Search Results (302)

Colorectal cancer (CRC) exhibits a highly heterogeneous tumor immune microenvironment (TME), ranging from “immune-inflamed” to “immune-desert” or “immune-excluded” phenotypes. Understanding how immune cell composition, cytolytic activity (CYT) and genomic alternations shape tumor-immune interactions is critical for improving immunotherapy outcomes. We analyzed TCGA-COAD and TCGA-READ datasets to evaluate immune competency, CYT, immune subtypes, microsatellite instability (MSI), and genomic instability, including somatic mutations, copy number aberrations (CNAs), and chromothriptic events. Immune cell infiltration was correlated with CYT levels, immune checkpoint expression, and immune-related gene signatures. Immune-competent (IC) tumors were predominantly CYT-high, enriched in stromal and immune scores, and exhibited distinct TME characteristics compared with immune-deficient (ID) tumors. IC/CYT-high tumors expressed higher levels of immune checkpoints (PD-1, PD-L1, CTLA-4, IDO1/2, LAG-3) and cytokines/chemokines (C1QA/B/C, CXCL9/10/11, CXCL13). Differences in immune infiltration were observed across tumors with significant mutations and copy number alterations. No prognostic difference was observed between CYT-high and CYT-low patients, indicating that CYT reflects immune activation rather than clinical outcome. Functionally, stimulated CD8⁺ T cells exhibited cytotoxicity activity against MSI-high (HCT-116) and microsatellite-stable (HT-29) CRC cells, with MSI-H cells showing higher sensitivity. Dynamic 3D co-culture demonstrated tumor-guided T cell infiltration and retention of CD8 expression, and co-culture was associated with moderate upregulation of cytotoxicity-related genes GZMA and PRF1 within the system. Cytotoxic activity decreased at lower effector-to-target ratios, highlighting the importance of effector dose. Overall, these findings link CYT, immune competency, MSI status, and genomic instability to T cell cytotoxic responses, providing insights into tumor-immune interactions, and suggest potential associations relevant for immunotherapy research in CRC. Full article

Background and Objectives: A subset of cancer patients treated with immune checkpoint inhibitors may experience rapid tumor progression rather than therapeutic benefit, a phenomenon described as hyperprogressive disease (HPD), which is linked to poor prognosis and shortened survival. Reliable biomarkers capable of predicting HPD remain lacking. To better understand the molecular background of HPD, we analyzed promoter region methylation and somatic mutation profiles in cancer-related genes in patients with malignant melanoma (MM) and renal cell carcinoma (RCC) undergoing anti-PD-1/PD-L1 treatment. Methods: Patients diagnosed with MM or RCC and treated with anti-PD-1/PD-L1 agents between 2011 and 2020 were included, and FFPE tumor samples along with paired normal tissues were analyzed. A diagnosis of HPD was assigned to patients with RECIST 1.1-defined progressive disease who demonstrated a ≥2-fold acceleration in tumor growth kinetics after initiation of immune checkpoint inhibitor therapy. Methylation-specific real-time PCR was performed on 54 samples (15 MM tumors, 22 RCC tumors, 17 RCC-matched adjacent normal samples) to assess promoter methylation of PIK3CA, BAP1, PTEN, and TP53. Next-generation sequencing (NGS) with an 86-gene pan-cancer panel was conducted on 9 HPD samples. Results: Promoter hypermethylation involving PIK3CA, BAP1, PTEN, and TP53 was more pronounced in HPD-associated tumor samples (n = 16) than in tumors without HPD (n = 21). Within the MM cohort, PTEN and TP53 methylation levels demonstrated statistically significant differences between the two groups (p = 0.005 and p = 0.028, respectively), while no comparable associations were observed in RCC patients. NGS analysis detected missense mutations classified as pathogenic or likely pathogenic in 5 of 9 HPD patients (55.6%), involving KIT, PTEN, and VHL. Conclusions: Promoter region hypermethylation in cancer-related genes may contribute to the aggressive tumor behavior observed in HPD. The somatic variants identified in HPD patients are consistent with known oncogenic pathways. These findings support further investigation of epigenetic and genomic biomarkers for HPD risk stratification in larger, prospective cohorts. Full article

