Whole genome and transcriptome profiling in advanced pancreatic cancer patients on the COMPASS trial

Abstract

Integrated whole genome and transcriptome sequencing can unveil distinct molecular subgroups in pancreatic cancer (PDAC). The COMPASS trial (NCT02750657) enrolled 268 patients with advanced PDAC; patients were given either modified (m) FOLFIRINOX or Gemcitabine-nab-paclitaxel (GnP) as per physicians choice. Median follow-up is 52 months and median overall survival in those receiving mFOLFIRINOX is 10.6 months and 8.4 months for GnP. KRAS specific mutants and allelic states alone are not prognostic; however basal-like PDAC are more likely to harbour major imbalances in mutant KRAS (KRAS^maj). In the presence of KRAS^maj, pre-existing type II DM is more common. Distinct prognostic cohorts include homologous-recombination deficient PDAC, predictive of mFOLFIRINOX response. Basal-like PDAC and patients exhibiting evidence of systemic inflammation as annotated using the Gustave Roussy Immune Score are unique poor prognostic cohorts. The latter associates with low CD8 T cell infiltration while basal-like PDAC documents an inflamed tumour microenvironment.

Fig. 1. CONSORT diagram of patients screened and enrolled on the COMPASS trial.

PDAC: Pancreatic ductal adenocarcinoma; WGS: Whole genomic sequencing; *none this refers to patients intended to receive combination chemotherapy post enrolment.

Fig. 2. KRAS mutational spectrum on the study.

Frequency of specific KRAS mutations of tumours (n = 249) included together with KRAS WT PDAC proportion (n = 19).

Fig. 3. Oncoprint depicting genomic characteristics of enrolled cases, including prevalence of the most common somatic mutations (top), COSMIC v2 mutational signatures, SNV, indel and SV patterns, tumour ploidy, KRAS allelic states.

PDAC subtypes are annotated and include the Waddell classifier, Moffitt basal-like vs classical subtype, HRDetect scores and the Menghi score identifying the tandem duplicator phenotype. The T cell inflamed signature evaluated in the cohort is also included. SNV: single nucleotide variants; indel: insertion/deletion, SV: structural variation.

Fig. 4. Molecular correlates of KRAS allelic states and overall survival.

A Frequency of tumour suppressors according to KRAS allelic states (balanced n = 108, minor imbalance n = 96, major imbalance n = 45, WT n = 19).Two-sided Fisher’s exact test ***p = 8.5e-06 *p = 0.02. B Frequency of Moffitt basal-like (n = 49) vs classical subtype (n = 204) in KRAS allelic states. P-value derived from two-sided Fisher’s exact test. C The median overall survival according to chemotherapy received in the intention to treat population (n = 261, mFFX n = 146, GnP n = 99, None=16), 7 patients who received ‘other’ treatments are excluded. D Median overall survival and 95% CI according to specific KRAS mutation (wt n = 19, G12D n = 114, G12R n = 36, G12V n = 77, others n = 22). E Median overall survival and 95% CI according to KRAS allelic state (major n = 45, minor n = 96, balanced n = 108, wt n = 19).

Fig. 5. Genomic predictors and cox regression analyses associated with overall survival in advanced PDAC (n = 268).

A Median overall survival and 95% CI according to presence of SBS3 (mutations >5% n = 40 vs <= 5% n = 228). B Overall survival according to HRDetect score and stratified by type of chemotherapy received (mFFX n = 144, GnP n = 96). C Median overall survival and 95% CI according to presence of SBS17 (mutations >5% n = 44 vs <= 5% n = 224). D Median overall survival and 95% CI according to presence of APOBEC SBS2 and SBS13 (mutations >5% n = 186 vs <= 5% n = 82). E Cox proportional hazards analysis of relevant variables, all variables were prespecified in the trial with the exception of the GRIm-S which was annotated retrospectively (n = 268). Error bars represent lower and upper 95% confidence interval. Chemo (mFFX p = 5.10e-20, GnP p = 3.84e-18); HRDetect high p = 2.10e-04; Moffitt basal-like p = 3.18e-05; GRIM high p = 5.50e-05; ECOG1 p = 1.32e-03. GnP= Gemcitabine/nab-paclitaxel; HRDetect hi is a score >0.7; GRIM= Gustave Roussy Immune Score.

Fig. 6. Baseline characteristics of LAPC compared to metastatic cases enrolled on COMPASS.

Boxplots in Panel A, B, D-F depict 1st quartile, median and 3rd quartile +/− 1.5 interquartile range. P-values derived from two-sided Wilcoxon rank sum test. A BMI in locally advanced (stage III, n = 37) compared to stage IV cases. B CA19.9 in locally advanced (stage III, n = 37) compared to stage IV cases. C Frequency of GRIm-S low (0) or high (2) in locally advanced (stage III, n = 37) compared to stage IV cases. Molecular features of LAPC (n = 37) compared to met PDAC (n = 231) D SNV count in locally advanced vs stage IV cases, E indel count and F structural variant count and G frequency of Moffitt basal-like vs classic subtype.

Fig. 7. Analyses of CD8 expression using immunohistochemistry (IHC, n = 149) or RNA-seq (n = 253) across cohorts included in COMPASS.

Boxplots in Panel B–F depict 1st quartile, median and 3rd quartile +/− 1.5 interquartile range. P-values derived from two-sided statistical tests. A Spearman correlation of CD8 IHC vs RNA-seq expression. B Comparison of CD8 IHC expression in primary biopsy sites vs metastatic sites. C CD8 expression according to specific KRAS mutation Left) analysis by IHC Right) analysis by RNA-seq. D CD8 expression (RNA-seq) in HRDetect hi vs lo cases. E CD8 expression according to Moffitt subtype (basal-like vs classical) in liver metastases Left) analysis by IHC, Right) analysis by RNA-seq. F CD8 expression by IHC in liver metastases comparing GRIm-S lo vs hi.

Fig. 8. Immune signatures and prognostic subgroups in advanced PDAC.

A–E T-cell Inflamed signature (RNA) in liver metastases according to A KRAS mutation (wt n = 19, G12D n = 114, G12R n = 36, G12Vn = 77, Q61 n = 16) (B) KRAS allelic states (wt n = 19, balanced n = 108, minor n = 96, major n = 45) C HRDetect hi (n = 227) vs lo (n = 34). D Moffitt subtype (basal-like n = 49, classical n = 204) E GRIm-S hi (n = 225) vs lo (n = 43) Boxplots depict 1st quartile, median and 3rd quartile +/− 1.5 interquartile range. P-values derived from two-sided statistical tests. F Expression of varying immune gene sets according to Moffitt subtype in liver metastases (basal-like n = 45, classical n = 122, see Supplementary Table 1 for genes).