Biology subjects

Flavell, R.

Publications and source records attributed to Flavell, R..

14 recordsLinked to original sources

bioRxiv2026

Reverse genetics in humanized mice reveals CARD8-mediated pyroptosis causing pancytopenia in human DPP9 deficiency

Loss of function mutation in the human DPP9 gene causes Hatipoglu syndrome leading to severe inflammasomopathy. A key feature of the disease is pancytopenia and patients require bone marrow transplantation, but the mechanism of cell loss is unclear since Dpp9 mutant mice have normal hematopoiesis, suggesting that a distinct mechanism of disease occurs in humans. Here, we present a model of human DPP9 deficiency leveraging reverse genetics in the MISTRG6 humanized mice. We found that CRISPR editing of human CD34+ hematopoietic stem and progenitor cells (HSPCs) led to very efficient and persistent gene deletion in vivo. Human DPP9 deletion recapitulated cytopenia in peripheral blood and in the bone marrow, and cell loss was cell intrinsic. However, DPP9 deletion led to little transcriptional changes suggesting post-transcriptional regulation in human HSPCs. Mechanistically, DPP9 deficiency led to the activation of the CARD8 inflammasome resulting in HSPC pyroptosis, whereas NLRP1 was dispensable for cell death. Thus, our results reveal a unique human mechanism of disease and offer therapeutic insight for this inflammasomopathy.

immunology↗

bioRxiv2025

Endothelial cell MHC molecules are necessary and sufficient to reject 3D-printed human skin grafts in an advanced human immune system mouse

Vascularized skins were 3D-printed using single donor human fibroblasts, pericytes, keratinocytes and endothelial cells (ECs), the latter either unmodified (WT-ECs) or deleted of MHC molecules (KO-ECs). Adult MISTRG6 immunodeficient mice neonatally inoculated with adult human hematopoietic stem cells (HSCs) received printed skin allogeneic to the HSCs and were boosted 3 weeks post-grafting with human peripheral blood mononuclear cells (PBMCs) autologous to the HSCs. HSC inoculation alone produced low levels of circulating human myeloid and lymphoid cells without affecting grafts; PBMC boosting dramatically increased circulating human CD4+ T cells and boosted CD8+ T cells only in mice with WT-EC grafts. These grafts became infiltrated by human macrophages, dendritic cells, CD4+ and CD8+ T cells, and showed evidence of rejection. Shared T cell clones were present in skin and spleen. KO-EC grafts had minimal infiltration of graft or spleen without rejection despite MHC molecule expression on other graft cell types.

immunology↗

bioRxiv2024

Linker histone regulates the myeloid versus lymphoid bifurcation of multipotent hematopoietic stem and progenitors

Myeloid-biased differentiation of multipotent hematopoietic stem and progenitor cells (HSPCs) occurs with aging or exhaustion. The molecular mechanism(s) responsible for this fate bias remain unclear. Here we report that linker histone regulates HSPC fate choice at the lymphoid versus myeloid bifurcation. HSPCs expressing H1.0 from a doxycycline (dox) inducible transgene favor the lymphoid fate, display strengthened nucleosome organization and reduced chromatin accessibility at genomic regions hosting key myeloid fate drivers. The transcription factor Hlf is located in one of such regions, where chromatin accessibility and gene expression is reduced in H1.0high HSPCs. Furthermore, H1.0 protein in HSPCs decreases in an aspartyl protease dependent manner, a process enhanced in response to interferon alpha (IFN) signaling. Aspartyl protease inhibitors preserve endogenous H1.0 levels and promote the lymphoid fate of wild type HSPCs. Thus, our work uncovers a point of intervention to mitigate myeloid skewed hematopoiesis.

developmental biology↗

bioRxiv2024

The Multiple Roles of Gamma Interferon in Intraepithelial T Cell-Villous Enterocyte Interactions in Active Celiac Disease

