Feb 4, 2021 / Oncology

Inside the marrow: exploring the immune microenvironment of multiple myeloma with single cell RNA-sequencing

Olivia Habern

In honor of World Cancer Day, we are spotlighting ongoing research into multiple myeloma, a blood cancer caused by overactive plasma cells in the bone marrow that crowd out healthy blood cells and weaken bone integrity. Learn how single cell technology is helping researchers explore the dynamic cellular composition of the tumor immune microenvironment over the course of disease progression and identify new potential targets for therapeutic intervention. In addition, find out more about the Immune Atlas initiative spearheaded by the Multiple Myeloma Research Foundation and five collaborating institutions—a research effort determined to advance precision immunotherapies for multiple myeloma through large-scale single cell immune profiling studies.

Microscopic images captured from bone marrow aspirate slides of patients diagnosed with multiple myeloma. CREDIT: Gupta, R., & Gupta, A. (2019). MiMM_SBILab Dataset: Microscopic Images of Multiple Myeloma [Data set]. The Cancer Imaging Archive. (CC BY 3.0)
Microscopic images captured from bone marrow aspirate slides of patients diagnosed with multiple myeloma. CREDIT: Gupta, R., & Gupta, A. (2019). MiMM_SBILab Dataset: Microscopic Images of Multiple Myeloma [Data set]. The Cancer Imaging Archive. (CC BY 3.0)

While most tumors have clear and potentially rapid stepwise developmental changes—in which cells begin to act abnormally, divide excessively, and create disorganization in their resident tissues—multiple myeloma is a quieter cancer. In fact, how myeloma appears and progresses is still largely unknown. The cancer originates in the bone marrow of typically older individuals, with a median age of diagnosis at 69 (1). It is uniquely characterized by asymptomatic precursor stages, including monoclonal gammopathy of undetermined significance (MGUS), followed by smoldering multiple myeloma (SMM). These stages are distinguished by a graded increase in blood measurements of M proteins, an abnormal immunoglobulin product of plasma cells in the bone marrow and a sign that those cells are growing abnormally. However, active multiple myeloma isn’t diagnosed until there is symptomatic evidence, including bone fractures or low blood cell counts caused by myeloma cells—cancerous, over-replicating plasma cells (1).

MGUS is present in about 1% of the general population in the US and 3% of healthy individuals older than 50; it progresses to active multiple myeloma, or another kind of blood cancer, in 20–25% of patients over the course of their lifetimes (1). The variability of these outcomes reveals a gap in our knowledge of multiple myeloma: it remains unclear when and how some patients will progress and others won't, necessitating a more comprehensive understanding of the underlying immune dysfunction driving the cancer and better predictors of outcome. Additionally, current treatment programs for multiple myeloma can, at their best, only control the cancer. Drug regimens accompanied by high-dose chemotherapy and autologous stem cell transplantation can kill myeloma cells in the bone marrow, then reinstate healthy hematopoietic stem cells derived from the patient’s own body. But even this cannot fully eradicate the errant plasma cells (2).

For these reasons, researchers are turning to single cell approaches to unravel the heterogeneous cellular composition of the bone marrow immune microenvironment in multiple myeloma. Discovering the factors at work in the asymptomatic progression of this cancer is a key area of focus. With the cellular and molecular insights provided by these methods, there is potential to more deeply inform current treatment programs by understanding the mechanisms of the early stages of this cancer’s evolution. And there is potential to find new immunotherapy targets that may restore the immune functions lost as a result of myeloma and give patients long-lasting treatment success.

Below, we describe some recent single cell studies of multiple myeloma presented at the American Society of Hematology (ASH) Annual Meeting & Exposition 2020 and catch up on developments with the Multiple Myeloma Research Foundation Immune Atlas initiative.

Exploring the immune microenvironment of multiple myeloma 

What immune cell dynamics are at work in the bone marrow of multiple myeloma patients? How do these dynamics change as the disease progresses, from asymptomatic abnormal plasma-cell growth to active cancer? To answer these questions, Irene Ghobrial, MD, Director of the Clinical Investigator Research Program at the Dana-Farber Cancer Institute and Professor of Medicine at Harvard Medical School, turned to single cell analysis. Presenting her research at the recent ASH Annual Meeting, she performed single cell RNA-sequencing on tumor and immune cells isolated from bone marrow samples from 23 multiple myeloma patients, including 5 MGUS, 11 SMM, 7 active MM, and 9 healthy donors. Annotation of single cell clusters revealed early compositional changes in the immune microenvironment. MGUS stage samples, in particular, showed significantly higher expression of natural killer (NK) cells and T regulatory cells (Tregs) compared to controls. Further characterization of T-cell clusters showed that memory cytotoxic T cells were lost as the cancer advanced to active multiple myeloma. These T-cell signatures suggest a rise in immune cell suppression activity during disease progression, which, if reversed, could possibly slow or prevent the progression of the cancer (3).

