Immune Profiling of MM Microenvironment at Single-Cell Resolution

Abstract

Background: The survival of multiple myeloma (MM) is highly dependent on the support of immune microenvironment. However, it is still a challenge to enhance the efficacy of immunotherapy and the underlying mechanism remains obscure. Thus, the aim of our study is to investigate into the dysfunction of immune cells associated with myelomagenesis and figure out the novel immunotherapeutic targets. Method: Single-cell RNA sequencing was utilized for bone marrow mononuclear cells of 7 healthy donors and 12 newly diagnosed MM patients. We analyze the various immune cell populations and their interaction network with tumor cells of NDMM patients by single-cell RNA sequencing data. Results: Firstly, we found a significant negative correlation between the proportion of T/NK cells and tumor burden. Especially, we observed a decrease of CD8+ effector T cells and skewed accumulation of CD8+ memory T cells in patients with high tumor burden. Further, via calculating the cytotoxicity and exhaustion score of T cells, we demonstrated that the dysfunction of CD8+ effector T cells is mostly related with the impaired cytotoxicity, but not the expression of classical exhausted genes, such as CTLA4, VSIR, LAG3, etc. PIM kinases PIM2/3 and KLRB1 seemed to play critical roles in the dysfunction of CD8+ effector T cells. Referring to NK cells, NK cells displayed similar pattern with effector T cells. NK cells also presented decreased cytotoxicity score in patients with high tumor burden and increased expression of PIM1 and KLRC1, which contributed to immunosuppression. Next, we investigated into myeloid compartment of MM patients. Conventional DC (cDC) cells expressed low level of genes including HLA-B, HLA-C, HLA-DRB1, and HLA-DQA1, etc., indicating the impaired antigen presentation by DCs in high-tumor-burden condition. By cell contact analysis, we evaluated the immune crosstalk among immune cells and tumor cells. We indicated the core role of myeloid cells in MM microenvironment. Consistently, the cellular interaction was active in low-tumor-burden condition, whereas suppressed in high-tumor-burden condition. Finally, we examined the metabolic status of immune cell of MM patients to elucidate the underlying mechanisms of dysfunction of immune cells. Our analysis suggested that aberrant metabolism including amino acid metabolism, lipid metabolism, oxidative phosphorylation caused by MM cells were involved in the defective immune response in MM. Conclusion: Our study delineated the immune profile of bone marrow in MM. We suggested an immunosuppressive microenvironment impacted by high tumor infiltration. The serine/threonine kinase PIM family were involved in the dysfunction of both innate and adaptive immune response. Reprogramming immune metabolism proved to be a hopeful immunotherapeutic strategy.