Biology subjects

Wasserfall, C. H.

Publications and source records attributed to Wasserfall, C. H..

11 recordsLinked to original sources

bioRxiv2026

Nanotherapy-mediated biased antigen-presenting cell reprogramming supports T cell anergy to prevent type 1 diabetes

Engineering immune tolerance using endogenously expressed autoantigens could enable early intervention in autoimmune disease. Present therapies suppress T cells to slow disease progression. Here, we develop rapamycin-loaded poly(ethylene glycol)-b-poly(propylene sulfide) polymersomes (rPS) to modulate antigen-presenting cells (APCs) during disease-associated antigen presentation. The rPS morphology enables lymphatic drainage following subcutaneous administration to access APCs in draining lymph nodes. Treatment reduced APC costimulatory marker coexpression and shifted CD4+ T cells toward an FR4hi CD73hi anergic phenotype. In a type 1 diabetes (T1D) nonobese diabetic (NOD) mouse model, rPS significantly delayed disease onset relative to the standard of care and selectively prevented hyperglycemia. Mediation via APCs, rPS avoids adverse effects including transient lymphopenia. These findings demonstrate how biomaterial-directed drug delivery can reshape APC--T cell interactions, supporting an antigen-agnostic strategy for delaying autoimmune diabetes without systemic lymphocyte depletion.

bioengineering↗

bioRxiv2025

Aberrant immune regulation and enrichment of stem-like CD8+ T cells in the pancreatic lymph node during type 1 diabetes development

Effector CD8+ T cells are key cellular drivers of type 1 diabetes (T1D) pathogenesis, yet questions remain regarding the molecular defects leading to altered cytotoxicity, their signature in peripheral tissues, and their receptor specificity. Thus, we analyzed human pancreatic lymph nodes (pLN) using mass cytometry and single cell RNA sequencing (scRNAseq) with combined proteomic and T cell receptor (TCR) profiling. Cytometric analysis revealed an enriched population of T stem-cell memory (TSCM)-like cells (CD8+CD45RA+CD27+CD28+CCR7+CXCR3+ T cells) in T1D pLNs. scRNAseq profiling indicated an elevated inflammatory cytokine gene signature (IFITM3, LTB) along with regulators of terminal differentiation (BCL6, BCL3), coupled with reduced expression of exhaustion-associated genes (DUSP2, NR4A2, TSC22D3) in CD8+ T cells in T1D pLN. Additionally, effector CD8+ T cells expressed features of progenitor exhausted cells (BCL2) in T1D pLN. Immune Response Enrichment Analysis (IREA) indicated IL-15 signaling as a significant driver of these phenotypes. Integrated TCR and transcriptomic analysis revealed a cluster of diverse naive-like CD8+ T cell clones in T1D pLN. When comparing pLN and pancreatic slice cellular isolates, we observed sharing of effector CD8+ T cells, with upregulation of terminal effector signatures detected within the pancreas relative to paired pLN samples. Multiplex imaging revealed differential localization of TCF1 and TOX expressing T cells in the pancreas, with TCF1+TOX+ cells located in closer proximity to the islets and displaying a mixture of activation and exhaustion-associated phenotypes. Thus, we provide multimodal cellular profiles enriched in T1D tissues for consideration in therapeutic targeting.

immunology↗

bioRxiv2025

3D imaging of human pancreas suggests islet size and endocrine composition influence their loss in type 1 diabetes

