Aksu, Murat

Abstract Background Molecular underpinnings and clinical characteristics of ERBB2/HER2-mutated colorectal cancers (CRCs) remain poorly understood. We aimed to comprehensively characterize the genomic landscape and clinical features of ERBB2/HER2-mutated CRC and to compare them with those of ERBB2/HER2-amplified CRC. Patients and methods We analyzed cBioPortal data from 4348 CRC patients with available ERBB2/HER2 profiling. Clinicodemographic features, microsatellite instability (MSI), tumor mutational burden, and alterations in 94 cancer-associated genes were evaluated using chi-square/Fisher’s exact test, Kruskal–Wallis test, and hierarchical clustering. Results ERBB2/HER2 putative driver mutations were identified in 95 patients (2.2%), amplifications in 87 (2.0%), and wild-type status in 4166 (95.8%). In the overall cohort, ERBB2/HER2-mutated tumors demonstrated significant KRAS enrichment (50.5%) compared to wild-type (37.7%; P = .014) and amplified tumors (18.4%; P < .001), alongside MSI enrichment (37.2% vs 1.6%; P < .001), elevated tumor mutational burden, and right-sided predominance. ERBB2/HER2-mutated tumors also showed broad driver co-alterations largely reflecting their MSI background. In contrast, ERBB2/HER2-amplified tumors exhibited left-sided predominance, with microsatellite stable (MSS)-restricted analyses revealing selective mutual exclusivity with KRAS (Log2 OR = −1.58; q = 0.019) and TP53 co-occurrence (Log2 OR = 2.04; q = 0.019). Hierarchical clustering confirmed that mutated and amplified tumors consistently occupy separate clusters across anatomical sites. Conclusion ERBB2/HER2 mutations and amplifications represent molecularly and clinically distinct subgroups. ERBB2/HER2-mutated tumors are characterized by an MSI-enriched, hypermutated background with frequent concurrent KRAS alterations, whereas amplified tumors exhibit selective KRAS mutual exclusivity and TP53 co-occurrence. These exploratory findings support alteration-specific therapeutic strategies in CRC.

Abstract Background Cholangiocarcinoma (CCA) is an aggressive primary liver cancer with remarkable molecular heterogeneity. Mutations in SWI/SNF chromatin remodeling components occur in > 20% of CCA cases, with ARID1A and PBRM1 being significantly co-mutated. However, how the dual loss of these subunits reshapes chromatin architecture and drives oncogenic programs remains unclear that we aimed to address by profiling SWI/SNF redistribution, chromatin accessibility, 3D chromatin structure, and transcriptome in a dual Arid1a/Pbrm1 knockout mouse model. Methods CCA was induced in Cas9 knock-in mice via biliary instillation of myr-AKT along with sgRNAs targeting Arid1a and Pbrm1, generating APAC cell line. AC cell line was derived from mice receiving myr-AKT alone. Isogenic dual knockout (AC-sgAP) and control (AC-NT) lines were then generated from AC cells. Multi-omics profiling included ChIP-seq for SMARCA4/BRG1 and DPF2, ATAC-seq, RNA-seq, and Hi-C. Results ChIP-seq revealed that AC-sgAP cells showed decreased BRG1 binding (9,217 vs. 20,769 peaks) but increased DPF2 binding (7,527 vs. 2,068 peaks) and co-occupancy (5,037 vs. 1,888 peaks) compared to AC-NT. In contrast, APAC cells exhibited depletion of both BRG1 (12,994 peaks) and particularly DPF2 (146 peaks) with minimal overlap (68 shared peaks). Genome-wide accessibility profiling demonstrated that APAC cells had 78,582 differentially accessible regions compared to AC-NT, the majority (>70%) representing loss of accessibility, whereas AC-sgAP cells showed only 6,587 differentially accessible regions. Transcriptional profiling identified both unique and common significantly differentially expressed genes in APAC and AC-sgAP relative to AC-NT controls. Interestingly, topologically associating domains (TADs) calling revealed that AC-sgAP cells displayed approximately three-fold more differential TADs compared to AC-NT than APAC cells relative to controls. Conclusions Concurrent Arid1a/Pbrm1 loss drives extensive chromatin and transcriptional reprogramming through SWI/SNF redistribution. APAC cells achieving greater transcriptional dysregulation with fewer TAD disruptions might suggest that intra-TAD regulatory changes are critical events in SWI/SNF-mutant cholangiocarcinoma.

