A gut microbiota rheostat to forecast response to PDL1-VEGF blockade in mesothelioma.
Authors: Fennell Dean Anthony , Bzura Aleksandra , Branson Amy , King Amy , Rogel Jan , Barber Shaun , Poile Charlotte , Harber James , Zhou Zisen , Pritchard Catrin , Kamata Tamihiro , Wells-Jordan Peter , Nusrat Nada , Baitei Essa , Dzialo Joanna , Thomas Anne , Barer Michael , Haldar Kairobi , Zhang Min ,   MIST investigators
Published: June 2023

e20534

Background: Targeting of the immune inhibitory PD1-PDL1 axis has proven clinically effective in mesothelioma, despite a low somatic mutation burden, and high rate of CDKN2A deletion. Tumour responses to anti PD1 or PDL1 immune checkpoint inhibition are heterogeneous, and the factors underpinning sensitivity remain poorly understood. We therefore addressed this knowledge gap through multi-omic interrogation of tumours from patients enrolled into arm 4 of the Mesothelioma Stratified Therapy umbrella trial (NCT03654833, MiST4), a multi-centre single arm phase IIA trial of atezolizumab and bevacizumab in patients with relapsed mesothelioma. Methods: Next generation sequencing of whole exomes (mesotheliomas and matched germline DNA), transcriptomes, and 16sRNA to profile gut microbiota were undertaken. Spatial phenotyping of the immune landscape employed multiplex immunofluorescence analysis using a 19x depth 4 panel detection. Tumour proportion score (TPS) for PDL1 was assessed using the 22C3 clone, and BAP1, p16ink4a assessed by immunohistochemistry. The MIST4 cohort was dichotomised by best tumour response (50:50) into those patients exhibiting any tumour reduction (R) versus those without (NR). Machine learning (boosting and bagging) was employed to decipher correlates of response. Results: Tumour responses correlated with progression-free survival (PFS, p = 0.0003). Neither PDL1 TPS or CDKN2A expression were predictive. The NR group exhibited a greater degree of genomic instability with higher somatic copy number burden (p = 0.02), homologous recombination deficiency (HRD, p = 0.03), and uniparental disomy (UPD, p = 0.01). Notably the burden of nonsynonymous mutations and neoantigens did not differ significantly between groups. The NR group was transcriptionally enriched for epithelial mesenchymal transition (p < 0.05). Conversely, 16s RNA sequencing revealed higher gut microbial diversity in the R group compared with NR (Shannon index p = 0.009) with R-group enrichment of the type 2 enterotype (provotella 33% vs 9%). R-group enriched genera comprised prevotella, butyricicoccus, bilophilla, Eubacterium ventriosum, whereas the NR group was enriched for erysipelatoclostidium. The log ratio of genera, ie. Log[GR/GNR] was 2-log higher for the R group (p < 0.0001) vs NR group, and was highly predictive of response (with an area under the receiver operator curve of 0.99). Log[GR/GNR] positively correlated with tumour CD8 T cell infiltration (r = 0.6, p = 0.05) and PFS (p = 0.04), but negatively with CD68 monocyte infiltration (p = 0.05), UPD (p = 0.008) and HRD (p = 0.05). Conclusions: We propose a model in which interacting tumour intrinsic and extrinsic factors correlate with response to PDL1-VEGF inhibition in patients with mesothelioma. Gut microbiota composition represents a new, potentially modifiable target with potential to improve immunotherapy outcomes in patients with mesothelioma. Clinical trial information: NCT03654833 .