Multiple Myeloma Publications

Pilcher, W. et al. Cross center single-cell RNA sequencing study of the immune microenvironment in rapid progressing multiple myeloma. NPJ Genom Med 8, 3 (2023). Lab Members Involved: William Pilcher, Beena Thomas, Swati Bhasin, Manoj Bhasin Other people involved: Madhav Dhodapkar, Li Ding
Despite advancements in understanding the pathophysiology of Multiple Myeloma (MM), the cause of rapid progressing disease in a subset of patients is still unclear. MM's progression is facilitated by complex interactions with the surrounding bone marrow (BM) cells, forming a microenvironment that supports tumor growth and drug resistance. Understanding the immune microenvironment is key to identifying factors that promote rapid progression of MM. To accomplish this, we performed a multi-center single-cell RNA sequencing (scRNA-seq) study on 102,207 cells from 48 CD138- BM samples collected at the time of disease diagnosis from 18 patients with either rapid progressing (progression-free survival (PFS) < 18 months) or non-progressing (PFS > 4 years) disease. Comparative analysis of data from three centers demonstrated similar transcriptome profiles and cell type distributions, indicating subtle technical variation in scRNA-seq, opening avenues for an expanded multicenter trial. Rapid progressors depicted significantly higher enrichment of GZMK+ and TIGIT+ exhausted CD8+ T-cells (P = 0.022) along with decreased expression of cytolytic markers (PRF1, GZMB, GNLY). We also observed a significantly higher enrichment of M2 tolerogenic macrophages in rapid progressors and activation of pro-proliferative signaling pathways, such as BAFF, CCL, and IL16. On the other hand, non-progressive patients depicted higher enrichment for immature B Cells (i.e., Pre/Pro B cells), with elevated expression for markers of B cell development (IGLL1, SOX4, DNTT). This multi-center study identifies the enrichment of various pro-tumorigenic cell populations and pathways in those with rapid progressing disease and further validates the robustness of scRNA-seq data generated at different study centers.

Yao, L. et al. Comprehensive Characterization of the Multiple Myeloma Immune Microenvironment Using Integrated scRNA-seq, CyTOF, and CITE-seq Analysis. Cancer Res Commun 2, 1255-1265 (2022). Lab Members Involved: William Pilcher, Beena Thomas, Swati Bhasin, Manoj Bhasin Other people involved: Lijun Yao, Kavita Dhodapkar, Madhav Dhodapkar, Li DIng

As part of the Multiple Myeloma Research Foundation (MMRF) immune atlas pilot project, we compared immune cells of multiple myeloma bone marrow samples from 18 patients assessed by single-cell RNA sequencing (scRNA-seq), mass cytometry (CyTOF), and cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) to understand the concordance of measurements among single-cell techniques. Cell type abundances are relatively consistent across the three approaches, while variations are observed in T cells, macrophages, and monocytes. Concordance and correlation analysis of cell type marker gene expression across different modalities highlighted the importance of choosing cell type marker genes best suited to particular modalities. By integrating data from these three assays, we found International Staging System stage 3 patients exhibited decreased CD4+ T/CD8+ T cells ratio. Moreover, we observed upregulation of RAC2 and PSMB9, in natural killer cells of fast progressors compared with those of nonprogressors, as revealed by both scRNA-seq and CITE-seq RNA measurement. This detailed examination of the immune microenvironment in multiple myeloma using multiple single-cell technologies revealed markers associated with multiple myeloma rapid progression which will be further characterized by the full-scale immune atlas project.

Pediatric Leukemias Publications

The obesity pandemic currently affects more than 70 million Americans and more than 650 million individuals worldwide. In addition to increasing susceptibility to pathogenic infections (eg, SARS-CoV-2), obesity promotes the development of many cancer subtypes and increases mortality rates in most cases. We and others have demonstrated that, in the context of B-cell acute lymphoblastic leukemia (B-ALL), adipocytes promote multidrug chemoresistance. Furthermore, others have demonstrated that B-ALL cells exposed to the adipocyte secretome alter their metabolic states to circumvent chemotherapy-mediated cytotoxicity. To better understand how adipocytes impact the function of human B-ALL cells, we used a multi-omic RNA-sequencing (single-cell and bulk transcriptomic) and mass spectroscopy (metabolomic and proteomic) approaches to define adipocyte-induced changes in normal and malignant B cells. These analyses revealed that the adipocyte secretome directly modulates programs in human B-ALL cells associated with metabolism, protection from oxidative stress, increased survival, B-cell development, and drivers of chemoresistance. Single-cell RNA sequencing analysis of mice on low- and high-fat diets revealed that obesity suppresses an immunologically active B-cell subpopulation and that the loss of this transcriptomic signature in patients with B-ALL is associated with poor survival outcomes. Analyses of sera and plasma samples from healthy donors and those with B-ALL revealed that obesity is associated with higher circulating levels of immunoglobulin-associated proteins, which support observations in obese mice of altered immunological homeostasis. In all, our multi-omics approach increases our understanding of pathways that may promote chemoresistance in human B-ALL and highlight a novel B-cell–specific signature in patients associated with survival outcomes.
Henry, C. Omics of Obesity in B-cell Acute Lymphoblastic Leukemia. Journal of the National Cancer Institute (2023).

Spatial Transcriptomics Publications

Michaud, M. E.;* Liang, P.;* Pilcher, W.; Mota, L.; Bakhtiari, M.; Thomas, B. E.; Tomeo, J.; Contreas, M.; Ferran, C. J.; Bhasin, S.; Pradhan-Nabzdyk, L.; Logerfo, F. W.; Bhasin, M. K. “An Integrated Single-Nuclei and Spatial Transcriptomic Analysis for Investigating Acute Distension Injury in Vein Graft Implantation.” Manuscript submitted to Circulation Research.
Lab Members Involved: Marina Michaud, William Pilcher, Mojtaba Bakhtiari, Beena Thomas, Swati Bhasin, Manoj Bhasin.
Other people involved: P. Liang, L. Mota, J. Tomeo, M. Contreas, J. C. Ferran, L. Pradhan-Nabzdyk, F. W. Logerfo
Autogenous vein is the most commonly used conduit for coronary and lower extremity arterial bypass grafting. Standard vein harvest technique involves pressure distention and manipulation of the vein conduit, and this process has been suspected to elicit early cell injury and lead to an increased risk of bypass graft failure. Utilizing single-nuclei and spatial transcriptomics, we profiled the genomic effects of distension during graft harvesting in a canine model. Saline distention of the vein graft resulted in acute injury and dysregulation of genes associated with extracellular matrix remodeling, cell proliferation and migration, and endothelial-mesenchymal transition (End MT). We further identified distinct subpopulations of endothelial cells (ECs) and fibroblasts (FBs) with disparate transcriptomic programs related to endothelial injury, EC activation, FB activation, and EndMT, which were present in altered proportions in distended veins compared to control veins. Lastly, we examined the spatial distribution and intercellular communication networks between the various cellular populations to elucidate the cellular and transcriptomic landscape of the vein following distension. The work presented herein represents the first applications of single-nuclei and spatial transcriptomic analyses to the investigation of vein graft implantation. Through this approach, we have unveiled a prompt genomic response to distension amongst distinct cellular populations, which were non-uniformly distributed throughout specific layers of vein, thus providing new molecular insights critical for guiding strategies to limit vein harvest injury.