Pembrolizumab activity in patients with Fanconi anemia repair pathway competent and deficient tumors

Abstract

Background: Given the observed antitumor activity of immune-checkpoint-inhibitors in patients with mismatch-repair deficient (MSI-H) tumors, we hypothesized that deficiency in homologous-recombination-repair (HRR) can also influence susceptibility.

Methods: Patients with disease progression on standard of care and for whom pembrolizumab had no FDA approved indication received pembrolizumab. Patients with MSI-H tumors were excluded. Objectives included immune-related objective response rate (iORR), progression-free survival (PFS) and 20-weeks-PFS. Pembrolizumab was given every 3 weeks and scans performed every six. We evaluated a triple-stain (FANCD2foci/DAPI/Ki67) functional assay of the Fanconi Anemia (FA) pathway: FATSI, in treated patients' archived tumors. The two-stage sample size of 20/39 patients evaluated an expected iORR≥20% in the whole population vs. the null hypothesis of an iORR≤5%, based on an assumed iORR≥40% in patients with functional FA deficiency, and < 10% in patients with intact HRR. An expansion cohort of MSI stable endometrial cancer (MS-EC) followed. Exploratory stool microbiome analyses in selected patients were performed.

Results: Fifty-two patients (45F,7M;50-evaluable) were enrolled. For the 39 in the two-stage cohort, response evaluation showed 2CR,5PR,11SD,21PD (iORR-18%). FATSI tumor analyses showed 29 competent (+) and 10 deficient (-). 2PR,9SD,17PD,1NE occurred among the FATSI+ (iORR-7%) and 2CR,3PR,2SD,3PD among the FATSI(-) patients (iORR-50%). mPFS and 20w-PFS were 43 days and 21% in FATSI+, versus 202 days and 70% in FATSI(-) patients. One PR occurred in the MS-EC expansion cohort.

Conclusions: Pembrolizumab has meaningful antitumor activity in malignancies with no current FDA approved indications and FA functional deficiency. The results support further evaluation of FATSI as a discriminatory biomarker for population-selected studies.

Keywords: Biomarkers; DNA repair; FancD2; Fanconi; Homologous recombination; Immune checkpoint inhibitor.

Fig. 1

A The Fanconi anemia pathway and formation of repair foci. Following DNA inter-strand crosslink damage, the FANCM-FAAP24-MHF1-MHF2 anchor complex recruits the FA core complex I, which functions to activate FANCD2 and FANCI by mono-ubiquitinating the proteins. The activated FANCD2 and FANCI heterodimers are subsequently transported to subnuclear foci (encircled), which in collaboration with additional genes result in homologous recombination DNA repair. B The Fanconi Anemia triple stain immunofluorescence method (FATSI) was performed in Paraffin Embedded Solid Tumor slides stained with FATSI as observed with immunofluorescence microscope (400x). Left, FATSI positive (competent pathway); Right, FATSI negative (deficient pathway). DAPI (blue), Ki67 (red) and FANCD2 (green)

Fig. 2

Kaplan Meier curves comparing progression free survival by FATSI status (P for logrank, 0.03). X-axis corresponds to progression free survival in months and Y-axis corresponds to survival probability. FATSI negative patients’ curve in blue; FATSI positives in red. + = censored

Fig. 3

“Swimmers Plot” for Individual Patients Progression Free Survival Divided According to Their Tumors FATSI status. Each bar represents one subject on study. X-axis, number of days progression free; Y-axis individual patients. Individuals’ best tumor response outcomes are indicated by labels

Fig. 4

Microbiome data from stool specimens of patients on the study. A Taxonomy bar plots of top 25 species. B LEfSe plot illustrating discriminating features between response groups. CR = complete response; PD = progressive disease; PR = partial response; SD = stable disease