Biology subjects

Hildeman, D. A.

Publications and source records attributed to Hildeman, D. A..

6 recordsLinked to original sources

bioRxiv2025

Co-Stimulatory Blockade Prevents Intragraft Accrual of Class-Switched, Activated B Cells Despite Failing to Prevent T-Cell Mediated Rejection

Previously, we defined the transcriptomes and clonality of intragraft CD8+ T cell during renal allograft rejection. Here, using single cell RNA sequencing (scRNAseq), we investigated non-CD8+ immune cells during T-cell-mediated rejection (TCMR) under different maintenance immunosuppression (mIS) regimens: tacrolimus, and co-stimulatory blockade (CoB) with belatacept (CTLA4-Ig) or iscalimab (anti-CD40). Myeloid cells comprised of DCs, monocytes and macrophages whose proportion and gene expression were similar between mIS regimens. Given their transcriptiomic similarities, we analyzed publicly-available scRNAseq/CITEseq datasets as well as immunofluorescence staining to resolve independent subpopulations of {gamma}/{delta} T cells and NK cells. Intragraft B cells consisted of clusters of naive, plasmablast, and class-switched B (BCS) cells, with the latter being diminished in CoB mIS. Intragraft CD4+ T cells consisted of FoxP3+ regulatory (Treg), exhausted, Th17, and CXCL13+ peripheral helper (Tph) cells whose proportions differed based in mIS, and the latter two had increased clonal expansion. Notably, cell-cell communication analysis indicated Th17 and Tph cell interactions with BCS cells in tacrolimus, but not CoB, samples. Thus, although failing to prevent TCMR, CoB mIS modulates the accrual of CD4+ T cells and inhibits the intragraft accrual of BCS cells, possibly reflective of clinical observations of less chronic antibody-mediated rejection under CoB mIS.

immunology↗

bioRxiv2025

A population-scale atlas of blood and tissue in lupus nephritis

One Sentence SummaryA single-cell atlas of paired blood and tissue samples from Lupus Nephritis patients and healthy controls identified stromal and immune populations within renal tissue, including the scar-associated macrophage populations, which correlate with and may drive renal disease activity. Lupus nephritis (LN), a severe manifestation of Systemic Lupus Erythematosus (SLE), is a heterogeneous disease driven by diverse immune and tissue cell types. We obtained 538K single-cell and 140K single-nuclear profiles from kidney biopsies of 155 LN patients and 30 pre-implantation transplant biopsy controls, along with 325K single-cell blood profiles overlapping many of these patients. We identified key tissue cell types and cell states, and immune cell states; we were able to determine cell states that were tissue specific, and those that were present in the blood. We observed that LN pathological features are significantly associated with cell states using differential gene expression and Covarying Neighborhood Analysis (CNA). These analyses revealed broad changes in cell states associated with irreversible chronic tissue damage. After controlling for the effects of ongoing tissue damage, we observed that expansion of key glomerular and Scar Associated Macrophages (SAMs) populations tracked with increasing inflammatory disease activity. SAMs appear to drive LN fibrosis and, in active disease, infiltrate the glomeruli more than other myeloid cells. These observations strongly support that therapeutic targeting of myeloid populations may offer an as-of-yet unproven strategy to prevent renal inflammation and ongoing kidney damage in LN.

molecular biology↗

bioRxiv2024

Defining the T cell transcriptional landscape in pediatric liver transplant rejection at single cell resolution

