Abstract
Background: The incidence of biliary system cancer is higher in the Chinese population than in the West. The overall prognosis of gallbladder cancer and cholangiocarcinoma is poor, and the current treatment is limited. In order to explore the pathogenesis of biliary tract cancers and potential targeted therapies, we mapped the mutation landscape of biliary tract cancer in the Chinese population and analyzed the molecular mechanism related to prognosis. Methods: A total of 59 formalin fixed paraffin-embedded (FFPE) tissue samples were obtained from patients with operable biliary tract cancer. We conducted targeted capture sequencing of 620 genes through high-throughput sequencing technology and analyzed the fusion information of 13 genes. Results: Mutations were detected in 88% samples, and the most frequent mutation base was C>T. Genes with higher single nucleotide variations (SNV) and copy number variations (CNV) frequency are TP53, KRAS, ARID1A, VEGFA, cyclin family related genes and cyclin-dependent kinase genes. Actionable mutations were detected in 59.3% samples, and germline mutations were detected in 22% samples. Patients with KRAS mutations, VEGFA pathway mutations and higher tumor mutation burden (TMB) may have poor prognosis. Conclusions: We explored the mutation characteristics and prognostic mechanism of biliary tract cancers in the Chinese population. This study provides potential evidence for targeted therapy and immunotherapy of biliary tract cancers.
Keywords: Gene mutation, somatic mutation, germline mutation, mutation landscape, biliary tract cancer, prognosis
Introduction
Biliary Tract Cancer (BTC) is a malignant tumor originating from the gallbladder and bile duct epithelium, including gallbladder cancer (GBC), intrahepatic cholangiocarcinoma (ICC) and extrahepatic cholangiocarcinoma (ECC). ECC consists of hilar cholangiocarcinoma and distal cholangiocarcinoma [1]. In Western countries, the incidence of cholangiocarcinoma is low, with an annual incidence of 0.35-2 per 100,000 [2]. In Asian countries, the incidence of cholangiocarcinoma is several times higher than that in Western countries. Gallbladder cancer is closely related to cholelithiasis and chronic cholecystitis, accounting for more than 80% of biliary system cancers. The global incidence of gallbladder cancer is 220,000, and the number of deaths is about 165,000 in 2018. In China, the incidence and mortality of gallbladder cancer are 52,800 and 40,700, and the morbidity and mortality are ranked 19th and 12th, respectively [3,4].
Regardless of location, BTC has potentially high transfer and invasion ability. Due to its anatomical location and distribution along the bile duct, it is difficult to remove completely by surgical resection. Even if it is diagnosed at an early stage, BTC is associated with poor prognosis [5,6]. Unfortunately, most BTC patients are diagnosed with advanced disease at their first visit and cannot be treated surgically. The 5-year survival rate of these patients is extremely low, about 10% for cholangiocarcinoma and less than 5% for gallbladder cancer [7-9].
There are no molecular markers related to clinical diagnosis, but drugs targeted to IDH1 and FGFR1/2/3 have shown superior performance recently [10-12]. The phase III clinical trial ClarlDHy demonstrated IDH1 inhibitor Ivosidenib improved the medium progression free survival (Ivosidenib 2.7 months vs. placebo 1.4 months) of patients with ICC who have been treated by chemotherapy [13]. FGFR2 target drugs such as infigratinib, derazantinib and TAS-120 showed good efficacy and controllable toxicity in phase II study [10-12]. The disease control rate of Infigratinib, a tyrosine kinase inhibitor, as a second-line drug for FGFR2 fusion-positive patients with advanced cholangiocarcinoma was 75.4% [12]. Irreversible pan-FGFR inhibitor, TAS-120, inhibited secondary mutations of FGFR2 and have efficacy in four patients with FGFR2-fusion-positive ICC who developed resistance to BGJ398 or Debio1347 [10]. On April 17th, 2020, the U.S. Food and Drug Administration (FDA) approved pemigatinib for FGFR2 fused cholangiocarcinoma and grants priority review to a variety of FGFR inhibitors for their superior efficacy. The pathogenesis of BTC is still unclear. Several previous studies [14-16] have presented common gene mutation spectrums in BTC in Japanese and western populations. Few studies outline genomic mutation characteristics of such tumors in the Chinese population. The next-generation sequencing with high throughput and high efficiency can perform parallel detection on multiple genes, which has been widely used in recent years. In order to explore the molecular mechanism of BTC and the population that would benefit from targeted therapy, we sequenced 620 genes related to tumorigenesis in 59 BTC samples.