We compared duodenal biopsies showing active celiac disease (CeD) to normal controls using single cell RNA sequencing, cyclic immunofluorescence, RNAScope and proximity ligation assays. There is increased infiltration of villous but not crypt epithelium T cells bearing either {beta} or {gamma}{delta} T cell receptors (TCRs) in CeD. Both T cell subsets are activated cytotoxic T lymphocytes (CTLs) and surprisingly are the predominant mucosal source of IFN{gamma}. In response to this IFN{gamma},villous but not crypt enterocytes show an IFN{gamma} signature, including nuclear phospho-STAT1 protein, class II HLA molecules and IFN{gamma}-inducible chemokines known to recruit CTLs (e.g., CCL3, CCL4, CXCL10, and CXCL11) and receptors for these chemokines are expressed on the infiltrating CTLs. Villous enterocytes also display increased HLA-E and HLA-B mRNAs and proteins. Bioinformatic analyses (NICHES) and proximity ligation assays show frequent binding of both {beta} and {gamma}{delta} TCRs with enterocyte HLA-E or HLA-B, but not HLA-DR. In contrast, NKG2C, proposed as an alternative trigger of CTL activation, is infrequently-expressed and shows few interactions with HLA-E. Our data suggest that activated intraepithelial CTLs produce IFN{gamma} which recruits additional CTLs and increases antigen-dependent killing of villous epithelium using either conventional or HLA-E antigen presentation. SignifanceAnalyses of diagnostic biopsies from celiac disease patients reveals critical roles for IFN{gamma} actions on enterocytes and a surprising role of HLA-E in antigen presntation. Activated cytotoxic T lymphocytes (CTLs) that are the primary source of mucosal IFN{gamma}, leading to IFN{gamma} signaling in villous enterocytes, including expression of phospho-STAT1 protein, class II HLA molecules, and chemokines that attract CTLs. Bioinformatic ligand receoptor analyses and proximity ligation assays showed frequent interactions between intraepithelial CTLs and enterocyte HLA-E or HLA-B, indicating that IFN{gamma} production by the CTLs likely promotes further CTL recruitment and antigen-dependent killing of the villous epithelium.

immunology↗

bioRxiv2024

TIF1γ regulates stability of T regulatory cells during inflammation

T regulatory cells are a suppressor population critical to control inflammation and maintain tissue homeostasis. The TGF-{beta} pathway is a fundamental signal for T regulatory cell differentiation, yet the molecular determinants of how TGF-{beta} signals regulate all these processes are not completely understood. TIF1{gamma} was demonstrated to promote a noncanonical TGF-{beta}/Smad pathway in HSC, however the role of TIF1{gamma} in Treg function has been largely ignored. Here we showed that TIF1{gamma} deficient Tregs lose stability and acquire an effector phenotype in the presence of an inflammatory stimuli or upon activation. TIF1{gamma} deficient T regs gain a Th1-like Treg phenotype or become pro-inflammatory exTregs, by losing Foxp3 expression and acquiring IFN{gamma} expression in an autoimmune model. Loss of TIF1{gamma} in Tregs was cell-intrinsic and was also accompanied by increased proliferation and enhanced glycolytic capacity upon activation. Additionally, we demonstrated that in the absence of TIF1{gamma}, there was an increased methylation status in the CNS2 enhancer region of the Foxp3 locus, further suggesting increased susceptibility for loss of Foxp3 expression. Mechanistically, TGF-{beta} was in part responsible to inhibit the Th1-like bias a Treg has in the absence of TIF1{gamma}, however, the proliferative phenotype observed in these cells was mostly independent of TGF-{beta} signaling. Finally, we identified the beta-catenin pathway as the molecular mechanism driving both TIF1{gamma}-dependent Treg stability and proliferation upon inflammation. Altogether, our data demonstrated that TIF1{gamma} is required for the maintenance of a suppressor phenotype and stability of Treg lymphocytes during inflammatory conditions in vivo and represents a new modulatory pathway to manipulate Treg cells for therapeutic purposes.