Abstract Background SWI/SNF chromatin remodeling complexes are frequently mutated across human cancers, including biliary tract cancers (BTC). Within the SWI/SNF complexes, loss-of-function (LOF) mutations in ARID1A and PBRM1 are the most common and frequently co-occur alongside PI3K/AKT pathway activation. Yet, how those mutations affect the intracellular signaling landscape and transcriptomic programs is underexplored and may yield novel therapeutic opportunities. Methods Clinicodemographic parameters and mutation profiles of 250 patients with BTC were retrospectively collected through electronic medical records. Advanced overall survival (OS) was assessed in a multivariable analysis. Transcriptomic data were obtained and differentially expressed genes (DEGs) and pathways associated with SWI/SNF mutation status were analyzed. Changes in the transcriptomic landscape were compared to a murine syngeneic model of intrahepatic cholangiocarcinoma (CCA) initiated by loss of ARID1A and/or PBRM1 for cross-species validation. Results After adjusting for age, sex, and anatomical subtype, patients with SWI/SNF LOF mutations were found to have a 30% reduction in mortality risk (HR = 0.70, 95% CI: 0.50-0.98, p = 0.037). The transcriptomic cohort of 233 BTC patients included 71 (30%) with SWI/SNF LOF mutations, 21 (9%) with variants of uncertain significance, and 141 (61%) with SWI/SNF wild-type tumors. Differential gene expression and pathway analysis revealed changes in adaptive immune response, extracellular matrix, and cancer-associated proteoglycans. RNA-sequencing of murine tumors revealed the dominant effect of ARID1A loss in single and double knock-out tumors and conserved pathway alterations between mouse and human tumors. Conclusion Both murine and human primary tumors with either ARID1A alone or ARID1A/PBRM1 co-mutations exhibited altered expression of critical genes and pathways associated with proteoglycan synthesis and extracellular matrix. Ongoing research is investigating how CCA cells depend on those pathways and their canonical regulators for tumor formation and progression.

e16486 Background: Allele-specific KRAS G12C inhibitors have revolutionized lung and colorectal cancer treatment, yet the biology of G12C in other gastrointestinal (GI) malignancies remains undefined. We aimed to elucidate the clinicopathologic and genomic landscape of KRAS G12C-mutated tumors compared to other G12 variants in a large non-colorectal GI cohort. Methods: We queried cBioPortal for pancreatic, esophagogastric, hepatobiliary, ampullary, and appendiceal adenocarcinomas. Following data quality control, the final cohort (n = 6,352) was stratified into KRAS wild-type (n = 3,293), G12C (n = 63), and other G12 variants (n = 2,996). Clinicopathologic features, tumor mutational burden (TMB), microsatellite instability status, and co-alteration in 96 key genes across 11 signaling pathways were compared. Statistical significance was assessed using Fisher’s exact or Chi-square tests for categorical variables and Kruskal-Wallis tests for continuous variables. The Benjamini-Hochberg method was applied to correct for multiple hypothesis testing. Results: KRAS G12C prevalence was 1.0% overall, with significant heterogeneity across cancer subtypes (p < 0.001). Appendiceal adenocarcinoma demonstrated the highest G12C prevalence at 5.71% (10/175), followed by ampullary (1.44%, 2/139), pancreatic (1.17%, 34/2906), hepatobiliary (0.88%, 12/1360), and esophagogastric cancers (0.28%, 5/1772). G12C patients were significantly older than wild-type patients (64.8±11.2 vs 62.5±12.9 years, mean±SD, p < 0.001) but younger than other G12 variant carriers (65.8±10.4 years). G12C tumors demonstrated intermediate genomic instability, with a TMB of 4.82±6.17 compared to 4.98±10.55 in wild-type tumors and 3.67±10.12 in other G12 variants (p < 0.001). Notably, G12C tumors