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Roberts, Lewis R.

https://orcid.org/0000-0001-7885-8574

Mayo Clinic

Mayo Clinic

Citations 276

Single-arm phase 2 study of the FGFR inhibitor futibatinib (Futi) in combination with pembrolizumab (Pem) in patients with FGF19 expressing advanced or metastatic hepatocellular carcinoma (aHCC).
Palmer, Mathias Earl, Ulrich, Angela, Babiker, Hani M., Revzin, Alexander , Gores, Gregory J., Jin, Zhaohui, Fonkoua, Lionel Aurelien Kankeu, Roberts, Lewis R. , Goenka, Ajit H. , Mahipal, A., Tran, Nguyen H., Roberts, Lewis R , Wee, Wen , Bekaii‐Saab, Tanios , Borad, Mitesh J. , Babiker, Hani M. , Majeed, Umair , Gores, Gregory J. , Hálfdánarson, Þorvarður R. , Jin, Zhaohui , Fonkoua, Lionel Aurelien Kankeu , McWilliams, Robert R. , Graham, Rondell P. , Heimbach, Julie K. , Mahipal, Amit , Ou, Fang‐Shu , Tran, Nguyen H.

Journal of Clinical Oncology | January 12, 2026 | Volume: 44 | Issue: 2_suppl | Pages: 561-561

10.1200/jco.2026.44.2_suppl.561 Get It

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 .
Low serum pseudocholinesterase levels are associated with mortality in patients with hepatocellular carcinoma
Sato-Espinoza, Karina , Chrysostome, Marie-Lise, Vierkant, Robert A., Miller, H. K., Chotiprasidhi, Perapa , Ilyas, Sumera, Roberts, Lewis R. , Wangensteen, Kirk J. , Sato‐Espinoza, Karina , Miller, Hunter B, Roberts, Lewis R , Wangensteen, Kirk J , Miller, Hunter B , Vierkant, Robert A., Ilyas, Sumera I.

Hepatology Communications | January 6, 2026 | Volume: 10 | Issue: 1 | Pages: No page available

10.1097/hc9.0000000000000879 Get It

Background: There is no consensus scoring system for staging and prognosis in hepatocellular carcinoma (HCC), which is the fourth leading cause of cancer-related mortality worldwide. Commonly used systems include the albumin–bilirubin (ALBI) score, the Barcelona staging classification (Barcelona Clinic Liver Cancer, BCLC), the Model for End-Stage Liver Disease (MELD), and the model to estimate survival in ambulatory HCC patients (MESIAH). Liver secretion of pseudocholinesterase (PCHE) has been linked to liver function but is poorly studied in the natural history of HCC. We evaluated whether serum PCHE level predicts HCC mortality and whether it enhances existing scoring systems. Methods: We conducted a retrospective cohort study of individuals diagnosed with HCC. We collected variables including PCHE level, clinical data used in scoring systems, and time to mortality or liver transplant. We then analyzed the association between these variables and survival using Kaplan–Meier curves, Cox proportional hazards regression models, receiver operating characteristic (ROC) curves, and area under the curve (AUC) calculations. Results: We identified 420 individuals with HCC who were tested for PCHE levels, with a follow-up time of more than 20 years. There was a strong inverse relationship between PCHE level and overall survival, with the lowest quartile having high mortality and poor outcomes. Low PCHE level was associated with hepatitis C virus (HCV) infection, vascular invasion, poor liver function, and a high likelihood of liver transplant. In contrast, the highest quartile was associated with metabolic dysfunction–associated steatotic liver disease (MASLD) as the underlying cause. Compared with validated scoring systems, ALBI, BCLC, MELD 3.0, and MESIAH, the PCHE level was an independent predictor of mortality. PCHE levels could predict 3-month survival as well as or better than the other scoring systems, with an AUC of 0.74. PCHE level could also predict mortality related to hepatectomy. The addition of PCHE level to MESIAH and ALBI scoring systems could further improve the ability to predict overall mortality in HCC. Conclusions: PCHE is a reliable stand-alone biomarker of HCC prognosis. It is an independent predictor of mortality and can improve the accuracy of existing scoring systems. Improved risk stratification could improve outcomes by informing treatment decisions regarding hepatectomy or other interventions.
Gastrointestinal cancer statistics in 2022 and projection to 2050: GLOBOCAN estimates across 185 countries
Danpanichkul, Pojsakorn , Pang, Yanfang , Tothanarungroj, Primrose , Dejvajara, Disatorn , Kim, Donghee, Saokhieo, Preenapun , Suparan, Kanokphong, Bernal, Diego Olavarria , Lui, Rashid N., Wijarnpreecha, Karn, Wallace, Michael, Roberts, Lewis R. , Singal, Amit G., Yang, Ju Dong, Kim, Donghee , Suparan, Kanokphong , Abou-Alfa, Ghassan K , Singal, Amit , Yang, Ju Dong , Roberts, Lewis R , Kim, Donghee , Danpanichkul, Pojsakorn , Muthiah, Mark D , Duangsonk, Kwanjit , Lui, Rashid , Wijarnpreecha, Karn , Abou‐Alfa, Ghassan K. , Singal, Amit G.

