Citations

Abstract Background: Most colorectal cancer (CRC) arises from polyps and is mainly prevented by polypectomy. The most important polyps to manage with colonoscopy are those with highest CRC risk- namely, advanced polyps (> 1cm, villous histology or high-grade dysplasia (HGD). Yet, 48% of advanced polyps recur within 1 to 3 years of removal, and up to 5% of advanced polyps under surveillance still progress to CRC. We performed this pilot study to investigate molecular and microenvironment heterogeneities of polyps and how they might impact their clinical behavior. Methods: GeoMx spatial transcriptomics was performed on FFPE tissues from three different polyp outcome phenotypes (POPs) including the polyp that does not recur (POP-NR), that recurs following polypectomy but cured by colonoscopy (POP-R) or the polyp despite polypectomy develops CRC at the polypectomy(ies) site (POP-CRC). Normal colon and polyp with low or HGD from the index polyp were assessed from 6 patients with POP-NR, 9 with POP-R and 12 with POP-CRC with a minimum of 2 follow up colonoscopies at 3-year intervals. Epithelium was identified as PanCK positive, and stroma identified as PanCK negative and positive nuclear staining. Cell type deconvolution was implemented using single-cell adult human intestinal tract catalogue (Elmentaite et al., https://www.gutcellatlas.org/). Differential gene expression (DEG), cell type abundance and functional enrichment analyses was performed using linear mixed effects model, and observations with p-value < 0.05 and log2FC >= |1| are reported. Results: The greatest number of DEGs were identified in stroma of the index POP-CRC compared to POP-NR polyps (n = 17 down and 11 upregulated genes), followed by epithelium of the index POP-CRC vs POP-NR polyps (n = 10 down and one upregulated gene(s)). Between the index POP-CRC and POP-R, epithelium showed downregulation of 7 genes, and upregulation of no genes. In stroma two genes were down and none upregulated. Four genes were downregulated in stroma of the index POP-R vs POP-NR polyp and 3 in epithelium, and one gene was upregulated in stroma and another in epithelium. MZT2B was upregulated in stroma of both the index POP-R (log2FC = 1.09, p-value = 0.0014) and POP-CRC (log2FC = 1.29, p-value = 0.0001) and has been implicated as a prognostic marker associated with worse prognosis in certain cancers. IgM and IgA plasma cells, proximal progenitors, MMP9+ inflammatory macrophages and myofibroblasts were found to be downregulated in epithelium of index POP-CRC and POP-R compared to POP-NR polyps; while microfold cells were downregulated in stroma of index POP-CRC and POP-R compared to POP-NR polyps. Conclusions: The stromal microenvironment and less so, epithelial features present in the index polyp differ based on a polyp’s future clinical behavior. The polyp-immune interaction warrants further study as a potential prevention target against polyp progression. Citation Format: Mrunal Dehankar, Lisa A. Boardman, Daniel O'Brien, E. Aubrey Thompson, Jennifer M. Kachergus, Ji Shi, Alexej Abyzov, Milovan Suvakov, Rondell P. Graham, Chen Wang. Stromal immune composition significantly contributes to adenomatous polyp recurrence or progression to cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 4018.

