Melika Golozar , Ali Valipour Motlagh , Mohammad Mahdevar , Maryam Peymani , Kolsoum InanlooRahatloo , Kamran Ghaedi
{"title":"结直肠癌中 TBX15 和 SDHB 的表达变化可作为潜在的预后生物标志物。","authors":"Melika Golozar , Ali Valipour Motlagh , Mohammad Mahdevar , Maryam Peymani , Kolsoum InanlooRahatloo , Kamran Ghaedi","doi":"10.1016/j.yexmp.2024.104890","DOIUrl":null,"url":null,"abstract":"<div><p>Alterations in the expression of certain genes could be associated with both patient mortality rates and drug resistance. This study aimed to identify genes in colorectal cancer (CRC) that potentially serve as hub genes influencing patient survival rates. RNA-Seq data were downloaded from the cancer genome atlas database, and differential expression analysis was performed between tumors and healthy controls. Through the utilization of univariate and multivariate Cox regression analyses, in combination with the MCODE clustering module, the genes whose expression changes were related to survival rate and the hub genes related to them were identified. The mortality risk model was computed using the hub genes. CRC samples and the RT-qPCR method were utilized to confirm the outcomes. PharmacoGx data were employed to link the expression of potential genes to medication resistance and sensitivity. The results revealed the discovery of seven hub genes, which emerged as independent prognostic markers. These included <em>HOXC6</em>, <em>HOXC13</em>, <em>HOXC8</em>, and <em>TBX15</em>, which were associated with poor prognosis and overexpression, as well as <em>SDHB</em>, <em>COX5A</em>, and <em>UQCRC1</em>, linked to favorable prognosis and downregulation. Applying the risk model developed with the mentioned genes revealed a markedly higher incidence of deceased patients in the high-risk group compared to the low-risk group. RT-qPCR results indicated a decrease in <em>SDHB</em> expression and an elevation in <em>TBX15</em> levels in cancer samples relative to adjacent healthy tissue. Also, PharmacoGx data indicated that the expression level of <em>SDHB</em> was correlated with drug sensitivity to Crizotinib and Dovitinib. Our findings highlight the potential association between alterations in the expression of genes such as <em>HOXC6</em>, <em>HOXC13</em>, <em>HOXC8</em>, <em>TBX15</em>, <em>SDHB</em>, <em>COX5A</em>, and <em>UQCRC1</em> and increased mortality rates in CRC patients. As revealed by the PPI network, these genes exhibited the most connections with other genes linked to survival.</p></div>","PeriodicalId":12176,"journal":{"name":"Experimental and molecular pathology","volume":"136 ","pages":"Article 104890"},"PeriodicalIF":2.8000,"publicationDate":"2024-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0014480024000091/pdfft?md5=81cba468dad9389365dfdf0369be2e8e&pid=1-s2.0-S0014480024000091-main.pdf","citationCount":"0","resultStr":"{\"title\":\"TBX15 and SDHB expression changes in colorectal cancer serve as potential prognostic biomarkers\",\"authors\":\"Melika Golozar , Ali Valipour Motlagh , Mohammad Mahdevar , Maryam Peymani , Kolsoum InanlooRahatloo , Kamran Ghaedi\",\"doi\":\"10.1016/j.yexmp.2024.104890\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>Alterations in the expression of certain genes could be associated with both patient mortality rates and drug resistance. This study aimed to identify genes in colorectal cancer (CRC) that potentially serve as hub genes influencing patient survival rates. RNA-Seq data were downloaded from the cancer genome atlas database, and differential expression analysis was performed between tumors and healthy controls. Through the utilization of univariate and multivariate Cox regression analyses, in combination with the MCODE clustering module, the genes whose expression changes were related to survival rate and the hub genes related to them were identified. The mortality risk model was computed using the hub genes. CRC samples and the RT-qPCR method were utilized to confirm the outcomes. PharmacoGx data were employed to link the expression of potential genes to medication resistance and sensitivity. The results revealed the discovery of seven hub genes, which emerged as independent prognostic markers. These included <em>HOXC6</em>, <em>HOXC13</em>, <em>HOXC8</em>, and <em>TBX15</em>, which were associated with poor prognosis and overexpression, as well as <em>SDHB</em>, <em>COX5A</em>, and <em>UQCRC1</em>, linked to favorable prognosis and downregulation. Applying the risk model developed with the mentioned genes revealed a markedly higher incidence of deceased patients in the high-risk group compared to the low-risk group. RT-qPCR results indicated a decrease in <em>SDHB</em> expression and an elevation in <em>TBX15</em> levels in cancer samples relative to adjacent healthy tissue. Also, PharmacoGx data indicated that the expression level of <em>SDHB</em> was correlated with drug sensitivity to Crizotinib and Dovitinib. Our findings highlight the potential association between alterations in the expression of genes such as <em>HOXC6</em>, <em>HOXC13</em>, <em>HOXC8</em>, <em>TBX15</em>, <em>SDHB</em>, <em>COX5A</em>, and <em>UQCRC1</em> and increased mortality rates in CRC patients. As revealed by the PPI network, these genes exhibited the most connections with other genes linked to survival.