Biology subjects

Hooper, L. V.

Publications and source records attributed to Hooper, L. V..

11 recordsLinked to original sources

bioRxiv2026

Intrinsic timekeeping in Escherichia coli

Circadian clocks allow organisms to anticipate predictable environmental changes across the day-night cycle. Here we show that the bacterium Escherichia coli exhibits intrinsic timekeeping that anticipates daily temperature cycles. E. coli biofilms entrained to daily temperature shifts, producing 24-hour rhythms in curli plaque formation that persisted under constant temperature. Mechanistically, genetic analyses localized the autonomous timing machinery to the Rcs phosphorelay, which exhibits structural and conceptual parallels with other circadian systems. The BluFR sensory pathway, which acts upstream of the Rcs phosphorelay, linked temperature and blue-light cycles to rhythmic curli production. Flagellar promoter activity and curli production peaked at opposite times of day, suggesting daily coordination of adhesion and motility programs. These findings identify an intrinsic timing system in E. coli that expands our understanding of biological timekeeping.

microbiology↗

bioRxiv2026

Epithelial sensing of vitamin A shapes intestinal antimicrobial defense

Vitamin A is a central regulator of intestinal adaptive immunity, but its role in innate immunity is less defined. Antimicrobial proteins form a chemical barrier that protects the intestinal epithelium from microbial invasion. Among these, REG3 family lectins are induced by the microbiota, yet how nutritional cues intersect with microbial signals to control their expression remains unclear. Here, we show that dietary vitamin A promotes expression of REG3 antimicrobial lectins, including REG3G, in intestinal epithelial cells from both mice and humans. This induction is mediated by retinoic acid and requires retinoic acid receptor (RAR) signaling. Mechanistically, RARs bind directly to the Reg3g promoter adjacent to a STAT3 binding site. As STAT3 mediates microbiota-induced IL-22 signaling in epithelial cells, this arrangement provides a molecular framework for integrating nutritional and microbial inputs at the level of REG3G transcription. Extending these findings, we demonstrate that vitamin A-retinoic acid signaling similarly promotes expression of -defensin antimicrobial proteins. Together, these findings define a transcriptional mechanism by which vitamin A enhances epithelial antimicrobial defenses and strengthens mucosal innate immunity. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=187 SRC="FIGDIR/small/710399v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@18dd8aforg.highwire.dtl.DTLVardef@18cf2fdorg.highwire.dtl.DTLVardef@a4dc89org.highwire.dtl.DTLVardef@18aa9c7_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIVitamin A promotes epithelial expression of REG3 antimicrobial proteins in the intestine C_LIO_LIRetinoic acid receptors (RARs) directly activate mouse Reg3g and human REG3G transcription C_LIO_LIRARs bind the Reg3g promoter adjacent to STAT3, integrating nutritional and microbial signals C_LIO_LIVitamin A-RAR signaling broadly regulates epithelial antimicrobial programs, including -defensins C_LI

immunology↗

bioRxiv2026

A single-cell atlas of intestinal immune cells across the day-night cycle reveals dynamic populations

The small intestine houses an array of immune cells that receive diverse inputs from food intake, microbiota, and other cues that vary by time of day. However, how diurnal variation influences intestinal immune cell proportions and functions is unclear. Here, we use flow cytometry and single cell RNA sequencing to establish an atlas of 815,073 mouse small intestine immune cells at four times across the day-night cycle. These data suggest possible temporal coordination of dendritic cell antigen processing and subsequent T cell antigen recognition. Most cells express circadian clock genes and have intrinsic oscillatory transcriptomes. However, differentiated antibody-producing plasma cells have minimal circadian gene expression and instead may receive extrinsic oscillatory cues from other cell types. Finally, certain populations of B cells are extremely dynamic, with broad transcriptional changes within a six hour time span. This dataset provides insight into the circadian dynamics of intestinal immunity. SummaryO_LIAn atlas of 815,073 small intestine immune cells across four time-points reveals a large proportion of naive B and T cells. C_LIO_LIGene expression profiles suggest coordination of antigen processing in dendritic cells prior to antigen recognition by T cells. C_LIO_LITh17 and innate lymphoid cells have high expression of circadian clock genes and most immune cells have rhythmic gene expression. C_LIO_LIPopulations of certain B cell subtypes, including transitional B cells and centrocytes, are extremely dynamic with large shifts over a six hour time frame. C_LIO_LITerminally differentiated antibody-producing plasma cells have minimal circadian gene expression and few oscillatory genes. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=121 SRC="FIGDIR/small/701519v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@162f451org.highwire.dtl.DTLVardef@1960711org.highwire.dtl.DTLVardef@a9fd4aorg.highwire.dtl.DTLVardef@341f42_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Timing of immune checkpoint blockade shapes anti-tumor immunity via a clock-dependent chemokine axis

