Single-Cell Analysis Reveals Depletion of Antigen-Presenting Cell (APC) and IFN-Stimulated CD4 T Cell Populations in High-Risk Newly Diagnosed Multiple Myeloma Patients
Authors: Vieira Junia , Park Alison S , Melnekoff David , Mouhieddine Tarek H. , D'anna Alessia , Aleman Adolfo , Ram Meghana , Kappes Katerina , Hamilton Mark , Mulligan George , Wiita Arun P , Chari Ajai , Martin Thomas , Slade Michael , Ding Li , Vij Ravi , Brown Brian , Tycko Benjamin , Feinman Rena , Siegel David S. , Jagannath Sundar , Parekh Samir , Lagana Alessandro 
Published: December 2024

Introduction: In the past 15 years, survival in multiple myeloma (MM) has greatly improved due to new treatments, including immunomodulatory drugs (IMiDs) and T cell therapies (CAR-T and BiTEs). Recent studies suggest the MM microenvironment (TME) plays a key role in disease and treatment outcomes. Understanding the MM-TME in high-risk cases is crucial for better patient risk stratification and management.
Methods: Bone marrow (BM) samples were collected at diagnosis from 72 NDMM patients, including 38 standard-risk (SR) and 34 high-risk (HR) patients. HR was defined by del(17p) and/or p53 mutations, biallelic del(1p32) or del(1p32) with gain(1q), t(4;14)/t(14;16)/t(14;20) with gain(1q) or del(1p), or B2M&gt; 5.5 mg/L with Creatinine &lt; 1.2mg/dL. We sequenced 567,340 BM cells using 10X 5' scRNA-seq, including 43,610 myeloid cells, 38,729 NK cells, 255,786 T cells, 35,626 B cells, and 90,688 myeloma cells. Tumor WES data from 40 patients (SR n = 22, HR n = 18) was integrated. Analysis was performed using R packages Seurat, InferCNV, and CellphoneDB.
Results: The 72 patients were classified as high-risk (HR; n = 34) or standard-risk (SR; n = 38), according to the IMWG criteria above. Exploratory copy number alteration (CNA) analysis on tumor scRNA-seq paired with WES data available for the HR cohort (n = 18) detected MM subclones with segmental deletion of chr 17 (n = 4), gain of 1q (n = 8), and gain of chr 14 (n = 4), showing congruency between scRNA-seq and WES findings.
ScRNA-seq identified 92 cell populations based on lineage markers as well as activation, exhaustion, senescence and proliferation markers. Overall, the SR group had a higher frequency of CD14+ S100+ monocytes, granulocyte-monocyte progenitors (GMP) and B memory cells (p &lt; 0.05) compared to the broad HR group, in alignment with previous findings (Pilcher et al, 2023).
To further stratify our cohort, we subdivided HR patients into three subgroups: del(17p) and/or p53 mutation (group 1, n = 10); t(4;14), t(14;16), or (14;20) with del(1p32) or gain(1q) (group 2, n = 17); and B2M&gt; 5.5 mg/L with Creatinine &lt; 1.2 (group 3, n = 10). The analysis revealed higher frequencies of pre-B, B naive and B memory cells in SR compared to HR groups 1 and 3 (p &lt; 0.05). Various myeloid subpopulations, including CD14+ S100+ monocytes, GMP, plasmacytoid and classic dendritic cells, were more frequent in SR compared to HR group 1 (p &lt; 0.05), suggesting a depletion of antigen presentation cells (APCs) in the presence of p53 alterations in MM cells.
In the NK/T cell compartment, we observed a lower frequency of IFN-stimulated CD4 central memory (CM) cells in HR group 2 (p = 0.02), while LEF1+ CD4 T helper cells were more frequent in HR group 3 (p = 0.03). Cell communication analysis revealed that LEF1+ CD4 T helper cells interact with TYROBP-expressing immunosuppressive myeloid cells (M2 Macrophages and CD14+ S100+ monocytes) via the CD44 receptor, indicating recruitment of these populations and migration to the MM-TME. These findings suggest that HR cytogenetics and clinical HR features correlate with a more immunosuppressive TME, characterized by more LEF1+ T helper cells and fewer IFN-stimulated CD4 CM cells.
Conclusions: Single cell profiling of the MM TME identified immunosuppressive subpopulations and a depletion of APC and IFN-stimulated CD4 populations, crucial for immunosurveillance and anti-tumoral response, in HR patients, potentially contributing to therapy resistance and worse outcomes. Ongoing work aims to validate these findings and analyze the interplay between tumor cells and TME in HR patients.