ID #322 Trans-species analysis of the unique immunobiology of DNA replication-repair deficient (RRD) medulloblastoma translates to novel therapeutic approaches: an IRRDC report
Anirban Das, Nicholas Fernandez, Adrian Levine, Kyle Smith, Evan Wang, Melissa Galati, Zoya Aamir, Brian Chung, Logine Negm, Hope Friedman, Katharine O’Flaherty, Owen Crump, Quang Trinh, Nuno Miguel, Vanessa Bianchi, Lucie Stengs, Melissa Edwards, Lincoln Stein, Eric Bouffet, Michael Taylor, Paul Northcott, Vijay Ramaswamy, Cynthia Hawkins, Uri TaboriAbstract
Background
Replication repair maintains genomic fidelity. Germline-inherited replication repair deficiency (RRD) leads to hypermutant, early-onset brain tumours. RRD medulloblastoma (MB) are reported but not well-characterized.
Methods
We performed multi-omic analyses to elucidate the impact of hypermutation on RRD-MB biology and treatment-outcomes.
Results
RRD-MB (n = 48) were enriched for anaplastic disease (61%). t-SNE analysis suggested SHH-subgroup affinity despite low confidence of classification on the Heidelberg Classifier (78%). Genomic profile displayed microsatellite instability and hypermutation, with frequent somatic mutations in polymerase proofreading genes (80%). Mutations were also common inTP53 (48%), SHH-pathway genes (56%) and, strikingly, glioma driver genes (ATRX,NF1,RB1; 50%). Copy number changes were infrequent. Comparative analysis of variant allele frequency in tumours with both SHH and glioma drivers indicated that SHH-drivers occur first, suggesting that primary tumor identity is defined by an initial combination of cell of origin and genetic alterations. Deconvolution of single-nuclei RNA-sequencing revealed enrichment for astro-glial expression programs exclusive to RRD-MB compared to non-RRD SHH-MB, suggesting a functional impact of glioma driver mutations. Representative RRD-MB mouse models (Nestin-Cre+/MSH2LoxP/LoxP/POLES459F/+) further substantiated human findings, harbouring both SHH- and glioma-drivers, with ultra-hypermutation and mixed embryonal-glial phenotypes. High levels of immune infiltrates (CD8+ T-cell), in both mouse and human tumors, provided biological insights into the immune mechanisms underlying the efficacy of anti-PD1 monotherapy in human RRD-MB, leading to radiological remission in refractory disease and prolonged survival (p = 0.02).
Conclusions
RRD-MB form a distinct subtype of SHH-activated MB. Their genetic phenotypes are modified by genomic instability leading to point mutations and indels in both SHH and glioma-pathways. Hypermutation and corresponding immune infiltration confer immune checkpoint inhibitor efficacy at recurrence, allowing the development of prospective combined chemo-immunotherapy treatment protocols for patients with high-risk disease.