Purpose: Biliary tract cancer (BTC) is a heterogeneous group of rare gastrointestinal malignancies with dismal prognosis often associated with inflammation. We assessed the prognostic value of IL6 and YKL-40 compared with CA19-9 before and during palliative chemotherapy. We also investigated in mice whether IL6R inhibition in combination with gemcitabine could prolong chemosensitivity. Experimental Design: A total of 452 Danish participants with advanced (locally advanced and metastatic) BTC were included from six clinical trials (February 2004 to March 2017). Serum CA19-9, IL6, and YKL-40 were measured before and during palliative treatment. Associations between candidate biomarkers and progression-free survival (PFS) and overall survival (OS) were analyzed by univariate and multivariate Cox regression. Effects of inhibiting IL6R and YKL-40 were assessed in vitro, and of IL6R inhibition in vivo. Results: High pretreatment levels of CA19-9, IL6, and YKL-40, and increasing levels during treatment, were associated with short PFS and OS in patients with advanced BTC. IL6 provided independent prognostic information, independent of tumor location and in patients with normal serum CA19-9. ROC analyses showed that IL6 and YKL-40 were predictive of very short OS (OS < 6 months), whereas CA19-9 was best to predict OS > 1.5 years. Treatment with anti-IL6R and gemcitabine significantly diminished tumor growth when compared with gemcitabine monotherapy in an in vivo transplant model of BTC. Conclusions: Serum IL6 and YKL-40 are potential new prognostic biomarkers in BTC. IL6 provides independent prognostic information and may be superior to CA19-9 in certain contexts. Moreover, anti-IL6R should be considered as a new treatment option to sustain gemcitabine response in patients with BTC.

Objective Cytotoxic agents are the cornerstone of treatment for patients with advanced intrahepatic cholangiocarcinoma (iCCA), despite heterogeneous benefit. We hypothesised that the pretreatment molecular profiles of diagnostic biopsies can predict patient benefit from chemotherapy and define molecular bases of innate chemoresistance. Design We identified a cohort of advanced iCCA patients with comparable baseline characteristics who diverged as extreme outliers on chemotherapy (survival 23 m in long survivors, LS). Diagnostic biopsies were characterised by digital pathology, then subjected to whole-transcriptome profiling of bulk and geospatially macrodissected tissue regions. Spatial transcriptomics of tumour-infiltrating myeloid cells was performed using targeted digital spatial profiling (GeoMx). Transcriptome signatures were evaluated in multiple cohorts of resected cancers. Signatures were also characterised using in vitro cell lines, in vivo mouse models and single cell RNA-sequencing data. Results Pretreatment transcriptome profiles differentiated patients who would become RPs or LSs on chemotherapy. Biologically, this signature originated from altered tumour-myeloid dynamics, implicating tumour-induced immune tolerogenicity with poor response to chemotherapy. The central role of the liver microenviroment was confrmed by the association of the RPLS transcriptome signature with clinical outcome in iCCA but not extrahepatic CCA, and in liver metastasis from colorectal cancer, but not in the matched primary bowel tumours. Conclusions The RPLS signature could be a novel metric of chemotherapy outcome in iCCA. Further development and validation of this transcriptomic signature is warranted to develop precision chemotherapy strategies in these settings.

