Abstract 2015: Single-cell atlas of tumor and immune cells in disease progression from MGUS to MM
Authors: Romanos Sklavenitis-Pistofidis, Ting Wu, Elizabeth Lightbody, Yoshinobu Konishi, Mahshid Rahmat, Michael Agius, Junko Tsuji, Jean-Baptiste Alberge, Ankit Dutta, Michelle Aranha, Nayda Bidikian, Hadley Barr, Nicholas Haradhvala, Gad Getz, Irene Ghobrial
Journal: Cancer Research (2025)

Introduction: Multiple Myeloma (MM) is a bone marrow (BM) plasma cell malignancy that is preceded by asymptomatic stages; Monoclonal Gammopathy of Undetermined Significance (MGUS) and Smoldering Multiple Myeloma (SMM). Despite their early stage, patients with MGUS/SMM exhibit immune dysregulation. Understanding how immune dysregulation evolves and how tumor and immune cells interact to promote progression to MM may help predict and intercept it. Methods: We performed single-cell RNA/BCR/TCR-seq (10X Genomics) on ∼6 million tumor and immune cells from 877 samples, 533 BM/blood specimens, and 365 patients with MGUS/SMM/MM and healthy donors. For 241 individuals, both tumor and immune cells were sequenced to enable integrative analyses of tumor and immune biology. Results: We observed a significant increase in the proportion of GZMB+ CD8+ effector memory T cells (TEMs) in MM compared to MGUS. This was due to increased clonal expansion and a differentiation bias in CD8+ TEMs, which also showed higher proliferative capacity and IFN-gamma expression. Despite these seemingly advantageous changes, GZMB+ CD8+ TEMs showed decreased activity of an expression signature marked by SLC7A5 and PIK3R1, genes critical for T cell functionality. Patients with lower activity of this signature showed higher risk of progression. To characterize its impact on tumor cells, we split patients into high and low T cell functionality groups and compared their tumor cell expression profiles. The top upregulated gene in tumor cells from patients with high T cell functionality was SERPINB9, which neutralizes granzymes and protects tumor cells from cytotoxic T cells. From this analysis, we derived the transcriptional footprint of T cell functionality on tumor cells, which we termed the “immune control” signature. We found that it, too, decreases with progression, and validated it in two external cohorts. To test whether this observed decrease could be the result of tumor-intrinsic genomic evolution or, alternatively, reflects the receding immune pressure by progressively more dysfunctional T cells, we constructed tumor phylogenetic trees and compared the activity of the immune control signature across ordered subclones within tumors. We observed stable expression of the immune control signature across subclones in our trees, suggesting that this signature may reflect external immune pressure, rather than tumor genomic evolution. Independent of the patient’s disease stage, tumors with higher immune control showed lower cycling capacity, demonstrating that high T cell functionality is associated with disease control. Conclusion: This study may have implications for: (i) the risk stratification of patients with MGUS/SMM/MM, (ii) patient selection for immunotherapy administration and interception of progression, (iii) preemptive T cell banking for future CAR-T cell therapy, and (iv) the development of novel immunotherapeutics. Citation Format: Romanos Sklavenitis-Pistofidis, Ting Wu, Elizabeth Lightbody, Yoshinobu Konishi, Mahshid Rahmat, Michael Agius, Junko Tsuji, Jean-Baptiste Alberge, Ankit Dutta, Michelle Aranha, Nayda Bidikian, Hadley Barr, Nicholas Haradhvala, Gad Getz, Irene Ghobrial. Single-cell atlas of tumor and immune cells in disease progression from MGUS to MM [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2015.