Materials and methods
Clinical samples
We collected 59 surgical tissue samples of BTC from Eastern Hepatobiliary Surgery Hospital of the Second Military Medical University (Shanghai, China). According to WHO 2015 classification criteria, the tumor samples including 17 cases of gallbladder cancer and 42 cases of cholangiocarcinoma. All tissue samples were paired with blood samples to rule out nonpathogenic germline mutations. Follow-up data of 26 samples were obtained from Eastern Hepatobiliary Surgery Hospital of the Second Military Medical University. The clinical features included sex, age, tumor location, TNM stage, ECOG score and other information that are presented in Table 1. All the patients in our study signed an informed consent.
Table 1.
Characteristic | Total (n=59) | Any mutation (n=52, 88.1%) | No mutation (n=7, 11.9%) |
---|---|---|---|
Age, median | 57.2 (34-75) | 56 | 65 |
Male gender | 33 | 29 (87.9) | 4 (12.1) |
Female gender | 26 | 23 (88.5) | 3 (11.5) |
ECOG | |||
0 | 9 | 8 (88.9) | 1 (11.1) |
1 | 26 | 23 (88.5) | 3 (11.5) |
2 | 12 | 10 (83.3) | 2 (16.7) |
Unknown | 12 | 11 (91.7) | 1 (8.3) |
Cancer type | |||
Cholangiocarcinoma | 42 | 37 (88.1) | 5 (11.9) |
Gallbladder cancer | 17 | 15 (88.2) | 2 (11.8) |
Stage | |||
I | 1 | 1 (100) | 0 (0) |
II | 7 | 5 (71.4) | 2 (28.6) |
III | 14 | 12 (85.8) | 2 (14.2) |
IV | 21 | 21 (100) | 0 (0) |
Unknown | 16 | 13 (81.3) | 3 (18.7) |
Library building and sequencing
DNA was extracted from FFPE-fixed tumor tissue or peripheral blood using QIAamp DNA FFPE Tissue Kit (Qiagen). NimbleGen SeqCap EZ choice capture panel was used to capture the coding region of 620 genes (Supplementary Table 1) and the splicing sites. The DNA libraries were built according to the procedure of KAPA Hyper Prep protocols (KAPA). The final libraries were sequenced on the Illumina Novoseq6000 (PE150) sequencer, and the original FASTQ file was obtained. The final libraries were sequenced by Illumina Novoseq6000 (PE150).
SNV and indel calling
Trimmomatic was used to filter the sequenced FASTQ files, and Burrows-Wheeler Aligner (BWA) was used to align the reads with the reference genome GRCh37 (hg19). Duplicates generated by PCR were removed by SAMtools. SNVs were called by Mutect2 with a paired workflow. ANNOVAR was used to annotate the variants. We filtered the obtained SNVs according to the following conditions: (1) base quality value ≥20; (2) mutation reads depth ≥4; (3) variant allele frequency ≥1%; (4) reads supporting variation <4 in normal, tumor abundance/normal abundance ≥8; (5) no strand bias (GATK parameter FS >60 for SNP and FS >200 for indel); (6) discard synonymous mutations; (7) variation not in the dbSNP database.
Copy number variation (CNV) analysis
When the dispersion is normal, we set the cutoff values for CNV as 1.5 and 0.5 copies. It is regarded as copy number amplification when the value is larger than 1.5, and it is regarded as copy number deletion when the value is smaller than 0.5.
