NGS-based targeted gene mutational profiles in Korean patients with pancreatic cancer

Baseline characteristics of the patients

Between March 2018 and August 2020, 87 patients were enrolled in this study. Patient characteristics and tumor specimen information are summarized in Table 1. The median age (range) of patients at diagnosis was 64 (35–86) years, and 54 patients (62.1%) were men. Meanwhile, 61 (70.1%) and 26 (29.9%) patients had metastatic and non-metastatic pancreatic cancers at the time of tissue acquisition, respectively. Adenocarcinoma was the dominant type of cancer (n = 82, 94.3%).

Table 1 Patient characteristics and tumor specimen information.

Tumor specimens for NGS were obtained from primary tumors and metastases in 41 (47.1%) and 46 patients (52.9%), respectively. The liver was the most frequent metastatic site for tissue acquisition (n = 33, 37.9%). Concerning the method of tissue acquisition, ultrasound-guided percutaneous needle biopsy (n = 36, 41.4%) was most common, followed by surgical resection (n = 25, 28.7%) and fine-needle aspiration or biopsy (n = 20, 23.0%). Meanwhile, 13 patients (14.9%) underwent additional biopsy for NGS after cancer progression or recurrence.

Landscape of genetic mutations

The mean depth of coverage in targeted gene sequencing ranged from 259 to 1,717. The most frequently reported mutation was KRAS mutation, which was found in 82 patients (94.3%), followed by TP53 mutations in 65 patients (74.7%), SMAD4 mutations in 26 patients (29.9%), and CDKN2A mutations in 20 patients (23.0%) (Fig. 1). The frequencies of these four mutations were similar to those reported in The Cancer Genome Atlas (TCGA) dataset (Table 2)14. Additionally, the frequencies of other significant recurrent mutations (which were previously reported in the TCGA dataset), such as RNF43 (10.3% vs. 6.0%), ARID1A (11.5% vs. 5.3%), TGFBR2 (4.6% vs. 5.3%), and GNAS (6.9% vs. 6.7%) mutations, were not significantly different from those of the TCGA dataset. CNVs were identified in 21 patients (24.1%), and KDM5A amplification (n = 5, 5.7%) was the most common amplification, followed by GATA6 (n = 4, 4.6%), RAD52 (n = 4, 4.6%), KRAS (n = 3, 3.4%), and MYC amplifications (n = 3, 3.4%) (Fig. 1). The mutation frequency was compared according to various clinical characteristics, including cancer stage, biopsy site, method of tissue acquisition, and prior chemotherapy; however, no significant differences in the frequencies of any mutations were identified (Supplementary Tables S3A and S3B).

Figure 1
figure 1

Landscape of genomic alterations in patients with pancreatic cancer (n = 87). Distribution of recurrent single nucleotides variants (SNVs)/insertions/deletions (INDELs) and copy number variation (CNV) as well as the total percentage of patients with SNVs/INDELs or CNV for each recurrent mutated gene.

Table 2 Comparison of the frequency of common recurrent mutations with TCGA dataset.

At least one Tier I or Tier II mutation was identified in 86 patients (98.9%). Other Tier I or II SNV/INDELs in oncogenes, such as BRAF (n = 1, 1.1%), GNAS (n = 1, 1.1%), and EGFR (n = 1, 1.1%), and tumor suppressor genes, such as ARID1A (n = 3, 3.4%) and RNF43 (n = 2, 2.3%), were observed, except for the four common mutations. Most common Tier I or Tier II CNVs were MYC and KRAS amplifications, where were observed in three patients (3.4%) each, followed by CDK6, CCND2, ERBB2, FGF6, FGF23, and MCL1 amplifications, which were observed in two patients (2.3%) each. Tier I or II mutations related to hereditary cancer syndrome in pancreatic cancer were identified in BRCA1 (n = 2, 2.3%), BRCA2 (n = 2, 2.3%), PRSS1 (n = 1, 1.1%), MSH6 (n = 2, 2.3%), PMS2 (n = 1, 1.1%), and APC (n = 1, 1.1%). Among them, two patients with BRCA1 mutations were confirmed to have germline pathogenic variants through paired germline testing using blood samples.

Potentially actionable mutations

In total, 27 patients (31.0%) were identified to have at least one potentially actionable mutation (Fig. 2A and Supplementary Table S4). Of these, highly actionable and modifies options mutations were found in 12 (13.8%) and 18 patients (20.7%), respectively. After excluding three patients (3.4%) who had both highly actionable and modifies options mutations, there were 15 patients with only modifies options mutations (17.2%).

