Methylation Heterogeneity and Gene Expression of SPG20 in Solid Tumors
Introduction. The downregulation of the Spastic Paraplegia-20 (<i>SPG20</i>) gene is correlated with a rare autosomal recessive disorder called Troyer Syndrome. Only in recent years has <i>SPG20</i> been studied and partially characterized in cancer. <i>SPG20</i>...
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MDPI AG
2022-05-01
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| Online Access: | https://www.mdpi.com/2073-4425/13/5/861 |
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| author | Vincenza Ylenia Cusenza Luca Braglia Raffaele Frazzi |
| author_facet | Vincenza Ylenia Cusenza Luca Braglia Raffaele Frazzi |
| author_sort | Vincenza Ylenia Cusenza |
| collection | DOAJ |
| description | Introduction. The downregulation of the Spastic Paraplegia-20 (<i>SPG20</i>) gene is correlated with a rare autosomal recessive disorder called Troyer Syndrome. Only in recent years has <i>SPG20</i> been studied and partially characterized in cancer. <i>SPG20</i> has been shown to be hypermethylated in colorectal cancer, gastric cancer, non-Hodgkin’s lymphoma and hepatocellular carcinoma. In this study, we analyze the methylation status and the gene expression of <i>SPG20</i> in different tumors of various histological origins. Methods. We analyzed the data generated through Infinium Human Methylation 450 BeadChip arrays and RNA-seq approaches extrapolated from The Cancer Genome Atlas (TCGA) database. The statistics were performed with R 4.0.4. Results. We aimed to assess whether the hypermethylation of this target gene was a common characteristic among different tumors and if there was a correlation between the m-values and the gene expression in paired tumor versus solid tissue normal. Overall, our analysis highlighted that <i>SPG20</i> open sea upstream the TSS is altogether hypermethylated, and the tumor tissues display a higher methylation heterogeneity compared to the solid tissue normal. The gene expression evidences a reproducible, higher gene expression in normal tissues. Conclusion. Our research, based on data mining from TCGA, evidences that colon and liver tumors display a consistent methylation heterogeneity compared to their normal counterparts. This parallels a downregulation of <i>SPG20</i> gene expression in tumor samples and suggests a role for this multifunctional protein in the control of tumor progression. |
| first_indexed | 2024-03-10T03:49:51Z |
| format | Article |
| id | doaj.art-f9d41bd038c647b48ee2a8104ccf0fce |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T03:49:51Z |
| publishDate | 2022-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-f9d41bd038c647b48ee2a8104ccf0fce2023-11-23T11:10:38ZengMDPI AGGenes2073-44252022-05-0113586110.3390/genes13050861Methylation Heterogeneity and Gene Expression of SPG20 in Solid TumorsVincenza Ylenia Cusenza0Luca Braglia1Raffaele Frazzi2Laboratory of Translational Research, Azienda Unità Sanitaria Locale—IRCCS di Reggio Emilia, 42123 Reggio Emilia, ItalyResearch and Statistics Infrastructure, Azienda Unità Sanitaria Locale—IRCCS di Reggio Emilia, 42123 Reggio Emilia, ItalyLaboratory of Translational Research, Azienda Unità Sanitaria Locale—IRCCS di Reggio Emilia, 42123 Reggio Emilia, ItalyIntroduction. The downregulation of the Spastic Paraplegia-20 (<i>SPG20</i>) gene is correlated with a rare autosomal recessive disorder called Troyer Syndrome. Only in recent years has <i>SPG20</i> been studied and partially characterized in cancer. <i>SPG20</i> has been shown to be hypermethylated in colorectal cancer, gastric cancer, non-Hodgkin’s lymphoma and hepatocellular carcinoma. In this study, we analyze the methylation status and the gene expression of <i>SPG20</i> in different tumors of various histological origins. Methods. We analyzed the data generated through Infinium Human Methylation 450 BeadChip arrays and RNA-seq approaches extrapolated from The Cancer Genome Atlas (TCGA) database. The statistics were performed with R 4.0.4. Results. We aimed to assess whether the hypermethylation of this target gene was a common characteristic among different tumors and if there was a correlation between the m-values and the gene expression in paired tumor versus solid tissue normal. Overall, our analysis highlighted that <i>SPG20</i> open sea upstream the TSS is altogether hypermethylated, and the tumor tissues display a higher methylation heterogeneity compared to the solid tissue normal. The gene expression evidences a reproducible, higher gene expression in normal tissues. Conclusion. Our research, based on data mining from TCGA, evidences that colon and liver tumors display a consistent methylation heterogeneity compared to their normal counterparts. This parallels a downregulation of <i>SPG20</i> gene expression in tumor samples and suggests a role for this multifunctional protein in the control of tumor progression.https://www.mdpi.com/2073-4425/13/5/861<i>SPG20</i>DNA methylationgene expression regulation |
| spellingShingle | Vincenza Ylenia Cusenza Luca Braglia Raffaele Frazzi Methylation Heterogeneity and Gene Expression of SPG20 in Solid Tumors Genes <i>SPG20</i> DNA methylation gene expression regulation |
| title | Methylation Heterogeneity and Gene Expression of SPG20 in Solid Tumors |
| title_full | Methylation Heterogeneity and Gene Expression of SPG20 in Solid Tumors |
| title_fullStr | Methylation Heterogeneity and Gene Expression of SPG20 in Solid Tumors |
| title_full_unstemmed | Methylation Heterogeneity and Gene Expression of SPG20 in Solid Tumors |
| title_short | Methylation Heterogeneity and Gene Expression of SPG20 in Solid Tumors |
| title_sort | methylation heterogeneity and gene expression of spg20 in solid tumors |
| topic | <i>SPG20</i> DNA methylation gene expression regulation |
| url | https://www.mdpi.com/2073-4425/13/5/861 |
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