Non-small cell lung cancer (NSCLC) exhibits genomic heterogeneity that affects tumor immunogenicity and PD-L1 expression. Patient clustering based on shared mutational profiles using social network analysis (SNA) has been narrowly explored. The study aimed to identify subgroups of NSCLC patients with similar somatic mutation profiles using network-based modularity clustering, and to compare these groups with respect to PD-L1 expression, Tumor mutation burden (TMB), and clinical variables. Data of patients with stage 4 (metastatic) NSCLC, whose tumor tissue samples were collected between 2022 and 2024, were analyzed. This retrospective study included NSCLC patients harboring actionable driver mutations in genes such as EGFR, KRAS, ALK, BRAF, MET. A social network of 129 patients was constructed. Two distinct genomic clusters were identified. Cluster 2 (n = 55) showed a higher prevalence of KRAS, TP53, BRAF, STK11 and additional mutations, while cluster 1 (n = 74) displayed a limited number of driver mutations. Cluster 2 had significantly higher PD-L1 expression (29.8% vs. 13.7%, p = 0.001) and higher TMB (7.8 vs. 5.8, p = 0.021). In multivariate logistic regression, both PD-L1 and TMB were associated with cluster assignment (p < 0.05). Mutation-based SNA clustering delineated two biologically distinct subgroups of NSCLC patients. The highly mutated cluster displayed higher PD-L1 expression and TMB, a profile consistent with a more immunogenic phenotype. This method offers a novel integrative approach that requires prospective validation before clinical implementation. Full article

Gastric adenocarcinomas with yolk sac tumor (YST) differentiation represent an exceptionally rare and poorly understood phenotype, characterized by the emergence of extraembryonic features within an epithelial malignancy. Their histogenesis remains debated, with increasing evidence supporting somatic lineage plasticity rather than germ cell origin. Here, we performed an integrated histopathologic and genomic characterization of three gastric adenocarcinomas with YST differentiation surgically treated at a tertiary cancer center. Histologically, all tumors showed a predominant adenocarcinoma component associated with variable YST differentiation, displaying reticular/microcystic and papillary patterns and expression of oncofetal markers, including alpha-fetoprotein (AFP) and Glypican-3. Targeted next-generation sequencing using a 523-gene panel revealed microsatellite-stable profiles with intermediate tumor mutational burden and substantial intertumoral heterogeneity. Despite gene-level variability, the detected alterations involved signaling pathways commonly implicated in epithelial tumorigenesis, including PI3K-AKT and RTK/RAS-MAPK signaling. Several recurrent alterations were identified across cases, including CCND3 variants and MDM2 copy number gains; however, their biological significance requires validation in larger cohorts. Functional enrichment analysis identified alterations involving developmental and proliferative signaling programs. Overall, these findings suggest that YST differentiation may represent a phenotypic manifestation of epithelial tumor plasticity arising within gastric adenocarcinoma and is associated with epithelial-related oncogenic programs, although broader genomic and comparative studies are required to clarify its histogenesis. This study provides preliminary molecular and histopathologic insights into this rare entity and supports the integration of molecular profiling into its diagnostic and translational management. Full article

Background: Outcomes in chronic myeloid leukemia (CML) remain heterogeneous despite effective BCR::ABL1 tyrosine kinase inhibitors (TKIs). Somatic mutations in epigenetic regulators, particularly additional sex combs-like 1 (ASXL1), have been implicated in adverse prognosis, but their clinical impact in CML has not been systematically defined. Methods: A systematic review was conducted using CINAHL, EMBASE, MEDLINE Ultimate, and PubMed from inception through August 2025. A total of 1339 records were identified; the eligible studies included adult and pediatric patients with chronic and advanced-phase (accelerated or blast) CML. After duplicate removal and screening, 11 studies met the inclusion criteria; these included adult patients only and were included in a qualitative synthesis and meta-analysis. ASXL1 mutation status was assessed using validated molecular methods. The outcomes included the molecular response, cytogenetic response, survival, and treatment resistance. Random-effects models were used to calculate the pooled odds ratios (ORs) with 95% confidence intervals (CIs). Statistical heterogeneity was assessed using the I² statistic. Results: Across the included studies, ASXL1 mutations were detected in approximately 15% of patients. At 12 months, patients with ASXL1 mutations had significantly lower odds of achieving a major molecular response (MMR) compared with ASXL1-wildtype patients (OR 0.29; 95% CI 0.16–0.51; p < 0.0001; I² = 30%). No statistically significant difference was observed in the complete cytogenetic response (CCyR) (OR 0.30; 95% CI 0.02–5.31; p = 0.41; I² = 68%). Compared with patients harboring other non-ASXL1 somatic mutations, an ASXL1 mutation was not associated with a significant difference in MMR (OR 0.49; 95% CI 0.23–1.05; p = 0.067; I² = 0%). Conclusions: ASXL1 mutations may be associated with an inferior molecular response to TKI therapy in CML, supporting their role as an adverse prognostic biomarker. These findings highlight the potential value of incorporating myeloid mutation profiling into future CML risk-stratification strategies. Full article

