Natural Killer Cells Are Active Against Myeloma, Leukemia or Lymphoma Cells with Loss of Tumor Suppressor Genes

The therapeutic targeting of tumor cells with loss of function (LOF) for tumor suppressor genes (TSGs) is challenging across cancers, including hematologic neoplasias, because pharmacological mechanisms to restore the function(s) of such genes are not readily feasible, in contrast to e.g., inhibition of oncogenic drivers. We reasoned, however, that, although LOF for TSGs leads to de-repressed growth of neoplastic hematopoietic cells, it may not necessarily protect them from immune attack. We thus explored the hypothesis that CRISPR-based loss of function of TSGs in cells from multiple myeloma (MM), leukemias or lymphoma may still be associated with substantial response to immune effector cells such as NK cells, which have the advantage to kill tumor cells across HLA barriers. We have conducted CRISPR-based studies in 7 cell lines that represent different hematologic malignancies and different levels of sensitivity to natural killer (NK) cells, namely the B-cell lymphoma (SUDHL4), precursor B cell acute lymphoblastic leukemia (NALM6), multiple myeloma (MM1.S, LP1, KMS11), chronic myeloid leukemia (K562), and acute myeloid leukemia (MOLM14). In these genome-scale or focused CRISPR screens for LOF (CRISPR-based gene editing) or gain of function (GOF, CRISPR activation), the blood cancer lines were exposed to allogeneic donor-derived NK cells (vs. control cultures without NK cells). We evaluated the performance of genes known to represent recurrent TSGs based on genomic data of patient samples or cell lines; as well as candidate TSGs, based on results from genome-scale CRISPR gene editing screens (e.g., CERES or CHRONOS scores >0.4 in multiple DepMap releases and TPM>1 [RNA-seq]) in the same cell lines as the NK cell resistance screens. These analyses sought to identify any TSGs whose LOF may potentially alter the response of blood cancer cells to NK cells. We also evaluated genes identified as top recurrent TSGs in patient samples from MM and other hematologic neoplasias (e.g., based on prior genomic studies). On aggregate, we evaluated a collection of known and recurrent TSGs (e.g., PTEN, TP53, RB1, CDKN2C, CDKN1B, TENT5C/FAM46C) as well as other, previously underappreciated candidate genes with TSG properties in hematologic neoplasias (e.g., HIF1A, DEPDC5). Perturbation of none of these genes was identified to meet criteria for association with significant resistance to allogeneic donor-derived NK cells (e.g., log2FC>1.0, at least 3-4 sgRNAs with enrichment