A high-definition description of pancreatic islets would prove beneficial for understanding the pathophysiology of type 1 diabetes (T1D), yet significant knowledge voids exist in terms of their size, endocrine cell composition, and number in both health and disease. Here, 3-dimensional (3D) analyses of pancreata from control persons without diabetes (ND) revealed heretofore underappreciated frequencies (approximately 50%) of insulin-positive (INS+) glucagon-negative (GCG-) islets. Non-diabetic individuals positive for a single Glutamic acid decarboxylase autoantibody (GADA+) yet at increased risk for disease consistently demonstrated endocrine features, including islet volume and cell composition, closely resembling the age-matched ND controls. In contrast, pancreata from individuals with short-duration T1D demonstrated significantly reduced islet density and a dramatic loss of INS+GCG- islets with preservation of large INS+GCG+ islets. The size and cellular composition of pancreatic islets may, therefore, represent influential factors that impact {beta}-cell loss during T1D disease progression. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/654045v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@1d2fdeaorg.highwire.dtl.DTLVardef@11c43edorg.highwire.dtl.DTLVardef@af8a82org.highwire.dtl.DTLVardef@ae8c58_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LI3D imaging of non-diabetic (ND) pancreas suggests up to 50% of INS+ islets lack GCG C_LIO_LIINS+GCG- islets are typically small-sized in ND and preferentially lost in T1D C_LIO_LIIn T1D pancreas, INS+ beta cells are preserved in large INS+GCG+ islets C_LIO_LIIslets from GADA+ individuals appear similar to ND for size and {beta}-to- cell ratios C_LI

pathology↗

bioRxiv2025

Rare Subset of T Cells Form Heterotypic Clusters with Circulating Tumor Cells to Foster Cancer Metastasis

The immune ecosystem is central to maintaining effective defensive responses. However, how immune cells in the periphery blood interact with circulating tumor cells (CTCs) - seeds of metastasis - remains largely understudied. Here, our analysis of the blood specimens (N=1,529) from patients with advanced breast cancer revealed that over 75% of the CTC-positive blood specimens contained heterotypic CTC clusters with CD45+ white blood cells (WBCs). Detection of CTC-WBC clusters correlates with breast cancer subtypes (triple negative and luminal B), racial groups (Black), and decreased survival rates. Flow cytometry and ImageStream analyses revealed diverse WBC composition of heterotypic CTC-WBC clusters, including overrepresented T cells and underrepresented neutrophils. Most strikingly, a rare subset of CD4 and CD8 double positive T (DPT) cells showed an up to 140-fold enrichment in the CTC clusters versus its frequency in WBCs. DPT cells shared part of the profiles with CD4+ T cells and others with CD8+ T cells but exhibited unique features of T cell exhaustion and immune suppression with higher expression of TIM-3 and PD-1. Single-cell RNA sequencing and genetic perturbation studies further pinpointed the integrin VLA4 (4{beta}1) in DPT cells and its ligand VCAM1 in tumor cells as essential mediators of heterotypic WBC-CTC clusters. Neoadjuvant administration of anti-4 (VLA4) neutralizing antibodies markedly blocked CTC-DPT cell clustering and inhibited metastasis for extended survival in preclinical mouse models in vivo. These findings uncover a pivotal role of rare DPT cells with immune suppressive features in fostering cancer dissemination through direct interactive clustering with CTCs. It lays a foundation for developing innovative biomarkers and therapeutic strategies to prevent and target cancer metastasis, ultimately benefiting cancer care. Brief summaryOur findings uncover a fostering role of immune-suppressive T cells in contact with circulating tumor cells and identify therapeutic approaches to eliminate devastating cancer metastasis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=191 SRC="FIGDIR/small/646421v1_ufig1.gif" ALT="Figure 1"> View larger version (67K): org.highwire.dtl.DTLVardef@13b7862org.highwire.dtl.DTLVardef@15c97b2org.highwire.dtl.DTLVardef@1eb4fd2org.highwire.dtl.DTLVardef@1c588e1_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Imaging mass cytometry reveals early β-cell dysfunction and changes in immune signatures during type 1 diabetes progression in human pancreata

The natural history and pathogenesis of type 1 diabetes, particularly during the autoantibody- positive stages preceding clinical onset, are not well understood, in part, due to limited availability of human pancreatic samples. Here, we studied 88 organ donors, including 28 single autoantibody-positive and 10 multiple autoantibody-positive donors, by imaging mass cytometry. Approximately 10,000 islets and 16 million single-cells were spatially analyzed using 79 antibodies revealing both {beta}-cell states and the islet-immune interface. We identified IAPP loss from {beta}-cells as an indicator of pre-clinical disease. Alterations in Interferon signatures and downregulation across lineage and functional markers, including markers of endoplasmic reticulum stress, were characteristic of recent-onset disease. Further, in single autoantibody- positive donors, we identified pro-inflammatory myeloid cells and PD1+ memory CD4+ T cells, and in multiple autoantibody-positive samples, found islet-specific and exhausted-like ebector CD8+ T cells. Multiple immune cell subtypes were associated with young age, disease severity and insulitis. This dataset is a major step toward creation of a multi-modal type 1 diabetes disease atlas that will be useful for identifying potential drug targets and association of disease features with clinical co-variates and trial outcomes.

