Related Experiment Video
Updated: Sep 21, 2025
Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer
Published on: September 18, 2020
Methylation Heterogeneity and Gene Expression of SPG20 in Solid Tumors
Vincenza Ylenia Cusenza1, Luca Braglia2, Raffaele Frazzi1
1Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy.
Introduction:
The downregulation of the Spastic Paraplegia-20 (SPG20) gene is correlated with a rare autosomal recessive disorder called Troyer Syndrome. Only in recent years has SPG20 been studied and partially characterized in cancer. SPG20 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 SPG20 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 SPG20 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 SPG20 gene expression in tumor samples and suggests a role for this multifunctional protein in the control of tumor progression.
Insights
The Spastic Paraplegia-20 (SPG20) gene is hypermethylated in tumors, showing decreased expression in colon and liver cancers. This suggests SPG20 may help control tumor progression.
Area of Science:
- Oncology
- Molecular Biology
- Epigenetics
Background:
- Spastic Paraplegia-20 (SPG20) gene downregulation is linked to Troyer Syndrome.
- SPG20 has recently been investigated for its role in various cancers.
- Hypermethylation of SPG20 is observed in colorectal, gastric, non-Hodgkin's lymphoma, and hepatocellular carcinomas.
Purpose of the Study:
- To investigate the methylation status and gene expression of SPG20 across diverse tumor types.
- To determine if SPG20 hypermethylation is a common feature in different cancers.
- To explore the correlation between SPG20 methylation levels and its gene expression in tumors versus normal tissues.
Main Methods:
- Utilized data from The Cancer Genome Atlas (TCGA) database.
- Employed Infinium Human Methylation 450 BeadChip arrays and RNA-seq.
- Statistical analysis performed using R 4.0.4.
Main Results:
- SPG20 is consistently hypermethylated upstream of the Transcription Start Site (TSS) in tumors.
- Tumor tissues exhibit greater methylation heterogeneity compared to normal tissues.
- SPG20 gene expression is significantly higher in normal tissues than in tumor samples.
Conclusions:
- Colon and liver tumors show notable SPG20 methylation heterogeneity compared to normal tissues.
- A consistent downregulation of SPG20 gene expression is observed in tumor samples.
- The findings suggest a potential role for SPG20 in regulating tumor progression.
