Abstract 751: Transcriptome profiling reveals novel gene fusions in early-onset sporadic rectal cancer

Abstract

Abstract Implementation of regular screening and adoption of a healthier lifestyle has resulted in a steady decline of colorectal cancer (CRC) incidence in the USA over the past few decades. On the contrary, early-onset sporadic rectal cancer (EOSRC) has exhibited an opposite trend in the more recent past. In addition, EOSRC appears to be the predominant CRC subtype in developing nations where CRC incidence has risen significantly during the past 2 decades. Our previous work revealed the absence of canonical CRC tumorigenesis pathways including Wnt (Wingless, Int-1) activation and mismatch repair inactivation in a significant proportion of EOSRC cases. More importantly, we revealed the enrichment of Ca2+/NFAT signaling leading to chromosomal instability in samples devoid of Wnt activation besides identifying ARID2 as a novel tumor suppressor for EOSRC. In order to improve our understanding of EOSRC driver events, we endeavored to characterize the landscape of gene fusions (GFs); given that the latter provide an attractive druggable target. To this end, we performed paired-end RNA Sequencing on 37 carefully selected and well annotated microsatellite stable EOSRC samples. We employed in silico prediction algorithms viz. FusionCatcher, SOAPFuse and EricScript to identify GFs after removing those predicted (GTEx and ConjoinG databases) to occur in normal tissues. The GFs were further filtered based on read support and identification through at least 2 of the 3 algorithms and validated using reverse transcription PCR and Sanger sequencing. Overall, we identified several known (EIF3E-RSPO2, NCEH1-SPATA16) and novel GFs that arose as inter- or intra-chromosomal events. Computational analyses revealed selective enrichment of Gene Ontologies (GOs) in the 5’- (as compared to 3’-) gene partners which differed from GOs enriched in GFs identified from the TCGA CRC data. More importantly, we analyzed the potential role of chromatin architecture in determining the fusion breakpoints. Analysis of CRC Hi-C data revealed that a majority of EOSRC GFs arose from genes located in open chromatin regions. Interestingly, fusions between 5’ ‘open’ and 3’ ‘closed’ partners often resulted in transcriptional activation of the latter revealing a novel mode of oncogenic activation in cancer. Further analyses to correlate the predicted fusion breakpoints with topologically associating domain (TAD) boundaries as well as with common fragile sites (CFSs) that associate with transcription-replication collision are currently ongoing. Validation of potential oncogenic role of few selected GFs using CRC cell lines and nude mice xenografts is also underway. The study is expected to provide significant insights into the patterns of genomic rearrangements in EOSRC besides highlighting the critical role GFs might play in propagating tumorigenesis in CRC. Citation Format: Asmita Gupta, Vasanth Kumar Mandla, Pratyusha Bala, Murali Dharan Bashyam. Transcriptome profiling reveals novel gene fusions in early-onset sporadic rectal cancer [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 751.