Late diagnosis is a critical factor undermining clinical management of patients with biliary tract cancer (BTC). While biliary tumours display extensive inter-patient heterogeneity, the host immune response may be comparatively homogenous, providing diagnostic opportunities. Herein, we investigated whether cancer-associated systemic reprogramming could be detected non-invasively to improve diagnosis of BTC. In this prospective Danish study, whole blood (WB) microRNA (miRNA) profiling was performed in samples from 218 patients with BTC, 99 healthy participants, and 69 patients with differential diagnoses split into discovery (small RNA-sequencing) and validation (RT-qPCR) cohorts. miRNA expression and activity were further investigated in 119 and 660 BTC tissues, respectively. Four WB miRNAs (let-7a-3p, miR-92b-5p, miR-145-3p, miR-582-3p) were identified and validated as diagnostic of BTC on univariable analysis. Two diagnostic miRNA indexes were subsequently identified that were elevated in patients with BTC and in patients with differential diagnoses, compared to healthy participants. The combination of these miRNA indexes with serum CA 19-9 significantly improved the diagnostic performance of CA 19-9 alone, consistently achieving superior AUC values irrespective of clinical setting (minimum AUC >0.84) or tumour location (minimum AUC >0.87). The diagnostic information captured by miRNA indexes was not recapitulated by routine clinical measurements. Index miRNA expression in BTC tissues was associated with distinct pathobiological and immune features. WB miRNA profiles are altered in patients with BTC. Quantification of miRNA indexes in combination with serum CA 19-9 has the potential to improve early diagnosis of BTC, pending further validation. Surgery is currently the only curative intervention for patients with biliary tract cancer (BTC). However, resection is not possible for most patients who are diagnosed with late-stage disease. With the aim of identifying new early diagnostic opportunities, we analysed circulating microRNAs (small non-coding RNAs whose role in cancer is being increasingly recognised) in whole blood samples. We identified a microRNA signature that could distinguish patients with BTC from healthy participants. These miRNAs significantly improved the diagnostic potential of the routinely measured biomarker, CA 19-9, and were implicated in distinct immune processes in tumour tissues.

Neoadjuvant chemotherapy can down-size or down-stage tumors, minimize post-surgical recurrence risk, or even replace surgery when deployed appropriately for patients with gastrointestinal cancers. However, accomplishing these goals is rate-limited by all-comer treatment protocols, median arm-based comparisons in clinical trials, and the persisting omission of precision approaches for cytotoxic agents. Despite heterogeneity in benefit from standard-of-care regimens, mounting biological data support the presence of actionable sensitivities or potentially targetable dependencies in most tumors. Conceptually, such tumor vulnerabilities could be a game changer. In treatment-resistant malignancies (biliary tract cancer and pancreatic ductal adenocarcinoma), individualized neoadjuvant treatment may increase the curative surgery frequencies that currently occur only in a minority of patients. For more treatment-sensitive gastrointestinal cancers, tailored chemotherapy strategies might reduce the need for high-intensity regimens, minimize post-surgical morbidity, and allow dose de-escalation for selected patients without compromising oncological outcomes. Personalizing chemotherapy strategies remains inferential from comparing outcomes of molecularly distinct patients receiving a single treatment or unselected patients (with comparable baseline characteristics) on different regimens. We discuss the critical importance of harnessing tumor biology to develop and implement predictive signatures for personalized neoadjuvant chemotherapy (alone or in combination with other modalities). This includes exploiting transcriptomics to retrospectively understand the molecular basis of treatment outcomes from patient biopsies, identifying existing agents to replace or supplement current standard of care for those unlikely to respond, and matching novel preclinical treatments to potential responder patients. Deploying mechanistically distinct cytotoxic regimens against gastrointestinal tumors with unique predispositions for DNA damage tolerance is a necessity for boosting neoadjuvant outcomes.

Advanced biliary tract cancers (BTCs) have gained notoriety among gastrointestinal tumours for their comparatively high incidence of actionable alterations and their compelling benefit from targeted therapies matched to these alterations. Such successes are exemplified by BTC-specific approvals of fibroblast growth factor receptor (FGFR) inhibitors for tumours with FGFR2 rearrangements, as well as mutant isocitrate dehydrogenase 1 inhibitors. Nevertheless, there is a clear absence of therapeutic benefit in a subset of patients despite their tumours fulfilling the current molecular criteria for treatment with these drugs. This results in inefficient management of patients with otherwise bleak prognosis, as well as considerable financial burden. Even among responders, the duration of response is limited, a clinical observation that could be considered unusual as these inhibitors typically target driver genes hypothesised to be responsible for tumour formation. However, BTCs exhibit oncogenic addiction to signalling networks rather than individual genes, and by extension, therapeutic response is dependent on these signalling networks rather than simply the status of the specific target gene. Primary resistance is mediated by co-occurring genetic (DNA) and non-genetic (transcriptional, translational, post-translational) alterations in members of signalling networks that are upstream, downstream, or in parallel pathways to the target alteration. Refining the molecular criteria to select patients is a necessary next step, by incorporating co-occurrence of resistance biomarkers as individual parameters or into predictors of treatment benefit. Characterising the molecular bases of resistance to targeted therapies will fuel next-generation combination treatments, maximising the catchment of responders and enhancing the duration of response.