Genetic Analyses of Cell-Free DNA in Pancreatic Juice or Bile for Diagnosing Pancreatic Duct and Biliary Tract Strictures

Abstract

Poor prognosis of pancreaticobiliary malignancies is attributed to intrinsic biological aggressiveness and the lack of reliable methods for early diagnosis. This study aimed to evaluate the feasibility and availability of pancreatic juice- and bile-derived cell-free DNA (cfDNA) for diagnosing pancreaticobiliary strictures. From October 2020 to February 2022, pancreatic juice or bile was obtained from 50 patients with pancreaticobiliary strictures during endoscopic retrograde cholangiopancreatography. cfDNAs extracted from the samples were analyzed using next-generation sequencing and a cancer gene panel. The obtained cfDNAs, genetic data and clinical information were analyzed for diagnosis. cfDNA concentrations in pancreatic juice were higher in the intraductal papillary mucinous neoplasm group than in the other groups, whereas those in bile were similar in all groups. In pancreatic juice, the sensitivity, specificity and positive and negative predictive values of cfDNA analyses were 33%, 100%, 100% and 71.4%, respectively, whereas those of cytological analyses were 0%, 100%, 0% and 62.5%, respectively. In bile, those of cell-free DNA analyses were 53%, 75%, 89.5% and 28.6%, respectively, whereas those of cytological analyses were 19%, 100%, 100% and 16%, respectively. In conclusion, pancreatic juice- and bile-derived cfDNA is a novel liquid biopsy tool that can diagnose pancreaticobiliary strictures.

Bile as a liquid biopsy matrix: potential applications and limitations

“…Firstly, in 2018 Kinugasa and colleagues [56] analyzed 49 genes in bile samples of patients with gallbladder cancer using a custom enrichment panel and demonstrated its better performance compared to cytology (58.3% versus 45.8%) [56]. Similar results using other commercialized or custom cancer related-gene panels were obtained for patients with different pancreato-biliary tumors, reaching sensitivities ranging from 53% to 96.2% [23,55,[112][113][114]. These panels include genes frequently mutated in multiple cancer types, including biliopancreatic malignancies such as TP53, KRAS, cyclin-dependent kinase inhibitor 2A (CDKN2A), erb-b2 receptor tyrosine kinase 2 (ERBB2), erb-b2 receptor tyrosine kinase 3 (ERBB3), mothers against decapentaplegic homolog 4 (SMAD4), phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA), among others.…”

Promise of bile circulating tumor DNA in biliary tract cancers

“…This may be due to the use of lower amounts of plasma (4 mL) than other studies 3 . It is also possible that the low plasma detection rate may be due to the larger proportion with less than stage III disease compared to the studies done in patients with advanced BTC 1,2,7 . Because studies done with dedicated gene panels have higher rates of oncogenic mutations and low‐coverage whole genome sequencing for the detection of aneuploidy reported higher plasma ctDNA detection, 9 the sequencing method used must also be considered.…”

“…[3][4][5] In 28 patients, Guo et al 4 found that bile outperformed plasma as a potential alternative to tissue biopsy in biliary tract cancer with a mutation detection rate of 71.4% in bile and 53.6% in plasma specimens. In 50 patients with PC and BTC, Nagai et al 7 found a 33% cfDNA mutation rate in the pancreatic juice of patients with pancreatic neoplasms compared with a 53% cfDNA mutation rate in the bile juice of BTC patients. Other prospective studies have shown low plasma ctDNA detection rates, but with low input volumes (Table 1).…”

Pancreatic Cancer and Detection Methods

“…Circulating cell-free DNA (cfDNA) can be found in the bloodstream from various cells, including hematopoietic cells, healthy cells, apoptotic cells, and circulating tumor cells (CTCs) [ 137 , 138 , 139 , 140 , 141 ]. In the context of cancer diagnosis, the cfDNA method may not be suitable for clinical decision making due to other factors that can alter cfDNA levels, such as inflammation, exercise, smoking, trauma, and innate chromosomal abnormalities [ 142 ].…”