Lei Qin

The bone marrow microenvironment is intimately linked to the biology that underpins the development and progression of multiple myeloma. However, the complex cellular and molecular features that form bone marrow niches are poorly defined. Here, we used subcellular spatial transcriptomics to profile the expression of 5001 genes in human bone marrow in the context of multiple myeloma. Using this approach, we explored the plasma cell and stroma ecosystem in bone marrow trephine biopsy specimens (herein referred to as trephines) from 21 individuals, including 7 with premalignant disease and 10 with newly diagnosed multiple myeloma. Using spatial transcriptomics in conjunction with an optimized trephine biobanking methodology, we could resolve major components of the human bone marrow microenvironment and reliably characterize distinct plasma cell populations in samples from healthy, premalignant disease and active myeloma. When plasma cells were visualized in the context of location, we detected spatially restricted subpopulations of plasma cells in 5 of 10 newly diagnosed myeloma trephines. Surprisingly, the composition of hematopoietic and stromal microenvironments varied significantly between newly diagnosed myeloma trephines. Furthermore, these differences in microenvironments were also observed within trephines that had spatially restricted plasma cell subpopulations. Thus, these data are not consistent with the hypothesis that a universal bone marrow microenvironment supports the expansion of malignant plasma cells in myeloma. Instead, we propose that myeloma subpopulations form distinct microenvironments and can vary both between patients and spatial locations.

Exhausted CD8⁺ T (T_EX) cell responses are maintained by precursors of exhausted T (T_PEX) cells that possess high self-renewal and developmental potential. T_PEX cells also drive the proliferative burst of effector T cells upon therapeutic immune checkpoint blockade (ICB). However, the spatial context and signals that regulate their differentiation and function are not well defined. Here we identify developmental and functional compartmentalization of T_PEX and T_EX cells across secondary lymphoid organs during chronic infection. We show that stem-like CD62L⁺ T_PEX and effector-like CX3CR1⁺ T_EX cells constitute a distinct developmental lineage that is promoted by the lymph node (LN) microenvironment and dependent on the transcription factor KLF2. LNs act as a niche in which migratory dendritic cells provide antigen and costimulatory signals to maintain the proliferative fitness of CD62L⁺ T_PEX cells and generation of CX3CR1⁺ T_EX cells. Moreover, LNs exclusively drive the proliferative burst and systemic dissemination of CX3CR1⁺ T_EX cells during ICB. Thus, our findings identify a unique role for LNs in the maintenance of T cell differentiation and function during systemic chronic infection and ICB therapy.

Fibroblastic reticular cells (FRCs) are specialized fibroblasts that construct secondary lymphoid organs where they provide crucial signals for immune cell homeostasis and migration. While splenic FRCs are thought to support antiviral T cell responses, their role remains unclear. Here, we found that ablation of splenic FRCs impaired virus-specific CD8 ⁺ T cell responses during lymphocytic choriomeningitis virus (LCMV) infection. Immunofluorescence imaging revealed that FRCs promote CD8 ⁺ T cell clustering with type 1 conventional dendritic cells (cDC1) in the T cell zone before migration to the infected marginal zone. Without FRCs, T cells instead clustered with cDC1 and virus-infected cells in the marginal zone, leading to suboptimal priming. Mechanistically, FRCs coordinated early viral replication and the inflammatory milieu for optimal DC activation, and an intact FRC network was crucial for generating effector T cells and maintaining protective memory T cells. Thus, splenic FRCs provide essential lymphoid niches for antiviral T cell responses.