immunology↗

bioRxiv2024

IL-4 Licenses B Cell Activation Through Cholesterol Synthesis

Lymphocyte activation involves a transition from quiescence and associated catabolic metabolism to a metabolic state with noted similarities to cancer cells such as heavy reliance on aerobic glycolysis for energy demands and increased nutrient requirements for biomass accumulation and cell division1-3. Following antigen receptor ligation, lymphocytes require spatiotemporally distinct "second signals". These include costimulatory receptor or cytokine signaling, which engage discrete programs that often involve remodeling of organelles and increased nutrient uptake or synthesis to meet changing biochemical demands4-6. One such signaling molecule, IL-4, is a highly pleiotropic cytokine that was first identified as a B cell co-mitogen over 30 years ago7. However, how IL-4 signaling mechanistically supports B cell proliferation is incompletely understood. Here, using single cell RNA sequencing we find that the cholesterol biosynthetic program is transcriptionally upregulated following IL-4 signaling during the early B cell response to influenza virus infection, and is required for B cell activation in vivo. By limiting lipid availability in vitro, we determine cholesterol to be essential for B cells to expand their endoplasmic reticulum, progress through cell cycle, and proliferate. In sum, we demonstrate that the well-known ability of IL-4 to act as a B cell growth factor is through a previously unknown rewiring of specific lipid anabolic programs, relieving sensitivity of cells to environmental nutrient availability.

immunology↗

bioRxiv2023

Chemoenzymatic syntheses of fluorine-18-labeled disaccharides from FDG yield potent sensors of living bacteria in vivo

Chemoenzymatic techniques have been applied extensively to pharmaceutical development, most effectively when routine synthetic methods fail. The regioselective and stereoselective construction of structurally complex glycans is an elegant application of this approach, that is seldom applied to positron emission tomography (PET) tracers. We sought a method to dimerize 2-deoxy-[18F]-fluoro-D-glucose ([18F]FDG), the most common tracer used in clinical imaging, to form [18F]-labeled disaccharides for detecting microorganisms in vivo based on their bacteria-specific glycan incorporation. When [18F]FDG was reacted with {beta}-D-glucose-1-phosphate in the presence of maltose phosphorylase, both the -1,4 and -1,3-linked products 2-deoxy-[18F]-fluoro-maltose ([18F]FDM) and 2-deoxy-2-[18F]-fluoro-sakebiose ([18F]FSK) were obtained. This method was further extended with the use of trehalose (,-1,1), laminaribiose ({beta}-1,3), and cellobiose ({beta}-1,4) phosphorylases to synthesize 2-deoxy-2-[18F]fluoro-trehalose ([18F]FDT), 2-deoxy-2-[18F]fluoro-laminaribiose ([18F]FDL), and 2-deoxy-2-[18F]fluoro-cellobiose ([18F]FDC). We subsequently tested [18F]FDM and [18F]FSK in vitro, showing accumulation by several clinically relevant pathogens including Staphylococcus aureus and Acinetobacter baumannii, and demonstrated their specific uptake in vivo. The lead sakebiose-derived tracer [18F]FSK was stable in human serum and showed high uptake in preclinical models of myositis and vertebral discitis-osteomyelitis. Both the synthetic ease, and high sensitivity of [18F]FSK to S. aureus including methicillin-resistant (MRSA) strains strongly justify clinical translation of this tracer to infected patients. Furthermore, this work suggests that chemoenzymatic radiosyntheses of complex [18F]FDG-derived oligomers will afford a wide array of PET radiotracers for infectious and oncologic applications.

microbiology↗

bioRxiv2022

Suppression of systemic T cell immunity to viral infection during liver injury is prevented by inhibition of interferon and IL-10 signaling

Patients with liver injury such as cirrhosis are at increased risk of intractable viral infections and are hyporesponsive to vaccination. Here, we report that liver injury leads to inhibition of systemic T cell immunity (LIST), which abrogated anti-viral immunity and caused persistent infection in preclinical liver injury models. Enhanced gut microbial-translocation but not dysbiosis induced tonic type-I-interferon (IFN) signaling in hepatic myeloid cells, which was responsible for their excessive production of IL-10 after viral infection. Antibiotic treatment reducing intestinal microbial burden or inhibition of IFN- and IL-10-signaling all restored anti-viral immunity without immune pathology. Importantly, inhibition of IL-10 restored virus-specific immune responses to vaccination in cirrhotic patients. Thus, LIST results from sequential events involving intestinal microbial translocation, hepatic myeloid cell-derived IFN-/IL-10 expression, and finally inhibitory IL-10 receptor-signaling in T cells, of which IL-10R-signaling may serve as target to reconstitute anti-viral T cell immunity in cirrhotic patients.

