Methylation-related genes involved in renal carcinoma progression
Renal carcinomas are a group of malignant tumors often originating in the cells lining the small tubes in the kidney responsible for filtering waste from the blood and urine production. Kidney tumors arise from the uncontrolled growth of cells in the kidneys and are responsible for a large share of...
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Frontiers Media S.A.
2023-08-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2023.1225158/full |
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| author | Jose María Zamora-Fuentes Enrique Hernández-Lemus Enrique Hernández-Lemus Jesús Espinal-Enríquez Jesús Espinal-Enríquez |
| author_facet | Jose María Zamora-Fuentes Enrique Hernández-Lemus Enrique Hernández-Lemus Jesús Espinal-Enríquez Jesús Espinal-Enríquez |
| author_sort | Jose María Zamora-Fuentes |
| collection | DOAJ |
| description | Renal carcinomas are a group of malignant tumors often originating in the cells lining the small tubes in the kidney responsible for filtering waste from the blood and urine production. Kidney tumors arise from the uncontrolled growth of cells in the kidneys and are responsible for a large share of global cancer-related morbidity and mortality. Understanding the molecular mechanisms driving renal carcinoma progression results crucial for the development of targeted therapies leading to an improvement of patient outcomes. Epigenetic mechanisms such as DNA methylation are known factors underlying the development of several cancer types. There is solid experimental evidence of relevant biological functions modulated by methylation-related genes, associated with the progression of different carcinomas. Those mechanisms can often be associated to different epigenetic marks, such as DNA methylation sites or chromatin conformation patterns. Currently, there is no definitive method to establish clear relations between genetic and epigenetic factors that influence the progression of cancer. Here, we developed a data-driven method to find methylation-related genes, so we could find relevant bonds between gene co-expression and methylation-wide-genome regulation patterns able to drive biological processes during the progression of clear cell renal carcinoma (ccRC). With this approach, we found out genes such as ITK oncogene that appear hypomethylated during all four stages of ccRC progression and are strongly involved in immune response functions. Also, we found out relevant tumor suppressor genes such as RAB25 hypermethylated, thus potentially avoiding repressed functions in the AKT signaling pathway during the evolution of ccRC. Our results have relevant implications to further understand some epigenetic–genetic-affected roles underlying the progression of renal cancer. |
| first_indexed | 2024-03-12T13:21:45Z |
| format | Article |
| id | doaj.art-d2c93d5a284e41b79ce6ee9578f3c7a8 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-03-12T13:21:45Z |
| publishDate | 2023-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-d2c93d5a284e41b79ce6ee9578f3c7a82023-08-25T18:51:31ZengFrontiers Media S.A.Frontiers in Genetics1664-80212023-08-011410.3389/fgene.2023.12251581225158Methylation-related genes involved in renal carcinoma progressionJose María Zamora-Fuentes0Enrique Hernández-Lemus1Enrique Hernández-Lemus2Jesús Espinal-Enríquez3Jesús Espinal-Enríquez4Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, MexicoComputational Genomics Division, National Institute of Genomic Medicine, Mexico City, MexicoCentro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, MexicoComputational Genomics Division, National Institute of Genomic Medicine, Mexico City, MexicoCentro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, MexicoRenal carcinomas are a group of malignant tumors often originating in the cells lining the small tubes in the kidney responsible for filtering waste from the blood and urine production. Kidney tumors arise from the uncontrolled growth of cells in the kidneys and are responsible for a large share of global cancer-related morbidity and mortality. Understanding the molecular mechanisms driving renal carcinoma progression results crucial for the development of targeted therapies leading to an improvement of patient outcomes. Epigenetic mechanisms such as DNA methylation are known factors underlying the development of several cancer types. There is solid experimental evidence of relevant biological functions modulated by methylation-related genes, associated with the progression of different carcinomas. Those mechanisms can often be associated to different epigenetic marks, such as DNA methylation sites or chromatin conformation patterns. Currently, there is no definitive method to establish clear relations between genetic and epigenetic factors that influence the progression of cancer. Here, we developed a data-driven method to find methylation-related genes, so we could find relevant bonds between gene co-expression and methylation-wide-genome regulation patterns able to drive biological processes during the progression of clear cell renal carcinoma (ccRC). With this approach, we found out genes such as ITK oncogene that appear hypomethylated during all four stages of ccRC progression and are strongly involved in immune response functions. Also, we found out relevant tumor suppressor genes such as RAB25 hypermethylated, thus potentially avoiding repressed functions in the AKT signaling pathway during the evolution of ccRC. Our results have relevant implications to further understand some epigenetic–genetic-affected roles underlying the progression of renal cancer.https://www.frontiersin.org/articles/10.3389/fgene.2023.1225158/fullclear cell renal carcinomagene co-expression networksRAB25ITKIGF2BP2TSFRN9 |
| spellingShingle | Jose María Zamora-Fuentes Enrique Hernández-Lemus Enrique Hernández-Lemus Jesús Espinal-Enríquez Jesús Espinal-Enríquez Methylation-related genes involved in renal carcinoma progression Frontiers in Genetics clear cell renal carcinoma gene co-expression networks RAB25 ITK IGF2BP2 TSFRN9 |
| title | Methylation-related genes involved in renal carcinoma progression |
| title_full | Methylation-related genes involved in renal carcinoma progression |
| title_fullStr | Methylation-related genes involved in renal carcinoma progression |
| title_full_unstemmed | Methylation-related genes involved in renal carcinoma progression |
| title_short | Methylation-related genes involved in renal carcinoma progression |
| title_sort | methylation related genes involved in renal carcinoma progression |
| topic | clear cell renal carcinoma gene co-expression networks RAB25 ITK IGF2BP2 TSFRN9 |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2023.1225158/full |
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