TMB calculating
TMB is defined as the number of SNV mutations per megabase. We kept mutations with mutation frequency ≥5% and removed synonymous mutations.
Driver mutation analysis
Driver genes were identified using oncodriveCLUST software, which is based on mutation frequency. The loss-of-function (LoF) gene mutations in the coding region were used as background. Gain-of-function (GoF) gene mutations were analyzed as key points.
Germline variant calling
Filter germline variants were obtained by GATK according to the following conditions: (1) mutation depth ≥50; (2) variation frequency ≥30%; (3) discard synonymous mutations; (4) population frequency ≤1/1,000 in ExAC, 1,000 genome and other database; (5) according to the ClinVar database, we reserved the splicing, stop-gain, frameshift, or (likely) pathogenic variants.
Survival analysis
All the analysis and graphs were based on R software. The survfit and survdiff functions in R were used to generate Kaplan-Meier survival curves and calculate the P value of the log-Rank test. Genes with more than 4 mutations were included in the survival analysis.
Results
Mutation signature
Target capture sequencing was conducted in all 59 BTC samples, with an average sequencing depth of 2,500X. At least one mutation was detected in 88% of tumor samples. In total, we identified 853 somatic mutations, including 736 SNVs and 99 indels. Among all the mutations, there were 649 missense, 77 nonsense, 78 frameshift, and 7 splicing mutations. The overall SNV mutation rate was 55.66 muts/Mb, and the Indel mutation rate was 7.49 muts/Mb. The mutation rates of cholangiocarcinoma and gallbladder cancer were 30.25 muts/Mb and 25.41 muts/Mb, respectively. In this study, C>T was found to be the most common type of mutation, accounting for 62.4% of all SNVs (Figure 1A). Non-negative matrix factorization (NMF) was used to identify mutant signatures of BTC. This analysis identified two different signatures: signature A is characterized by (A/C/T/G) CG> (A/C/T/G) TG, and signature B is characterized by TC (A/C/T) <TG (A/C/T) and TC (A/T/C/G) <TT (A/T/C/G) (Figure 1A). We compared the identified signature with the COSMIC signature and found that signature A is similar to COSMIC signature SBS1 and SBS6 (cosine similarity is 0.66 and 0.68 respectively), and that signature B is similar to COSMIC SBS13 (cosine similarity is 0.78) (Figure 1B).
We profiled the somatic mutation maps of BTC (Figure 2A). A total of 603 genes were mutated in all BTC samples, and most of the gene mutations appeared at least in one sample. We found 47% of all 59 patients harbored the TP53 mutation, significantly higher than previously reported (33%, 26%) [15,16]. The mutation frequencies of TP53 in cholangiocarcinoma and gallbladder cancer were 43% and 80%, respectively (Figure 2B, 2C), and both are higher than previously reported. TP53 gene mutations had no hot spot, but were mainly in the DNA binding domain (Figure 3). In previous reports, KRAS, with mutation frequency ranging from 5% to 18%, was the gene with the second most significant number of mutations after TP53 [15-17]. In this study, the KRAS mutation frequency was 19%, and the frequencies in cholangiocarcinoma and gallbladder cancer were 24% and 13%, respectively (Figure 2B, 2C). We used oncodriverCLUST to analyze the possible driver genes and found that KRAS and IDH1 mutations were driver mutations (Supplementary Table 3).
In addition to the above genes, other frequently mutated genes in this study included ARID1A, KMT2C, ATM, BRCA2, PBRM1, SMARCA4 et al. We estimated that ARID1A was mutated in 17% of all patients in this study, slightly higher than that was recorded in the COSMIC database (12%). The proteins encoded by the ARID1A, ARID1B, PBRM1 and ARID2 genes are all parts of the large ATP-dependent chromatin remodeling complex SNF/SWI. ARID1A is the largest subunit in the SWI/SNF chromatin remodeling complex, which has activities of helicase and ATPase, and regulates transcription by changing the chromatin structure of specific genes [18].