Abstract Background: Hepatocellular carcinoma (HCC) is largely refractory to immune checkpoint blockade due to immune exclusion, stromal barriers, and aberrant vasculature. We evaluated whether multimodal therapy - external beam radiotherapy (EBRT) for antigen release, intratumoral dendritic cell (DC) vaccination for antigen presentation, PD-L1 blockade for immune activation, and VEGF inhibition for vascular normalization - could convert “cold” HCC tumors into sustained immune-inflamed states. Methods: Serial biopsies (baseline, post-EBRT, end-of-treatment [EOT], and progression [PD] when available) from three patients enrolled in an ongoing phase II trial (NCT03942328) underwent multiplex immunofluorescence, spatial neighborhood analysis, and transcriptomic profiling. Longitudinal changes in cellular composition, immune-stromal architecture, spatial contact networks, and pathway activity were compared. Results: Baseline tumor microenvironments (TMEs) were strongly immune-excluded, dominated by tumor (PanCK+60-70%) and stroma (SMA+/Vimentin+25-30%) with sparse immune infiltration (<10-15%). Post-therapy, immune complexity and spatial connectivity increased 2-3-fold in all patients. Patient 1 showed robust cold-to-hot conversion with CD8+(3x), CD4+(2.2x), and DC (2.3x) expansion, increased CD8-DC interactions (2.5x), and reduced tumor fraction (-40%). Transcriptomics showed marked upregulation of IFN-γ (↑3.4x), HLA-DRA (↑2.7x), and reductions in VEGFR2 (↓50%) and HIF1A (↓40%), consistent with vascular normalization. Patient 2 exhibited stromal/vascular remodeling and improved T-cell infiltration but restricted immune diversity, with CD4+/CD8+ dyads (↑2.2x) and B/NK cells(↓ 60%). Neighborhood diversity rose (3→7 communities) and immune-tumor proximity improved (distance ↓ 35%). Patient 3 showed transient inflaming with CD8+(↑3x), DC(↑2x), and new CD4-CD20/CD4-CD56 interactions, followed by relapse marked by stromal/myeloid re-expansion (SMA+↑1.8x, CD14+↑2.5x), angiogenic resurgence (VEGFR2/CD34+↑2.2x), contraction of immune networks, and genomic shift from activating CTNNB1 mutation loss to ATM gain. DCs accumulated but localized mainly to DC-DC or DC-myeloid niches, indicating non-productive antigen presentation. Conclusions: Multimodal EBRT+DC+PD-L1/VEGF blockade induces four-sided synergistic TME reprogramming - antigen release, immune priming, checkpoint release, and vascular normalization - promoting cold-to-hot conversion in HCC. Durable inflaming correlates with sustained T-cell/DC expansion and vascular remodeling, whereas relapse reflects stromal/myeloid reinforcement and genomic adaptation. These findings define mechanistic trajectories of TME remodeling and highlight actionable barriers to sustained immunotherapy response in HCC. Citation Format: Lionel Aurelien Kankeu Fonkoua, Christopher L. Hallemeier, Basim Salem, Arina Tkachuk, Kaitlynn McCay, Panwen Wang, Ying Li, Thomas D. Atwell, Krishan R. Jethwa, Caitlin Conboy, Nguyen H. Tran, Leslie A. Washburn, Melody Wu, Chen Wu, Andre De Menezes Silva Corraes, Rondell P. Graham, Jose Caetano Villasboas, Kevin Regan, Zuoyi Shao, Rayaan Kamal, Nathan R. Foster, Haidong Dong, Sean Park, Yi Lin, Lewis R. Roberts. Multimodal immunotherapy remodels the tumor microenvironment in hepatocellular carcinoma: Integrative spatial and transcriptomic profiling from a Phase II trial [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 7935.

Abstract Background: Aberrations in telomere length have important implications in cancer development and progression. This study aimed to determine whether leukocyte telomere length (LTL) in patients with colorectal cancer (CRC) is associated with survival outcomes. We also investigated whether genetic variants in telomere maintenance genes are associated with survival in these patients. Methods: Blood specimens were collected from 1,007 patients prior to receiving chemotherapy or radiation. Genomic DNA was extracted using the Promega Maxwell RSC instrument. LTL was measured in triplicate using monochrome multiplex PCR, where the average amplification value of telomeric repeats was termed T. Similarly, PCR amplification of a single-copy reference gene was performed, and its average amplification value was termed S. The telomere length for each sample was expressed as the T/S ratio. Genotyping of single-nucleotide polymorphisms (SNPs) in TERC, TERT, and OBFC1 genes was conducted at the institutional Genome Analysis Core facility. Kaplan-Meier survival curves were generated to evaluate patient survival outcomes. Results: Younger individuals (∼25 years) exhibited nearly a twofold longer LTL compared with older individuals (∼75 years). No significant difference in LTL was observed between stage II and stage III CRC patients. A strong inverse correlation was observed between patient age and LTL (Spearman’s r = -0.48; p = 1.13 × 10-58). Females had significantly longer LTL than males (p = 3.97 × 10-5). The TERC SNP rs1317082 was significantly associated with both overall survival (OS) and disease-free survival (DFS) in the combined stage II and stage III patient cohort (p = 