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1. Introduction

Pancreatic cancer and biliary tract cancer are malignant tumours with the worst prognosis. By 2020, the number of new cases of pancreatic cancer is estimated to be 57,600 and biliary tract cancer would be 42,810, which accounts for 3.2 and 2.4% of all new cancer cases, respectively. In contrast, the estimated deaths due to pancreatic and biliary tract cancers in 2020 would be 47,050 and 30,160, accounting for 7.8 and 5.0% of all cancer-related deaths in the United States ^[1].

The poor prognoses of pancreatic and biliary tract cancers are attributable to their low sensitivity to systemic chemotherapy. FOLFIRINOX ^[2] or combination therapy with gemcitabine and nab-paclitaxel ^[3] is the first-line therapy for unresectable or metastatic pancreatic cancer, and gemcitabine and CDDP (cisplatin) for biliary tract cancer [4^[4]]. These treatments are not based on gene mutation profiles, and the median overall survival is less than one year with either treatment.

However, in recent years, with the advancements in the next-generation sequencing (NGS) technology, the genome profiles of a considerable number of tumour specimens have been markedly improved, thereby making it an era wherein therapeutic targets can be explored based on these data, in a so-called tumour-agnostic or histology-agnostic manner [5–9] ^{[5][6][7][8][9]}.

Generally, the amount of DNA required for a gene panel test is 10 to 500 ng, and the proportion of tumour cells contained in the sample is important for ensuring the quality of the test ^[10]. Previously, it was difficult to collect samples for pancreatic cancer and biliary tract cancer, but with the development of endoscopic ultrasonography (EUS) guided biopsy technology, clinically useful samples can now be collected [11,12]^[11][12]. Furthermore, it has been reported that NGS analysis results are obtained from specimens collected by EUS guided biopsy, and that the results are comparable to surgical specimens [13,14]^[13][14]. Therefore, it is expected that gene panel tests will be actively performed in pancreatic cancer and biliary tract cancer.

The cancer panel test introduced in clinical practice has led to the identification of druggable mutations in approximately 10% of the pancreatic cancers and 40% of the biliary tract cancers ^[15]. Therefore, utilisation of tumour multigene NGS is recommended for the detection of actionable alterations in cholangiocarcinoma ^[16].

Here, we review the genome profiles of pancreatic cancers and biliary tract cancers and the approaches used for the development of drugs for the indicated actionable mutations.

2. Gene Mutation Profiles of Pancreatic Cancers

A considerable number of the gene mutations reported in pancreatic cancer are attributed to KRAS, tumour protein p53 (TP53), SMAD4, and cyclin-dependent kinase inhibitor 2A (CDKN2A), and KRAS mutations account for approximately 90% of the pancreatic cancers [17,18]^[17][18]. The results of all exon analyses and single-nucleotide polymorphism (SNP) arrays using samples obtained from 24 pancreatic cancer patient indicate that pancreatic cancer exhibits an average of 63 genetic changes, most of which are point mutations and such gene mutations are concentrated in 12 cellular signalling pathways ^[19].

Furthermore, Biankin, AV et al. ^[20] performed copy number variation (CNV) analysis using exome sequences and arrays of 142 cases of early pancreatic cancer and reported gene mutations in the molecules of the Axon Guidance signal during the embryonic period in addition to the abovementioned 12 cellular signals (slit guidance ligand 2 (SLIT2), roundabout homolog 2 (ROBO2) gene mutation, ROBO1 and SLIT2 copy number decrease, semaphorin 3A (SEMA3A), and plexin-A2 (PLXNA2) copy number increase). The decrease in the expression level of these genes caused by the gene structural mutation is found to be associated with a poor prognosis.

Waddell et al. performed whole-genome analysis and CNV analysis of 100 cases of pancreatic cancer and classified pancreatic cancer based on the pattern of chromosomal structural changes into “stable”, “locally rearranged”, “scattered”, and “unstable” types [21] ^[21]. Among the locally rearranged types, which account for 30% of all pancreatic cancers, there are cases that show amplification of the protooncogenes such as ERBB2, MET, fibroblast growth factor receptor 1 (FGFR1), cell division protein kinase 6 (CDK6), phosphoinositide-3-kinase regulatory subunit 3 (PIK3R3), and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA), which are likely to be treated by molecular targeted therapies. Additionally, the unstable type, which accounts for 14% of all pancreatic cancers, contains several abnormal DNA repair-related genes. Furthermore, it was reported that cases with abnormalities in these genes were sensitive to platinum-based drugs.

