Biology subjects

Pope, S. D.

Publications and source records attributed to Pope, S. D..

7 recordsLinked to original sources

bioRxiv2026

Non-cell-autonomous removal of protein aggregates via trogocytosis

Protein aggregate formation can cause cell damage and contribute to tissue pathologies including neurodegeneration. Protein aggregates are normally eliminated by cell-intrinsic mechanisms of lysosomal (autophagic) degradation. However, degradative capacity varies between cell types, raising the possibility that high-capacity cell types, such as macrophages, may contribute to aggregate disposal from the low-capacity cells. Here, we show that cellular protein aggregates are removed by macrophages via trogocytosis -- a partial engulfment of the target cells. Lysosomal stress upon protein aggregate accumulation promotes cell surface expression of the transmembrane isoform of the macrophage growth factor CSF1 (tmCSF1), which is detected by macrophages through the CSF1 receptor to drive trogocytosis. Insufficient or impaired degradation of protein aggregates in lysosomes results in their transport along microtubules to the plasma membrane where they physically associate with tmCSF1. This enables macrophages to specifically trogocytose protein aggregates. These findings reveal a protein homeostasis system that eliminates protein aggregates in a non-cell-autonomous manner.

cell biology↗

bioRxiv2024

Control of Inflammatory Response by Tissue Microenvironment

Inflammation is an essential defense response but operates at the cost of normal tissue functions. Whether and how the negative impact of inflammation is monitored remains largely unknown. Acidification of the tissue microenvironment is associated with inflammation. Here we investigated whether macrophages sense tissue acidification to adjust inflammatory responses. We found that acidic pH restructured the inflammatory response of macrophages in a gene-specific manner. We identified mammalian BRD4 as a novel intracellular pH sensor. Acidic pH disrupts the transcription condensates containing BRD4 and MED1, via histidine-enriched intrinsically disordered regions. Crucially, a decrease in macrophage intracellular pH is necessary and sufficient to regulate transcriptional condensates in vitro and in vivo, acting as negative feedback to regulate the inflammatory response. Collectively, these findings uncovered a pH-dependent switch in transcriptional condensates that enables environment-dependent control of inflammation, with a broader implication for calibrating the magnitude and quality of inflammation by the inflammatory cost. HighlightsO_LIAcidic pH regulates a switch-like gene-specific inflammatory response in macrophages C_LIO_LIAcidic pH impacts chromatin remodeling and transcription circuits to control inflammatory programs C_LIO_LIBRD4 transcriptional condensates are regulated by intracellular pH via the histidine-enriched intrinsically disordered region C_LIO_LITissue inflammation decreases intracellular pH and disrupts BRD4 condensates as a negative feedback C_LI

immunology↗

bioRxiv2024

Stepwise neofunctionalization of the NF-κB family member c-Rel during vertebrate evolution

Adaptive immunity and the five vertebrate NF-{kappa}B/Rel family members first appeared in cartilaginous fish, suggesting that divergence and specialization within the NF-{kappa}B family helped facilitate the evolution of adaptive immunity. One specialized function of the NF-{kappa}B c-Rel protein in macrophages is the activation of Il12b, which encodes a key regulator of T-cell development. We found that c-Rel is a far more potent regulator of Il12b than of any other inducible genes in macrophages, with c-Rel regulation of Il12b dependent on its heightened intrinsic DNA-binding affinity. c-Rel homodimers regulate Il12b transcription in part via motifs with little resemblance to canonical NF-{kappa}B motifs. ChIP-seq experiments further defined distinct c-Rel DNA-binding preferences genome-wide, and X-ray crystallography of a c-Rel/RelA chimeric protein identified key amino acid changes that support the unique c-Rel properties. Unexpectedly, these changes, along with the c-Rel/RelA binding affinity differences, were largely restricted to mammalian species. Together, our findings reveal how a transcription factor family member can undergo a structural transition at a late stage of vertebrate evolution, resulting in an increased intrinsic DNA binding affinity and with clear functional consequences, presumably to support the increasing complexity of immune regulation.

immunology↗

bioRxiv2023

Macrophages control pathological interferon responses during viral respiratory infection

Antiviral immune mediators, including interferons and their downstream effectors, are critical for host defense yet can become detrimental when uncontrolled. Here, we identify a macrophage-mediated anti-inflammatory mechanism that limits type I interferon (IFN-I) responses. Specifically, we found that cellular stress and pathogen recognition induce Oncostatin M (OSM) production by macrophages. OSM-deficient mice succumbed to challenge with influenza or a viral mimic due to heightened IFN-I activation. Macrophage-derived OSM restricted excessive IFN-I production by lung epithelial cells following viral stimulation. Furthermore, reconstitution of OSM in the respiratory tract was sufficient to protect mice lacking macrophage-derived OSM against morbidity, indicating the importance of local OSM production. This work reveals a host strategy to dampen inflammation in the lung through the negative regulation of IFN-I by macrophages. One-Sentence SummaryType I interferons induced by viral stimuli are negatively regulated by macrophage-derived Oncostatin M.