0.017 and p = 0.023, respectively). Similarly, the OBFC1 SNP rs9419958 was significantly associated with OS (p = 0.016). Importantly, LTL itself was significantly associated with both OS and DFS (p = 0.008 and p = 0.044, respectively) among the combined stage II and stage III patients. Kaplan-Meier survival analyses demonstrated that age- and sex-adjusted LTL was predictive of long-term survival outcomes. Conclusions: Survival among patients with stage II and III colorectal cancer is significantly influenced by LTL. Additionally, specific allelic variants of telomere maintenance genes, including TERC and OBFC1, are independently associated with improved survival, irrespective of LTL. These findings suggest that peripheral blood LTL measurement, along with telomere-related genotyping, may serve as a valuable prognostic marker for colorectal cancer outcomes. Funding: Individualizing colorectal cancer patient care using the host and tumor telomere phenotype (RO1 CA204013), Curtiss Fund (92541775), C-SiG Core(s): Epigenomics & Spatial Biology Core, and Clinical Core of the Mayo Clinic Center for Cell Signaling in Gastroenterology (P30DK084567) Citation Format: Estela M. Cruz Garcia, Gobinda Sarkar, Jun Chen, Shubham Sood, Kim Kossick, Daniel Schupack, Rondell Graham, Brooke Druliner, Zahra Heydari, Lauren Helgeson, Richard G. Cawthon, Lisa A. Boardman. Longer leukocyte telomeres and specific alleles of telomere maintenance genes are independently associated with improved survival of colon cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 1919.

Abstract Background: Spatial cellular ecosystems in the tumor microenvironment (TME) form dynamic signaling hubs that critically influence cancer disease progression and response to therapy, including response to immune checkpoint inhibitors (ICIs). However, tumor sampling bias and the impracticality of acquiring serial tumor biopsies have made it challenging to profile the TME clinically. To address this challenge, we developed Liquid EcoTyper, a multi-analyte AI framework to quantify TME spatial cellular ecosystems—termed spatial ecotypes (SEs)—noninvasively from cell-free DNA (cfDNA) methylation data. Methods: In previous work, we discovered nine spatial ecotypes, including SEs associated with ICI response (e.g., SE7 with benefit, SE4 with resistance), and quantified them from 1,249 bulk tumor RNA-seq profiles of melanoma, non-small cell lung cancer (NSCLC), and bladder cancer (BC) patients (Cancer Res (2025) 85 (8_Supplement_1): 153). Here we trained Liquid EcoTyper, an interpretable deep learning model, to transfer SE profiling to cell-free DNA using CpG methylation profiles. Performance was quantified using simulated and real data, including methylation profiles (EM-seq) of plasma cfDNA paired with tumor biopsy-derived SE levels determined by EM-seq (n=20 pairs) or 10x Visium (n=15 pairs). Clinical outcome prediction was evaluated using pretreatment plasma from patients treated with ICI alone (n=78 melanoma pts), chemotherapy and ICI (n=25 NSCLC pts), and enfortumab vedotin and ICI (n=10 localized muscle-invasive BC (MIBC) pts). Tumor mutational burden (TMB), tumor PD-L1, or circulating tumor DNA (ctDNA) were profiled as a comparator where possible. Results: We observed striking concordance between plasma-derived SE levels and tumor biopsy-confirmed SE levels from the same patients, demonstrating that liquid biopsy analysis of cfDNA methylomes can recapitulate TME spatial biology. Underscoring specificity, no reliable SE signal was detectable from peripheral blood mononuclear cells. In pre-ICI plasma, liquid SE levels were significantly associated with ICI-based response (SE7) versus resistance (SE4) in patients with melanoma, NSCLC, and MIBC, with a mean cross-cancer area under the curve (AUC) of 0.87 for SE7 (range 0.8-0.97) and 0.81 for SE4 (range 0.76-0.85)—far surpassing TMB, tumor PD-L1, and ctDNA in evaluable patients, both in binary analyses of response and multivariable models of survival. Our results also showed potential to predict pathologic complete response in the neoadjuvant setting. Conclusion: Liquid EcoTyper is a scalable noninvasive AI-based framework for spatiotemporal assessment of the TME. By enabling TME-informed risk stratification without surgical biopsies, Liquid EcoTyper has potential to enable more precise and actionable decision making in patients with solid tumors. Citation Format: Erin L. Brown, Wubing Zhang, Abul Usmani, Noah Earland, Ayesha Hashmi, Chibuzor Olelewe, Anushka Viswanathan, Pradeep S. Chauhan, Minji Kang, Chloé B. Steen, Hyun Soo Jeon, Susanna Avagyan, Irfan Alahi, Nicholas P. Semenkovich, Matteo Bergsagel, Janella C. Schwab, Chloe M. Sachs, Faridi Qaium, Peter K. Harris, Antonella Bacchiocchi, Qingyuan Cai, Andrew J. Gentles, Rondell P. Graham, Peter C. Lucas, Ryan C. Fields, Jacob J. Orme, Aaron S. Mansfield, Mario Sznol, Ruth Halaban, David Y. Chen, Aaron M. Newman, Aadel A. Chaudhuri. Liquid biopsy profiling of the tumor microenvironment to determine response to immunotherapy regimens across solid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 94.