Cancer | December 30, 2025 | Volume: 132 | Issue: 1 | Pages: No page available

10.1002/cncr.70245 Get It

Abstract Background Gastrointestinal (GI) cancer remains a major global health challenge. This study provides updated 2022 estimates of GI cancer incidence and mortality worldwide, along with projections of incident cases and deaths through 2050 to inform cancer control strategies. Methods In this population‐based study, data from the GLOBOCAN 2022 database were used to examine incidence and deaths associated with GI cancer. By using global demographic projections, this study estimated the projected number of incident cases and deaths until the year 2050. Results By 2050, the global burden of GI cancer is projected to reach 9.06 million incident cases (+85%) and 6.42 million deaths (+93%) from 2022. Increases in incidence are projected for both females (+87%) and males (+83%), as are increases in mortality for both females (+97%) and males (+91%). Whereas the Western Pacific region will have the highest absolute burden, with 3.88 million new cases and 2.79 million deaths, the greatest relative increase is expected in Africa, with incidence and deaths rising by 157% and 160%, respectively. As measured by the Human Development Index (HDI), the steepest increases are projected in low (+151% incidence; +152% deaths) and medium (+112% incidence; +114% deaths) HDI countries. Overall, all GI cancer types are projected to increase, led by pancreatic cancer in incidence (+95%) and colorectal cancer in deaths (+103%). Conclusions GI cancer incidence and deaths are expected to nearly double by 2050, with increases across sexes, cancer types, and regions, especially in lower HDI countries.
Association of Epigenetic Aging Biomarkers With Risk of MASLD ‐Related HCC
Perkin, Alani, Armasu, Sebastian M. , Fan, Winnie Z. , Yalley, Naana N. , Ahmed, Fowsiyo , Boix, Loreto , Bañales, Jesús M. , Reig, María , Roberts, Lewis R. , Wangensteen, Kirk J. , Berglund, Anders , Antwi, Samuel O. , Yan, Irene K. , Ahmed, Fowsiyo Y , Banales, Jesus M , Romero-Gómez, Manuel , Singal, Amit , Roberts, Lewis R , Antwi, Samuel O , Berglund, Anders E , Wangensteen, Kirk J , Reig, Maria , Izquierdo‐Sánchez, Laura , Rojas, Ángela , Stål, Per , Singal, Amit G. , Patel, Tushar P

Liver International | November 29, 2025 | Volume: 46 | Issue: 1 | Pages: No page available

