Toward personalized medicine for intrahepatic cholangiocarcinoma: Pharmacogenomic stratification of patients
Authors: Paula Olaizola, Maria J. Perugorria, Jesus M. Banales
Journal: Hepatology (2018)

Potential conflict of interest: Nothing to report. See Article on Page 950 Supported by the Spanish Ministries of Economy and Competitiveness (grants FIS PI12/00380 and FIS PI15/01132 and Miguel Servet Programme CON14/00129 [to J.M.B.]; grants FIS PI14/00399 and FIS PI17/00022; and Ramon y Cajal Programme RYC‐2015‐17755) [to M.J.P.] cofinanced by "Fondo Europeo de Desarrollo Regional"; ISCIII (CIBERehd), Spain (to J.M.B. and M.J.P.); "Diputación Foral Gipuzkoa" (grants DFG15/010 and DFG16/004 [to J.M.B.]), BIOEF (Basque Foundation for Innovation and Health Research: EiTB Maratoia BIO15/CA/016/BD [to J.M.B.]); Department of Health of the Basque Country (grants 2013111173 and 2017111010 [to J.M.B.]; grant 2015111100 [to M.J.P.]); and the AECC Scientific Foundation (to J.M.B.). P.O. was funded by the Basque Government. Cholangiocarcinoma (CCA) includes a heterogeneous group of biliary tumors characterized by dismal prognosis.1 The incidence of this cancer is increasing worldwide, representing the second most frequent primary liver tumor and a significant health, social, and economic problem.1 CCAs are traditionally classified according to their anatomical location as intrahepatic (iCCA), perihilar (pCCA), or distal (dCCA). However, their origin and features seem to be diverse.1 Because CCAs are commonly asymptomatic in early stages, they are frequently diagnosed in advanced phases when the disease is found disseminated. Late diagnosis highly compromises the current potentially curative options based on surgery or liver transplantation, although tumor recurrence risk is elevated. Moreover, the refractory nature of CCA makes conventional chemotherapy mainly palliative. All of these data emphasize the need for new noninvasive diagnostic and therapeutic strategies based on personalized medicine. Previous "omics" approaches, including genomic, epigenomic, transcriptomic, and metabolomic analyses, enabled the profiling of different iCCA subtypes.2 The most frequently mutated genes in iCCA include TP53, KRAS, IDH1/2, FGFR2 fusions, and chromatin remodeling enzymes (ARID1A and BAP1), among others.3 Indeed, the identification of the oncogenic networks influenced by individual driver mutations could facilitate future therapeutic interventions within a specific subgroup. In this regard, IDH1/2 mutations and FGFR2 fusions seem to enhance tumor sensitivity to specific pharmacological targeting, resulting in improved patient outcome.7 Nonetheless, the broader integration of genomic, epigenomic, molecular features, and therapeutic implications remains to be elucidated. In this issue of Hepatology, Nepal, O'Rourke, et al.9 provide a novel, deep, and integrated characterization of iCCA at genomic, epigenomic, and pharmacomolecular levels. The study highlights the unprecedented cancer program consequences of having a mutation in either of three genes—IDH, KRAS, and TP53—resulting in a way to stratify patients based on the mutational status of key driver genes. This approach could be valuable for personalized clinical management. Moreover, this mutation‐based classification might be useful to unveil the fundamental networks that orchestrate cholangiocarcinogenesis. The authors integrated whole exome sequencing, targeted exome sequencing, and epigenomic data, which resulted in the identification of four iCCA subgroups based on the most prevalent somatic mutations. In agreement with previous publications, TP53, KRAS, and IDH1/IDH2 were identified as the most recurrently mutated genes in two independent cohorts of iCCA patients comprising 427 individuals. The distribution of mutations differed between genes, with IDH1 and KRAS alterations mainly localized in specific hotspots (R132C/G/L and G12A/C/D, respectively), whereas TP53 mutations occurred across the full length of the gene. Notably, the presence of dual IDH1/KRAS or IDH1/TP53 mutants was infrequent, whereas KRAS and TP53 mutations cooccurred in a small set of patients. Of note, risk factors such as hepatitis B virus infection were associated with the presence of TP53 mutations, which is comparable to previously reported data on liver fluke‐related iCCA.6 Other less frequently mutated genes in this cohort of iCCA patients included chromatin regulators such as ARID1A, BAP1, KDM6B, and SETD2. Based on these data, Nepal et al. stratified iCCA patients into four subgroups: IDH‐gr, KRAS‐gr, TP53‐gr, and undetermined (Udt)‐gr, which consists of iCCAs with wild‐type status for the three driver genes. In addition, single nucleotide variants (SNVs) along the entire genome were described for each group, with the predominance of C>A transversions in IDH‐gr and Udt‐gr, enrichment of C>T transitions in KRAS‐gr, and preferential T>A transversions in TP53‐gr. Each classifier gene was also accompanied by different comutated genes, with BCLAF1 being enhanced in IDH‐gr; SMAD4 in KRAS‐gr; PTEN, RB1, and LATS2 in TP53‐gr; and