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Cheraghi-Shavi T, Jalal R, Minuchehr Z. TGM2, HMGA2, FXYD3, and LGALS4 genes as biomarkers in acquired oxaliplatin resistance of human colorectal cancer: A systems biology approach. PLoS One 2023; 18:e0289535. [PMID: 37535601 PMCID: PMC10399784 DOI: 10.1371/journal.pone.0289535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 07/20/2023] [Indexed: 08/05/2023] Open
Abstract
Acquired resistance to oxaliplatin is considered as the primary reason for failure in colorectal cancer (CRC) therapy. Identifying the underlying resistance mechanisms may improve CRC treatment. The present study aims to identify the key genes involved in acquired oxaliplatin-resistant in CRC by confirming the oxaliplatin resistance index (OX-RI). To this aim, two public microarray datasets regarding oxaliplatin-resistant CRC cells with different OX-RI, GSE42387, and GSE76092 were downloaded from GEO database to identify differentially expressed genes (DEGs). The results indicated that the OX-RI affects the gene expression pattern significantly. Then, 54 common DEGs in both datasets including 18 up- and 36 down-regulated genes were identified. Protein-protein interaction (PPI) analysis revealed 13 up- (MAGEA6, TGM2, MAGEA4, SCHIP1, ECI2, CD33, AKAP12, MAGEA12, CALD1, WFDC2, VSNL1, HMGA2, and MAGEA2B) and 12 down-regulated (PDZK1IP1, FXYD3, ALDH2, CEACAM6, QPRT, GRB10, TM4SF4, LGALS4, ALDH3A1, USH1C, KCNE3, and CA12) hub genes. In the next step, two novel up-regulated hub genes including ECI2 and SCHIP1 were identified to be related to oxaliplatin resistance. Functional enrichment and pathway analysis indicated that metabolic pathways, proliferation, and epithelial-mesenchymal transition may play dominant roles in CRC progression and oxaliplatin resistance. In the next procedure, two in vitro oxaliplatin-resistant sub-lines including HCT116/OX-R4.3 and HCT116/OX-R10 cells with OX-IR 3.93 and 10.06 were established, respectively. The results indicated the up-regulation of TGM2 and HMGA2 in HCT116/OX-R10 cells with high OX-RI and down-regulation of FXYD3, LGALS4, and ECI2 in both cell types. Based on the results, TGM2, HMGA2, FXYD3, and LGALS4 genes are related to oxaliplatin-resistant CRC and may serve as novel therapeutic targets.
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Affiliation(s)
- Tayebeh Cheraghi-Shavi
- Faculty of Science, Department of Chemistry, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Razieh Jalal
- Faculty of Science, Department of Chemistry, Ferdowsi University of Mashhad, Mashhad, Iran
- Institute of Biotechnology, Novel Diagnostics and Therapeutics Research Group, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Zarrin Minuchehr
- Systems Biotechnology Department, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
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Vieira GM, Gellen LPA, da Veiga Borges Leal DF, Pastana LF, Vinagre LWMS, Aquino VT, Fernandes MR, de Assumpção PP, Burbano RMR, dos Santos SEB, dos Santos NPC. Correlation between Genomic Variants and Worldwide Epidemiology of Prostate Cancer. Genes (Basel) 2022; 13:genes13061039. [PMID: 35741800 PMCID: PMC9222668 DOI: 10.3390/genes13061039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/28/2022] [Accepted: 06/06/2022] [Indexed: 12/19/2022] Open
Abstract
Prostate cancer (PCa) incidence and mortality vary across territories and populations. This can be explained by the genetic factor of this disease. This article aims to correlate the epidemiological data, worldwide incidence, and mortality of PCa with single-nucleotide polymorphisms (SNPs) associated with the susceptibility and severity of this neoplasm in different populations. Eighty-four genetic variants associated with prostate cancer susceptibility were selected from the literature through genome association studies (GWAS). Allele frequencies were obtained from the 1000 Genomes Project, and epidemiological data were obtained from Surveillance, Epidemiology, and End Results (SEER). The PCa incidence, mortality rates, and allele frequencies of variants were evaluated by Pearson’s correlation. Our study demonstrated that 12 SNPs (rs2961144, rs1048169, rs7000448, rs4430796, rs2066827, rs12500426, rs6983267, rs11649743, rs2075110, rs114798100, rs855723, and rs2075109) were correlated with epidemiological data in different ethnic groups. Ten SNPs (rs2961144, rs1048169, rs7000448, rs4430796, rs2066827, rs12500426, rs11649743, rs2075110, rs114798100, and rs2075109) were positively correlated with the mortality rate. Seven SNPs (rs1048169, rs2961144, rs7000448, rs4430796, rs2066827, rs12500426, and rs114798100) were positively correlated with incidence. Positive correlations of incidence and mortality rates were more frequent in the African population. The genetic variants investigated here are likely to predispose to PCa and could play a role in its progression and aggressiveness. This genetic study demonstrated here is promising for implementing personalized strategies to screen for prostate cancer in diverse populations.