10.1111/liv.70464 Get It

ABSTRACT Introduction Hepatocellular carcinoma (HCC) development in patients with metabolic dysfunction‐associated steatotic liver disease (MASLD) is a growing health concern, but the underlying mechanisms are not fully understood. Epigenetic aging biomarkers, reflecting cellular and tissue aging, have been linked to various age‐related pathologies, but their association with MASLD‐HCC is unknown. We investigated associations between five epigenetic aging biomarkers and MASLD‐HCC risk. Methods We performed whole blood DNA methylation assay (Infinium 850k array) and calculated principal components‐based (PC) versions of HorvathAge, HannumAge, PhenoAge and GrimAge and the DunedinPACE aging rate. We further calculated relative age accelerations for PCHorvathAge, PCHannumAge, PCPhenoAge and PCGrimAge. The aging biomarkers were modelled as continuous variables and categorised into tertiles based on distributions among controls. Associations between each aging biomarker and MASLD‐HCC were examined using logistic regression, calculating odds ratios (ORs) and 95% confidence intervals (CIs), adjusting for covariates. Results Data on 272 MASLD‐HCC cases and 316 cancer‐free MASLD controls recruited from six sites and matched on chronological age, sex and study site were analysed. Higher relative age accelerations of PCPhenoAge (OR T3 vs. T1 = 2.25, 95% CI: 1.45–3.50; OR continuous = 1.04, 95% CI: 1.02–1.07, p = 0.009), PCGrimAge (OR T3 vs. T1 = 3.97, 95% CI: 2.41–6.64; OR continuous = 1.16, 95% CI: 1.10–1.24, p = 8.76 × 10 −07 ) and DunedinPACE (OR T3 vs. T1 = 3.45, 95% CI: 2.17–5.55; OR continuous = 1.72, 95% CI: 1.43–2.10, p = 2.58 × 10 −08 ) were associated with MASLD‐HCC, but not PCHorvathAge or PCHannumAge. Conclusion Higher relative age accelerations of PCPhenoAge, PCGrimAge and DunedinPACE aging rate are associated with risk of MASLD‐HCC. These aging biomarkers could improve HCC risk assessment and facilitate risk stratification in patients with MASLD.
Immune modulation in cholangiocarcinoma through targeted Sulfatase-2 Inhibition for therapeutic intervention 4711
Brooks, Tayla Rashanaye , Campbell, Nellie A. , Smoot, Rory L., Roberts, Lewis R. , Roberts, Lewis R , Luo, Xin

The Journal of Immunology | November 21, 2025 | Volume: 214 | Issue: Supplement_1 | Pages: No page available

10.1093/jimmun/vkaf283.2350 Get It

Abstract Description Cholangiocarcinoma (CCA) is an aggressive epithelial malignancy of the bile duct, with rising global incidence and poor prognosis. Current treatments achieve only 20-30% response rates in advanced cases, highlighting the need for novel therapeutic approaches. The tumor microenvironment (TME) has emerged as a critical focus for innovative therapies. Sulfatase 2 (SULF2) is a heparan sulfate (HS)-editing enzyme that alters HS chain affinity for growth factors and receptors, modulating heparan sulfate proteoglycans (HSPG) in cell signaling pathways. Specific sulfatases in HSPGs have been implicated as therapeutic targets in CCA. This study investigates the potential of anti-SULF2 antibodies to modulate immune cells within the TME using a C57BL6 syngeneic mouse model. Anti-SULF2-treated mice were compared to untreated controls, with tumors analyzed via CyTOF. Treatment resulted in reduced immunosuppressive cells and increased anti-tumor immune cells, suggesting that SULF2 inhibition shifts the TME toward an anti-tumorigenic state. These findings highlight SULF2 as a promising target for therapeutic intervention. Future studies will explore spatial transcriptomic and proteomics to elucidate the interplay between SULF2 expression in the TME makeup. We will also explore the molecular mechanisms of SULF2 suppression and its influence on cytokine signaling pathways within the TME. Funding Sources Supported by CTSA Grant Number TL1 TR002380 from the National Center for Advancing Translational Science (NCATS). Topic Categories Tumor Immunology: Cellular Responses and Tumor Microevironment (TIME)
Associations of S-Adenosylmethionine and S-Adenosylhomocysteine with Hepatocellular Carcinoma
Yalley, Naana N. , Armasu, Sebastian M. , Fan, Winnie Z. , Ahmed, Fowsiyo , Stål, Per , Roberts, Lewis R. , Antwi, Samuel O. , Yan, Irene K. , Ahmed, Fowsiyo Y, Stål, Per , Roberts, Lewis R , Patel, Tushar , Antwi, Samuel O , Patel, Tushar

