Methylation Heterogeneity and Gene Expression of SPG20 in Solid Tumors

Abstract

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.

Keywords: DNA methylation; SPG20; gene expression regulation.

Figure 1

Algorithm of the workflow applied and described in the present research on The Cancer Genome Atlas (TCGA). The inclusion and exclusion criteria are specified.

Figure 2

Quantitative methylation and gene expression analysis of bladder and colorectal datasets. (A) Bladder m-values of the 7 probes located at the open sea region of the locus SPG20. (B) Bladder expression levels of SPG20 in normal versus tumor tissues. The p-value indicates the statistical significance of the data. (C) Colorectal m-values of the 7 probes located at the open sea region of the locus SPG20. (D) Colorectal expression levels of SPG20 in normal versus tumor tissues. The p-value indicates the significance of the data. Green boxplots represent the nontumoral tissues (solid tissue normal datasets), while red boxplots represent the tumor tissues. The black dots represent the outliers. Each probe is identified with a specific alphanumeric code. The tumor delta is a value that represents the variation between the two groups. The higher the value of tumor delta, the greater the variation between the two groups. Each box plot displays the median value, and the whiskers are the interval between the 1st and 3rd quartiles.

Figure 3

Quantitative methylation and gene expression analysis of the KIRP and KIRC datasets. (A) KIRP m-values of the 7 probes located at the open sea region of the locus SPG20. (B) KIRP expression levels of SPG20 in normal versus tumor tissues. The p-value indicates the statistical significance of the data. (C) KIRC m-values of the 7 probes located at the open sea region of the locus SPG20. (D) KIRC expression levels of SPG20 in normal versus tumor tissues. The p-value indicates the significance of the data. Green boxplots represent the nontumoral tissues (solid tissue normal datasets), while red boxplots represent the tumor tissues. The black dots represent the outliers. Each probe is identified with a specific alphanumeric code. The tumor delta is a value that represents the variation between the two groups. The higher the value of the tumor delta, the greater the variation between the two groups. Each box plot displays the median value and the whiskers the interval between the 1st and 3rd quartiles.

Figure 4

Quantitative methylation and gene expression analysis of hepatocellular, lung and prostate carcinomas. (A) Hepatocellular m-values of the 7 probes located at the open sea region of the locus SPG20. (B) Hepatocellular expression levels of SPG20 in normal versus tumor tissues. The p-value indicates the statistical significance of the data. (C) Lung m-values of the 7 probes located at the open sea region of the locus SPG20. (D) Lung expression levels of SPG20 in normal versus tumor tissues. The p-value indicates the significance of the data. (E) Prostate m-values of the 7 probes located at the open sea region of the locus SPG20. (F) Prostate expression levels of SPG20 in normal versus tumor tissues. Green boxplots represent the nontumoral tissues (solid tissue normal datasets), while red boxplots represent the tumor tissues. The black dots represent the outliers. Each probe is identified with a specific alphanumeric code. The tumor delta is a value that represents the variations between the two groups. The higher the value of the tumor delta, the greater the variations between the two groups. Each box plot displays the median value and the whiskers the interval between the 1st and 3rd quartiles.

Figure 5

(A) Schematic representation of the SPG20 gene with the localization of the two analyzed regions: CpG_121 and open sea. (B,C) m-values analysis of the methylation status of the canonical CpG island (CpG_121) in colorectal and hepatocellular carcinoma. Blue boxplots represent nontumoral tissues, while orange boxplots represent the tumor tissues. The tumor delta represents the variations between the two groups; the p-value indicates the statistical significance of the data. Each box plot displays the median value and the whiskers the interval between the 1st and 3rd quartiles.