Seth Winfree
A5013589380- Single-cell and spatial transcriptomics
- Chronic Kidney Disease and Diabetes
- Cell Image Analysis Techniques
- Kidney Stones and Urolithiasis Treatments
- Pediatric Urology and Nephrology Studies
- AI in cancer detection
- Renal and related cancers
- Acute Kidney Injury Research
- Advanced Fluorescence Microscopy Techniques
- Dialysis and Renal Disease Management
- Radiomics and Machine Learning in Medical Imaging
- Medical Imaging Techniques and Applications
- Health, Environment, Cognitive Aging
- Renal and Vascular Pathologies
- Angiogenesis and VEGF in Cancer
- Vector-borne infectious diseases
- Renal cell carcinoma treatment
- Machine Learning in Healthcare
- Immune Response and Inflammation
- Cancer Genomics and Diagnostics
- Advanced Biosensing Techniques and Applications
- Neuroinflammation and Neurodegeneration Mechanisms
- Medical Image Segmentation Techniques
- Vibrio bacteria research studies
- 3D Printing in Biomedical Research
National Institutes of Health
2008-2025
National Institute of Allergy and Infectious Diseases
2011-2025
University of Nebraska Medical Center
2021-2024
Indiana University School of Medicine
2017-2024
Indiana University – Purdue University Indianapolis
2017-2024
Indiana University
2018-2023
Indiana University Bloomington
2022
University School
2020-2022
University of Nebraska System
2022
University of Nebraska at Omaha
2022
Salmonella enterica is an intracellular bacterial pathogen that resides and proliferates within a membrane-bound vacuole in epithelial cells of the gut gallbladder. Although essential to disease, how escapes from its niche spreads secondary same host, or new not known. Here, we demonstrate subpopulation hyperreplicating cytosol serves as reservoir for dissemination. These bacteria are transcriptionally distinct intravacuolar . They induced invasion-associated type III secretion system...
Abstract Understanding kidney disease relies on defining the complexity of cell types and states, their associated molecular profiles interactions within tissue neighbourhoods 1 . Here we applied multiple single-cell single-nucleus assays (>400,000 nuclei or cells) spatial imaging technologies to a broad spectrum healthy reference kidneys (45 donors) diseased (48 patients). This has provided high-resolution cellular atlas 51 main types, which include rare previously undescribed...
Single-cell sequencing studies have characterized the transcriptomic signature of cell types within kidney. However, spatial distribution acute kidney injury (AKI) is regional and affects cells heterogeneously. We first optimized coordination transcriptomics single-nuclear data sets, mapping 30 dominant to a human nephrectomy. The predicted cell-type spots corresponded with underlying histopathology. To study implications AKI on transcript expression, we then 2 murine models:...
Kidney Precision Medicine Project (KPMP) is building a spatially specified human kidney tissue atlas in health and disease with single-cell resolution. Here, we describe the construction of an integrated reference map cells, pathways, genes using unaffected regions nephrectomy tissues undiseased biopsies from 56 adult subjects. We use single-cell/nucleus transcriptomics, subsegmental laser microdissection transcriptomics proteomics, near-single-cell 3D CODEX imaging, spatial metabolomics to...
Sepsis is a dynamic state that progresses at variable rates and has life-threatening consequences. Staging patients along the sepsis timeline requires thorough knowledge of evolution cellular molecular events tissue level. Here, we investigated kidney, an organ central to pathophysiology sepsis. Single-cell RNA-sequencing in murine endotoxemia model revealed involvement various cell populations be temporally organized highly orchestrated. Endothelial stromal cells were first responders. At...
There is a need to define regions of gene activation or repression that control human kidney cells in states health, injury, and repair understand the molecular pathogenesis disease design therapeutic strategies. Comprehensive integration expression with epigenetic features regulatory elements remains significant challenge. We measure dual single nucleus RNA chromatin accessibility, DNA methylation, H3K27ac, H3K4me1, H3K4me3, H3K27me3 histone modifications decipher landscape regulation...
ABSTRACT Coxiella burnetii infects mononuclear phagocytes, where it directs biogenesis of a vacuolar niche termed the parasitophorous vacuole (PV). Owing to its lumenal pH (∼5) and fusion with endolysosomal vesicles, PV is considered phagolysosome-like. However, degradative properties mature are unknown, there conflicting reports on maturation state growth permissiveness harboring virulent phase I or avirulent II C. variants in human phagocytes. Here, we employed infection primary...
Salmonella enterica serovar Typhimurium invades and proliferates within epithelial cells. Intracellular bacteria replicate a membrane bound vacuole known as the containing vacuole. However, this bacterium can also efficiently in cytosol of cells net intracellular growth is product both vacuolar cytosolic replication. Here we have used semi-quantitative single-cell analyses to investigate contribution each these replicative niches proliferation cultured We show that replication account for...
Abstract Understanding kidney disease relies upon defining the complexity of cell types and states, their associated molecular profiles, interactions within tissue neighborhoods. We have applied multiple single-cell or -nucleus assays (>400,000 nuclei/cells) spatial imaging technologies to a broad spectrum healthy reference (n = 42) kidneys. This has provided high resolution cellular atlas 100 that include rare novel populations. The multi-omic approach provides detailed transcriptomic...
