McCarroll, Steven A.

Significance By evaluating children with a malformed cerebral cortex, we identified an ATPase pump (ATP1A3) with an early role in brain development. The ATP1A3 pump maintains the physiological concentration of sodium and potassium ions in cells, a process critical for osmotic equilibrium and membrane potential across several developing cell populations. We employed single-cell sequencing approaches to identify key enrichments for ATP1A3 expression during human cortex development. Unravelling this early cell-type–specific pathophysiology in the developing brain offers a potential basis for the treatment of ATP1A3 -related diseases affecting prenatal and early childhood development.

Abstract In multiple myeloma (MM), despite well-characterized precursor states such as monoclonal gammopathy of undetermined significance (MGUS) and smoldering multiple myeloma (SMM), there is a lack of sufficient biomarkers to predict disease progression. Most genomic analyses have studied the malignant plasma cells, however, cancers form a complex ecosystem with the immune and stromal microenvironment. To characterize the cellular composition and transcriptional programs of each component of the tumor and microenvironment at different stages of MM progression, we employed single-cell RNA sequencing on 48K plasma and 40.8K immune microenvironmental cells from a cohort of 22 patients with varying stages of disease progression and 9 healthy donors. Expression profiles of plasma cells revealed clear tumor-specific differences in known oncogenic drivers in MM (MMSET/FGFR3, CCND1 and MAFB) as well as other clonally expressed genes (LAMP5, HIST1H1C, and AREG), distinguishing them from healthy plasma cells. We identified a subset of cycling plasma cells in malignant samples, observing a range of proliferative capacity across disease stages. Furthermore, our approach allowed a unique head-to-head comparison of gene expression changes in normal and malignant plasma cells from the same individual, revealing early alterations in genes related to immune modulation (NKBIA) or controlling transcription and differentiation (EID1). Some alterations were patient-specific, while others, such as MHC I overexpression and CD27 loss, were recurrently observed across subsets of the cohort. Analysis of the BM microenvironment demonstrated significant infiltration of natural killer cells, non-classical monocytes/macrophages, and T cells, even in the earliest stages of the disease. Further investigation revealed upregulation of MHC II expression at the mRNA level in CD14+ monocytes/macrophages and yet, intriguingly, analysis by CyTOF and immunohistochemistry revealed a shift towards intracellular localization of MHC II in these cells. Co-culture with MM cell lines was sufficient to induce the decrease of extracellular MHC II, providing strong evidence for MM-induced compromised antigen presentation by macrophages, and hinting at a mechanism of immune evasion. Together, our results provide a comprehensive view at the complex interplay of the immune and malignant cells in different stages of the disease. We demonstrate the immune response beginning in premalignant conditions to be heterogeneous, including compromised antigen presentation as well as alterations in cellular composition and signaling. Consideration of the type of immunological response may prove valuable in determination of progression risk, as well as open up potential strategies for therapy. Citation Format: Nicholas J. Haradhvala, Oksana Zavidij, Tarek H. Mouhieddine, Romanos Sklavenitis-Pistofidis, Jihye Park, Mairead Reidy, Abdallah Flaifel, Benjamin Ferland, Salomon Manier, Mark Bustoros, Daisy Huynh, Marzia Capelletti, Brianna Berrios, Mahshid Rahmat, Chia-Jen Liu, Meng Xiao He, Esteban Braggio, Rafael Fonseca, Yosef Maruvka, Jennifer Guerriero, Melissa Goldman, Eliezer Van Allen, Steven McCarroll, Jamil Azzi, Gad Getz, Irene M. Ghobrial. Single-cell RNA sequencing reveals compromised immune microenvironment in precursor stages of multiple myeloma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 139.