immunology↗

bioRxiv2022

Gene Trajectory Inference for Single-cell Data by Optimal Transport Metrics

Single-cell RNA-sequencing has been widely used to investigate cell state transitions and gene dynamics of biological processes. Current strategies to infer the sequential dynamics of genes in a process typically rely on constructing cell pseudotime through cell trajectory inference. However, the presence of concurrent gene processes in the same group of cells and technical noise can obscure the true progression of the processes studied. To address this challenge, we present GeneTrajectory, an approach that identifies trajectories of genes rather than trajectories of cells. Specifically, optimal-transport distances are calculated between gene distributions across the cell-cell graph to extract gene programs and define their gene pseudotemporal order. Here, we demonstrate that GeneTrajectory accurately extracts progressive gene dynamics in myeloid lineage maturation. Moreover, we show that GeneTrajectory deconvolves key gene programs underlying mouse skin hair follicle dermal condensate differentiation that could not be resolved by cell trajectory approaches. GeneTrajectory facilitates discovery of gene programs that control the changes and activities of biological processes.

bioinformatics↗

bioRxiv2022

Antigen-dependent inducible T cell reporter system for PET imaging of breast cancer and glioblastoma

For the past several decades, chimeric antigen receptor T cell (CAR T) therapies have shown promise in the treatment of cancers. These treatments would greatly benefit from companion imaging biomarkers to follow the trafficking of T cells in vivo. Using synthetic biology, we engineered T cells with a chimeric receptor SyNthetic Intramembrane Proteolysis Receptor (SNIPR) that induces overexpression of an exogenous reporter gene cassette upon recognition of specific tumor markers. We then applied a SNIPR-based positron emission tomography (PET) reporter system to two cancer-relevant antigens, human epidermal growth factor receptor 2 (HER2) and epidermal growth factor receptor variant III (EGFRvIII), commonly expressed in breast and glial tumors respectively. Antigen-specific reporter induction of the SNIPR-PET T cells was confirmed in vitro using GFP fluorescence, luciferase luminescence, and the HSV-TK PET reporter with [18F]FHBG. T cells associated with their target antigens were successfully imaged using PET in dual xenograft HER2+/HER2- and EGFRvIII+/EGFRvIII-animal models, with > 10-fold higher [18F]FHBG signals seen in antigen-expressing tumors versus the corresponding controls. The main innovation described is therefore PET detection of T cells via specific antigen-induced signals, in contrast to reporter systems relying on constitutive gene expression.

synthetic biology↗

bioRxiv2021

A hierarchical GBP network promotes cytosolic LPS recognition and sepsis

Bacterial lipopolysaccharide (LPS) is one of the most bioactive substances known. Trace amounts trigger robust immunity to infection but also life-threatening sepsis causing millions of deaths each year. LPS contamination of the cytosol elicits a caspase-dependent inflammasome pathway promoting cytokine release and host cell death. Here, we report an immune GTPase network controls multiple steps in this pathway by genome-engineering mice to lack 7 different guanylate-binding proteins (GBPs). Gbp2-/- and Gbp3-/- mice had severe caspase-11-driven defects that protected them from septic shock. Gbp2 recruited caspase-11 for LPS recognition whereas Gbp3 assembled and trafficked the pyroptotic pore-forming protein, gasdermin D, after caspase-11 cleavage. Together, our results identify a new functional hierarchy wherein different GBPs choreograph sequential steps in the non-canonical inflammasome pathway to control Gram-negative sepsis. One-Sentence SummaryImmune GTPase network orchestrates hierarchical immunity to bacterial products in vivo

immunology↗

bioRxiv2020

Cyclic gallium-68 labeled peptides for specific detection of human angiotensin-converting enzyme 2

