Single-Cell Multi-Omic Profiling of Patients with BCMA-Targeted Therapy Identifies Molecular and Cellular Factors Associated with Responsiveness and Treatment Effects
Authors: Dang Minghao , Lee Hans C. , Bansal Hima , Acevedo-Calado Maria , Qin Li , Tan Wei , Moreno Rueda Luz Yurany , Berrios David , Patel Krina K. , Lin Pei , Thomas Sheeba K. , Weber Donna M. , Wang Linghua , Orlowski Robert Z. 
Published: December 2024

Background:
Immunotherapeutics targeting B cell maturation antigen (BCMA), including antibody drug conjugate (ADC), bispecific T cell engager (BiTE) and chimeric antigen receptor T-cell (CAR-T) have revolutionized treatment in relapsed and/or refractory myeloma (RRMM). However, our understanding of how these therapies change the molecular and immune characteristics of myeloma cells and their tumor microenvironment (TME) is incomplete and hinders our ability to predict patient responsiveness and rationally sequence therapies.
Methods:
We performed paired single-cell RNA sequencing (scRNA-seq), single-cell T/B cell receptor sequencing (scTCR-seq and scBCR-seq) on 89 fresh bone marrow (BM) aspirate samples from 54 RRMM patients with prior and/or post BCMA-targeted therapies. For each sample, the BM mononuclear cells (BMMNCs) were isolated and plasma cells (PCs) were enriched by CD138+ selection. cDNA libraries from BMMNCs and PCs were used for scRNA-seq, scBCR-seq and/or scTCR-seq. Single-cell data was processed as previously described (Dang et al., Cancer Cell, 2023). Samples were classified as responders and non-responders at baseline, in responding and relapse/refractory according to their best response to the therapy.
Results:
Among the 54 patients, 8 received ADC therapy, 20 received BiTE therapy, 8 received CAR-T therapy, the remaining 18 received more than one BCMA-targeted therapies. We profiled 583,684 high-quality cells including 287,960 TME cells (among which 6,843 have paired scBCR-seq and 68,792 have paired scTCR-seq data) and 295,724 PCs (among which 261,777 have paired scBCR-seq data). Unsupervised clustering analysis revealed 24 different TME cell types which were further resolved into 74 cell subsets. Malignant cells were identified based on BCR clonotypes as well as inferred copy number alterations. We compared baseline characteristics of responders (n=23) versus non-responders (n=12), as well as characteristics across baseline (n=30), responding (n=21), and relapse/refractory (n=33) states in both TME and myeloma cells.
At baseline, responders exhibited higher levels of monocytes (with low MDSC and phagocytosis signature) and cDCs (with low M1 and M2 signature) compared to non-responders. In contrast, non-responders showed an increased proportion of interferon stimulated CD8+ T and NK cells, exhausted CD8+ T cells, and elevated expression of chemokines and their receptors. Macrophages in non-responders showed higher M1 and M2 signature. Myeloma cells in responders were enriched for B cell activation pathways, while those from non-responders were enriched for interferon response pathways. Regulatory T cells showed no significant difference between the two groups.
Comparing baseline, responding, and relapse/refractory states, we found that mature B cells and pDCs were significantly depleted in responding samples. Baseline samples had higher proportions of naïve/memory T cells (both CD4+ and CD8+) and Th17 cells, whereas responding samples were characterized by a higher proportion of effector T and NKT cells. Relapse/refractory samples showed an overall decrease in T cells but increase in myeloid and erythrocyte progenitors. Additionally, the diversity of TCR clonotypes in responding samples was significantly lower than in baseline and relapse/refractory samples. Monocytes in relapse/refractory samples had a higher MDSC signature, while cDCs in responding samples exhibited higher M1 and phagocytosis signature. Myeloma cells from responding samples were enriched for B cell activation and apoptosis pathways, whereas those from relapse/refractory samples were enriched for energy metabolism pathways.
Conclusions:
We comprehensively characterize the cellular and molecular properties of TME and myeloma cells and find distinct landscapes associated with responsiveness to BCMA-targeted therapy. Responders at baseline have more monocytes and cDCs while non-responder show a global interferon stimulated signature; samples in responding have a higher level of cytotoxic lymphocytes and a decreased TCR clonotype diversity, suggesting the expansion of tumor-killing T cells; relapse/refractory samples show a more suppressed immune microenvironment. These observations provide valuable insights into mechanisms underlying patient responsiveness and treatment effects and highlight potential targets for further investigation.