Metabolites | November 14, 2025 | Volume: 15 | Issue: 11 | Pages: 740

10.3390/metabo15110740 Get It

Background: Hepatocellular carcinoma (HCC) is a leading cause of cancer-related deaths worldwide, increasingly arising in patients with metabolic dysfunction-associated steatotic liver disease (MASLD). Epigenetic dysregulation, particularly DNA methylation, has been implicated in MASLD-HCC development, yet the roles that the principal DNA methylation precursor metabolites, S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH), play in this association are unclear. Objective: We investigated associations of circulating SAM, SAH, the SAM/SAH ratio, with MASLD-HCC. Methods: In a multi-center pilot case–control study, we evaluated 69 MASLD-HCC cases and 136 cancer-free MASLD controls. Plasma SAM and SAH levels were quantified by liquid chromatography–tandem mass spectrometry. Metabolite levels were categorized as greater than or less than the median based on distribution in controls. Logistic regression was used to calculate odds ratios (ORs) and 95% confidence intervals (CIs), adjusting for age, sex, body mass index, smoking status, and type 2 diabetes. Results: MASLD-HCC cases had significantly higher plasma SAM levels (mean 121 vs. 96 nmol/L; p = 0.001) and SAM/SAH ratios (2.09 vs. 1.48; p = 6.42 × 10−7) than MASLD controls. In multivariable-adjusted models, elevated SAM levels (OR≥median vs. <median = 2.76; 95% CI: 1.38–5.72) and higher SAM/SAH ratio (OR≥median vs. <median = 2.30; 95% CI: 1.15–4.73) were associated with higher odds of MASLD-HCC. SAH alone was associated with MASLD-HCC. Conclusions: Higher plasma SAM levels and SAM/SAH ratios are independently linked to MASLD-HCC development. These metabolites might serve as noninvasive markers for HCC risk stratification in patients with MASLD and improve early detection efforts for MASLD-HCC.
Circulating cell‐free DNA methylation biomarkers for hepatocellular carcinoma risk prediction in HIV ‐positive Nigerian population
Zheng, Yinan , Han, Jingzhe , Qu, Yishu , Wang, Jun , Okeke, Edith, Davwar, Pantong , Duguru, Mary, Nyam, David, Oyeleke, Ganiyat K. , Sulaimon, Akanmu A., Hawkins, Claudia , Badmos, Kabir, Gursel, Demirkan, Silas, Olugbenga A. , Kocherginsky, Masha , Sun, Zequn , Achenbach, Chad J. , Yang, Hushan , Sagay, Atiene S. , Roberts, Lewis R., Hou, Lifang , Roberts, Lewis R. , Yang, Hushan , Roberts, Lewis R , Zheng, Yinan , Hou, Lifang , Wang, Jun , Joyce, Brian , Odeghe, Emuobor , Lesi, Olufunmilayo , Imade, Godwin , Abdulkareem, Fatimah Biade , Wei, Jian‐Jun , Kim, Kwang‐Youn A. , Zhang, Xuehong , Ogunsola, Folasade Tolulope , Murphy, Robert L. , Roberts, Lewis R.

