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Kuk SK, Kim K, Lee JI, Pang K. Prognostic DNA mutation and mRNA expression analysis of perineural invasion in oral squamous cell carcinoma. Sci Rep 2024; 14:2427. [PMID: 38287071 PMCID: PMC10825128 DOI: 10.1038/s41598-024-52745-6] [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: 10/11/2023] [Accepted: 01/23/2024] [Indexed: 01/31/2024] Open
Abstract
This study analyzed oral squamous cell carcinoma (OSCC) genomes and transcriptomes in relation to perineural invasion (PNI) and prognosis using Cancer Genome Atlas data and validated these results with GSE41613 data. Gene set enrichment analysis (GSEA), gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes were conducted. We identified 22 DNA mutations associated with both overall survival (OS) and PNI. Among them, TGFBR1 and RPS6KA4 mRNAs were overexpressed, while TYRO3 and GPR137 mRNAs were underexpressed in PNI patients. Among the 141 mRNA genes associated with both OS and PNI, we found overlap with PNI-related DNA mutations, including ZNF43, TEX10, TPSD1, and PSD3. In GSE41613 data, TGFBR1, RPS6KA4, TYRO3, GPR137, TEX10 and TPSD1 mRNAs were expressed differently according to the prognosis. The 22 DNA-mutated genes clustered into nervous system development, regulation of DNA-templated transcription, and transforming growth factor beta binding. GSEA analysis of mRNAs revealed upregulation of hallmarks epithelial mesenchymal transition (EMT), TNFα signaling via NF-κB, and IL2 STAT5 signaling. EMT upregulation aligned with the TGFBR1 DNA mutation, supporting its significance in PNI. These findings suggest a potential role of PNI genes in the prognosis of OSCC, providing insights for diagnosis and treatment of OSCC.
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Affiliation(s)
- Su Kyung Kuk
- Division of Biomedical Informatics, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Kitae Kim
- Department of Molecular Genetics, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Jae Il Lee
- Department of Oral Pathology, School of Dentistry and Dental Research, Seoul National University, Seoul, Republic of Korea
| | - KangMi Pang
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Seoul National University, 101, Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
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Cervena K, Siskova A, Jungwirth J, Volarić M, Kral J, Kohout P, Levy M, Vymetalkova V. MALAT1 in Liquid Biopsy: The Diagnostic and Prognostic Promise for Colorectal Cancer and Adenomas? Int J Gen Med 2023; 16:3517-3531. [PMID: 37601809 PMCID: PMC10439781 DOI: 10.2147/ijgm.s420127] [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: 05/05/2023] [Accepted: 07/27/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction The development of colorectal cancer (CRC) is a multistep process accompanied by the accumulation of mutations that start from specific precancerous lesion - colorectal adenomas (CA). CRC incidence and mortality can be reduced by the early identification of these neoplasm. Colonoscopy is the most widely used screening method for CRC identification. Nowadays, clinical research interest is shifting to the use of liquid biopsy that may help with the early diagnosis of CA and CRC. In our previous study, we identified long non-coding RNA MALAT1 gene amplification associated with the development of CA. Methods This study aimed to describe the potential of MALAT1 expression levels in the adenoma tissue of patients used in the previous study by real-time qPCR. Furthermore, we analysed the plasma samples of an independent group of patients with CA (n=97), CRC (n=101), and cancer-free individuals (CFI, n=48). Results There was no difference in the MALAT1 expression level between CA patients with or without MALAT1 amplification. However, the plasma MALAT1 expression levels were significantly upregulated in patients with CRC and CA compared to CFI (for both p<0.001). Moreover, a correlation between MALAT1 expression and histological types of adenomas was identified- high-CRC-risk adenomas also displayed the highest MALAT1 expression levels. Furthermore, in CRC patients, MALAT1 levels were associated with a response to therapy. Conclusion MALAT1 expression levels could serve as a promising circulating biomarker for early CA and CRC diagnosis, and even as a predictor of therapy response in CRC patients.
