Immunophenotypic Changes in the Tumor and Tumor Microenvironment During Progression to Multiple Myeloma
Isabelle Bergiers, Murat Cem Köse, Sheri Skerget, Milan Malfait, Nele Fourneau, Jenna-Claire Ellis, Greet Vanhoof, Tina Smets, Bie Verbist, Dries De Maeyer, Jeroen Van Houdt, Koen Van der Borght, Raluca Verona, Bradley Heidrich, William Kurth, Michel Delforge, Nathalie Meuleman, Jan Van Droogenbroeck, Philip Vlummens, Christoph J. Heuck, Yves Beguin, Nizar Bahlis, Tineke Casneuf, Jo Caers
Abstract:
Investigation of the cellular and molecular mechanisms of disease progression from precursor plasma cell disorders to active disease increases our understanding of multiple myeloma (MM) pathogenesis and supports the development of novel therapeutic strategies. In this analysis, single-cell RNA sequencing, surface protein profiling, and B lymphocyte antigen receptor profiling of unsorted, whole bone marrow (BM) mononuclear cell samples was used to study molecular changes in tumor cells and the tumor microenvironment (TME).
Introduction:
Multiple myeloma (MM), a hematologic malignancy of bone marrow (BM) plasma cells, is the second most common blood cancer in the USA and is primarily considered a disease of the elderly (median age at diagnosis is 69 years). Over the past 15 years, the prognosis of patients with MM has improved due to the emergence of new therapies providing deep and durable responses. However, these therapies are not curative, and patients will eventually relapse, underscoring the urgent need for new treatment options and a better understanding of disease progression.
Materials and Methods:
Samples were thawed at 37ºC and diluted in a prewarmed RPMI-1640 medium before centrifugation. Cell pellets were resuspended in cold PBS + 1% bovine serum albumin. For each sample, 0.2 × 106 cells were stained using a tagged-antibody pool (see S1 Appendix for additional details) following the manufacturer’s procedure (BioLegend, San Diego, California, USA). After staining, cells were resuspended in PBS + 0.04% bovine serum albumin at a concentration of 1000 cells/µl, filtered using a FACS tube with a cell strainer cap and processed immediately according to the 10x Genomics Chromium Single Cell V(D)J with Feature Barcoding protocol.
Discussion:
Despite recent treatment advancements, MM remains an incurable disease. Comprehensive and deep molecular profiling of the tumor plasma cells and surrounding immune populations advance our understanding of disease progression and can inform the identification of novel therapeutic targets. In this study, a single-cell transcriptomic atlas comprising >120 subjects from 4 cohorts, including healthy volunteers and patients with MGUS, SMM and MM, was generated. A multi-modal single-cell omics approach was applied to investigate the molecular changes that take place in tumoral plasma cells and immune populations present in the tumor microenvironment during disease progression.
Acknowledgments:
We thank the clinical trial operational team and particularly Audrey Hanegreefs, Claudia Bollekens, Kathleen Mascarenhas, and Nicole Shipitofsky (Janssen Pharmaceuticals) for their continuous support; Evi Van Dijck and Kato Verwilt (Janssen Research & Development, Beerse, Belgium) for supporting the methodology development; Cheryl Sweeney, Hans Wils, and Yann Abraham (Janssen Research & Development, Beerse, Belgium) for technical support and fruitful scientific discussions; Gary Borzillo (Janssen Research & Development, Spring House, PA) for support and insights; and Jan Slabbaert and Aniko Meijer for their valuable contributions to CyTOF analyses. We thank the Janssen Beerse Biobank team for their support with sample management. We thank the Multiple Myeloma Research Foundation Immune Atlas network for generating CoMMpass study data and for fruitful collaboration.
Citation: Bergiers I, Köse MC, Skerget S, Malfait M, Fourneau N, Ellis J-C, et al. (2025) Immunophenotypic changes in the tumor and tumor microenvironment during progression to multiple myeloma. PLoS Genet 21(10): e1011848. https://doi.org/10.1371/journal.pgen.1011848
Editor: SNEHAL M. GAIKWAD, National Cancer Institute, UNITED STATES OF AMERICA
Received: July 19, 2024; Accepted: August 21, 2025; Published: October 7, 2025.
Copyright: © 2025 Bergiers et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: Data files are available at the Gene Expression Omnibus with accession number GSE232988.
Funding: Clinical trial NOPRODMMY0001 was conducted and funded by Janssen Research & Development LLC with support of VLAIO (Flanders Innovation & Entrepreneurship) (HBC.2018.2291) awarded to Janssen Pharmaceuticals. Janssen Research & Development LLC contributed to study design, data collection and analysis, decision to publish, and preparation of the manuscript. VLAIO had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. JC is supported by a grant from the Fondation contre le Cancer and from ERA-NET TRANSCAN-3 (EC co-funded call 2021, SmartCAR-T).
Competing interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: IB, SS, NF, GV, TS, BV, DDM, JVH, KVdB, RV, BH, CJH, and TC were employees of Janssen Research & Development LLC at the time the study was conducted and may hold stock and/or stock options. MCK and NB received research support from Janssen Research & Development LLC. JC has a research mandate funded by the Fondation contre le Cancer. MM, J-CE, WK, MD, NM, JVD, PV and YB have declared that no competing interests exist.