International Journal of Cancer | October 23, 2025 | Volume: 158 | Issue: 5 | Pages: 1281-1291

10.1002/ijc.70204 Get It

Abstract Hepatocellular carcinoma (HCC) is a leading cause of cancer mortality globally, with particularly high burdens among people living with HIV (PLWH) in low‐resource settings like Nigeria. Effective early detection remains a major challenge due to limited access to imaging‐based surveillance and the low sensitivity of current biomarkers such as alpha‐fetoprotein (AFP). We conducted an epigenome‐wide association study (EWAS) of circulating cell‐free DNA (ccfDNA) methylation in a Nigerian cohort of HIV‐positive individuals ( n = 245), spanning HCC, cirrhosis (FibroScan ≥12.3 kPa), fibrosis (FibroScan ≥7.6 and <12.3 kPa), and HCC‐free without fibrosis (FibroScan <7.6 kPa) groups. Using random forest modeling, we developed and evaluated a ccfDNA methylation classifier (ccfDNAmRF) for HCC risk prediction. We identified 73 CpG sites significantly associated with HCC (false discovery rate <0.01). The ccfDNAmRF model demonstrated strong discriminatory power, achieving 100% sensitivity and 80%–91% specificity for distinguishing HCC from cirrhosis, fibrosis, and HCC‐free groups (area under the curve [AUC]: 92%–97%). Combining ccfDNA methylation risk scores with AFP further improved classification accuracy (AUC up to 98.5%). Notably, ccfDNA methylation patterns displayed clear dose–response relationships across the disease spectrum, supporting their utility for early‐stage detection and risk stratification. Our findings highlight the promise of ccfDNA methylation biomarkers as a non‐invasive, blood‐based screening tool for improving early identification of HCC cases among PLWH.
Targeted Therapy Improves Real-World Survival in Patients with Molecularly Matched Advanced Biliary Tract Cancer
Bekaii‐Saab, Tanios , Zheng-Lin, Binbin , Eslinger, Cody , Ramaker, Ryne C. , Itoh, Shinji , Hashimoto, Tadayoshi , Imai, Mitsuho , Pirozzi, Angelo , Hoyek, Celine , Moyer, Ashley , Ueno, Makoto , Morizane, Chigusa, Ahn, Daniel H. , Gottam, Madhuri, Bekaii-Saab, Tanios S , Shibuki, Taro , Kosiorek, Heidi , Abidoye, Oluseyi , Kawamoto, Yasuyuki , Fujisawa, Takao , Sonbol, Mohamad Bassam , Wu, Christina , Tran, Nguyen, Babiker, Hani M. , Roberts, Lewis R. , Nakamura, Yoshiaki , Bando, Hideaki , Yoshino, Takayuki , Morizane, Chigusa , Borad, Mitesh J. , Strickler, John H. , Ikeda, Masafumi

No container title available | October 12, 2025 | Volume: No volume available | Issue: No issue available | Pages: No page available

10.21203/rs.3.rs-7744614/v1 Get It

Abstract Molecular profiling reveals that up to 40% of advanced biliary tract cancers (BTCs) harbor actionable genomic alterations amenable to matched targeted therapies. However, conventional trial designs typically evaluate these agents in pretreated populations, resulting in approvals for later-line use. Notably, 25–44% of patients with advanced BTC may become ineligible for treatment after first-line therapy due to disease progression or functional decline, thus the real-world survival outcomes with matched therapies remains poorly characterized. This international collaborative study includes data from Mayo Clinic, Duke Cancer Institute, and National Cancer Center East (Japan), as well as a combined dataset from the SCRUM-Japan GOZILA, MONSTAR-SCREEN-1, and MONSTAR-SCREEN-2 projects. We assessed overall survival (OS) of patients based on the presence of actionable alterations and the receipt of matched therapy. To adjust for confounding, we applied propensity score weighting with inverse probability of treatment and multivariate Cox regression modeling, controlling for age, sex, tumor location, prior resection, and mutational subgroup. Among 1,049 patients that were analyzed, 358 (34.1%) harbored actionable alterations, with 160 (44.7%) receiving matched targeted therapy. The matched group (patients with actionable tumors who received a matched therapy) were significantly associated with longer median OS (23.3 months; 95% CI: 19.5–30.4) compared to the unmatched group (14.7 months; 95% CI: 12.8–17.9) and those with non-actionable tumors (17.1 months; 95% CI: 15.5–18.7; HR 0.57, 95% CI: 0.46–0.71; p < 0.0001). The unmatched group also was associated with the lowest three-year OS rate (13% vs. 35% in matched and 19% in actionable groups, respectively; p<0.0001). On multivariable analysis with patients who received ≥2 lines of therapy, receipt of matched therapy remained an independent predictor of improved OS (HR 0.62; 95% CI 0.43–0.90). These findings support the early integration of targeted therapies in BTC management and underscore the need to overcome systemic barriers to treatment access.
Performance of the multi-target hepatocellular carcinoma blood test: Design and rationale of the ALTUS study
John, Binu V. , Camardo, Mark, Elias, Paul Z. , Kielar‐Grevstad, Elle, Rego, Seema P., Parikh, Neehar D. , Roberts, Lewis R. , Silva, Alvin C. , Yang, Ju Dong , Elias, Paul Z , Roberts, Lewis R , John, Binu V , Parikh, Neehar D , Porter, Kyle M. , Singal, Amit G., Yang, Ju Dong , Limburg, Paul J.