Circadian clocks regulate immunity, yet how they shape the tumor immune microenvironment and influence cancer immunotherapy remains unclear. Here, we show that tumor immune infiltration and immune checkpoint inhibitor efficacy vary by time of day in mice, driven by intrinsic clocks in dendritic cells and CD8+ T cells. Time-of-day modulates the abundance, spatial organization, and cytokine-chemokine production of tumor-infiltrating immune cells. Mechanistically, dendritic cell clocks control expression of Cx3cl1, driving recruitment of CX3CR1+CD8+ T cells and thereby reshaping the tumor immune microenvironment to enhance immunotherapy efficacy. Disruption of this axis abolishes time-of-day-dependent differences in treatment response. These findings identify a circadian mechanism of immune cell recruitment to tumors and provide mechanistic insight into clinical observations linking treatment timing to immunotherapy outcomes. One sentence summaryTime of day determines cancer immunotherapy efficacy through a circadian clock-dependent chemokine axis.

immunology↗

bioRxiv2025

The gut microbiota directs vitamin A flux to regulate intestinal T cell development

The intestinal microbiota shapes adaptive immunity, but the mechanisms remain incompletely defined. Here, we show that the microbiota initiates the movement of retinoids--dietary vitamin A derivatives including retinol and retinoic acid--through a sequential pathway from epithelial cells to myeloid cells and ultimately to T cells in the mesenteric lymph nodes (mLNs). This cellular axis is traversed over three days. Microbe-associated molecular patterns (MAMPs) initiate retinoid flux by inducing expression of serum amyloid A (SAA) proteins. These epithelial retinol-binding proteins are necessary and sufficient for epithelial-to-myeloid cell retinoid transfer and for myeloid cell migration to the mLNs. In the mLNs, microbial antigen drives retinoid transfer from myeloid cells to developing T cells, culminating in T cell retinoid uptake and transcriptional programming. This pathway is activated during postnatal development, when gut adaptive immunity is first established. These findings reveal that the microbiota programs intestinal adaptive immunity by regulating immune cell access to a nutrient-derived developmental signal. HighlightsO_LIThe gut microbiota enables vitamin A flux to developing intestinal CD4 T cells. C_LIO_LIMicrobiota-induced SAA initiates vitamin A flux along a gut myeloid-T cell axis. C_LIO_LIMicrobial molecular patterns and antigen drive distinct steps of vitamin A flux. C_LIO_LIMicrobiota-driven vitamin A flux programs intestinal T cell homing and maturation. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=192 HEIGHT=200 SRC="FIGDIR/small/674524v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@13b3906org.highwire.dtl.DTLVardef@11ceee3org.highwire.dtl.DTLVardef@87913forg.highwire.dtl.DTLVardef@50c9a0_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Microbiota-derived short-chain fatty acids mediate Candida albicans gastrointestinal colonization resistance

