Abstract 3759: Recurrent methylation heterogeneity and reduced expression of SPG20 is a common characteristic of different tumors
Authors: Cusenza Vincenza Ylenia , Frazzi Raffaele 
Published: June 2022

Background: The Spastic Paraplegia-20 (SPG20, also known as SPART), is a gene that encodes spartin protein. When SPG20 is mutated, spartin expression is downregulated and leads to a rare autosomal recessive disorder called Troyer Syndrome. We recently demonstrated that this gene is epigenetically silenced and downregulated in Diffuse Large B Cell Lymphoma (DLBCL) cell lines. In recent years, other authors demonstrated independently the epigenetic regulation of SPG20 in hepatocellular, gastric and colorectal cancers. In order to assess whether the differential methylation of SPG20 is a common characteristic of tumors of different histological origin, we analysed the methylation of 9 probes upstream of the transcription starting site (TSS) and the gene expression of SPG20 in tumor samples affecting 6 different anatomical sites.

Methods: Illumina Infinium Human Methylation 450 BeadChip and RNAseq data extrapolated from The Cancer Genome Atlas (TCGA) database were used to evaluate the methylation levels and expression of SPG20. Bladder, Colon, Kidney, Liver, Lung and Prostate datasets were selected. At least 30 independent tumor and at least 5 normal tissue samples for each tumor site were analysed. The tumor and normal tissues were paired in each specific cohort. Transcriptome profiling was analysed only in datasets where both tumor and normal counterparts were available. Statistical analysis was performed by two-way ANOVA with a Sidak’s post hoc test for methylation analysis and multiple t-test with Holm-Sidak’s post hoc test for expression analysis.

Results: SPG20 β-values ranging from 0.19 to 0.96 among the different tumor samples were observed in the promoter region covered by the 9 probes that we previously identified (Illumina 450k platform). In the normal group, the β-values were higher than 0.63. Statistically significant differences between the tumor and normal counterpart were observed in colon, liver and prostate and mainly in the probes closest the TSS. The heterogeneity in the methylation status of SPG20 was a common characteristic among the different tumor groups. The variability range of β-values between tumor and normal groups was significantly different with a p value &lt;0.05. Differential expression was observed between tumor and normal counterpart in almost all sites. SPG20 was more expressed in normal than in tumor tissues and the differences were significant in bladder, lung and colon.

Conclusion: Our analysis unveils that the methylation heterogeneity of SPG20 is a common hallmark in all the tumor samples, while the normal counterpart results homogenously distributed. In tumor samples there is an inverse correlation between SPG20 promoter methylation heterogeneity and gene expression. SPG20 is down-regulated in almost all the tumors of different histological origins. SPG20 could have a relavant but still undefined role in cancer as a tumor-suppressor gene.

Citation Format: Vincenza Ylenia Cusenza, Raffaele Frazzi. Recurrent methylation heterogeneity and reduced expression of SPG20 is a common characteristic of different tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3759.