were universally microsatellite stable (0% MSI-H vs 4.0% wild-type vs 0.9% other G12, p < 0.001). Genomic analysis revealed that AKT1 mutations were significantly enriched in the G12C cohort (6.3% vs 0.4%; q = 0.025) as compared to other G12 variants. A trend of increased mutation frequency in HRAS was observed specifically in pancreatic cancers in G12C tumors as compared to other variants (8.8% vs 0.7%; q = 0.083). In pancreatic adenocarcinoma, G12C tumors were enriched for chromatin modifiers, notably ARID1A (17.6% vs 7.7%, p = 0.045) and SETD2 / SETD26 (8.8% vs 1.1%, p = 0.006), though these did not reach FDR significance. Notably, the immunotherapy-resistance drivers STK11 and KEAP1 were absent (0%) in the whole G12C cohort. Conclusions: KRAS G12C represents a biologically distinct subgroup of exon 2 KRAS mutations compared to other KRAS G12 pathogenic variants. The absence of resistance markers and enrichment of actionable AKT1 and chromatin-modifier mutations suggest distinct therapeutic vulnerabilities in non-colorectal KRAS G12C-mutated GI cancers.

210 Background: ERBB2/HER2 amplification defines a rare but clinically distinct subtype of colorectal cancer (CRC), associated with favorable responses to HER2-targeted therapies. In contrast, ERBB2/HER2 -mutant CRCs show limited therapeutic benefit, and their clinical and molecular features remain poorly defined. This study investigated the molecular and clinical features of ERBB2/HER2 -mutant CRCs to provide insight into the molecular basis of their differential therapeutic vulnerabilities compared to amplified CRC. Methods: CRC cases were identified from cBioPortal studies with available clinical and ERBB2/HER2 genomic data. After quality control and deduplication, the cohort included 4407 unique cases: 97 with driver mutation(s) only (2.2%), 86 with amplification only (2%), and 4224 wild-type (95.9%). Demographic, clinical, and molecular features, including microsatellite instability (MSI), tumor mutational burden (TMB), and alterations in 94 oncogenic pathway genes, were compared across groups. Statistical analyses used chi-square/Fisher’s exact tests for categorical data, Kruskal-Wallis tests for continuous variables, and the Benjamini-Hochberg correction for multiple comparisons. Odds ratios and FDR-adjusted p-values were calculated to assess associations. Results: Across groups, the distributions of gender, race, and primary cancer site (colon or rectal cancer) were comparable. However, significant differences were observed in age (mean 58.7 ± 15.0 years for ERBB2/HER2 -mutant, 55 ± 13.9 for amplified, and 59 ± 14.8 for wild-type; p = 0.035) and tumor sidedness (among ERBB2/HER2 -mutant cases: right-colon 30.8%, left-colon 15.2%; among ERBB2/HER2 -amplified: right-colon 12.1%, left-colon 37.9%, p = 0.011). KRAS alterations were significantly more common in ERBB2/HER2 -mutant CRCs (50.5%) compared with both amplified (19.8%) and wild-type (37.6%). MSI-H was detected in 34.5% of ERBB2/HER2 -mutant cases, whereas no MSI-H was observed among amplified tumors (p < 0.001). Expectedly, ERBB2/HER2 -mutant tumors exhibited a hypermutated phenotype, with significantly higher TMB (30.3 ± 45.5) and total mutation count (232.8 ± 926.0), compared to amplified (6.1 ± 9.7 and 15.3 ± 28.4) and wild-type (10.5 ± 20.3 and 126.3 ± 424.5; both p < 0.001). Conversely, ERBB2/HER2 -amplified tumors had the highest fraction of overall genomic alterations including chromosomal changes (0.24 ± 0.17 in amplified vs 0.14 ± 0.17 in mutants and 0.20 ± 0.16 in wild-type; p < 0.001). Hierarchical clustering demonstrated that ERBB2/HER2 -mutant tumors form a distinct molecular cluster, whereas amplified tumors cluster closely with wild-type CRC. Conclusions: ERBB2/HER2 - mutant and amplified CRCs show highly distinct genomic and clinical features, supporting the need for tailored treatment approaches.

