Abstract 5675: An intronic SINE-VNTR-Alu element insertion in CASP8 alters gene expression and confers resistance to induction of cell death in gastrointestinal cancer
Authors: Lin Eric W. , Kocher Joshua R. , Chu Chong , Park Peter J. , Ting David T. 
Published: March 2024

Transposable elements are a major source of variation in the human genome. SINE-VNTR-Alus (SVAs), the hominid-specific and youngest active retrotransposon family, are highly polymorphic within the human germline and can contribute to disease risk and progression. In fact, polymorphic SVAs have previously been linked to several human diseases, including rare cases of hereditary cancer syndromes such as neurofibromatosis type I and Lynch syndrome. These examples illustrate that the mobility of SVAs in the genome can significantly impact gene function. Here, we sought to evaluate the potential of SVAs inserting into known tumor suppressors and oncogenes. To this end, we surveyed genomic data from Pan-Cancer Analysis of Whole Genomes (PCAWG) and identified 1956 unique germline SVA insertions in the introns of 1933 genes. Among these, we discovered a highly prevalent polymorphic SVA_E (subfamily) in an intronic region of CASP8. Given caspase-8’s canonical role in apoptosis, we hypothesized that this SVA may impact both caspase-8 expression as well as cell death in cancer.

We first created a panel of colon and gastric cancer cell lines genotyped by PCR for the presence or absence of the CASP8-SVA (SVA+/+: RKO, NCI-N87, HT29, NCI-H747, OCUM-1; SVA-/-: HCT116, LoVo, SNU-407, 23132/87, KM12). RT-qPCR analysis showed significantly higher CASP8 expression in SVA+/+ cell lines, which was concordant with caspase-8 protein expression by immunoblot. Treatment of these cell lines with cytotoxic chemotherapy (FOLFOXIRI) in vitro demonstrated increased resistance to cell death in SVA+/+ cell lines. Direct induction of caspase-8-mediated apoptosis via TRAIL (TNF-related apoptosis-inducing ligand) revealed decreased TRAIL-mediated cell death in SVA+/+ cell lines; interestingly, caspase-8 enzymatic activity was also decreased in SVA+/+ cell lines upon TRAIL stimulation despite increased pro-caspase-8 expression. To further isolate the effects of the CASP8-SVA, we generated an isogenic cell line (RKO CASP8-SVA knockout) model via CRISPR-Cas9. Deletion of the CASP8-SVA redemonstrated decreased CASP8 expression at the mRNA and protein levels. Treatment with FOLFOXIRI in the CASP8-SVA KO cell line exhibited increased sensitivity compared to empty vector control.

In summary, our findings indicate that an intronic SVA insertion in CASP8 increases gene and protein expression but decreases canonical caspase-8 activity, which was associated with increased resistance to FOLFIRINOX or TRAIL induced cell death. Additional interrogation of SVA-induced effects on transcriptional regulation (e.g., epigenetic effects) as well as non-canonical functions of caspase-8 (e.g., activation of NF-κB) is ongoing. To our knowledge this is the first report describing the mechanistic effects of a germline SVA insertion in the context of cancer and therapeutic resistance.

Citation Format: Eric W. Lin, Joshua R. Kocher, Chong Chu, Peter J. Park, David T. Ting. An intronic SINE-VNTR-Alu element insertion in CASP8 alters gene expression and confers resistance to induction of cell death in gastrointestinal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5675.