CRISPR-based screens uncover determinants of immunotherapy response in Multiple Myeloma

Abstract

Cancer cells commonly develop resistance to immunotherapy by loss of antigen expression. Combinatorial treatments that increase levels of the target antigen on the surface of cancer cells have the potential to restore efficacy to immunotherapy. Here, we use our CRISPR interference and CRISPR activation-based functional genomics platform to systematically identify pathways controlling cell-surface expression of the multiple myeloma immunotherapy antigen - B cell maturation antigen, BCMA. We discovered that pharmacological inhibition of HDAC7 and the Sec61 complex increased cell-surface BCMA, including in primary patient cells. Importantly, pharmacological Sec61 inhibition enhanced the anti-myeloma efficacy of a BCMA-targeted antibody-drug conjugate. A CRISPR interference CAR-T coculture screen enabled us to identify both antigen-dependent and -independent mechanisms controlling response of myeloma cells to BCMA-targeted CAR-T cells. Thus, our study demonstrates the potential of CRISPR screens to uncover mechanisms controlling response of cancer cells to immunotherapy and to suggest potential combination therapies.Key PointsUsing CRISPR screens, we systematically identify mechanisms increasing expression of the immunotherapy target BCMA and ADC efficacy.We also identify antigen-independent mechanisms regulating response of cancer cells to BCMA-CAR-T cells.

Determinants of Response and Mechanisms of Resistance of CAR T-cell Therapy in Multiple Myeloma

“…This is in line with prior studies showing that sialic acids, present on the tumor cell surface, impair T-cellmediated tumor immunity (58). This study also showed that ICAM-1 expression is important for BCMA CAR T-cellmediated tumor cell lysis, whereas knockdown of genes belonging to the family of diacylglycerol kinases (DGK) increased sensitivity to BCMA CAR T cells (53).…”

“…In addition, a CRISPR-based screen in an MM cell line identified several novel mechanisms that control the response to BCMA CAR T cells (53). Knockdown of genes in the sialic acid biosynthesis pathway sensitized MM cells to BCMA CAR T cells (53). This is in line with prior studies showing that sialic acids, present on the tumor cell surface, impair T-cellmediated tumor immunity (58).…”

“…However, there was also a high rate of cytokine release syndrome (CRS) and neurotoxicity (52). Inhibitors of HDAC7 or the Sec61 complex also increase BCMA cell-surface expression (53).…”

“…In addition, a CRISPR-based screen in an MM cell line identified several novel mechanisms that control the response to BCMA CAR T cells (53). Knockdown of genes in the sialic acid biosynthesis pathway sensitized MM cells to BCMA CAR T cells (53).…”

Defining the cell surface proteomic landscape of multiple myeloma reveals immunotherapeutic strategies and biomarkers of drug resistance

“…For example, our group (45) and others (46)(47)(48) have used small molecules to increase expression of CD38 on myeloma plasma cells to enhance efficacy of daratumumab. Other examples include small molecule treatment to boost surface BCMA in myeloma (49,50) or CD22 in B-ALL (51). Furthermore, it has been suggested that acute responses to PI treatment, in particular marked chaperone upregulation and ER stress response, may translate into mechanisms of long-term cellular adaptation and resistance (52)(53)(54).…”