Copy number variation (CNV)
CNV is one of the driver factors of carcinogenesis and can directly affect gene transcription and protein expression. In this study, CNV was calculated based on the relative coverage of tumor samples and normal samples. We used GISTIC2.0 to analyze statistically significant local amplifications or deletions, and found that CNV occurred in 35.6% of patient samples (Figure 4A). Frequently amplified or deleted genes included vascular endothelial growth factor A encoding gene VEGFA, cyclin family genes (CCND1, CCND2, CCND3), cyclin dependent kinase genes (CDK12, CDK6), cyclin dependent kinase inhibition genes (CDKN2A, CDKN2B), Erb-B2 receptor tyrosine kinase encoding gene ERBB2 and other genes such as MYC, MDM4, MDM2.
Statistical analysis showed that the chromosome segments that are more prone to amplification and deletion were 6p21.1 and 5q35.3, respectively (Figure 4B). The 6p21.1 region occurs in a variety of cancer types in Chinese population, including lung cancer and esophageal cancer, and is also associated with various familial genetic diseases such as hypertension and atherosclerosis [19]. CNV in the 5q35.3 region is relatively rare and has been reported in pancreatic cancer [20].
Pathway enrichment analysis
In order to explore the molecular mechanism of BTC, KEGG pathway enrichment analysis was used to enrich somatic mutant genes into important signaling pathways. Among these pathways, the tumor associated signal pathways with frequent gene mutations are PI3K-Akt, MAPK and Ras signaling pathways (Figure 5). PI3K-AKT signaling pathway (Supplementary Figure 1A) not only regulates tumor cell proliferation, but also is closely related to tumor angiogenesis [21]. The Ras-Raf-MAPK signal transduction pathway (Supplementary Figure 1B) is involved in the signal transduction of various activated growth factors, cytokines, mitogens and hormone receptors, and plays an important role in regulating cell proliferation, growth and differentiation. Mitogen activated protein kinase (MAPK) can promote vascular endothelial cell proliferation and neovascularization, which can provide more nutrients for tumors, accelerate tumor growth, and promote the spread of cancer cells [22].
Germline variants in BTC patients
In order to explore the genetic characteristics of cancer in the biliary system, we analyzed germline mutations in 61 genes (Supplementary Table 2) associated with genetic susceptibility. Germline mutations in BTC have been reported in several studies, and the reported detection frequency is 10%-20% [23]. Germline mutations were found in 13 (22%) patients’ samples in this study. Each germline mutation was detected in only one patient sample, and most of them were truncated, frameshift or splicing variations with high evidence of pathogenicity. Germline mutations are mostly DNA damage repair related genes, such as Lynch syndrome related mismatch repair genes MLH3, MSH6 [24,25], nucleotide excision repair gene ERCC4, DNA single-strand damage repair gene XRCC1. Germline mutations have also occurred in other genes including POLD1, XRCC1, IKZF1, ERCC4, TLR4, EPPK1, CDKN1A, NCOA3 and FGFR1. So far all these mutation nucleotide sites above have not been reported in biliary tract cancers (Table 2).
Table 2.