Background and aims: Aberrations in telomere length can have important implications in cancer. Using a cohort of 1007 patients, we investigated whether leukocyte telomere length (LTL) in patients with colorectal cancer (CRC) is associated with survival. We also investigated whether some telomere maintenance genes are associated with survival in these patients. Methods: The Biobank for Gastrointestinal Health Research (BGHR), an ongoing project involving collection of biospecimens at the Mayo Clinic, was utilized to obtain data from patients diagnosed with stage II or III CRC. Blood samples were collected prior to chemotherapy/radiation and DNA was extracted for measuring median LTL. The main outcome measures were overall survival (OS) and disease-free survival (DFS) by disease stage. Results: A significant inverse relationship was observed with patient age and LTL (spearman correlation coefficient (r) = −0.48, 95%; p = 1.13 × 10−58). Females had significantly longer LTL than males (p = 3.97 × 10−5). The rs1317082 SNP in the TERC gene was significantly associated with both OS and DFS in combined stage II and stage III patients (p = 0.017 and p = 0.023, respectively). A statistically significant association of the OBFC1 SNP (rs9419958) was observed for OS for the combined stage II and stage III patients (p = 0.016). Importantly, LTL was significantly associated with both OS and DFS (p = 0.008 and 0.044 respectively) in combined stage II and stage III patients. Conclusions: Our results show that LTL is predictive of OS and DFS for stage II and III CRC patients, particularly over a longer follow-up, extending beyond five years after a diagnosis of CRC, and certain SNPs in genes involved in telomere maintenance are significantly associated with patient outcomes, independent of telomere length.

561 Background: For patients with aHCC, second-line treatment options are not well established. The primary aim of this study was to evaluate the efficacy of Futi, an FGFR 1-4 inhibitor, in combination with Pem as a second line therapy in patients with FGF19-expressing aHCC. Methods: Patients aged ≥ 18 years, with histological/cytological diagnosis or radiological diagnosis of HCC, Child-Pugh (CP) class A-B7, Barcelona Clinic Liver Cancer (BCLC) A, B or C, ECOG performance status of 0-2, and FGF19+, by in-situ hybridization or immunohistochemistry, received Futi 20 mg once daily plus i.v. Pem 200mg every 3 weeks. The primary endpoint was progression-free survival at 6 months (PFS6). Secondary endpoints include overall survival (OS). The study was designed to enroll 22 evaluable patients to detect PFS6 from 25% (historical control) to 47%, assuming a 1-sided alpha of 0.1 with 80% power. All patients provided written consent. Eligible patients with consent who started treatment are considered evaluable. Results: The study was closed to enrollment early at the request of funding agency due to poor accrual. Between 8/2021 and 3/2024, 14 patients enrolled with 1 patient withdrawing consent before beginning protocol treatment. Among 13 evaluable patients, median age was 72 (range: 60-87) years, 7 (53.8%) were male, 12 CP A (92.3%), 7 BCLC C (53.8%), with 7 (53.8%) having received prior liver directed therapy. Median PFS was 15 weeks (95% confidence interval [CI]: 9.0-Not Estimable) and PFS6 was 23.1% (95% CI: 8.6%, 62.3%). Objective response rate was 0% (95% CI: 0%, 24.71%) and stable disease occurred in 7 (53.9%) of patients. Median OS was 55.7 weeks (95% CI: 47.3-NE). Nine (69.2%) patients experienced at least 1 grade 3+ adverse event (AE), and 2 (15.4%) patients experienced at least a grade 4+ AE. One patient had a grade 5 AE unrelated to study treatment (acute kidney injury). Most commonly reported AEs (occurring in more than 31% of patients) were hyperphosphatemia (76.9%), fatigue (69.3%), diarrhea (61.6%), AST (53.9%) and ALT (46.2%), dry eye (38.5%), nail changes (38.5%), rash-maculo-papular (38.5%), and mucositis oral (38.5%). Conclusions: This prospective study evaluated the use of a targeted treatment in combination with immunotherapy following first line immune-based therapy. This combination had modest activity as a second line therapy for patients with aHCC but did not meet the primary endpoint. The safety profile was acceptable and consistent with prior reports. An optimal second-line regimen remains a critical need. Clinical trial information: NCT04828486 .

