Predictive Values of Blood-Based RNA Signatures for the Gemcitabine Response in Advanced Pancreatic Cancer

Abstract

Pancreatic ductal adenocarcinoma (PDAC) is expected to be the second cause of cancer death by 2022. For nearly 80% of patients, diagnosis occurs at an advanced, nonsurgical stage, making such patients incurable. Gemcitabine is still an important component in PDAC treatment and is most often used as a backbone to test new targeted therapies and there is, to date, no routine biomarker to predict its efficacy. Samples from a phase III randomized trial were used to develop through a large approach based on blood-based liquid biopsy, transcriptome profiling, and machine learning, a nine gene predictive signature for gemcitabine sensitivity. Patients with a positive test (41.6%) had a significantly longer progression free survival (PFS) (3.8 months vs. 1.9 months p = 0.03) and a longer overall survival (OS) (14.5 months vs. 5.1, p < 0.0001). In multivariate analyses, this signature was independently associated with PFS (HR = 0.5 (0.28–0.9) p = 0.025) and OS (HR = 0.39 (0.21–0.7) p = 0.002).

Performance of a blood-based RNA signature for gemcitabine-based treatment in metastatic pancreatic adenocarcinoma

“…The following quality requirements were applied: a minimum of 300 ng of total RNA with an absorbance ratio (260/280 nm) of >1.8. The gene expression analyses were performed using a LightCycler ® 480 SYBR Green I Master (Roche Diagnostics, Santa Clara, CA, USA) in a 10 µL final reaction volume, according to the manufacturer’s protocol, using a LightCycler ® 480 System II Instrument (Roche Diagnostics) and an established qPCR assay ( 19 ). The targeted genes were ATP-binding cassette subfamily C member 1 (ABCC1), ADP Ribosylation Factor-Like GTPase 4C (ARL4C), LYN proto-oncogene, Src family tyrosine kinase (LYN), NME/NM23 nucleoside diphosphate kinase 4 (NME4), peptidylprolyl isomerase B (PPIB), ubiquitin-conjugating enzyme E2 H (UBE2H), and transporters such as solute carrier family 35 member E2B (SLC35E2B).…”

“…The normalization of gene expression levels was done using two housekeeping genes, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and beta-2-microglobulin (B2M). We defined the acceptance criteria for real-time PCR analysis ( 19 ), including five replicate measures for all genes in compliance with the defined limit of quantification (LoQ), the melting temperature (Tm), and negative controls.…”

“…The GE score was previously established (19) with the exact methodology described in previous article (19). We then used signature built upon two components that aim to predict the OS (Comp1) and PFS (Comp2) and used it to compute prediction.…”

“…In 2020, we developed an innovative blood-based RNA signature to predict gemcitabine-based efficacy in patients suffering from mPDAC ( 19 ). This test, called the GemciTest, is a non-invasive test based on a nine-gene blood-based RNA signature.…”

An EMT-Related Gene Signature for Predicting Response to Adjuvant Chemotherapy in Pancreatic Ductal Adenocarcinoma

“…Several genes participating in drug uptake and metabolism have emerged as powerful predictors of drug sensitivity (Bird et al, 2017;Raffenne et al, 2019;Okamura et al, 2020). Recently, with the adventure of high throughput sequencing and bioinformatic technology, more and more gene expression signatures have been identified to evaluate drug sensitivity in PDAC (Kaissis et al, 2019;Clayton et al, 2020;Piquemal et al, 2020;Nicolle et al, 2021;Nishiwada et al, 2021).…”