Patient ID | Cancer Type | Gene | Chrom | Start_Position | End_Position | Nucleotide change | Protein change | Location | Variant classification |
---|---|---|---|---|---|---|---|---|---|
1810276 | cholangiocarcinoma | IKZF1 | chr7 | 50459525 | 50459525 | c.688G>A | p.A230T | exon6 | Missense |
1810285 | gallbladder carcinoma | TLR4 | chr9 | 120476505 | 120476505 | c.2099dupT | p.P701fs | exon3 | Frame_Shift_Ins |
1810285 | gallbladder carcinoma | POLD1 | chr19 | 50912119 | 50912119 | c.1853dupA | p.Y618_T619delinsX | exon15 | Nonsense |
1810455 | cholangiocarcinoma | EPPK1 | chr8 | 144947313 | 144947313 | c.108dupC | p.R37fs | exon2 | Frame_Shift_Ins |
1810558 | gallbladder carcinoma | RFWD2 | chr1 | 176054978 | 176054978 | c.1075C>T | p.R359X | exon10 | Nonsense |
1830007 | gallbladder carcinoma | XRCC1 | chr19 | 44079097 | 44079097 | c.109A>T | p.K37X | exon2 | Nonsense |
1830027 | cholangiocarcinoma | CDKN1A | chr6 | 36652317 | 36652317 | c.439A>G | p.M147V | exon2 | Missense |
1910201 | cholangiocarcinoma | NCOA3 | chr20 | 46279949 | 46279949 | c.3875T>C | p.M1292T | exon20 | Missense |
1910783 | cholangiocarcinoma | FGFR1 | chr8 | 38271190 | 38271190 | c.2518C>T | p.R840X | exon19 | Nonsense_Mutation |
1912566 | cholangiocarcinoma | ERCC4 | chr16 | 14026143 | 14026143 | c.1102+1G>A | . | intron6/7 | Splice_Site |
1912694 | cholangiocarcinoma | INSRR | chr1 | 156816322 | 156816322 | c.1798dupA | p.T600fs | exon8 | Frame_Shift_Ins |
1912695 | cholangiocarcinoma | TRAF3 | chr14 | 103342048 | 103342048 | c.385A>G | p.M129V | exon4 | Translation_Start_Site |
1930095 | cholangiocarcinoma | MLH3 | chr14 | 75513610 | 75513610 | c.2749C>T | p.Q917X | exon2 | Nonsense |
1930184 | cholangiocarcinoma | MSH6 | chr2 | 48033987 | 48033987 | c.4068_4071dupGATT | p.K1358fs | exon10 | Frame_Shift_Ins |
Survival impacts of molecular characteristics
To analyze the relationship between molecular characteristics and prognosis, we obtained survival information of 26 patients and plotted Kaplan-Meier survival curves by univariate analysis. Patients with KRAS mutations had worse median overall survival (OS, 108 d vs. 320.5 d, p=0.00057) (Figure 6A) among all patients in this study. We also compared the effects of mutations in various signaling pathways on survival and found that gene mutations in the VEGFR signal pathway had a significantly negative impact on OS (144.5 d vs. 324.5 d, p=0.0077) (Figure 6B). In addition, we analyzed the correlation between TMB and survival in stage IV patients. Patients whose TMB was higher than the median TMB had worse prognosis than those below (172.5 d vs. 474 d, p=0.05) (Figure 6C).
Discussion
We identified some molecular characteristics of biliary tract cancers through targeted capture sequencing. Among all the mutated bases, C>T bases accounted for the largest proportion, which is consistent with previous reports [15-17]. The mutation signatures were similar to COSMIC signature SBS1, SBS6 and SBS13. Signature SBS1 is an endogenous mutation process, triggered by spontaneous or enzymatic deamination of 5-methylcytosine to thymine, resulting in G:T mismatch in double-stranded DNA. Failure to detect and eliminate these mismatches before DNA replication always causes C to replace T. Signature SBS6 is associated with DNA mismatch repair deficiency, and often occurs in microsatellite unstable tumors. SBS13 is related to the cytosine deaminase activity of the AID/APOBEC family which may be caused by the replication of the basic site generated by the error-prone polymerase (such as REV1) during base excision and repair of uracil [26]. Series of DNA damage and repair deficiency may be the internal cause of biliary tract cancers.