Immunotherapy has transformed cancer treatment; however, clinical benefit remains limited to a subset of patients, underscoring the need for robust biomarkers that capture tumor-immune interactions across cancer types. In this study, we performed a comprehensive pan-cancer, multi-omics characterization of the immune checkpoint–related molecules CD70, CD80, and TIGIT to evaluate their diagnostic, prognostic, and immunological relevance. Using integrative analyses of transcriptomic, epigenomic, genomic, pharmacogenomic, and single-cell RNA-sequencing data from The Cancer Genome Atlas and complementary resources, we assessed expression patterns, DNA methylation, somatic mutations, copy number alterations, immune infiltration, tumor stemness, and drug sensitivity. CD70, CD80, and TIGIT were broadly dysregulated across multiple malignancies, with coordinated overexpression particularly evident in kidney renal clear-cell carcinoma. Elevated expression of these immune checkpoints was associated with advanced tumor stage, aggressive molecular subtypes, and unfavorable survival outcomes in selected cancers, including uveal melanoma and renal malignancies. Functional analyses revealed significant associations between checkpoint expression and key oncogenic pathways, including epithelial–mesenchymal transition, apoptosis, and hormone receptor signaling, suggesting links with tumor progression and immune activation states. Immune deconvolution analyses indicated that TIGIT expression is associated with a T-cell–inflamed microenvironment and reduced neutrophil infiltration, while CD80 exhibited methylation-dependent associations with immune cell composition. Genomic and epigenetic alterations were found to correlate with checkpoint expression patterns and immune phenotypes across tumor types. Pharmacogenomic profiling identified associations between checkpoint expression and sensitivity to multiple anticancer agents; however, these findings are based on cell line datasets and should be considered predictive. Single-cell transcriptomic analyses further resolved cell-type–specific expression patterns, distinguishing tumor-intrinsic from immune-restricted expression profiles. Collectively, our findings establish CD70, CD80, and TIGIT as integrative biomarkers of tumor progression, immune contexture, and therapeutic response, providing a rationale for their clinical exploitation in precision immuno-oncology. Full article

Background: Oral squamous cell carcinoma (OSCC) remains a major public health challenge, particularly in South Asian populations where environmental exposures such as tobacco and areca nut consumption contribute significantly to disease burden. Although genomic studies have improved understanding of oral cancer biology, population-specific genomic data from high-risk Indian populations remain limited. This study aimed to characterize the genomic landscape of OSCC using whole-exome sequencing (WES) of fresh biopsy specimens obtained from patients residing along the southwest coast of Karnataka, India. Methods: Paired tumor and adjacent normal tissues from ten OSCC samples (total n = 20 samples) were subjected to WES to identify somatic and germline-associated variants. Matched tumor–normal comparative analysis, variant annotation, and population frequency assessment using established genomic databases, including gnomAD, were performed to characterize the mutational profile. The findings were further compared with a previously analyzed regional cohort comprising 66 OSCC patients to evaluate recurrence patterns and population relevance. Results: The analysis identified a broad background of recurrent germline-associated variants alongside a comparatively limited number of tumor-specific somatic mutations, consistent with the expected predominance of constitutional genetic variation relative to acquired coding alterations in tumor samples. Recurrent variants were observed in genes associated with DNA repair, immune signaling, inflammatory responses, and pharmacogenomic pathways, including XRCC1, ITPKB, ABCB1, and OPRM1, whereas somatic alterations were primarily detected in established cancer-associated genes such as TP53, CDKN2A, and TERT. Conclusions: Several recurrent variants demonstrated high frequencies in South Asian populations, suggesting that they may represent recurrent population-associated variants of potential biological or pharmacogenomic relevance that require validation in larger cohorts. KEGG pathway enrichment analysis identified pathways related to cancer, chemical carcinogenesis, metabolic regulation, and xenobiotic response. Overall, these findings provide preliminary insights into the population-specific genomic characteristics of OSCC in this regional cohort and highlight the need for larger validation studies to determine the biological significance and reproducibility of these findings. Full article