KDM6B in Udt‐gr. Furthermore, ARID1A mutations were enriched in Udt‐gr and were also present in IDH‐gr and KRAS‐gr, whereas BAP1 mutations were predominantly present within IDH‐gr. In contrast, no chromatin modifiers were associated with TP53‐gr. The analysis of the clinical data from both cohorts indicated that KRAS‐gr and TP53‐gr were both associated with poor prognosis (i.e., reduced overall survival and higher recurrence rates in both independent cohorts). To gain deeper knowledge of the association between the gene mutation pattern and the oncogenic networks guiding iCCA development and progression, dysregulated signaling pathways were evaluated within each subgroup. Metabolic pathways including glutathione and citrate cycles were perturbed in IDH‐gr, whereas disarrangement of immune‐related pathways was described in KRAS‐gr. Alternatively, mitogen‐activated protein kinase, Wnt, and p53 pathways were found enriched in TP53‐gr, and mechanistic target of rapamycin kinase (mTOR) pathway was the only deregulated signaling cascade in Udt‐gr, suggesting the potential involvement of additional genomic (e.g., somatic copy number alteration [SCNA]) or epigenetic alterations. In contrast, a different stratification based on the next most predominantly mutated genes, such as ARID1A‐gr, CDC27‐gr, and BAP1‐gr, did not show consistent common pathway activation. Nepal et al. analyzed SCNAs, indicating an inverse correlation between SNVs and SCNAs. Furthermore, while deletions were enriched in all four iCCA subgroups, amplifications preferentially occurred in TP53‐gr and Udt‐gr. On the other hand, SCNAs contained within IDH‐gr and TP53‐gr did not seem to contribute to the pathogenesis, as there was a lack of enriched signaling pathways associated with the affected genes. Nevertheless, SCNAs in KRAS‐gr and Udt‐gr displayed an increase in several immunological processes, complementing the information derived from SNVs in KRAS‐gr and compensating the absence of SNV‐mediated pathway defects in Udt‐gr. The contribution of epigenomics could also have a role in cholangiocarcinogenesis. By studying an additional cohort of patients (n = 69 iCCAs), the authors revealed prevalent genomic DNA hypermethylation, with IDH‐gr presenting the highest number of differentially methylated regions, followed by Udt‐gr. Next, and in order to determine the value of predictions on pharmacogenomics targeting of key molecular pathways activated by specific mutated genes, high‐throughput screening was conducted on eight human CCA cell lines using 525 compounds that have been approved by the US Food and Drug Administration or are in the later stages of clinical trials. As predicted by in silico analyses, RNA synthesis inhibitors, microtubule‐targeting drugs, topoisomerase and polo‐like kinase 1 inhibitors, and mTOR pathway modulators exhibited the greatest regulatory efficacy in IDH‐gr, KRAS‐gr, TP53‐gr, and Udt‐gr, respectively. Taken together, these observations contribute to gain new knowledge of potential personalized treatment options for CCA patients, demonstrating the importance of patient stratification based on their integrated genomic, epigenomic, and pharmacomolecular profiles (Fig. 1). However, these findings also present new questions that must be addressed. For instance, the accuracy of liquid biopsy for genomic screening and stratification of iCCA needs to be explored, and the therapeutic value of pharmacological targeting of specific signaling pathways after genetic screening should be clinically evaluated. In addition, the genomic, epigenomic, and molecular characterization of CCA tumors originated from different risk conditions such as primary sclerosing cholangitis, cholelithiasis, or choledochal cysts needs to be assessed, as it may provide valuable information for tailored therapy. Because this study was based on iCCAs, future analyses should compare these data with results obtained from pCCA and dCCA. Moreover, future correlations between the integrative genomic, epigenomic, and molecular profiles of CCAs with their histopathological features (e.g., grade of tumor differentiation, perineural invasion, metastasis, stroma, etc.) at diagnosis and patient outcome after target treatments could increase their value. In this study, the Udt‐gr comprised a large proportion of patients, which could mask additional genetic alterations that need to be determined. Notably, METTL13 amplifications were found in more than 70% of the Udt‐gr iCCAs, suggesting METTL13 as a potential RNA methylation promoter involved in cholangiocarcinogenesis.Figure 1: Current available diagnostic techniques and future directions. Abbreviations: CA19.9, carbohydrate antigen 19.9; CEA, carcinoembryogenic antigen; CT, computed tomography; iCCA, intrahepatic cholangiocarcinoma; IDH, isocitrate dehydrogenase; KRAS, KRAS proto‐oncogene; MRI, magnetic resonance imaging; TP53, tumor protein p53; Udt, undetermined.In conclusion, the study by Nepal et al. outlines that the screening of IDH1/2, KRAS, and TP53 gene mutations, as well as FGFR2 fusions, may be of value for future therapeutic approaches.