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Affiliation(s)
- Giovana Miranda Vieira
- Research Center of Oncology, Federal University of Pará Belém, Belém 66073-000, Brazil; (G.M.V.); (L.P.A.G.); (D.F.d.V.B.L.); (L.F.P.); (L.W.M.S.V.); (V.T.A.); (P.P.d.A.); (R.M.R.B.); (S.E.B.d.S.); (N.P.C.d.S.)
| | - Laura Patrícia Albarello Gellen
- Research Center of Oncology, Federal University of Pará Belém, Belém 66073-000, Brazil; (G.M.V.); (L.P.A.G.); (D.F.d.V.B.L.); (L.F.P.); (L.W.M.S.V.); (V.T.A.); (P.P.d.A.); (R.M.R.B.); (S.E.B.d.S.); (N.P.C.d.S.)
| | - Diana Feio da Veiga Borges Leal
- Research Center of Oncology, Federal University of Pará Belém, Belém 66073-000, Brazil; (G.M.V.); (L.P.A.G.); (D.F.d.V.B.L.); (L.F.P.); (L.W.M.S.V.); (V.T.A.); (P.P.d.A.); (R.M.R.B.); (S.E.B.d.S.); (N.P.C.d.S.)
| | - Lucas Favacho Pastana
- Research Center of Oncology, Federal University of Pará Belém, Belém 66073-000, Brazil; (G.M.V.); (L.P.A.G.); (D.F.d.V.B.L.); (L.F.P.); (L.W.M.S.V.); (V.T.A.); (P.P.d.A.); (R.M.R.B.); (S.E.B.d.S.); (N.P.C.d.S.)
| | - Lui Wallacy Morikawa Souza Vinagre
- Research Center of Oncology, Federal University of Pará Belém, Belém 66073-000, Brazil; (G.M.V.); (L.P.A.G.); (D.F.d.V.B.L.); (L.F.P.); (L.W.M.S.V.); (V.T.A.); (P.P.d.A.); (R.M.R.B.); (S.E.B.d.S.); (N.P.C.d.S.)
| | - Vitória Teixeira Aquino
- Research Center of Oncology, Federal University of Pará Belém, Belém 66073-000, Brazil; (G.M.V.); (L.P.A.G.); (D.F.d.V.B.L.); (L.F.P.); (L.W.M.S.V.); (V.T.A.); (P.P.d.A.); (R.M.R.B.); (S.E.B.d.S.); (N.P.C.d.S.)
| | - Marianne Rodrigues Fernandes
- Research Center of Oncology, Federal University of Pará Belém, Belém 66073-000, Brazil; (G.M.V.); (L.P.A.G.); (D.F.d.V.B.L.); (L.F.P.); (L.W.M.S.V.); (V.T.A.); (P.P.d.A.); (R.M.R.B.); (S.E.B.d.S.); (N.P.C.d.S.)
- Ophir Loyola Hospital, Belém 66063-005, Brazil
- Correspondence:
| | - Paulo Pimentel de Assumpção
- Research Center of Oncology, Federal University of Pará Belém, Belém 66073-000, Brazil; (G.M.V.); (L.P.A.G.); (D.F.d.V.B.L.); (L.F.P.); (L.W.M.S.V.); (V.T.A.); (P.P.d.A.); (R.M.R.B.); (S.E.B.d.S.); (N.P.C.d.S.)
| | - Rommel Mario Rodríguez Burbano
- Research Center of Oncology, Federal University of Pará Belém, Belém 66073-000, Brazil; (G.M.V.); (L.P.A.G.); (D.F.d.V.B.L.); (L.F.P.); (L.W.M.S.V.); (V.T.A.); (P.P.d.A.); (R.M.R.B.); (S.E.B.d.S.); (N.P.C.d.S.)
- Ophir Loyola Hospital, Belém 66063-005, Brazil
| | - Sidney Emanuel Batista dos Santos
- Research Center of Oncology, Federal University of Pará Belém, Belém 66073-000, Brazil; (G.M.V.); (L.P.A.G.); (D.F.d.V.B.L.); (L.F.P.); (L.W.M.S.V.); (V.T.A.); (P.P.d.A.); (R.M.R.B.); (S.E.B.d.S.); (N.P.C.d.S.)
| | - Ney Pereira Carneiro dos Santos
- Research Center of Oncology, Federal University of Pará Belém, Belém 66073-000, Brazil; (G.M.V.); (L.P.A.G.); (D.F.d.V.B.L.); (L.F.P.); (L.W.M.S.V.); (V.T.A.); (P.P.d.A.); (R.M.R.B.); (S.E.B.d.S.); (N.P.C.d.S.)