Background/Objectives: To date, no validated scoring system can accurately predict the responses of acute myeloid leukaemia (AML) patients to induction chemotherapy (CTX). Current risk assessment relies on complex cytogenetic and molecular abnormalities and focuses on mutations in genes considered fundamental to leukaemogenesis. Methods: We performed bioinformatic analysis of targeted sequencing (TS) data from 111 genes in 1552 AML patients, focusing on mutational patterns derived from single-nucleotide variant (SNV) catalogues. The SNV catalogues were analysed using non-negative matrix factorisation (NNMF), a linear dimensionality-reduction approach, to extract risk-defining recursive signatures (RSs) and to distinguish responders from resistant patients following induction CTX. To enable patient-level prediction, we complemented NNMF with a Random Forest (RF) model. Given the class imbalance between responders and resistant cases, model performance was improved by applying the Synthetic Minority Over-sampling Technique (SMOTE) and by incorporating germline variants alongside somatic mutations. Results: NNMF-derived RSs captured clinically relevant structures in patients’ mutational profiles and clustered patients by treatment response, indicating that the diagnostic targeted sequencing data contain sufficient information for risk stratification and treatment response prediction. At the single-patient level, RF models incorporating balanced data and germline variation improved predictive performance compared with unbalanced somatic-only models. Conclusions: These findings demonstrate that machine learning applied to targeted sequencing data can extract clinically informative mutational structures and improve risk stratification in AML, supporting its potential integration into precision treatment decision-making. Full article

Background: Muscle-invasive bladder cancer (MIBC) is an aggressive disease with heterogeneous responses to neoadjuvant chemotherapy and emerging chemo-immunotherapy combinations. Reliable biomarkers to predict treatment responsiveness before therapy initiation are needed to guide patient selection. Objective: The objective of this study was to identify genomic and immune-related features associated with immune-active tumor phenotypes in MIBC using The Cancer Genome Atlas bladder cancer cohort (TCGA-BLCA). Methods: A retrospective bioinformatics analysis of TCGA-BLCA data was performed, evaluating gene expression, somatic mutations, tumor mutational burden (TMB), DNA damage response (DDR) gene status, and immune infiltration signatures. Immune enrichment metrics were derived from transcriptomic data. In the absence of direct treatment response data, a surrogate immune response classification was applied. Associations were analyzed using descriptive statistics and Firth’s penalized logistic regression. Results: Tumors classified as immune-high phenotype group based on immune-related features exhibited significantly higher global immune infiltration, including increased ImmuneScore and enrichment of cytotoxic and innate immune cells. In multivariable analysis, ImmuneScore was the only independent predictor of inferred responsiveness (p = 0.003). Conclusions: Global immune infiltration showed the strongest association with immune-active tumor phenotypes among the features examined in this TCGA-based analysis. These exploratory findings suggest that immune profiling may warrant further investigation as a component of tumor characterization in MIBC, pending validation in cohorts with clinical treatment and outcome data. Full article

Understanding germline genetic variation is essential for improving human cancer care. Cancer predisposition genetic testing has become a part of the landscape of healthcare. Clinical guidelines have been established to identify individuals with monogenic risk, support variant classification, and guide enhanced cancer surveillance and prevention strategies. However, genetic mechanisms, cancer syndromes, genetic testing, patient education, and high-risk cancer management are often addressed in separate professional domains leading to limited cross-disciplinary understanding and confusion. A review tailored to a broad spectrum of clinicians is necessary to synthesize information, connect key concepts, and clearly define the principles and reasoning underlying recommended practice. Advanced genetic technology identified numerous genes and countless pathogenic variants contributing to a wide range of cancer predispositions. Rapid and accurate next-generation sequencing has enabled the routine use of multi-gene panel testing to stratify cancer risk. In precision cancer therapies, tumor genomic profiling frequently uncovers not only somatic alterations but also germline mutations, revealing additional cancer risk for the patients and their biological relatives. Beyond monogenic risks, the cumulative effect of numerous common polygenic factors can also significantly influence cancer susceptibility. Despite major advances in integrating germline genetic information into cancer care, substantial challenges remain in variant interpretation, precise risk stratification, and implementing personalized screening and prevention strategies. Using several cancer predisposition syndromes as examples, such as breast and ovarian cancer syndrome, Lynch syndrome, and Li-Fraumeni syndrome, the review provides a high-level overview of key concepts, the evolution of knowledge and technology, and the rationale underlying the current clinical management strategies. Full article

