Functional Oncogenomic and Immune Response Landscape for Genes Recurrently Mutated in Myeloma

For many genes that are recurrently mutated in patient-derived samples or cell lines from multiple myeloma (MM), the functional roles of these genes have remained incompletely understood. We have sought to address the functional implications of these genes through extensive CRISPR-Cas9-based functional genomics studies for loss-of-function (LOF, e.g. CRISPR-based gene editing) and gain of function (GOF, e.g. CRISPR-based gene activation) in MM cell lines in vitro and in vivo. We focused on 96 genes mutated in >2% of newly diagnosed MM patients in the CoMMpass (IA17) study (after excluding non-expressed genes [<1 FPKM in 95% of samples] and immunoglobulin/MHC genes) and specifically examined the performance of these genes in a series of in vitro genome-scale studies for CRISPR gene editing or activation (n=19 and n=5 MM lines, respectively); in vitro validation studies with subgenome-scale focused sgRNA libraries of individual sgRNAs; and in vivo focused subgenome-scale CRISPR screens (in 3 cell lines) in conventional subcutaneous (s.c.) xenograft or in bone marrow (BM)-like scaffolds with “humanized” mesenchymal BM stromal cell compartment (seeking a more translationally-relevant simulation of the BM microenvironment in MM patients).