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Single-cell landscape analysis unravels molecular programming of the human B cell compartment in chronic GVHD
Jonathan C. Poe, Jiyuan Fang, Dadong Zhang, Marissa R. Lee, Rachel A. DiCioccio, Hsuan Su, Xiaodi Qin, Jennifer Y. Zhang, Jonathan Visentin, Sonali J. Bracken, Vincent T. Ho, Kathy S. Wang, Jeremy J. Rose, Steven Z. Pavletic, Frances T. Hakim, Wei Jia, Amy N. Suthers, Itaevia M. Curry-Chisolm, Mitchell E. Horwitz, David A. Rizzieri, William C. McManigle, Nelson J. Chao, Adela R. Cardones, Jichun Xie, Kouros Owzar, Stefanie Sarantopoulos
Jonathan C. Poe, Jiyuan Fang, Dadong Zhang, Marissa R. Lee, Rachel A. DiCioccio, Hsuan Su, Xiaodi Qin, Jennifer Y. Zhang, Jonathan Visentin, Sonali J. Bracken, Vincent T. Ho, Kathy S. Wang, Jeremy J. Rose, Steven Z. Pavletic, Frances T. Hakim, Wei Jia, Amy N. Suthers, Itaevia M. Curry-Chisolm, Mitchell E. Horwitz, David A. Rizzieri, William C. McManigle, Nelson J. Chao, Adela R. Cardones, Jichun Xie, Kouros Owzar, Stefanie Sarantopoulos
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Resource and Technical Advance Immunology

Single-cell landscape analysis unravels molecular programming of the human B cell compartment in chronic GVHD

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Abstract

Alloreactivity can drive autoimmune syndromes. After allogeneic hematopoietic stem cell transplantation (allo-HCT), chronic graft-versus-host disease (cGVHD), a B cell–associated autoimmune-like syndrome, commonly occurs. Because donor-derived B cells continually develop under selective pressure from host alloantigens, aberrant B cell receptor (BCR) activation and IgG production can emerge and contribute to cGVHD pathobiology. To better understand molecular programing of B cells in allo-HCT, we performed scRNA-Seq analysis on high numbers of purified B cells from patients. An unsupervised analysis revealed 10 clusters, distinguishable by signature genes for maturation, activation, and memory. Within the memory B cell compartment, we found striking transcriptional differences in allo-HCT patients compared with healthy or infected individuals, including potentially pathogenic atypical B cells (ABCs) that were expanded in active cGVHD. To identify intrinsic alterations in potentially pathological B cells, we interrogated all clusters for differentially expressed genes (DEGs) in active cGVHD versus patients who never had signs of immune tolerance loss (no cGVHD). Active cGVHD DEGs occurred in both naive and BCR-activated B cell clusters. Remarkably, some DEGs occurred across most clusters, suggesting common molecular programs that may promote B cell plasticity. Our study of human allo-HCT and cGVHD provides understanding of altered B cell memory during chronic alloantigen stimulation.

Authors

Jonathan C. Poe, Jiyuan Fang, Dadong Zhang, Marissa R. Lee, Rachel A. DiCioccio, Hsuan Su, Xiaodi Qin, Jennifer Y. Zhang, Jonathan Visentin, Sonali J. Bracken, Vincent T. Ho, Kathy S. Wang, Jeremy J. Rose, Steven Z. Pavletic, Frances T. Hakim, Wei Jia, Amy N. Suthers, Itaevia M. Curry-Chisolm, Mitchell E. Horwitz, David A. Rizzieri, William C. McManigle, Nelson J. Chao, Adela R. Cardones, Jichun Xie, Kouros Owzar, Stefanie Sarantopoulos

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Figure 9

Assessment of DEGs occurring across many clusters provides additional insight into altered B cell functions in active cGVHD.

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Assessment of DEGs occurring across many clusters provides additional in...
(A) scRNA-Seq DEGs (Padj < 0.05) occurring in 4 or more B cell clusters, either up or down in active cGVHD. Colored squares indicate significance. Crosses indicate DEGs also depicted in Figure 7, C and D. (B) scRNA-Seq DEGs (Padj < 0.05) in total untreated B cells, up or down in active cGVHD. Asterisks indicate genes also represented in A. (C) qPCR analysis of CKS2 on B cells from patients with active cGVHD (n = 10) or no cGVHD (n = 7). Results indicate fold-change CKS2 expression with the mean value in no cGVHD normalized to 1. ACTB was the housekeeping gene. Statistical comparison: 2-tailed Mann-Whitney test (GraphPad Prism 9; **, P < 0.01; error bars, mean ± SD). (D) CKS2 UMAP transcript density plots between active cGVHD and no cGVHD. Representative regions (boxes) are enlarged to visualize single B cells. (E) Normalized CKS2 expression values across the 10 B cell clusters for all allo-HCT patients, by disease group. (F) Representative phosphoprotein arrays on whole-cell lysates of untreated B cells from active cGVHD (n = 3) and no cGVHD (n = 3) patients. Boxes and protein IDs indicate the location (duplicate spots) of P27KIP1 (phospho-T198), AMPKα2 (phospho-T172), and RSK1/2/3 (phospho-S380/S386/S377, respectively). Reference control spots are indicated as “ref.” (G) Combined results from 3 independent phosphoprotein arrays shown in F and Supplemental Figure 7. Each bar indicates results from 1 experiment, representing average dual spot intensity for active cGVHD over no cGVHD B cells (dashed line = ratio of 1 as a guide). (H) Western blot of total P27KIP1 relative to β-ACTIN in blood B cell lysates from patients with active cGVHD (n = 4) and no cGVHD (n = 4). Statistical comparison: 2-tailed, unpaired t test (GraphPad Prism 9 software; **, P < 0.01; error bars represent mean ± SD). (I) Model depicting heightened P27KIP1 accumulation in active cGVHD B cells.

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