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Affiliation(s)
- Klara Cervena
- Institute of Experimental Medicine, Czech Academy of Sciences, Prague, 142 00, Czech Republic
- Institute of Biology and Medical Genetics, 1 Medical Faculty, Charles University, Prague, 128 00, Czech Republic
| | - Anna Siskova
- Institute of Experimental Medicine, Czech Academy of Sciences, Prague, 142 00, Czech Republic
- Institute of Biology and Medical Genetics, 1 Medical Faculty, Charles University, Prague, 128 00, Czech Republic
| | - Jiri Jungwirth
- Institute of Physiology, 1st Faculty of Medicine Charles University, Prague, 121 08, Czech Republic
- Department of Surgery, Weiden Clinic, Weiden in der Oberpfalz, 92637, Germany
| | - Marin Volarić
- Laboratory for Non-Coding DNA, Ruđer Bošković Institute, Zagreb, 10000, Croatia
| | - Jan Kral
- Department of Hepatogastroenterology, Institute for Clinical and Experimental Medicine, Prague, 140 21, Czech Republic
| | - Pavel Kohout
- Department of Internal Medicine, 3rd Faculty of Medicine Charles University and Faculty Thomayer Hospital Prague, Prague, 140 00, Czech Republic
| | - Miroslav Levy
- Department of Surgery, First Faculty of Medicine, Charles University and Thomayer Hospital Prague, Prague, 140 59, Czech Republic
| | - Veronika Vymetalkova
- Institute of Experimental Medicine, Czech Academy of Sciences, Prague, 142 00, Czech Republic
- Institute of Biology and Medical Genetics, 1 Medical Faculty, Charles University, Prague, 128 00, Czech Republic
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University in Prague, Pilsen, 323 00, Czech Republic
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Ren J, Yuan Q, Liu J, Zhong L, Li H, Wu G, Chen F, Tang Q. Identifying the role of transient receptor potential channels (TRPs) in kidney renal clear cell carcinoma and their potential therapeutic significances using genomic and transcriptome analyses. BMC Med Genomics 2022; 15:156. [PMID: 35831825 PMCID: PMC9277847 DOI: 10.1186/s12920-022-01312-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 07/08/2022] [Indexed: 11/17/2022] Open
Abstract
Kidney renal clear cell carcinoma (KIRC) is among the major causes of cancer-caused mortality around the world. Transient receptor potential channels (TRPs), due to their role in various human diseases, might become potential drug targets in cancer. The mRNA expression, copy number variation, single-nucleotide variation, prognostic values, drug sensitivity, and pathway regulation of TRPs were studied across cancer types. The ArrayExpress and The Cancer Genome Atlas (TCGA) databases were used to retrieve KIRC samples. Simultaneously, training, internal, and external cohorts were grouped. In KIRC, a prognostic signature with superior survival prediction in contrast with other well-established signatures was created after a stepwise screening of optimized genes linked to TRPs using univariate Cox, weighted gene co-expression network analysis, multivariate Cox, and least absolute shrinkage and selection operator regression analyses. Subsequent to the determination of risk levels, the variations in the expression of immune checkpoint genes, tumor mutation burden, and immune subtypes and response between low-risk and high-risk subgroups were studied using a variety of bioinformatics algorithms, including ESTIMATE, XCELL, EPIC, CIBERSORT-ABS, CIBERSORT, MCPCOUNTER, TIMER, and QUANTISEQ. Gene set enrichment analysis helped in the identification of abnormal pathways across the low- and high-risk subgroups. Besides, high-risk KIRC patients might benefit from ABT888, AZD6244, AZD7762, Bosutinib, Camptothecin, CI1040, JNK inhibitor VIII, KU55933, Lenalidomide, Nilotinib, PLX4720, RO3306, Vinblastine, and ZM.447439; however, low-risk populations might benefit from Bicalutamide, FH535, and OSI906. Finally, calibration curves were used to validate the nomogram with a satisfactory predictive survival probability. In conclusion, this research provides useful insight that can aid and guide clinical practice and scientific research.
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Affiliation(s)
- Jie Ren
- Department of Oncology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Qihang Yuan
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Jifeng Liu
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Lei Zhong
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Hanshuo Li
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Guangzhen Wu
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China.
| | - Feng Chen
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China.
| | - Qizhen Tang
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China.