Leveraging large cohort studies to understand multiple myeloma

Dr. Ghobrial’s work pointed to a crucial readout of the underlying immune dysfunction that could be driving multiple myeloma progression. However, she also noted a need for larger cohort studies to confirm the observed correlation between disease progression and T-cell compositional changes. Such data would be necessary to advance potential immunotherapies that would address these immune cell dynamics.

Answering this call for larger cohort studies to accelerate immunotherapy development, the Multiple Myeloma Research Foundation (MMRF) has initiated an Immune Atlas project in collaboration with Beth Israel Deaconess Medical Center, Emory University, Mayo Clinic Rochester, Mount Sinai School of Medicine, and Washington University, forming the MMRF Immune Profiling Consortium. Through large-scale single cell immune profiling studies, the consortium hopes to fully profile the immune microenvironment in multiple myeloma in order to accelerate insights to clinical research and practice. One of the Immune Atlas’ inaugural initiatives will be to profile samples from the MMRF's CoMMpass Study, a longitudinal study collecting genomic and clinical information from recently diagnosed myeloma patients—to date, 1150 patients from 76 sites worldwide—over the course of their disease and treatment.

Led by Manoj Bhasin, PhD, of Emory School of Medicine, members of the MMRF Immune Profiling Consortium presented findings at the recent ASH Annual Meeting. Looking to uncover the mechanisms underlying multiple myeloma progression, the research team compared the bone marrow immune microenvironment of patients with rapidly progressing multiple myeloma to those whose disease had not progressed, even for several years, at the time of analysis. A total of 18 patients were sampled; with technical replicates for each sample and analysis distributed across three institutions from the consortium, the team profiled approximately 102,207 cells from 48 samples via single cell RNA-sequencing. Analysis revealed multiple transcriptionally diverse clusters of CD138+ plasma tumor cells. Significant inter-patient heterogeneity was observed in these clusters for patients with rapidly progressing cancer. A closer look at the gene expression of plasma tumor cells revealed increased expression of pathway genes related to the epithelial-mesenchymal transition and p38 MAPK signaling, both of which were associated with poorer outcome in multiple myeloma. They also identified 22 distinct immune cell clusters from the bone marrow samples. Among non-progressing patients, the team observed enrichment of GZMB+ T cells and NK cells, which overexpressed genes associated with natural killer cell signaling, CD28 signaling in T helper cells, NF-kB signaling, and the Th17 activation pathway. Additionally, they noted enrichment of other immune cell types, including macrophages, monocytes, and myeloid cells with significant activation of metabolic and immune response pathways. Together, their insights suggest that a bone marrow immune microenvironment rich in activated T cells and myeloid lineage populations slows multiple myeloma progress and supports better patient outcomes (4).

Working together to find long-lasting solutions for multiple myeloma 

Ongoing research into the cellular composition and dynamic transcriptional signatures of the bone marrow immune microenvironment in multiple myeloma is opening up new insights into the reasons why this cancer progresses in some patients but remains quiet in others. Evidence of early-onset immune suppression at the MGUS stage may pose new therapeutic routes to unleash immune activity that could be the key to slowing the uncontrolled replication of cancerous plasma cells. At 10x Genomics, we’re very honored to see our technology supporting the cause of finding long-lasting therapeutic solutions for patients with multiple myeloma. We look forward to the collaborative, multi-site research that will continue to pave the way towards this end.

For World Cancer Day, we’d like to thank the doctors, researchers, and patients working together to find cures for multiple myeloma and other blood cancers.


  3. Irene Ghobrial. The Immune Microenvironment in Myeloma. ASH Annual Meeting & Exposition 2020.
  4. Manoj Bhasin et al. Characterization of Plasma and Immune Cells Molecular Landscape That Play a Role in Rapid Progression of Multiple Myeloma Using Cross Center Scrna-Seq Study. ASH Annual Meeting & Exposition 2020. Oral and Poster Abstracts 1357.