Background: Colorectal cancer (CRC) is the third most diagnosed malignancy and the second leading cause of cancer-related mortality worldwide. Recent therapeutic advancements have significantly improved clinical management, underscoring the importance of routine molecular profiling to guide personalised treatment strategies. This study aims to evaluate the prognostic impact of main molecular alterations—including allele frequency (AF) of RAS mutations—on survival outcomes in a real-world hospital-based cohort of patients with metastatic CRC. Methods: A total of 208 consecutive patients with a histologically confirmed diagnosis of CRC and complete clinical, molecular, and survival data were retrospectively analysed. Somatic mutations in KRAS, NRAS, BRAF, and the occurrence of microsatellite instability (MSI) were assessed using pyrosequencing and real-time PCR assays, respectively, on formalin-fixed, paraffin-embedded tumour samples. Associations between mutational status, clinicopathological parameters, and overall survival (OS) were evaluated. Results: Overall, 138 patients (66.3%) harboured at least one somatic mutation: 115 (55.3%) in KRAS, 8 (3.8%) in NRAS, and 15 (7.2%) in BRAF. MSI was detected in 17/208 (8.2%) patients. A statistically significant improvement in OS was observed in patients lacking mutations in any of the three genes—referred to as wild-type (WT) patients—with BRAF mutated cases showing the worst survival (p = 0.041). Increasing age at the time of first-line therapy for advanced disease stage was associated with a statistically significant increase in the hazard of death (p = 0.031). Conclusions: In the advanced disease stage, RAS/BRAF wild-type colorectal cancers were significantly associated with a survival advantage. Full article

Background: Diffuse Large B-cell Lymphoma (DLBCL) is a biologically heterogeneous subtype of non-Hodgkin’s lymphoma (NHL), accounting for 30–40% of cases worldwide. Despite the incorporation of rituximab into standard chemo-immunotherapy regimen, approximately one-third of patients present with relapsed or refractory disease, implicating the need for improved prognostic markers and therapeutic targets. Gene expression profiling successfully classified DLBCL into Germinal Center B-cell-like (GCB) and non-GCB subtypes, which differ in genetic alterations, response to therapy, and clinical outcome. While intrinsic tumor biology has been extensively studied, the contribution of the tumor microenvironment (TME) to disease progression and therapeutic resistance still remains incompletely understood. Methods: In this study, we investigated the mutational landscape of stromal-related genes in DLBCL and evaluated their impact on gene expression, downstream signaling pathways, and tumor progression. Results: A total of 176 DLBCL patients were screened, of which 113 were enrolled based on availability of complete clinical data. The cohort demonstrated male predominance (male:female ratio: 2.1:1), advanced disease stage in 72.6% of patients, and elevated serum lactate dehydrogenase levels in 57.5%. Based on immunohistochemistry, 43.4% cases were classified as GCB-DLBCL and 56.6% as non-GCB DLBCL. Although the International Prognostic Index (IPI) retained prognostic significance for event-free survival (EFS) and overall survival (OS), considerable heterogeneity was observed within similar risk groups. Whole-exome sequencing (WES) uncovered recurrent somatic mutations in key oncogenic and epigenetic regulators, including TNFAIP3, NFIB, NOTCH1, TSC2, EZH2, EP300, KMT2D, and B2M, with subtype-specific distribution. Pathway enrichment analysis implicated role of Notch, Wnt, mTOR, JAK-STAT, TGF-β, and antigen-presentation pathways. Comprehensive WES analysis identified multiple novel mutations in genes associated with the stromal/extracellular matrix with distinct patterns in GCB and non-GCB DLBCL, accompanied by concordant alterations in gene expression profiles, suggesting functional relevance within the TME. Functional validation through primary cell culture demonstrated significantly elevated Th2 (IL-4, IL-6, IL-10) and Th17 (IL-17) cytokines in co-cultures containing both neoplastic cells and stromal components, underscoring the role of TME in DLBCL progression. Conclusions: Taken together, this study provides novel insights into stromal mutational signatures and cytokine-mediated tumor–stroma interactions, offering potential prognostic biomarkers and therapeutic targets for the improved management of DLBCL. Full article

