A5088515016- RNA modifications and cancer
- Epigenetics and DNA Methylation
- interferon and immune responses
- Tuberculosis Research and Epidemiology
- Liver Diseases and Immunity
- Trace Elements in Health
- Inflammatory Bowel Disease
- HIV Research and Treatment
- Immune Cell Function and Interaction
- Cancer-related molecular mechanisms research
- Genetic Associations and Epidemiology
- T-cell and B-cell Immunology
- Veterinary Orthopedics and Neurology
- Neonatal Respiratory Health Research
- IL-33, ST2, and ILC Pathways
- Helicobacter pylori-related gastroenterology studies
- Tracheal and airway disorders
- Medical Imaging and Analysis
- Digestive system and related health
- Infectious Diseases and Tuberculosis
- Immune cells in cancer
- Pneumocystis jirovecii pneumonia detection and treatment
- Immunodeficiency and Autoimmune Disorders
- Systemic Lupus Erythematosus Research
- Gut microbiota and health
University of Chicago
2021-2025
Resident-tissue macrophages (RTMs) arise from embryonic precursors1,2, yet the developmental signals that shape their longevity remain largely unknown. Here we demonstrate in mice genetically deficient 12-lipoxygenase and 15-lipoxygenase (Alox15-/- mice) neonatal neutrophil-derived 12-HETE is required for self-renewal maintenance of alveolar (AMs) during lung development. Although seeding differentiation AM progenitors remained intact, absence led to a significant reduction AMs adult lungs...
Abstract Primary sclerosing cholangitis (PSC) is an immune-mediated disease of the bile ducts that co-occurs with inflammatory bowel (IBD) in almost 90% cases. Colorectal cancer a major complication patients PSC and IBD, these are at much greater risk compared to IBD without concomitant PSC. Combining flow cytometry, bulk single-cell transcriptomics, T B cell receptor repertoire analysis right colon tissue from 65 PSC, 108 48 healthy individuals we identified unique adaptive transcriptional...
Influenza A virus (IAV) infections are frequent every year and result in a range of disease severity. Here, we wanted to explore the potential contribution transposable elements (TEs) variable human immune response. Transcriptome profiling monocyte-derived macrophages from 39 individuals following IAV infection revealed significant inter-individual variation viral load post-infection. Using transposase-accessible chromatin using sequencing (ATAC-seq), identified set TE families with either...
Transcriptome-wide association studies (TWASs) help identify disease-causing genes but often fail to pinpoint disease mechanisms at the cellular level because of limited sample sizes and sparsity cell-type-specific expression data. Here, we propose scPrediXcan, which integrates state-of-the-art deep learning approaches that predict epigenetic features from DNA sequences with canonical TWAS framework. Our prediction approach, ctPred, predicts high accuracy captures complex gene-regulatory...
SUMMARY Influenza A virus (IAV) infections are frequent every year and result in a range of disease severity. Given that transposable elements (TEs) contribute to the activation innate immunity, we wanted explore their potential role this variability. Transcriptome profiling monocyte-derived macrophages from 39 individuals following IAV infection revealed significant inter-individual variation viral load post-infection. Using ATAC-seq identified set TE families with either enhanced or...
Summary Humans display remarkable inter-individual variation in immune response when exposed to identical challenges. Yet, our understanding of the genetic and epigenetic factors contributing such remains limited. Here we carried out in-depth genetic, epigenetic, transcriptional profiling on primary macrophages derived from a panel European African-ancestry individuals before after infection with influenza A virus (IAV). We show that baseline profiles are strongly predictive IAV across...
Severe combined immunodeficiency (SCID) comprises rare inherited disorders of immunity that require definitive treatment through hematopoietic cell transplantation (HCT) or gene therapy for survival. Despite successes allogeneic HCT, many SCID patients experience incomplete immune reconstitution, persistent T-cell lymphopenia, and poor long-term outcomes.
Antituberculosis drugs, mostly developed over 60 years ago, combined with a poorly effective vaccine, have failed to eradicate tuberculosis. More worryingly, multiresistant strains of Mycobacterium tuberculosis (MTB) are constantly emerging. Innovative strategies thus urgently needed improve treatment. Recently, host-directed therapy has emerged as promising strategy be used in adjunct existing or future antibiotics, by improving innate immunity limiting immunopathology. Here, using...
Transcriptome-wide association studies (TWAS) help identify disease causing genes, but often fail to pinpoint mechanisms at the cellular level because of limited sample sizes and sparsity cell-type-specific expression data. Here we propose scPrediXcan which integrates state-of-the-art deep learning approaches that predict epigenetic features from DNA sequences with canonical TWAS framework. Our prediction approach, ctPred, predicts high accuracy captures complex gene regulatory grammar...
Summary Different regions of the gastrointestinal tract have distinct digestive and absorptive functions, which may be locally disrupted by infection or autoimmune disease. Yet, mechanisms underlying intestinal regionalization its dysregulation in disease are not well understood. Here, we used mouse models, transcriptomics, immune profiling to show that regional epithelial expression transcription factor GATA4 prevented adherent bacterial colonization inflammation proximal small intestine...
Abstract Anti-tuberculosis drugs, mostly developed over 60 years ago, combined with a poorly effective vaccine, have failed to eradicate tuberculosis. More worryingly, multi-resistant strains of Mycobacterium tuberculosis are constantly emerging. Innovative strategies thus urgently needed improve treatment. Recently, host-directed therapy has emerged as promising strategy be used in adjunct existing or future antibiotics, by improving innate immunity limiting immunopathology. Here, using...
Abstract Primary sclerosing cholangitis (PSC) is an autoimmune-like disease of the bile ducts that co-occurs with inflammatory bowel (IBD) in almost 90% cases. Colorectal cancer a major complication patients both PSC and IBD, these are at much greater risk compared to IBD without concomitant PSC. Combining flow cytometry, bulk single cell transcriptomics, T- B-cell receptor repertoire analysis right colon tissue from PSC, healthy controls we identified unique adaptive transcriptional...
In the pharmaceutical industry, micro-CT images of Dutch-Belted rabbit fetuses have been used for assessment compound-induced skeletal abnormalities in developmental and reproductive toxicology (DART) studies. automated approach proposed to assess morphology each bone, localization segmentation vertebral bone is a critical task. this work, we are extending our previous work cervical vertebrae entire spine following multivariate regression framework based on 3D convolutional neural network...