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Comprehensive quantitative analysis of alternative splicing variants reveals the HNF1B mRNA splicing pattern in various tumour and non-tumour tissues. Sci Rep 2022; 12:199. [PMID: 34997048 PMCID: PMC8741901 DOI: 10.1038/s41598-021-03989-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 12/13/2021] [Indexed: 11/24/2022] Open
Abstract
Hepatocyte nuclear factor-1-beta (HNF1B) is a transcription factor and putative biomarker of solid tumours. Recently, we have revealed a variety of HNF1B mRNA alternative splicing variants (ASVs) with unknown, but potentially regulatory, functions. The aim of our work was to quantify the most common variants and compare their expression in tumour and non-tumour tissues of the large intestine, prostate, and kidney. The HNF1B mRNA variants 3p, Δ7, Δ7–8, and Δ8 were expressed across all the analysed tissues in 28.2–33.5%, 1.5–2%, 0.8–1.7%, and 2.3–6.9% of overall HNF1B mRNA expression, respectively, and occurred individually or in combination. The quantitative changes of ASVs between tumour and non-tumour tissue were observed for the large intestine (3p, Δ7–8), prostate (3p), and kidney samples (Δ7). Decreased expression of the overall HNF1B mRNA in the large intestine and prostate cancer samples compared with the corresponding non-tumour samples was observed (p = 0.019 and p = 0.047, respectively). The decreased mRNA expression correlated with decreased protein expression in large intestine carcinomas (p < 0.001). The qualitative and quantitative pattern of the ASVs studied by droplet digital PCR was confirmed by next-generation sequencing, which suggests the significance of the NGS approach for further massive evaluation of the splicing patterns in a variety of genes.
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Kukkonen K, Taavitsainen S, Huhtala L, Uusi-Makela J, Granberg KJ, Nykter M, Urbanucci A. Chromatin and Epigenetic Dysregulation of Prostate Cancer Development, Progression, and Therapeutic Response. Cancers (Basel) 2021; 13:3325. [PMID: 34283056 PMCID: PMC8268970 DOI: 10.3390/cancers13133325] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 02/07/2023] Open
Abstract
The dysregulation of chromatin and epigenetics has been defined as the overarching cancer hallmark. By disrupting transcriptional regulation in normal cells and mediating tumor progression by promoting cancer cell plasticity, this process has the ability to mediate all defined hallmarks of cancer. In this review, we collect and assess evidence on the contribution of chromatin and epigenetic dysregulation in prostate cancer. We highlight important mechanisms leading to prostate carcinogenesis, the emergence of castration-resistance upon treatment with androgen deprivation therapy, and resistance to antiandrogens. We examine in particular the contribution of chromatin structure and epigenetics to cell lineage commitment, which is dysregulated during tumorigenesis, and cell plasticity, which is altered during tumor progression.
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Affiliation(s)
- Konsta Kukkonen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Sinja Taavitsainen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Laura Huhtala
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Joonas Uusi-Makela
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Kirsi J. Granberg
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Alfonso Urbanucci
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway
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Němejcová K, Bártů M, Hojný J, Hájková N, Michálková R, Krkavcová E, Stružinská I, Bui HQ, Dundr P, Cibula D, Jirsová K. A comprehensive analysis of the expression, epigenetic and genetic changes of HNF1B and ECI2 in 122 cases of high-grade serous ovarian carcinoma. Oncol Lett 2021; 21:185. [PMID: 33574924 PMCID: PMC7816296 DOI: 10.3892/ol.2021.12446] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 12/03/2020] [Indexed: 11/28/2022] Open
Abstract
High-grade serous ovarian cancer (HGSC) is the most common subtype of ovarian cancer, with a poor prognosis; however, most studies concerning ovarian carcinoma have focused mainly on clear cell carcinoma. The involvement of hepatocyte nuclear factor 1β (HNF1B) in the carcinogenesis of HGSC has not yet been fully elucidated. To the best of our knowledge, the present study is the first to analyse the expression of the possible downstream target of HNF1B, enoyl-CoA (Δ) isomerase 2 (ECI2), in HGSC. The present study performed a comprehensive analysis of HNF1B mRNA and protein expression, and epigenetic and genetic changes, as well as an analysis of ECI2 mRNA and protein expression in 122 cases of HGSC. HNF1B protein expression was detected in 28/122 cases, and was positively associated with lymphovascular invasion (P=0.025). Protein expression of ECI2 was detected in 115/122 cases, but no associations with clinicopathological variables were revealed. Therefore, ECI2 does not seem to function as a suitable prognostic marker for HGSC. In the sample set, a positive correlation between HNF1B and ECI2 protein expression was detected (P=0.005). HNF1B mRNA was also positively correlated with HNF1B protein expression (P=0.001). HNF1B promoter methylation was detected in 26/67 (38.8%) of cases. A novel pathogenic somatic HNF1B mutation was detected in 1/61 (1.6%) of the analysed HGSC cases. No other correlations between the examined SNPs (rs4430796, rs757210 and rs7405776), HNF1B promoter methylation, HNF1B/ECI2 expression or clinicopathological characteristics were found.
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Affiliation(s)
- Kristýna Němejcová
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
| | - Michaela Bártů
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
| | - Jan Hojný
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
| | - Nikola Hájková
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
| | - Romana Michálková
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
| | - Eva Krkavcová
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
| | - Ivana Stružinská
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
| | - Hiep Quang Bui
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
| | - Pavel Dundr
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
| | - David Cibula
- Gynecologic Oncology Center, Department of Obstetrics and Gynecology, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
| | - Kateřina Jirsová
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
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