylmethionine, 3-indolebutyric acid, and doxycycline. Finally, a link between pathological processes of PD and BD is identified at transcriptional level. This study may help us to predict the development of PD among the people suffering from BD and gives some clue to understand significant pathological mechanisms.
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Affiliation(s)
- Md Bipul Hossain
- Department of Information and Communication Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh.,Department of Information and Communication Technology, Islamic University, Kushtia, Bangladesh
| | - Md Kobirul Islam
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Apurba Adhikary
- Department of Information and Communication Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Abidur Rahaman
- Department of Information and Communication Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Md Zahidul Islam
- Department of Information and Communication Technology, Islamic University, Kushtia, Bangladesh
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