Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy

Abstract

Pancreatic ductal adenocarcinoma (PDA) is a lethal disease. Overall survival is typically 6 months from diagnosis. Numerous phase 3 trials of agents effective in other malignancies have failed to benefit unselected PDA populations, although patients do occasionally respond. Studies in other solid tumors have shown that heterogeneity in response is determined, in part, by molecular differences between tumors. Furthermore, treatment outcomes are improved by targeting drugs to tumor subtypes in which they are selectively effective, with breast and lung cancers providing recent examples. Identification of PDA molecular subtypes has been frustrated by a paucity of tumor specimens available for study. We have overcome this problem by combined analysis of transcriptional profiles of primary PDA samples from several studies, along with human and mouse PDA cell lines. We define three PDA subtypes: classical, quasimesenchymal and exocrine-like, and we present evidence for clinical outcome and therapeutic response differences between them. We further define gene signatures for these subtypes that may have utility in stratifying patients for treatment and present preclinical model systems that may be used to identify new subtype specific therapies.

Figure 1. Subtypes of PDA in tumors and cell lines and their prognostic significance

A. Heatmap (HM) showing three subtypes of PDA in a DWD-merged UCSF and Badea et al. PDA microarray datasets using the PDAssigner geneset. B. Kaplan-Meier Survival curve comparing survival of classical (red), QM-PDA (blue) and exocrine-like (green) subtype patients. Survival time is in days (d). p-value is by Log-rank test. C. HM showing three subtypes of PDA in a DWD-merged core clinical and human PDA cell line microarray datasets using the PDAssigner geneset. D. HM showing three subtypes of PDA in a DWD-merged core clinical PDA and mouse PDA cell line microarray datasets using PDAssigner geneset. In the top bar, magenta marks classical subtype PDA, yellow marks QM-PDA and light blue marks exocrine-like (by NMF). The second from top bar denotes sample set of origin, with brown samples originating from UCSF, orange samples originating from Badea et al. PDA datasets and gray samples originating from either human (C) or mouse (D) PDA cell lines. The bars on the side denote PDAssigner genes upregulated in classical (violet), QM-PDA (gray) and exocrine-like (green).

Figure 2. Classical PDA subtype and the GATA6 transcription factor

A. Relative log expression of GATA6 in PDA cell lines, transduced with shRNA against GATA6 or control, was determined by qRT-PCR. Black columns are classical lines, gray columns are QM-PDA lines, note log scale. B. Colonies per Low Powered Field (LPF) in PDA cell lines transduced with shRNA against GATA6 or control.

Figure 3. Classical subtype cells depend on KRas

A. PDA lines (all with GTPase inactivating KRAS mutations), were transduced with lentiviruses encoding either control (shLUC) or KRAS (shKRAS) directed RNAi. Relative proliferation is plotted. Black columns are classical lines and gray columns are QM-PDA lines. B. Box plot of relative proliferation of classical and QM-PDA human PDA cell lines. p-values by the Kruskal-Wallis test.

Figure 4. Drug Responses Differ by Subtype

IC₅₀ in negative log₁₀ of drug concentration is plotted for each cell line tested with A. gemcitabine and C. erlotinib. Black columns are classical lines and gray columns are QM-PDA lines. Box Plot of IC₅₀ of classical and QM-PDA human PDA cell lines for B. gemcitabine and D. erlotinib, p-values represent statistics using Kruskal-Wallis test.