Juvenile myelomonocytic leukemia (JMML) is a rare, aggressive myeloproliferative neoplasm of early childhood characterized by constitutive activation of the RAS-MAPK signaling pathway. RASopathies are a heterogeneous group of complex genetic disorders arising from germline mutations that dysregulate RAS-MAPK signaling. Noonan syndrome, CBL syndrome, and neurofibromatosis type 1 (NF1) are the three major RASopathies predisposing to JMML. More than 90% of JMML cases harbor germline or somatic mutations in one of five canonical driver genes—PTPN11, NRAS, KRAS, NF1, or CBL—establishing JMML as the prototypical malignant manifestation of RASopathy biology. The fifth edition of the World Health Organization Classification of Tumours reclassified JMML as a myeloproliferative neoplasm while the International Consensus Classification adopted JMML under pediatric and/or germline mutation-associated disorders, introducing a JMML-like category for cases lacking five canonical mutations but harboring emerging drivers such as SH2B3::LNK alterations and ALK::ROS1 fusions. The distinction between germline and somatic mutations profoundly influences prognosis: e.g., germline PTPN11-associated myeloproliferations and many germline CBL cases undergo spontaneous resolution, whereas somatic PTPN11- and NF1-mutated JMML is more aggressive and requires prompt allogeneic hematopoietic stem cell transplantation. DNA methylation profiling has emerged as the most robust prognostic framework, with consensus defining high-, intermediate-, and low-methylation subgroups that independently predict outcome. Both genotype and DNA methylation subclassification have been integrated into clinical decision-making, incorporating pretransplant azacitidine, watch-and-wait approaches for favorable-risk patients, and emerging targeted therapies including MEK inhibitors. This review synthesizes recent advances in understanding JMML as a bona fide RASopathy; provides a diagnostic algorithm, molecular landscapes, and prognostic models; and highlights opportunities for molecularly targeted therapeutic intervention. Full article

The genomic landscape of myelodysplastic syndromes/neoplasms (MDS), a heterogeneous group of myeloid malignancies defined by bone marrow cell dysplasia with ineffective hematopoiesis, includes somatic and, less frequently, germline mutations in hematopoietic stem and progenitor cells, along with chromosomal abnormalities. The latest World Health Organization 2022 classification of myeloid neoplasms, as well as stratification in lower-risk (LR) and higher-risk (HR) MDS using either the Revised International Prognostic Scoring System (IPSS-R) or the Molecular International Prognostic Scoring System (IPSS-M), guide prognostic assessment and risk-adjusted therapy. We report the case of an 81-year-old patient diagnosed with LR-MDS according to IPSS-R that exhibited direct progression to acute myeloid leukemia. The retrospective analysis of paired DNA samples from MDS and leukemic phases, obtained four months apart, using both targeted next-generation sequencing and single nucleotide polymorphism array, indicated swift alterations in the genomic profile, being suggested that the leukemic clone emerged from the clone harboring homozygous TET2 and heterozygous SRSF2 variants that acquired RUNX1, BCOR, BCORL1 likely pathogenic mutations and trisomy 13. By employing IPSS-M for prognostic evaluation at the MDS phase, the patient would have been assigned to the HR-MDS category with a possible benefit from hypomethylating agent therapy. Risk stratification is of pivotal importance in a patient-centered approach to MDS treatment being significantly improved by incorporating the molecular genetic findings. Full article

Pancreatic ductal adenocarcinoma (PDAC) and biliary tract cancers (BTCs) remain highly lethal gastrointestinal malignancies because of late presentation, marked molecular heterogeneity, and limited durable benefit from conventional systemic therapy. This narrative review summarizes recent advances in both diseases, focusing on practice-informing clinical trials, biomarker-driven treatment strategies, and translational insights into tumor biology and resistance. In PDAC, progress includes refinement of perioperative management, broader germline and somatic testing, recognition of DNA damage repair-deficient subsets, and development of KRAS-directed therapies and rational combination strategies. In BTCs, especially intrahepatic cholangiocarcinoma, comprehensive molecular profiling has expanded precision oncology through actionable alterations such as FGFR2 rearrangements, IDH1 mutations, HER2 amplification/overexpression, BRAF V600E, NTRK fusions, and MSI-high/dMMR status. Immunotherapy has a clearer role in selected BTC populations, whereas in PDAC benefit remains largely restricted to rare biomarker-defined subsets. Across both diseases, circulating tumor DNA is emerging as a promising tool for prognostication, minimal residual disease assessment, response monitoring, and early resistance detection. Contemporary care increasingly depends on early molecular profiling, individualized treatment sequencing, and integration of targeted therapies, biomarker-guided immunotherapy, and clinical trials. Full article