immunology↗

bioRxiv2024

Impaired islet function with normal exocrine enzyme secretion is consistent across the head, body, and tail pancreas regions in type 1 diabetes

Histopathological heterogeneity in human pancreas has been well documented; however, functional evidence at the tissue level is scarce. Herein we investigated in situ glucose-stimulated islet and carbachol-stimulated acinar cell secretion across the pancreas head (PH), body (PB), and tail (PT) regions in no diabetes (ND, n=15), single islet autoantibody-positive (1AAb+, n=7), and type 1 diabetes donors (T1D, <14 months duration, n=5). Insulin, glucagon, pancreatic amylase, lipase, and trypsinogen secretion along with 3D tissue morphometrical features were comparable across the regions in ND. In T1D, insulin secretion and beta-cell volume were significantly reduced within all regions, while glucagon and enzymes were unaltered. Beta-cell volume was lower despite normal insulin secretion in 1AAb+, resulting in increased volume-adjusted insulin secretion versus ND. Islet and acinar cell secretion in 1AAb+ were consistent across PH, PB and PT. This study supports low inter-regional variation in pancreas slice function and potentially, increased metabolic demand in 1AAb+.

pathology↗

bioRxiv2023

Characterizing cell-type spatial relationships across length scales in spatially resolved omics data

Spatially resolved omics (SRO) technologies enable the identification of cell types while preserving their organization within tissues. Application of such technologies offers the opportunity to delineate cell-type spatial relationships, particularly across different length scales, and enhance our understanding of tissue organization and function. To quantify such multi-scale cell-type spatial relationships, we developed CRAWDAD, Cell-type Relationship Analysis Workflow Done Across Distances, as an open-source R package with source code and additional documentation at https://jef.works/CRAWDAD/. To demonstrate the utility of such multi-scale characterization, recapitulate expected cell-type spatial relationships, and evaluate against other cell-type spatial analyses, we applied CRAWDAD to various simulated and real SRO datasets of diverse tissues assayed by diverse SRO technologies. We further demonstrate how such multi-scale characterization enabled by CRAWDAD can be used to compare cell-type spatial relationships across multiple samples. Finally, we applied CRAWDAD to SRO datasets of the human spleen to identify consistent as well as patient and sample-specific cell-type spatial relationships. In general, we anticipate such multi-scale analysis of SRO data enabled by CRAWDAD will provide useful quantitative metrics to facilitate the identification, characterization, and comparison of cell-type spatial relationships across axes of interest.

bioinformatics↗

bioRxiv2023

Serum from pregnant donors induces human beta cell proliferation and insulin secretion

Pancreatic beta cells are among the slowest replicating cells in the human body. Human beta cells usually do not increase in number with exceptions being during the neonatal period, in cases of obesity, and during pregnancy. This project explored maternal serum for stimulatory potential on human beta cell proliferation and insulin output. Gravid, full-term women who were scheduled to undergo cesarean delivery were recruited for this study. A human beta cell line was cultured in media supplemented with serum from pregnant and non-pregnant donors and assessed for differences in proliferation and insulin secretion. A subset of pregnant donor sera induced significant increases in beta cell proliferation and insulin secretion. Pooled serum from pregnant donors also increased proliferation in primary human beta cells but not primary human hepatocytes indicating a cell-type specific effect. This study suggests stimulatory factors in human serum during pregnancy could provide a novel approach for human beta cell expansion.