The gut microbiota plays a critical role in constraining Candida albicans (Ca) colonization of the gastrointestinal (GI) tract, a key precursor to disseminated fungal infection in immunocompromised hosts. Depletion of commensal microbiota increases Ca burden and promotes dissemination, yet the mechanisms of microbiota-mediated Ca colonization resistance remain poorly defined. Here, we show that gut microbiota-derived short-chain fatty acids (SCFAs) directly inhibit Ca growth by impairing hexose uptake, disrupting central carbon metabolism, and inducing intracellular acidification. In vivo, SCFAs enhance Ca colonization resistance only in the presence of an intact gut microbiome, which is required to drive SCFA-induced taxonomic shifts that further augment resistance. Commensal microbiota lacking SCFA production exhibit diminished capacity to restrict Ca colonization, while prebiotic therapy that increases luminal SCFA levels enhances Ca clearance. These findings define a critical microbiota-metabolite mechanism underlying Ca colonization resistance and suggest strategies to modulate GI fungal burden and prevent invasive disease.

microbiology↗

bioRxiv2022

Coinfection with Intestinal Parasite Expands Resident Macrophages and Impairs Control of Chronic Herpesvirus Infection

In addition to a range of homeostatic functions, resident macrophages are essential for immune surveillance in tissues. Therefore, anything that alters the phenotype or function of these cells potentially impacts their response to infectious challenges. Parasite infections cause proliferation of large peritoneal macrophages (LPMs), which are the resident macrophages of the peritoneal cavity. However, the functional consequences of LPM expansion on the control of secondary infectious challenge is unknown. Using a coinfection model with the intestinal parasite Heligmosomoides polygyrus (HP) and the virus, murine gammaherpesvirus-68 (MHV68), we investigated the impact of LPM expansion on viral infection. We determined that LPM expansion induced by HP required retinoic acid signaling. When we challenged HP-infected mice with MHV68, we observed increased herpesvirus infection and latency. Coinfection of mice with macrophage-specific deletion of GATA6, the retinoic acid-responsive transcription factor that drives LPM transcriptional programming, eradicated the increase in viral infection. In addition to increased MHV68 infection, parasite coinfected mice displayed increased herpesvirus reactivation from latency, indicating impaired control of chronic herpesvirus infection. Elimination of dietary vitamin A, which depletes retinoic acid and LPMs, abolished the increased MHV68 reactivation in parasite coinfected mice. These results indicate that parasite- and retinoic acid-mediated resident macrophage expansion drives increased herpesvirus infection, latency, and reactivation.

immunology↗

bioRxiv2022

Macrophages regulate gastrointestinal motility through complement component 1q

Peristaltic movement of the intestine propels food down the length of the gastrointestinal tract to promote nutrient absorption. Interactions between intestinal macrophages and the enteric nervous system regulate gastrointestinal motility, yet we have an incomplete understanding of the molecular mediators of this crosstalk. Here we identify complement component 1q (C1q) as a macrophage product that regulates gut motility. Macrophages were the predominant source of C1q in the mouse intestine and most extraintestinal tissues. Although C1q mediates complement-mediated killing of bacteria in the bloodstream, we found that C1q was not essential for immune defense of the intestine. Instead, C1q-expressing macrophages were localized to the intestinal submucosal plexus where they closely associated with enteric neurons and expressed surface markers characteristic of nerve-adjacent macrophages in other tissues. Mice with a macrophage-specific deletion of C1qa showed changes in enteric neuronal gene expression, increased peristaltic activity, and accelerated intestinal transit. Our findings identify C1q as a key regulator of gastrointestinal motility and provide enhanced insight into the crosstalk between macrophages and the enteric nervous system.

immunology↗

bioRxiv2020

Microbial DNA on the move: sequencing based detection and analysis of transduced DNA in pure cultures and microbial communities

