Proteomic Analysis of Pancreatic Ductal Adenocarcinoma Response to BRCA-Targeted Therapy

Pancreatic-ductal-adenocarcinoma(PDAC) is a lethal malignancy. Germline-BRCA1/2 mutation carriers are the most well-defined DNA-damage-repair (DDR) deficient subgroup and present up-to ~15% of PDAC. A portion of these patients are highly susceptible to DNA-damage agents and PARP-inhibition (PARPi), however, responses are heterogeneous and clinical resistance evolves. Over 90% of PDAC-tumors display activating KRAS mutations, which activate the downstream PI3K/AKT pathway. PI3K plays a role in DNA-repair, and PI3K inhibitors (PI3Ki) showed to increase DNA-damage in tumor cells, suggesting addition PI3Ki may enhance sensitivity to PARPi and overcome resistance.

We hypothesized that addition of PI3Ki will enhance sensitivity to PARPi in BRCA-mut PDAC and will sensitize WT-BRCA PDAC tumors to PARPi. Our goal is to identify the differentially expressed proteins upon PARPi and PI3Ki treatment and to examine the variability in PDAC patient`s response.

We analyzed the proteome of 108 patient-derived PDAC xenografts (PDX), exposed to PARPi and/or PI3Ki treatment. Laser-capture-microdissection was used to separate the cancer-cells from FFPE-tumor-blocks, followed by protein extraction, digestion, Tandem-Mass-Tags labeling and high-resolution mass-spectrometric analysis. Supervised and unsupervised analysis was used to investigate the changes upon treatment and association with response.

High inter-patient variance in response to treatments was observed. PARPi-resistant PDXs showed upregulation of SRC-proteins upon treatment, and two PDXs with PARPi+PI3Ki synergic effect, demonstrated an increase in interferon response and decrease in lipids and sterol metabolism. We speculate that the increased DNA-damage upon treatment, together with high IFN signaling in responding tumors, reflects activation of the innate immune pathway, which may be further targeted in patients.