Comprehensive and spatially mapped molecular atlases of organs at a cellular level are critical resource to gain insights into pathogenic mechanisms personalized therapies for diseases. The Kidney Precision Medicine Project (KPMP) is an endeavor generate three-dimensional (3-D) healthy diseased kidney biopsies by using multiple state-of-the-art omics imaging technologies across several institutions. Obtaining rigorous reproducible results from disparate methods different sites interrogate...
Kidney stone disease causes significant morbidity and increases health care utilization. In this work, we decipher the cellular molecular niche of human renal papilla in patients with calcium oxalate (CaOx) healthy subjects. addition to identifying cell types important papillary physiology, characterize collecting duct subtypes an undifferentiated epithelial type that was more prevalent patients. Despite focal nature mineral deposition nephrolithiasis, uncover a global injury signature...
Salmonella Typhimurium is a facultative intracellular pathogen that causes acute gastroenteritis in man. Intracellular survive and replicate within modified phagosome known as the Salmonella-containing vacuole (SCV). The onset of replication accompanied by appearance membrane tubules, called Salmonella-induced filaments (Sifs), extending from SCV. Sifs are enriched late endosomal/lysosomal proteins such lysosome-associated protein 1, but their formation ability to interact with endosomal...
The Gram-negative bacterium Salmonella enterica has developed an array of sophisticated tools to manipulate the host cell and establish intracellular niche, for successful propagation as a facultative pathogen. While exerts diverse effects on its cell, only biology classic "trigger"-mediated invasion process subsequent development Salmonella-containing vacuole have been investigated extensively. These processes are dependent cohorts effector proteins translocated into cells by two type III...
In the live animal, tissue autofluorescence arises from a number of biologically important metabolites, such as reduced form nicotinamide adenine dinucleotide. Because changes with metabolic state, it can be harnessed label-free imaging tool which to study metabolism in vivo Here, we used combination intravital two-photon microscopy and frequency-domain fluorescence lifetime (FLIM) map cell-specific signatures kidneys animals. The FLIM images are analyzed using phasor approach, requires no...
Tamm-Horsfall protein (THP), also known as uromodulin, is a kidney-specific produced by cells of the thick ascending limb loop Henle. Although predominantly secreted apically into urine, where it becomes highly polymerized, THP released basolaterally, toward interstitium and circulation, to inhibit tubular inflammatory signaling. Whether, through this latter route, can regulate function renal interstitial mononuclear phagocytes (MPCs) remains unclear, however. Here, we show that primarily in...
Analysis of the immune system in kidney relies predominantly on flow cytometry. Although powerful, process tissue homogenization necessary for cytometry analysis introduces bias and results loss morphologic landmarks needed to determine spatial distribution cells. An ideal approach would support three-dimensional (3D) cytometry: an automated quantitation cells associated parameters 3D image volumes collected from intact tissue. However, widespread application this is limited by lack...
Uromodulin inhibits systemic oxidative stress via TRPM2.
Abstract Background Image-based machine learning tools hold great promise for clinical applications in pathology research. However, the ideal end-users of these computational (e.g., pathologists and biological scientists) often lack programming experience required setup use which rely on command line interfaces. Methods We have developed Histo-Cloud , a tool segmentation whole slide images (WSIs) that has an easy-to-use graphical user interface. This runs state-of-the-art convolutional...
The Salmonella type III effector, SopB, is an inositol polyphosphate phosphatase that modulates host cell phospholipids at the plasma membrane and nascent Salmonella-containing vacuole (SCV). Translocated SopB persists for many hours after infection ubiquitinated but significance of this covalent modification has not been investigated. Here we identify by mass spectrometry six lysine residues are mono-ubiquitinated. Substitution these with arginine, SopB-K(6)R, almost completely eliminated...
Yersinia pestis, the bacterial agent of plague, is transmitted by fleas. The bite an infected flea deposits Y. pestis into dermis and triggers recruitment innate immune cells, including phagocytic PMNs. can subvert this PMN response survive at flea-bite site, disseminate, persist in host. Although its genome encodes a number antiphagocytic virulence factors, phagocytosis PMNs has been observed. This study tests hypotheses that grown ambient temperature vector (21°C), where major factors are...
ABSTRACT Coxiella burnetii is an intracellular bacterial pathogen and a significant cause of culture-negative endocarditis in the United States. Upon infection, nascent phagosome fuses with host endocytic pathway to form large lysosome-like vacuole called parasitophorous (PV). The PV membrane rich sterols, drugs perturbing cell cholesterol homeostasis inhibit formation growth. Using supplementation cholesterol-free model system, we found smaller PVs reduced growth as cellular concentration...
The kidney interstitial gene signature is interrogated by laser microdissection, snRNA sequencing, and in situ hybridization.
The primary step in tissue cytometry is the automated distinction of individual cells (segmentation). Since cell borders are seldom labeled, generally segmented by their nuclei. While tools have been developed for segmenting nuclei two dimensions, segmentation three-dimensional volumes remains a challenging task. lack effective methods represents bottleneck realization potential cytometry, particularly as clearing present opportunity to characterize entire organs. Methods based on deep...