Abstract Background: The transcriptional cofactor Yes-associated protein (YAP) is activated in CCA pathophysiology. While canonical regulation by the Hippo pathway resulting in phosphorylation at serine 127 (S127) is inhibitory, SRC-family kinases (SFKs) phosphorylate YAP at tyrosine 357 (Y357), causing activation. Previously, cholangiocytes, hepatic progenitor cells (HPCs), and even mature hepatocytes were suggested as potential cells of origin of CCA, which highlights the plasticity in the liver. However, the role of YAP activation in selecting the cell of origin and lineage commitment during hepatobiliary oncogenesis is unknown. Aim: To determine if YAP Y357 phosphorylation is required for CCA tumorigenesis, we utilized an in vivo model. Unexpectedly, a shift in tumor phenotype to hepatocellular carcinoma (HCC) was identified. Subsequently, we further explored cell signaling and cell of origin contributions to this phenotypic switch. Method: C57BL/6 mice underwent biliary transfection with Sleeping Beauty transposase and transposons encoding myr-AKT and either YAP S127A (YAP-S) or YAP S127A/Y357F (YAP-SY), followed by IL-33 treatment. Tumor nodule count, histologic classification, and liver-to-body ratio were assessed at necropsy after 10 weeks. RNA sequencing and ingenuity pathway analysis (IPA) were performed on HCC and CCA nodules. To determine the cell of origin, tumors were generated in lineage tracing mice (Rosa26 mT/mG mice treated with AAV8-TBG-Cre). Finally, two tumor-derived cell lines with YAP-SY and constitutive AKT expression were isolated. Results: Both YAP-S and YAP-SY models developed similar tumor numbers and bulk. YAP-S mice generated frequent CCA (25.3%) in addition to combined HCC-CCA (cHCC-CCA) tumors (10.7%) and HCC (64%), whereas YAP-SY mice developed predominantly HCC (86.7%), with rare CCA (8.8%) and mixed tumors (4.5%). Transcriptome analysis identified 3,367 differentially expressed genes (DEGs) between HCC from YAP-SY mice and CCA from YAP-S mice. Notably, YAP-regulated genes had decreased expression in the HCC from YAP-SY mice. IPA revealed key upstream regulators, including cytokines and growth factors (e.g., TGFB1, TNF, INFG, CSF2, IL6, IL1B, IL4) and transcription factors (e.g., TP53, JUN, SP1, NFKBIA, STAT3). Lineage tracing demonstrated HCC originated from hepatocytes and CCA from cholangiocytes in both models. Finally, gene expression analysis of novel syngeneic cancer cell lines from YAP-SY mice showed mixed features of both HCC and CCA. Conclusion: In this murine model, we found that sub-maximal YAP activation is associated with increased formation of HCC from hepatocytes, while a higher level of YAP activation due to YAP Y357 phosphorylation is associated with efficient formation of CCA. We identified cytokines and growth factors that may orchestrate this phenotypic switch. Finally, we developed novel syngeneic cancer cell lines with cHCC-CCA characteristics. Citation Format: Muhammed D. Aksu,Jayla T. Millender,Ryan D. Watkins,Jennifer A. Yonkus,EeeLN H. Buckarma,Nathan W. Werneburg,Daniel R. O'Brien,Chantal E. McCabe,Rondell P. Graham,Gregory J. Gores,Rory L. Smoot,Caitlin B. Conboy. YAP tyrosine phosphorylation regulates lineage commitment in liver tumorigenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 1457.