Acute cellular rejection (ACR) affects >80% of pediatric liver transplant recipients within 5 years, and late ACR is associated with graft failure. Traditional anti-rejection therapy for late ACR is ineffective and has remained unchanged for six decades. Although CD8+ T cells promote late ACR, little has been done to define their specificity and gene expression. Here, we used single-cell sequencing and immune repertoire profiling (10X Genomics) on 30 cryopreserved 16G liver biopsies from 14 patients (5 pre-transplant or with no ACR, 9 with ACR). We identified expanded intragraft CD8+ T cell clonotypes (CD8EXP) and their gene expression profiles in response to anti-rejection treatment. Notably, we found that expanded CD8+ clonotypes (CD8EXP) bore markers of effector and CD56hiCD161- NK-like T cells, retaining their clonotype identity and phenotype in subsequent biopsies from the same patients despite histologic ACR resolution. CD8EXP clonotypes localized to portal infiltrates during active ACR, and persisted in the lobule after histologic ACR resolution. CellPhoneDB analysis revealed differential crosstalk between KC and CD8EXP during late ACR, with activation of the LTB-LTBR pathway and downregulation of TGF{beta} signaling. Therefore, persistently-detected intragraft CD8EXP clones remain active despite ACR treatment and may contribute to long-term allograft fibrosis and failure of operational tolerance. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/582173v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@50a954org.highwire.dtl.DTLVardef@19ccc02org.highwire.dtl.DTLVardef@115be16org.highwire.dtl.DTLVardef@72a858_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2023

An atlas of gene regulatory networks for T memory cells in youth and old age

Aging profoundly affects immune-system function, promoting susceptibility to pathogens, cancers and chronic inflammation. We previously identified a population of IL-10-producing, T follicular helper-like cells ("Tfh10"), linked to suppressed vaccine responses in aged mice. Here, we integrate single-cell (sc)RNA-seq, scATAC-seq and genome-scale modeling to characterize Tfh10 - and the full CD4+ memory T cell (CD4+TM) compartment - in young and old mice. We identified 13 CD4+TM populations, which we validated through cross-comparison to prior scRNA-seq studies. We built gene regulatory networks (GRNs) that predict transcription-factor control of gene expression in each T-cell population and how these circuits change with age. Through integration with pan-cell aging atlases, we identified intercellular-signaling networks driving age-dependent changes in CD4+TM. Our atlas of finely resolved CD4+TM subsets, GRNs and cell-cell communication networks is a comprehensive resource of predicted regulatory mechanisms operative in memory T cells, presenting new opportunities to improve immune responses in the elderly.

immunology↗

bioRxiv2023

Single cell transcriptomic analysis of renal allograft rejection reveals novel insights into intragraft TCR clonality

Bulk analysis of renal allograft biopsies (rBx) identified RNA transcripts associated with acute cellular rejection (ACR); however, these lacked cellular context critical to mechanistic understanding. We performed combined single cell RNA transcriptomic and TCR/{beta} sequencing on rBx from patients with ACR under differing immunosuppression (IS): tacrolimus, iscalimab, and belatacept. TCR analysis revealed a highly restricted CD8+ T cell clonal expansion (CD8EXP), independent of HLA mismatch or IS type. Subcloning of TCR/{beta} cDNAs from CD8EXP into Jurkat76 cells (TCR-/-) conferred alloreactivity by mixed lymphocyte reaction. scRNAseq analysis of CD8EXP revealed effector, memory, and exhausted phenotypes that were influenced by IS type. Successful anti-rejection treatment decreased, but did not eliminate, CD8EXP, while CD8EXP were maintained during treatment-refractory rejection. Finally, most rBx-derived CD8EXP were also observed in matching urine samples. Overall, our data define the clonal CD8+ T cell response to ACR, providing novel insights to improve detection, assessment, and treatment of rejection.

immunology↗

bioRxiv2018

The immune cell landscape in kidneys of lupus nephritis patients

Lupus nephritis is a potentially fatal autoimmune disease, whose current treatment is ineffective and often toxic. To gain insights into disease mechanisms, we analyzed kidney samples from lupus nephritis patients and healthy controls using single-cell RNA-seq. Our analysis revealed 21 subsets of leukocytes active in disease, including multiple populations of myeloid, T, NK and B cells, demonstrating both pro-inflammatory and resolving responses. We found evidence of local activation of B cells correlated with an age-associated B cell signature, and of progressive stages of monocyte differentiation within the kidney. A clear interferon response was observed in most cells. Two chemokine receptors, CXCR4 and CX3CR1, were broadly expressed, pointing to potential therapeutic targets. Gene expression of immune cells in urine and kidney was highly correlated, suggesting urine may be a surrogate for kidney biopsies. Our results provide a first comprehensive view of the complex network of leukocytes active in lupus nephritis kidneys.

immunology↗