cell biology↗

bioRxiv2023

Human immune phenotyping reveals accelerated aging in type 1 diabetes

The composition of immune cells in peripheral blood is dramatically remodeled throughout the human lifespan, as environmental exposures shape the proportion and phenotype of cellular subsets. These dynamic shifts complicate efforts to identify disease-associated immune signatures in type 1 diabetes (T1D), which is variable in age of onset and rate of {beta}-cell decline. Herein, we conducted standardized flow cytometric immune profiling on peripheral blood from a cross-sectional cohort of T1D participants (n=240), their first-degree relatives (REL, n=310), those at increased risk with two or more islet autoantibodies (RSK, n=24), and autoantibody negative healthy controls (CTR, n=252). We constructed an immune-age predictive model in healthy subjects and developed an interactive data visualization portal (ImmScape; https://ufdiabetes.shinyapps.io/ImmScape/). When applied to the T1D cohort, this model revealed accelerated immune aging (p<0.001) as well as phenotypic signatures of disease after age correction. Of 192 investigated flow cytometry and complete blood count readouts, 46 were significantly associated with age only, 25 with T1D only, and 23 with both age and T1D. Phenotypes associated with T1D after age-correction were predictive of T1D status (AUROC=82.3%). Phenotypes associated with accelerated aging in T1D included increased CXCR3+ and PD-1+ frequencies in naive and memory T cell subsets, despite reduced PD-1 expression levels (mean fluorescence intensity) on memory T cells. Additionally, quantitative trait locus analysis linked an increase in HLA-DR expression on monocytes with the T1D-associated HLA-DR4/DQ8 genotype, regardless of clinical group. Our findings demonstrate advanced immune aging in T1D and highlight disease-associated phenotypes for biomarker monitoring and therapeutic interventions. One Sentence SummaryPeripheral blood characterization reveals accelerated immune-age and age-adjusted proinflammatory immune phenotypes in type 1 diabetes.

immunology↗

bioRxiv2022

A streamlined tandem tip-based workflow for sensitive nanoscale phosphoproteomics

Effective phosphoproteome of nanoscale sample analysis remains a daunting task, primarily due to significant sample loss associated with non-specific surface adsorption during enrichment of low stoichiometric phosphopeptide. We developed a novel tandem tip phosphoproteomics sample preparation method that is capable of sample cleanup and enrichment without additional sample transfer, and its integration with our recently developed SOP (Surfactant-assisted One-Pot sample preparation) and iBASIL (improved Boosting to Amplify Signal with Isobaric Labeling) approaches provides a streamlined workflow enabling sensitive, high-throughput nanoscale phosphoproteome measurements. This approach significantly reduces both sample loss and processing time, allowing the identification of >3,000 (>9,500) phosphopeptides from 1 (10) {micro}g of cell lysate using the label-free method without a spectral library. It also enabled precise quantification of [~]600 phosphopeptides from 100 cells sorted by FACS (single-cell level input for the enriched phosphopeptides) and [~]700 phosphopeptides from human spleen tissue voxels with a spatial resolution of 200 {micro}m (equivalent to [~]100 cells) in a high-throughput manner. The new workflow opens avenues for phosphoproteome profiling of mass-limited samples at the low nanogram level.

biochemistry↗

bioRxiv2021

Tissue Registration and Exploration User Interfaces in support of a Human Reference Atlas

Several international consortia are collaborating to construct a human reference atlas, which is a comprehensive, high-resolution, three-dimensional atlas of all the cells in the healthy human body. Laboratories around the world are collecting tissue specimens from donors varying in sex, age, ethnicity, and body mass index. However, integrating and harmonizing tissue data across 20+ organs and more than 15 bulk and spatial single-cell assay types poses diverse challenges. Here we present the software tools and user interfaces developed to annotate ("register") and explore the collected tissue data. A key part of these tools is a common coordinate framework, which provides standard terminologies and data structures for describing specimens, biological structures, and spatial positions linked to existing ontologies. As of December 2021, the "registration" user interface has been used to harmonize and make publicly available data on 6,178 tissue sections from 2,698 tissue blocks collected by the Human Biomolecular Atlas Program, the Stimulating Peripheral Activity to Relieve Conditions program, the Human Cell Atlas, the Kidney Precision Medicine Project, and the Genotype Tissue Expression project. The second "exploration" user interface enables consortia to evaluate data quality and coverage, explore tissue data in the context of the human body, and guide data acquisition.

bioinformatics↗