Abstract 484: Molecular drivers of tumor progression in microsatellite stable APC mutation-negative colorectal cancers
Authors: Padi Megha , Bellomo Dante , Grant Adam , Xicola Rosa M. , Thorne Curtis , Salhia Bodour , Llor Xavier , Ellis Nathan 
Published: June 2022

Background: The tumor suppressor gene adenomatous polyposis coli (APC) is the initiating mutation in approximately 80% of all colorectal cancers (CRC). Recent studies have found that early-onset CRC exhibits an increased proportion of tumors lacking an APC mutation. We set out to identify regulatory mechanisms underlying APC mutation-negative (APCmut-) CRCs.

Methods: We analyzed data from The Cancer Genome Atlas to compare clinical phenotypes, somatic mutations, copy number variations, gene fusions, RNA expression, and DNA methylation profiles between APCmut- and APC mutation-positive (APCmut+) microsatellite stable CRCs. We also constructed and compared regulatory networks between APCmut- and APCmut+ CRCs by integrating transcription factor (TF) binding motifs, protein-protein interactions, and gene co-expression using the algorithms PANDA and LIONESS. Single sample networks were used to identify each tumor’s contribution to the differences in transcriptional regulation observed between the APCmut- and APCmut+ groups.

Results: APCmut- CRC expression profiles clustered into two approximately equal groups. Cluster One was associated with enhanced mitochondrial activation. Cluster Two was strikingly associated with genetic inactivation or decreased RNA expression of the WNT antagonist RNF43, increased expression of the WNT agonist RSPO3, activating mutation of BRAF, or increased methylation and decreased expression of AXIN2. APCmut- CRCs exhibited evidence of increased immune cell infiltration, with significant correlation between M2 macrophages and RSPO3. Consistent with this, APCmut-CRC regulatory networks showed strong activation of immune pathways relative to APCmut+ CRCs. The second most prominently targeted pathway was RAS signaling, with the TFs TCF15 and RUNX2 regulating key pathway members including RAF1, GEFs, and GAPs. Single sample networks revealed that tumors with the strongest transcriptional regulation of RAS genes tend to lack a KRAS mutation and exhibit a slight skew towards earlier onset.

Conclusions: APCmut- CRCs comprise two groups of tumors characterized by enhanced mitochondrial activation or increased sensitivity to extracellular WNT, suggesting that they could be respectively susceptible to inhibition of these pathways. APCmut- tumors exhibit increased regulation of RAS pathway genes compared to APCmut+ tumors. The samples contributing most to this regulatory signature tend to lack a KRAS mutation, suggesting that APCmut- tumors have developed ways to modulate RAS pathway activity through non-mutational mechanisms. Focal emphasis on the RAF1 gene suggests these tumors may be more vulnerable to inhibition of the downstream MAPK pathway. Network analysis implicates TCF15 and RUNX2 as regulators of RAS pathway genes, suggesting a possible WNT-RAS crosstalk occurring in APCmut- CRC that warrants further investigation.

Citation Format: Megha Padi, Dante Bellomo, Adam Grant, Rosa M. Xicola, Curtis Thorne, Bodour Salhia, Xavier Llor, Nathan Ellis. Molecular drivers of tumor progression in microsatellite stable APC mutation-negative colorectal cancers [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 484.