Hepatology Communications | October 7, 2025 | Volume: 9 | Issue: 11 | Pages: No page available

10.1097/hc9.0000000000000800 Get It

Background: Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death in the United States and worldwide. HCC screening among patients at elevated risk is associated with improved early detection and overall survival, but current ultrasound-based screening strategies are challenged by low adherence and suboptimal sensitivity. Blood-based screening tests have the potential to enhance adherence and improve early-stage HCC detection if they can demonstrate favorable performance compared with ultrasound-based screening. Here we present the design and rationale for ALTUS (A lternative to Ultrasound), a prospective, longitudinal, multicenter study in the United States to investigate the performance of the multi-target HCC blood test (mt-HBT) for the detection of HCC in a screening population. Methods: Adults with liver cirrhosis or chronic hepatitis B infection will be enrolled to undergo standard-of-care screening imaging and concurrent blood collection for the mt-HBT. All participants will undergo contrast-enhanced CT or MRI imaging with central radiology LI-RADS assessment as the reference method to determine HCC status. Participants without an identified malignancy will undergo a second screening visit and blood collection, and longitudinal clinical and imaging data will be collected up to 18 months from enrollment. The primary study objectives are to demonstrate that the mt-HBT is non-inferior to ultrasound for early-stage HCC sensitivity and to assess mt-HBT HCC specificity. The secondary objective is to assess mt-HBT overall sensitivity. Results: ALTUS is in progress with readout of the primary analysis expected in 2025. Conclusions: This prospective head-to-head comparison of the mt-HBT versus ultrasound will provide novel data regarding the performance and utility of the mt-HBT for HCC screening.
Multiomics combined with machine learning defines unique molecular subtypes of cholangiocarcinoma and identifies TNK1 as a therapeutic target
Mun, Dong‐Gi , Jessen, Erik , Carlson, Danielle M. , Watkins, Ryan , Gregory, Lindsey A., McCabe, Chantal E. , Golkowski, Martin , Baker, Marshall S., Conboy, Caitlin B. , Ozmert, Enis H., Kandasamy, Richard K. , Roberts, Lewis R. , Andersen, Joshua L. , Smoot, Rory L. , Tomlinson, Jennifer L. , Abdelrahman, Amro , Gregory, Lindsey, Conboy, Caitlin, Larson, Ellen L. , Roberts, Lewis, Pandey, Akhilesh , Jessen, Erik , Roberts, Lewis R , Smoot, Rory L , Kandasamy, Richard K , Conboy, Caitlin B , Mun, Dong-Gi , Carlson, Danielle Marie , Budhraja, Rohit , Alva‐Ruiz, Roberto , Abdelrahman, Amro M. , Wang, Chen , Graham, Rondell P. , Woods, Kathryn, Gores, Gregory J. , Ilyas, Sumera I. , Sample, Jack W. , Borad, Mitesh J. , Pandey, Akhilesh

Hepatology | September 29, 2025 | Volume: 84 | Issue: 2 | Pages: 396-410

10.1097/hep.0000000000001535 Get It

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.