In this study, we developed ACE2-specific, peptide-derived 68Ga-labeled radiotracers, motivated by the hypotheses that (1) ACE2 is an important determinant of SARS-CoV-2 susceptibility, and (2) that modulation of ACE2 in COVID-19 drives severe organ injury. MethodsA series of NOTA-conjugated peptides derived from the known ACE2 inhibitor DX600 were synthesized, with variable linker identity. Since DX600 bears two cystine residues, both linear and cyclic peptides were studied. An ACE2 inhibition assay was used to identify lead compounds, which were labeled with 68Ga to generate peptide radiotracers ([68Ga]NOTA-PEP). The aminocaproate-derived radiotracer [68Ga]NOTA-PEP4 was subsequently studied in a humanized ACE2 (hACE2) transgenic model. ResultsCyclic DX-600 derived peptides had markedly lower IC50s than their linear counterparts. The three cyclic peptides with triglycine, aminocaproate, and polyethylene glycol linkers had calculated IC50s similar to, or lower than the parent DX600 molecule. Peptides were readily labeled with 68Ga, and the biodistribution of [68Ga]NOTA-PEP4 was determined in a hACE2 transgenic murine cohort. Pharmacologic concentrations of co-administered NOTA-PEP ("blocking") showed significant reduction of [68Ga]NOTA-PEP4 signals in the in the heart, liver, lungs, and small intestine. Ex vivo hACE2 activity in these organs was confirmed as a correlate to in vivo results. ConclusionsNOTA-conjugated, cyclic peptides derived from the known ACE2 inhibitor DX600 retain their activity when N-conjugated for 68Ga chelation. In vivo studies in a transgenic hACE2 murine model using the lead tracer [68Ga]NOTA-PEP4 showed specific binding in the heart, liver, lungs and intestine - organs known to be affected in SARS-CoV-2 infection. These results suggest that [68Ga]NOTA-PEP4 could be used to detect organ-specific suppression of ACE2 in SARS-CoV-2 infected murine models and COVID-19 patients. TOC figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=44 SRC="FIGDIR/small/412809v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@f3047org.highwire.dtl.DTLVardef@12ab9a9org.highwire.dtl.DTLVardef@33f43org.highwire.dtl.DTLVardef@12e77ed_HPS_FORMAT_FIGEXP M_FIG For Table of Contents use only C_FIG

biochemistry↗

bioRxiv2019

Map3k2-Regulated Intestinal Stromal Cells (MRISC) Define a Distinct Sub-cryptic Stem Cell Niche for Damage Induced Wnt Agonist R-spondin1 Production

Intestinal stem cell propagation and differentiation are essential for rapid repair of tissue damage in the gut. While intestinal stromal cells were recently identified as key mediators of this process, the cellular and molecular mechanisms by which this diverse population induces tissue repair remains poorly understood. Here we show that Map3k2 has a colon stromal cell specific function critically required for maintenance of Lgr5+ intestinal stem cells and protection against acute intestinal damage. This Map3k2-specific function is mediated by enhancing Wnt agonist R-spondin1 production. We further reveal a unique novel cell population, named Map3k2-regulated intestinal stromal cells (MRISC), as the primary cellular source of R-spondin1 following intestinal injury. Together, our data identify a novel intestinal stem cell niche organized by MRISC, which specifically dependent on the Map3k2-signaling pathway to augment the production of Wnt agonist R-spondin1 and promote regeneration of the acutely damaged intestine.\n\nHighlightsO_LIMap3k2 protects mice from DSS-induced colitis by promoting intestinal stem cell regeneration.\nC_LIO_LIMap3k2-MAPK pathway cross-talks with Wnt signaling pathway via upregulation of R-spondin1.\nC_LIO_LIMap3k2-Regulated Intestinal Stromal Cells (MRISC) marked by co-expression of CD90, CD34 and CD81 defines a novel colonic stem cell niche.\nC_LI

cell biology↗

bioRxiv2019

Detecting regions of differential abundance betweenscRNA-Seq datasets

Traditional cell clustering analysis used to compare the transcriptomic landscapes between two biological states in single cell RNA sequencing (scRNA-seq) is largely inadequate to functionally identify distinct and important differentially abundant (DA) subpopulations between groups. This problem is exacerbated further when using unsupervised clustering approaches where differences are not observed in clear cluster structure and therefore many important differences between two biological states go entirely unseen. Here, we develop DA-seq, a powerful unbiased, multi-scale algorithm that uniquely detects and decodes novel DA subpopulations not restricted to well separated clusters or known cell types. We apply DA-seq to several publicly available scRNA-seq datasets on various biological systems to detect differences between distinct phenotype in COVID-19 cases, melanomas subjected to immune checkpoint therapy, embryonic development and aging brain, as well as simulated data. Importantly, we find that DA-seq not only recovers the DA cell types as discovered in the original studies, but also reveals new DA subpopulations that were not described before. Analysis of these novel subpopulations yields new biological insights that would otherwise be neglected.

bioinformatics↗