TP53 encodes a tumor suppressor protein which contains transcriptional activation, DNA binding and oligomeric domains. The protein encoded by TP53 responds to various cell pressures, regulates target gene expression, and thereby induces cell cycle arrest, apoptosis, aging, DNA repair or metabolic changes. TP53 mutations are ubiquitous in many cancer types, most of which are frameshift or nonsense mutations that lead to protein inactivation. These mutations are widely distributed throughout the whole gene, and occur most frequently in the DNA binding domain [27,28]. KRAS mutation is a key driver of oncogenesis [29]. We also found that frequently mutation of KRAS might be the driver mutation of BTC. Ongoing cancer driver gene discovery efforts have identified many new drivers within the RAS pathway [30,31]. In addition, there are already preliminary results of clinical trials, and AMG510 targeting KRAS G12C is particularly prominent [32]. It has opened a historic gap and helped patients with KRAS mutation. Adagrassib (mrtx849) has excellent clinical data recently [33]. Genes encoding SWI/SNF chromatin remodeling complexes such as ARID1A, ARID1B, PBRM1 and ARID2 were also frequently mutated in this study. Recent studies have found that ARID1A mutation is associated with microsatellite instability, C>T mutation pattern, and increased mutational burden in many kinds of tumors. Those tumors formed by ARID1A-deficient ovarian cancer cell lines in mice have increased mutations, more tumor-infiltrating lymphocytes and PD-L1 expression. PD-L1 monoclonal antibodies can reduce tumor burden and prolong survival of mice, but it cannot inhibit ARID1A wild-type ovarian tumors. ARID1A deficiency may lead to tumor MMR deficiency, and patients with ARID1A deficiency may benefit from immune checkpoint inhibitors [34].
Genes encoding vascular endothelial growth factor A (VEGFA), cyclin family, cyclin-dependent kinase, cyclin-dependent kinase inhibitor and others had higher frequency of CNV than others. The protein encoded by VEGFA belongs to the PDGF/VEGF family whose products play an important role in angiogenesis and endothelial cell growth. The expression of VEGFA is upregulated in various tumors including cholangiocarcinoma, which can induce endothelial cell proliferation, promote tumor cell migration and inhibit apoptosis [35-37]. Given the importance of CCND and CDK, the development of CDK4/CDK6 inhibitors has been a strategy for the generation of new anticancer drugs [38,39].
In this study, the incidence of germline mutations was 22%, slightly higher than previously reported [23]. Germline mutations of DDR genes are associated with increased mutation load, which causes patients with these mutations to possibly be more sensitive to PARP inhibitors and platinum-based treatments. Germline mutations may be a susceptible factor for the occurrence of BTC. Screening for germline mutations in susceptible people is of great importance in prevention and treatment of biliary tract cancers.
Patients with KRAS mutations and VEGF signaling pathway mutations have shorter overall survival. As a cancer-driven event, KRAS mutation is a predictor of drug resistance and poor prognosis for various cancers [29]. Abnormal VEGF signaling pathway promotes tumor cell proliferation and migration, often leading to poor prognosis [40,41]. In addition, TMB-H patients also exhibited poor OS in this study, possibly due to complicated tumor clone composition and carcinogenesis mechanism. In clinical practice, patients with poor prognosis are suggested to adopt more aggressive treatment and rigorous and regular follow up. Patients with high TMB may be eligible for immunotherapy such as PD-1/PD-L1 inhibitors.
According to the classification of oncoKB, the proportion of actionable gene mutations in the study was up to 59.3% (Supplementary Table 4). As more therapeutic targets are in research and more targeted drugs are being approved, there are more opportunities for biliary tract cancer patients with actionable gene mutations to receive precision medicine in the future. With the rapid development of the next-generation genome sequencing technology, defining of somatic or germline mutation in BTC patients could help accurately identify patients benefiting from drugs such as PARP inhibitors and immune checkpoint inhibitors.
The limited number of samples, insufficient clinical information and not using the whole exon sequencing may be deficiencies of this study. In later research, it is necessary to expand the research cohort with comprehensive clinical information and analyze samples with the whole exon sequencing and other necessary methods. Future prospective research is needed to verify the correlation between specific molecular characteristics and prognosis.
Acknowledgements
We acknowledge the work of geneticists involved in the analysis of the gene mutations of samples in this study (Zhiyong Li, Ning He, Panpan Song).
Disclosure of conflict of interest
None.
Supporting Information
References
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