Raphael et al. performed integrated genomic, transcriptomic, and proteomic profiling of 150 pancreatic ductal adenocarcinomas [6]. They reported that abnormalities in genes of the RAS pathway other than KRAS were observed in approximately 60% of the KRAS wild-type pancreatic cancers. The proteomic profiling revealed that the TSC/mTOR (mammalian target of rapamycin) signalling pathway showed increased activation in the KRAS wild-type pancreatic cancer compared to that in the mutant type, and it was considered as one of the molecular targets of the KRAS wild-type pancreatic cancer.

Based on the abovementioned findings, it can be implied that pancreatic cancer is dominated by KRAS mutations or RAS pathway genes, but other gene mutations have also been observed that may be targeted for treatment ^[22]. In the future, it will be necessary to conduct studies to devise strategies for identification of these patients.

3. Gene Mutation Profiles in Biliary Tract Cancers

Based on the results of comprehensive genetic analysis of biliary tract cancer, the mutant genes of biliary tract cancer constitute a heterogeneous population consisting of common genetic abnormalities and unique genetic abnormalities in gallbladder cancer, intrahepatic cholangiocarcinoma, and extrahepatic cholangiocarcinoma [7–9,23–26]^{[23][24][25][26]}.

Li et al. performed a paired analysis with normal specimens of 57 cases of gallbladder cancer and found that gene mutations such as TP53 (47.1%), KRAS (7.8%), and ERBB3 (11.8%) were frequently observed, and patients with ERBB pathway mutations, which comprised 36.8% of the cohort, had a worse outcome ^[23]. Roa et al. also reported that patients with gallbladder cancer with HER2 overexpression (ERBB2 amplification) demonstrated a worse overall survival ^[24].

Ross et al. analysed 3320 exons of 182 cancer-related genes and 36 introns of 14 genes in 28 cases of intrahepatic cholangiocarcinoma ^[25]. Structural abnormalities in AT-rich interaction domain 1A (ARID1A; 36%), isocitrate dehydrogenase 1/2 (IDH1/2; 36%), TP53 (36%), and induced myeloid leukaemia cell differentiation protein (MCL1; 21%) were observed frequently, and fusion genes of FGFR2 and neurotrophic tyrosine kinase (NTRK) were also reported.

Nakamura et al. reported results of the whole-exome analysis of 260 cases of biliary tract cancer (145 cases of intrahepatic cholangiocarcinoma, 86 cases of extrahepatic bile duct cancer, and 29 cases of cholangiocarcinoma) [7]. Compared to the intrahepatic cholangiocarcinoma cases, gallbladder cancer and extrahepatic cholangiocarcinoma cases exhibit a higher frequency of gene mutations and an apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC)-associated mutational signature ^[27]. Significant mutations occurred in 32 genes, including KRAS, PIK3CA, IDH1, NRAS, guanine nucleotide binding protein, alpha stimulating activity polypeptide (GNAS), and ERBB2. Among these, TP53, BRCA1, BRCA2, and PIK3CA were observed as gene mutations common to the biliary tract cancers. Site-specific gene abnormalities of EGFR, ERBB3, phosphatase, and tensin homolog (PTEN), ARID2, mixed-lineage leukaemia protein 2 (MLL2), MLL3, telomerase reverse transcriptase (TERT) promoter mutations were found in gallbladder cancer, PRKACA or PRKACB fusion, ELF3, ARID1B in extrahepatic bile duct cancer, and FGFR2 fusion, IDH1/2, EPHA2, and BRCA1 associated protein-1 (BAP1) in intrahepatic bile duct cancer. KRAS, SMAD4, ARID1A, and GNAS mutations were commonly observed in intrahepatic cholangiocarcinoma and extrahepatic cholangiocarcinoma.

Similar to the gene mutation profile of biliary tract cancer, molecular abnormalities related to the RAS pathway are most frequently reported in pancreatic cancer. However, the abnormality of the RAS pathway is only 51.9%, and other pathways or modules include the TGF-β-SWI/SNF-MYC module (40.2%), p53 module (33.9%), epigenetic module (29.3%), and RB-cell cycle module (11.7%). Taken together, it can be inferred that nearly 40% of the indicated genes harbour druggable mutations.

Genetic structural mutations associated with the poor prognosis include deletions of CDKN2A/B, ERBB2, TP53, KRAS, ARID1A, and deletion of 7q22.1 [8,9,26]. Nakamura et al. also reported that the subgroup that exhibited the gene expression profile similar to that of the immune system and cytokine activation had a poor prognosis [7].

The major druggable gene mutations are shown in Table 1, and the related clinical trials are shown in Table 2.

Table 1. Druggable mutation profiles of pancreatic cancer and biliary tract cancer.

Table 2. Clinical trials for druggable mutations in pancreatic cancer and biliary tract cancer.

Selected clinical trial identfied on clinicalTrials.gov on January 31, 2021.