immunology↗

bioRxiv2023

Macrophages sense ECM mechanics and growth factor availability through cytoskeletal remodeling to regulate their tissue repair program

Tissue resident macrophages play important roles in tissue homeostasis and repair. However, how macrophages monitor and maintain tissue integrity is not well understood. The extracellular matrix (ECM) is a key structural and organizational component of all tissues. Here, we find that macrophages sense the mechanical properties of the ECM in order to regulate a specific tissue repair program. We show that macrophage mechanosensing is mediated by cytoskeletal remodeling and can be performed in three-dimensional environments through a non-canonical, integrin-independent mechanism analogous to amoeboid migration. We find that these cytoskeletal dynamics also integrate biochemical signaling by CSF1 and ultimately regulate chromatin accessibility to control the mechanosensitive gene expression program. This study suggests a distinct mode of ECM mechanosensing and growth factor signaling through which macrophages may regulate tissue repair and fibrosis.

immunology↗

bioRxiv2022

Microenvironmental sensing by fibroblasts controls macrophage population size

Animal tissues are comprised of diverse cell types. However, the mechanisms controlling the number of each cell type within tissue compartments remain poorly understood. Here, we report that different cell types utilize distinct strategies to control population numbers. Proliferation of fibroblasts, stromal cells important for tissue integrity, is limited by space availability. In contrast, proliferation of macrophages, innate immune cells involved in defense, repair, and homeostasis, is constrained by growth factor availability. Examination of density-dependent gene expression in fibroblasts revealed that Hippo and TGF-{beta} target genes are both regulated by cell density. We found YAP1, the transcriptional co-activator of the Hippo signaling pathway, directly regulates expression of Csf1, the lineage-specific growth factor for macrophages, through an enhancer of Csf1 that is specifically active in fibroblasts. Activation of YAP1 in fibroblasts elevates Csf1 expression and is sufficient to increase the number of macrophages at steady state. Our data also suggest that expression programs in fibroblasts that change with density may result from sensing of mechanical force through actin-dependent mechanisms. Altogether, we demonstrate that two different modes of population control are connected and coordinated to regulate cell numbers of distinct cell types. Sensing of the tissue environment may serve as a general strategy to control tissue composition. Significance StatementCollections of distinct cell types constitute animal tissues. To perform their unique functions, each cell type must exist in the correct number and proportion in a given tissue compartment. However, many of the mechanisms regulating and coordinating cell population sizes remain enigmatic. Our study characterizes two different modes of population size control, utilized by two ubiquitous cell types, macrophages and fibroblasts. Macrophage populations are more sensitive to the presence of growth factors in the environment and fibroblasts are more sensitive to space limitations. Intriguingly, space-sensing mechanisms in fibroblasts directly control the production of growth factor for macrophages and thus macrophage numbers. This link suggests a mechanism by which macrophage compartment size is controlled by stromal cells according to the microenvironment.

immunology↗

bioRxiv2018

The lupus susceptibility locus Sgp3 encodes the suppressor of endogenous retrovirus expression SNERV

Elevated endogenous retrovirus (ERV) transcription and anti-ERV antibody reactivity are implicated in lupus pathogenesis. Overproduction of non-ecotropic ERV (NEERV) envelope glycoprotein, gp70, and resultant nephritis occur in lupus-prone mice. However, a NEERV repressor has not been identified to test if this association is causal. Here we identified suppressor of NEERV (Snerv) 1 & 2, Kruppel-associated box zinc finger proteins (KRAB-ZFP) that repressed NEERV by binding the NEERV long terminal repeat to recruit the transcriptional regulator KAP1. Germline Snerv1/2 deletion increased activating chromatin modifications, transcription, and gp70 expression from NEERV loci. F1 crosses of lupus-prone NZB and 129 mice to Snerv1/2-/- mice failed to restore NEERV repression, demonstrating that loss of SNERV underlies the lupus autoantigen gp70 overproduction that promotes nephritis in susceptible mice. Increased ERV expression in lupus patients was inversely correlated with expression of three putative ERV-suppressing KRAB-ZFP, suggesting that KRAB-ZFP-mediated ERV misexpression may contribute to human lupus pathogenesis.

immunology↗