Horizontal gene transfer (HGT) plays a central role in microbial evolution. Our understanding of the mechanisms, frequency and taxonomic range of HGT in polymicrobial environments is limited, as we currently rely on historical HGT events inferred from genome sequencing and studies involving cultured microorganisms. We lack approaches to observe ongoing HGT in microbial communities. To address this knowledge gap, we developed a DNA sequencing based "transductomics" approach that detects and characterizes microbial DNA transferred via transduction. We validated our approach using model systems representing a range of transduction modes and show that we can detect numerous classes of transducing DNA. Additionally, we show that we can use this methodology to obtain insights into DNA transduction among all major taxonomic groups of the intestinal microbiome. This work extends the genomic toolkit for the broader study of mobile DNA within microbial communities and could be used to understand how phenotypes spread within microbiomes. Significance StatementMicrobes can rapidly evolve new capabilities by acquiring genes from other organisms through a process called horizontal gene transfer (HGT). HGT occurs via different routes, one of which is by the transfer of DNA carried by microbe infecting viruses (phages) or virus-like agents. This process is called transduction and has primarily been studied in the lab using pure cultures or indirectly in environmental communities by analyzing signatures in microbial genomes revealing past transduction events. The transductomics approach that we present here, allows for the detection and characterization of genes that are potentially transferred between microbes in complex microbial communities at the time of measurement and thus provides insights into real-time ongoing horizontal gene transfer.

microbiology↗

bioRxiv2019

The intestinal microbiota programs diurnal rhythms in host metabolism through histone deacetylase 3

Circadian rhythmicity is a defining feature of mammalian metabolism that synchronizes metabolic processes to day-night light cycles. Here, we show that the intestinal microbiota programs diurnal metabolic rhythms in the mouse small intestine through histone deacetylase 3 (HDAC3). The microbiota induced expression of intestinal epithelial HDAC3, which was recruited rhythmically to chromatin and produced synchronized diurnal oscillations in histone acetylation, metabolic gene expression, and nutrient uptake. HDAC3 also functioned non-canonically to coactivate estrogen related receptor (ERR), inducing microbiota-dependent rhythmic transcription of the lipid transporter gene Cd36 and promoting lipid absorption and diet-and jet lag-induced obesity. Our findings reveal that HDAC3 integrates microbial and circadian cues to regulate diurnal metabolic rhythms, and pinpoint a key mechanism by which the microbiota controls host metabolism. One sentence summaryThe intestinal microbiota induces daily metabolic rhythms and controls lipid uptake through the enzyme histone deacetylase 3.

microbiology↗

bioRxiv2019

Epithelial retinoid acid receptor β regulates serum amyloid A expression and vitamin A-dependent intestinal immunity

Vitamin A is a dietary component that is essential for the development of intestinal immunity. Vitamin A is absorbed and converted to its bioactive derivatives retinol and retinoic acid by the intestinal epithelium, yet little is known about how epithelial cells regulate vitamin A-dependent intestinal immunity. Here we show that epithelial cell expression of the transcription factor retinoic acid receptor {beta} (RAR{beta}) is essential for vitamin A-dependent intestinal immunity. Epithelial RAR{beta} activated vitamin A-dependent expression of serum amyloid A (SAA) proteins by binding directly to Saa promoters. In accordance with the known role of SAAs in regulating Th17 cell effector function, epithelial RAR{beta} promoted IL-17 production by intestinal Th17 cells. More broadly, epithelial RAR{beta} was required for the development of key vitamin A-dependent adaptive immune responses, including CD4+ T cell homing to the intestine and the development of immunoglobulin A-producing intestinal B cells. Our findings provide insight into how the intestinal epithelium senses dietary vitamin A status to regulate adaptive immunity and highlight the role of epithelial cells in regulating intestinal immunity in response to diet. Significance StatementVitamin A is a nutrient that is essential for the development of intestinal immunity. It is absorbed by gut epithelial cells which convert it to retinol and retinoic acid. Here we show that the transcription factor retinoic acid receptor {beta} (RAR{beta}) allows epithelial cells to sense vitamin A in the diet and regulate vitamin A-dependent immunity in the intestine. We find that epithelial RAR{beta} regulates several intestinal immune responses, including production of the immunomodulatory protein serum amyloid A, T cell homing to the intestine, and B cell production of immunoglobulin A. Our findings provide new insight into how epithelial cells sense vitamin A to regulate intestinal immunity and highlight why vitamin A is so important for immunity to infection.

immunology↗