Figure 2
figure 2

(A) The percentage of patients with potentially actionable mutations (n = 87). (B) Therapeutic options according to the mutational profile (n = 87). (C) Tumor mutation burden profiling (n = 84).

Highly actionable mutations included mutations in BRCA1 (n = 2), BRCA2 (n = 2), ATM (n = 2), and BRAF (n = 1) and amplification in CDK6 (n = 2), ERBB2 (n = 2), and AKT2 (n = 1). Mutations in DDR genes such as BRCA1, BRCA2, and ATM, which were observed in six patients, were the most frequent highly actionable mutations. Concerning modifies options, mutations in ARID1A (n = 7) were the most frequent, followed by RNF43 mutations (n = 5), GNAS mutations (n = 2), and CCND2 amplification (n = 2). When classified by therapeutic options, mTOR/AKT inhibitors represented the most common drug class (n = 10, 11.5%), followed by poly(adenosine diphosphate-ribose) polymerase (PARP) inhibitors (n = 7, 8.0%), WNT inhibitors (n = 5, 5.7%), CDK inhibitors (n = 4, 4.6%), and MEK inhibitors (n = 4, 4.6%) (Fig. 2B). The MSI status and TMB were analyzed in 84 patients profiled with the SNUBH panel ver. 2.0. No patient had MSI-high tumors, but high TMB was reported in one patient (1.2%) (Fig. 2C).

Clinical implications of NGS results

In this study, three patients (3.4%) received matched therapy based on their molecular profiles. Of these, one patient was a 65-year-old man who was diagnosed with metastatic pancreatic cancer with an EGFR exon 19 deletion. He received a combination treatment, including gemcitabine and an EGFR tyrosine kinase inhibitor erlotinib (Roche, Basel, Switzerland); however, he showed rapid aggravation just after one cycle of the treatment.

The remaining two patients were diagnosed with metastatic pancreatic cancer using percutaneous needle biopsy of liver metastasis, and targeted gene profiling with the SNUBH panel ver. 2.0 was conducted at the time of diagnosis. The profiling results illustrated that both patients had tumors with Tier I BRCA1 mutations. With additional germline testing, they were confirmed to have germline pathogenic BRCA1 mutations, and they received the PARP inhibitor olaparib (AstraZeneca, Cambridge, United Kingdom) as maintenance therapy after FOLFIRINOX chemotherapy, as introduced in the POLO trial15.

The first patient who received olaparib maintenance treatment was a 54-year-old man with metastatic pancreatic cancer and a germline BRCA1 mutation (c.3412 + 1G > T). He received nine cycles of FOLFIRINOX and displayed a partial response with a 70% reduction of the tumor burden versus baseline according to RECIST ver. 1.1 (Fig. 3A). Subsequently, he received maintenance treatment with a PARP inhibitor. The tumor burden gradually decreased during maintenance treatment, and the lesion became indiscernible on computed tomography scan after 1 year of PARP inhibitor treatment. He has consistently responded to PARP inhibitor therapy, which he has received for 18 months. He had a sister with ovarian cancer and a germline BRCA1 mutation and a niece (the daughter of the sister with ovarian cancer) with breast cancer and a germline BRCA1 mutation. He had three children, and genetic testing revealed a germline BRCA1 mutation in one child.

Figure 3
figure 3

(A) and (B) Clinical course of two patients with germline pathogenic BRCA1 mutations who were treated with PARP inhibitors. Changes in tumor burden (left y-axis) and the level of CA 19–9 (right y-axis) over time of treatment (months, x-axis) were presented together with specific computed tomography imaging.

The other patient was a 64-year-old woman with metastatic pancreatic cancer and a germline BRCA1 mutation (c.5467 + 1G > A). She received nine cycles of FOLFIRINOX and displayed a partial response with a 50% reduction of the tumor burden versus baseline according to RECIST ver. 1.1 (Fig. 3B). She received maintenance therapy with a PARP inhibitor, but the tumor progressed after 3 months of treatment. Subsequently, considering the germline BRCA1 pathogenic variant, she received third-line gemcitabine and cisplatin chemotherapy, but the tumor progressed after four cycles of treatment. She is currently receiving nanoliposomal irinotecan with fluorouracil as fourth-line therapy. She had a family history of variant cancers, including two first-degree relatives with gastric cancer (father and younger brother), two second-degree relatives with gastric cancer (father’s brother) and pancreatic cancer (mother’s brother), and a nephew (the child of a younger brother with gastric cancer) who was diagnosed with cholangiocarcinoma at the age of 28 years. Of her two children, one underwent germline BRCA1 mutation testing, and the result was negative.

Source link

Back to top button