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Jungwirth J, Urbanova M, Boot A, Hosek P, Bendova P, Siskova A, Svec J, Kment M, Tumova D, Summerova S, Benes Z, Buchler T, Kohout P, Hucl T, Matej R, Vodickova L, van Wezel T, Vodicka P, Vymetalkova V. Mutational analysis of driver genes defines the colorectal adenoma: in situ carcinoma transition. Sci Rep 2022; 12:2570. [PMID: 35173208 PMCID: PMC8850440 DOI: 10.1038/s41598-022-06498-9] [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: 10/19/2021] [Accepted: 01/13/2022] [Indexed: 01/07/2023] Open
Abstract
A large proportion of colorectal carcinomas (CRC) evolve from colorectal adenomas. However, not all individuals with colonic adenomas have a risk of CRC substantially higher than those of the general population. The aim of the study was to determine the differences or similarities of mutation profile among low- and high-grade adenomas and in situ carcinoma with detailed follow up. We have investigated the mutation spectrum of well-known genes involved in CRC (such as APC, BRAF, EGFR, NRAS, KRAS, PIK3CA, POLE, POLD1, SMAD4, PTEN, and TP53) in a large, well-defined series of 96 adenomas and in situ carcinomas using a high-throughput genotyping technique. Besides, the microsatellite instability and APC and MLH1 promoter methylation were studied as well. We observed a high frequency of pathogenic variants in the studied genes. The APC, KRAS and TP53 mutation frequencies were slightly lower in adenoma samples than in in situ carcinoma samples. Further, when we stratified mutation frequency based on the grade, the frequency distribution was as follows: low-grade adenoma—high-grade adenomas—in situ carcinoma: APC gene 42.9–56.0–54.5%; KRAS gene 32.7–32.0–45.5%; TP53 gene 8.2–20.0–18.2%. The occurrence of KRAS mutation was associated with the presence of villous histology and methylation of the APC promoter was significantly associated with the presence of POLE genetic variations. However, no association was noticed with the presence of any singular mutation and occurrence of subsequent adenoma or CRC. Our data supports the multistep model of gradual accumulation of mutations, especially in the driver genes, such as APC, TP53 and KRAS.
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Affiliation(s)
- Jiri Jungwirth
- Institute of Biology and Medical Genetics, Institute of Physiology, 1st Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic.,Department of Surgery, Weiden Clinic, Söllnerstraße 16, 92637, Weiden in der Oberpfalz, Germany
| | - Marketa Urbanova
- Institute of Biology and Medical Genetics, Institute of Physiology, 1st Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic.,Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
| | - Arnoud Boot
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Petr Hosek
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 323 00, Pilsen, Czech Republic
| | - Petra Bendova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic.,Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 323 00, Pilsen, Czech Republic
| | - Anna Siskova
- Institute of Biology and Medical Genetics, Institute of Physiology, 1st Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic.,Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
| | - Jiri Svec
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, Czech Republic.,Department of Radiotherapy and Oncology, Third Faculty of Medicine, Charles University, Srobarova 50, 100 34, Prague 10, Czech Republic
| | - Milan Kment
- Second Department of Internal Medicine, Third Faculty of Medicine, Charles University, Srobarova 50, 100 34, Prague 10, Czech Republic
| | - Daniela Tumova
- DT Gastroenterology, Roskotova 1/1225, Prague 4, Czech Republic
| | - Sandra Summerova
- Department of Internal Medicine, Third Faculty of Medicine Charles University and Thomayer University Hospital, Ruska 87, 100 00, Prague, Czech Republic
| | - Zdenek Benes
- Department of Internal Medicine, Third Faculty of Medicine Charles University and Thomayer University Hospital, Ruska 87, 100 00, Prague, Czech Republic
| | - Tomas Buchler
- Department of Oncology, First Faculty of Medicine, Charles University and Thomayer University Hospital, Videnska 800, 140 59, Prague, Czech Republic
| | - Pavel Kohout
- Department of Internal Medicine, Third Faculty of Medicine Charles University and Thomayer University Hospital, Ruska 87, 100 00, Prague, Czech Republic
| | - Tomas Hucl
- Department of Hepatogastroenterology, Institute for Clinical and Experimental Medicine, Videnska 1958/9, 140 21, Prague, Czech Republic
| | - Radoslav Matej
- Department of Pathology and Molecular Medicine, Third Faculty of Medicine, Charles University and Thomayer University Hospital, Videnska 800, 140 59, Prague, Czech Republic.,Department of Pathology, Third Faculty of Medicine, Charles University and University Hospital Kralovske Vinohrady, Srobarova 50, 100 34, Prague 10, Czech Republic
| | - Ludmila Vodickova
- Institute of Biology and Medical Genetics, Institute of Physiology, 1st Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic.,Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic.,Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 323 00, Pilsen, Czech Republic
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Pavel Vodicka
- Institute of Biology and Medical Genetics, Institute of Physiology, 1st Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic.,Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic.,Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 323 00, Pilsen, Czech Republic
| | - Veronika Vymetalkova
- Institute of Biology and Medical Genetics, Institute of Physiology, 1st Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic. .,Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic. .,Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 323 00, Pilsen, Czech Republic.
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