Abstract Objective β-Catenin–mutated hepatocellular adenomas (HCAs) carry an increased malignant transformation risk and are screened by interpreting glutamine synthetase (GS) and β-catenin by immunohistochemistry (IHC). Our study aims to assess GS and β-catenin interpretation guidelines for applicability and reproducibility in predicting high-risk HCA and other relevant molecular alterations. Methods Hematoxylin and eosin (H&E), β-catenin, GS, and CD34 stains from 75 HCAs were interpreted by three pathologists using Method A (GS interpretation: negative, perivenular patchy, map-like, diffuse, and indeterminate) and Method B criteria (similar GS interpretation scheme based on a recent publication, with and without CD34 expression patterns). Ease of application and interpretation confidence level were assessed. High-risk IHC was defined as nuclear β-catenin and/or diffuse homogeneous GS. Molecular testing was performed on a subset of HCAs and controls. Results There were 57 resections and 18 biopsy specimens examined. Methods A and B (GS only) were rated as easy to apply, with high interpretation confidence (≥90% using both methods). Consensus rate was comparable in biopsy specimens (100% for both methods) and resections (88% for Method A, 93% for Method B). While the same cases were stratified into high-risk GS categories using both systems, clinically significant genetic alterations (TERT promoter, EGFR, MTOR, and TP53) were identified in 25% of cases stratified as not high risk by IHC. Conclusions Both methods have a similar ease of application and level of interpretation confidence, and they also detected β-catenin mutations as expected. Other relevant molecular alterations associated with risk of neoplastic progression and/or bleeding were detected in 25% of HCAs with the non-high-risk IHC phenotype, suggesting the value of molecular testing in this subset.

PURPOSE Immunotherapy has demonstrated limited efficacy in the treatment of microsatellite-stable (MSS) metastatic colorectal cancer (mCRC) to date. We evaluated whether an off-the-shelf, multipeptide vaccine, PolyPEPI1018, in conjunction with standard chemotherapy can induce broad antitumor immune responses, potentially improving disease control in refractory mCRC. PATIENTS AND METHODS This single-arm, open-label study enrolled adults with MSS mCRC who had progressed after ≤2 previous lines of therapy for metastatic disease. PolyPEPI1018 was administered subcutaneously to four anatomical sites on days 1 and 15 and TAS-102 orally twice a day on days 1-5 and 8-12 of a 28-day cycle. Patients were treated for seven cycles or until disease progression. The primary end point was safety. Secondary end points were overall response rate, progression-free survival (PFS), overall survival (OS), and immune and genetic correlates. RESULTS Fifteen patients were enrolled; 80% had liver metastases and 67% had KRAS mutations. Adverse events (AEs) related to PolyPEPI1018 were grade 1 and 2 local skin reactions (n = 14). Grade 3 AEs (n = 15) at least possibly related to treatment were fatigue, decreased lymphocyte and neutrophil counts, and diarrhea. None had objective tumor response; the disease control rate was 53.3%. The median PFS (mPFS) was 4.0 (95% CI, 2.2 to 6.1) months and the median OS (mOS) was 8.7 (95% CI, 6.4 to 15.2) months. In post hoc subgroup analyses, patients without active liver metastasis had improved mPFS of 9.7 months and mOS of 14.8 months. In addition, patients who were predicted to have broader immune responses to vaccine based on human leukocyte antigen genotype had longer mOS (10.3 v 4.6 months, hazard ratio, 0.29 [95% CI, 0.07 to 1.17]). CONCLUSION The addition of PolyPEPI1018 to TAS-102 was safe and induced immunological responses that were associated with improved clinical outcomes. Further investigation of this chemo-immunotherapeutic is warranted.