</p></div>\",\"PeriodicalId\":12176,\"journal\":{\"name\":\"Experimental and molecular pathology\",\"volume\":\"136 \",\"pages\":\"Article 104890\"},\"PeriodicalIF\":2.8000,\"publicationDate\":\"2024-02-22\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.sciencedirect.com/science/article/pii/S0014480024000091/pdfft?md5=81cba468dad9389365dfdf0369be2e8e&pid=1-s2.0-S0014480024000091-main.pdf\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Experimental and molecular pathology\",\"FirstCategoryId\":\"3\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S0014480024000091\",\"RegionNum\":4,\"RegionCategory\":\"医学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"PATHOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Experimental and molecular pathology","FirstCategoryId":"3","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S0014480024000091","RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"PATHOLOGY","Score":null,"Total":0}
TBX15 and SDHB expression changes in colorectal cancer serve as potential prognostic biomarkers
Alterations in the expression of certain genes could be associated with both patient mortality rates and drug resistance. This study aimed to identify genes in colorectal cancer (CRC) that potentially serve as hub genes influencing patient survival rates. RNA-Seq data were downloaded from the cancer genome atlas database, and differential expression analysis was performed between tumors and healthy controls. Through the utilization of univariate and multivariate Cox regression analyses, in combination with the MCODE clustering module, the genes whose expression changes were related to survival rate and the hub genes related to them were identified. The mortality risk model was computed using the hub genes. CRC samples and the RT-qPCR method were utilized to confirm the outcomes. PharmacoGx data were employed to link the expression of potential genes to medication resistance and sensitivity. The results revealed the discovery of seven hub genes, which emerged as independent prognostic markers. These included HOXC6, HOXC13, HOXC8, and TBX15, which were associated with poor prognosis and overexpression, as well as SDHB, COX5A, and UQCRC1, linked to favorable prognosis and downregulation. Applying the risk model developed with the mentioned genes revealed a markedly higher incidence of deceased patients in the high-risk group compared to the low-risk group. RT-qPCR results indicated a decrease in SDHB expression and an elevation in TBX15 levels in cancer samples relative to adjacent healthy tissue. Also, PharmacoGx data indicated that the expression level of SDHB was correlated with drug sensitivity to Crizotinib and Dovitinib. Our findings highlight the potential association between alterations in the expression of genes such as HOXC6, HOXC13, HOXC8, TBX15, SDHB, COX5A, and UQCRC1 and increased mortality rates in CRC patients. As revealed by the PPI network, these genes exhibited the most connections with other genes linked to survival.
期刊介绍：
Under new editorial leadership, Experimental and Molecular Pathology presents original articles on disease processes in relation to structural and biochemical alterations in mammalian tissues and fluids and on the application of newer techniques of molecular biology to problems of pathology in humans and other animals. The journal also publishes selected interpretive synthesis reviews by bench level investigators working at the "cutting edge" of contemporary research in pathology. In addition, special thematic issues present original research reports that unravel some of Nature''s most jealously guarded secrets on the pathologic basis of disease.
Research Areas include: Stem cells; Neoangiogenesis; Molecular diagnostics; Polymerase chain reaction; In situ hybridization; DNA sequencing; Cell receptors; Carcinogenesis; Pathobiology of neoplasia; Complex infectious diseases; Transplantation; Cytokines; Flow cytomeric analysis; Inflammation; Cellular injury; Immunology and hypersensitivity; Athersclerosis.
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