Mutational profiling of patient tumor organoids for clinical variable association and markers of therapeutic response in mucinous appendiceal cancers

Background : Mucinous Appendiceal Cancer (mAC) is a rare and poorly characterized malignancy with no known molecular targets and is treated using colorectal cancer protocols. In this study, we employed whole-exome sequencing (WES) on 3D cultures to investigate how mAC-specific oncogenic programming associates with patient clinical variables and therapeutic responses. Methods : Patient-derived tumor organoids (PTOs) were generated from multiple mAC lesions from patients undergoing cytoreductive surgery and hyperthermic intraperitoneal chemotherapy under IRB approval. PTOs were treated with FOLFOX or FOLFIRI for 72 hours with response measured by Cell TiterGlo to determine a response phenotype. A subset of PTOs from 10 patients and 31 tumor deposits were treated with DMSO vehicle, FOLFOX, or FOLFIRI, after which genomic DNA was isolated and sequenced on an Illumina NextSeq 6000. GATK and DRAGEN pipelines were used for mutation calling, and alterations associated with drug response were analyzed by Ingenuity Pathway Analysis (IPA), with stratification informed by relevant patient clinical variables. Results : Across the 10 mAC cases profiled, WES identified a total of 28,245 mutations, including therapeutically actionable KRAS G12D variants in 40% of cases. No targetable alterations were detected in BRAF, EGFR, or ALK. When pooling all pre-treated PTOs and averaging the variant allele frequency (VAF) across all 31 lesions, with a focus on mutations with an average VAF >=10% and present in at least 2/10 patients, individual gene mutations that were undetectable (i.e. VAF=0%) after FOLFIRI treatment included TAX1BP1, PDXK, ZFPM2, and H1FX-AS1. The lone genetic mutation undetectable after FOLFOX treatment was LINC01197, with mutations in SORD and ZBTB24 associated with a complete clonal loss after either FOLFIRI or FOLFOX treatment. Of note, SORD overexpression is implicated in the migration of CRC via upregulation of the mevalonate pathway. IPA canonical pathway analysis of patients progressing within 2 years revealed alterations in D-Myo-Inositol regulation associated pathways, whereas progression-free patients displayed alterations in pathways related to insulin-like growth factor uptake and iron regulation. Further pathway analysis was performed to discover mutations that differentiate pathways by sex, race, tumor grade, TNM scores, obesity status, among other clinical variables. Conclusions : Comprehensive mutational profiling of mAC using paired PTO models via WES is feasible and clinically informative, enabling the detection of actionable oncogenic drivers and chemotherapy-sensitive clonal populations. These data provide the first integrated framework linking mAC-specific genomic alterations to patient outcomes and therapeutic responses and offers new biological insight into the molecular underpinnings of mAC.