Abstract Background The term “incomplete microscopic colitis” (MCi) has been suggested to define patients with chronic watery diarrhea not fulfilling the complete histologic criteria for MC. There are inconsistent data on the epidemiology of MCi and the optimal management of these patients. Methods A systematic search of randomized control trials (RCTs) and observational studies of adults with biopsy-proven MCi (incomplete lymphocytic colitis and collagenous colitis) was conducted using Cochrane, Medline, Scopus, and Embase from inception to May 6, 2025. Data were extracted on (1) incidence and prevalence of MCi, (2) patient features and risk factors, (3) clinical response with treatment, and (4) relapse after treatment cessation. Data were pooled using the random-effects model to calculate weighted pooled estimates and 95% confidence intervals (CIs). Results Of 136 potentially relevant publications identified, 49 passed abstract screening, and 17 studies (1 RCT and 16 observational) were included, with a total of 1370 patients with MCi (median age of 62 years and 69.6% women). The incidence rate of MCi ranged from 0.96 to 5.0 cases per 100 000 person-years. The pooled proportion of concurrent autoimmune disease with MCi was 18% (95% confidence interval [CI], 0.07-0.28; I2 = 95%), and 46% (95% CI, 0.28-0.64; I2 = 95%) were on medications associated with microscopic colitis (MC). The pooled clinical remission rate with any induction therapy was 78% (95% CI, 0.68-0.89; I2 = 81%) and 85% (95% CI, 0.72-0.98; I2 = 88%) with budesonide. Conclusions Patients with MCi share similar characteristics with full MC including demographics, risk factors, and response to therapy, indicating that the histologic criteria for MC should potentially be broadened.

Background and Aims: Cholangiocarcinoma (CCA) is one of the most lethal cancers, characterized by molecular heterogeneity and treatment resistance. To uncover new biological signals and therapeutic opportunities, we employed multiomic characterization combined with machine learning. Approach and Results: We profiled all anatomical CCA subtypes using whole exome sequencing, mRNA sequencing, and proteome/phosphoproteome analysis. Integrative dimensional reduction revealed RNA, protein, and phosphoprotein features driving tumor heterogeneity, enabling clustering. Machine learning algorithms identified molecular features for each cluster and mapped external datasets and patient-derived xenograft (PDX) models onto these clusters. Kinase enrichment analysis highlighted targetable kinases active in each cluster. In vivo validation was performed in cluster-specific PDX models using the selective TNK1 inhibitor, TP-5801. We identified 3 molecular clusters with distinct pathway characterization: immunomodulatory (cluster 1), metabolic (cluster 2), and gene regulation/cellular fate (cluster 3). Cluster assignment was independent of anatomic subtype but correlated with overall survival following curative-intent resection. We also identified multiomic features and pathways linked to overall survival and lymph node metastases, crucial for patient treatment selection. Kinase enrichment analysis pinpointed TNK1 as a highly active kinase in the metabolic cluster. Treatment with TP-5801 significantly reduced tumor growth in a metabolic PDX model, but not in models representing the other clusters. Combining internal data with publicly available datasets, we identified the immunomodulatory cluster as most responsive to gemcitabine/cisplatin therapy, confirmed in vivo using cluster-specific PDX models. Conclusions: Integrated multiomic characterization provides translational insights by defining unique molecular subtypes associated both with therapeutic response and overall clinical outcomes. This approach identified TNK1 as a previously unrecognized therapeutic target in a defined subset of CCA tumors.