Biology subjects

Schwartz, C.

Publications and source records attributed to Schwartz, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Preserved Type 2 Immune Cell Plasticity in Human Obesity and Differential Immune Reconstitution After Bariatric Surgery

BackgroundObesity disrupts type 2 immune cell populations in white adipose tissue, replacing the homeostatic network of group 2 innate lymphoid cells (ILC2s), eosinophils, T helper 2 (Th2) cells, and alternatively activated macrophages (AAMs) with pro-inflammatory type 1 populations. Whether this remodelling reflects permanent immune impairment or a reversible shift in cellular equilibrium, and to what extent bariatric surgery restores type 2 immunity, remain incompletely understood. MethodsWe performed comprehensive immunophenotyping of visceral white adipose tissue (WAT) and peripheral blood from persons with severe obesity (people with obesity, PWO) scheduled for or having undergone bariatric surgery (sleeve gastrectomy, gastric bypass), combined with lean controls. Using flow cytometry, quantitative PCR, and in vitro polarization assays, we assessed immune cell frequencies, transcription factor expression, cytokine profiles, and functional polarization capacity across lean, pre-operative, and post-operative states. ResultsObesity was associated with decreased eosinophil and CD8+ T cells frequencies in WAT, accompanied by an increase in CD4+ frequency and a shift from Th2 toward Th1 predominance, as well as elevated PD-1 expression on T cell subsets. Bariatric surgery partially normalised peripheral immune cell composition, reducing CD8+ T cell frequencies while increasing CD4+ T cells. Macrophage polarization capacity, dampened in pre-operative PWO, recovered after surgery. Conversely, Th2 polarization capacity and IL-13 production were reduced in post-operative T cells despite preserved function pre-operatively, indicating divergent trajectories of innate and adaptive immune reconstitution. ConclusionType 2 immune cells retain functional plasticity in human obesity despite reduced frequency. Bariatric surgery differentially reconstitutes immune function, restoring macrophage plasticity while paradoxically reducing Th2 polarization capacity, arguing against uniform immune normalisation after weight loss. FundingGerman Federal Ministry of Research, Technology and Space (BMFTR, FKZ 01KI2109), Interdisciplinary Center for Clinical Research (IZKF, Faculty of Medicine, Friedrich-Alexander Universitat (FAU) Erlangen-Nurnberg).

immunology↗

bioRxiv2026

Obesity selectively disrupts long-lasting type 2 immune cell depots in white adipose tissue

White adipose tissue (WAT) has emerged as a tissue-resident niche for immunological memory, but whether this depot function extends to type 2 immune memory and how it is modulated by metabolic disease remains incompletely understood. Here, we show that Nippostrongylus brasiliensis infection, in which the parasite transits and damages the lung, establishes a long-lasting immune cell depot in distal abdominal WAT comprising eosinophils, group 2 innate lymphoid cells (ILC2s), and memory T cells that persists after parasite clearance. Intranasal papain administration recapitulates this depot phenotype, demonstrating that depot formation is a general feature of pulmonary type 2 inflammation rather than a response restricted to live infection. Adoptive transfer of OT-II T cells together with ovalbumin-coated N. brasiliensis larvae confirms that WAT accumulates bona fide antigen-experienced T cells. Diet-induced obesity selectively disrupts depot establishment, while leaving acute lung-stage immune cell recruitment, parasite clearance, and the intrinsic competence of cells that do accumulate largely intact. Despite preserved early lung recruitment, obese mice show exacerbated peri-alveolar tissue damage, consistent with an uncoupling of immune cell infiltration from productive type 2-dependent wound repair. Together, these findings establish WAT as a broadly competent type 2 immunological memory niche, identify obesity as a selective disruptor of depot formation rather than effector function, and provide a cellular framework for the impaired vaccine and infection responses associated with obesity.

immunology↗

bioRxiv2026

POLQ-driven repair scars shape the immunogenic landscape of homologous recombination-deficient pancreatic cancer

Pancreatic cancer (PC) is broadly resistant to immune checkpoint blockade, although a subset of homologous recombination-deficient (HRD) tumors exhibits durable immune engagement. The genomic features that distinguish these immune-responsive tumors from immune-inert HRD tumors remain poorly understood. Here we identify a microhomology-mediated end joining (MMEJ) repair scar, the MMEJ Deletion Footprint (MDF), as a genomic readout of POLQ-associated error-prone repair that enriches for frameshift indels. Across the multi-omic discovery cohort integrating tumor genomics, single-nucleus transcriptomics and spatial immune profiling, MDF-high HRD PC exhibited increased frameshift-indel-derived neoantigens and interferon programs. MDF was further associated with remodeling of the myeloid compartment toward MHC II-high dendritic cell-like antigen-presenting macrophage states and the immune synapse architecture marked by increased spatial interaction between APC-like macrophages and cytotoxic CD8+ T cells. These tissue-level features aligned with a functional trajectory shift of CD8+ T cells, consistent with effective anti-tumor immunity and was associated with favorable clinical outcomes of patients. Together, our findings position MMEJ-linked repair scarring as actionable biology that connects an HRD genotype to immune organization and suggests rational immunotherapy combinations that may enhance antigen presentation and myeloid activation to extend durable benefit in HRD-lineage cancers.

cancer biology↗

bioRxiv2026

Hormone signaling and immune programs define differential endocrine responsiveness in high-risk breast tissue

Hormone therapies are frequently used to reduce breast cancer risk in individuals at increased risk for primary or subsequent disease; however, tissue-level responses to these therapies are heterogeneous and incompletely understood. Background parenchymal enhancement (BPE) on breast magnetic resonance imaging (MRI) provides a non-invasive radiologic readout of breast tissue features associated with endocrine responsiveness and cancer risk. Although BPE is associated with hormonal exposure, a subset of patients with BPE do not show a response to preventive endocrine therapy and therefore may remain at increased breast cancer risk. In this study, we integrated single-nucleus RNA sequencing and spatial transcriptomics to define the determinants of endocrine responsiveness in the setting of BPE. We identify hormone-driven epithelial cells with high levels of estrogen signaling and endocrine responsiveness, together with immune-associated epithelial programs characterized by diminished luminal identity and increased expression of immune-modulatory pathways, including major histocompatibility complex (MHC) class II and CD74. Functional organoid assays validate that these epithelial states exhibit differential sensitivity to tamoxifen and demonstrate that inflammatory signals can induce immune-modulatory epithelial programs. Together, our findings identify hormone signaling and immune programs as key determinants of endocrine responsiveness in breast tissue and provide a biological basis for interpreting radiologic markers relevant to cancer prevention.

cancer biology↗

bioRxiv2026

Identification of a key residue in the cellular transcription factor BCL11b important for its global acetylation and its nuclear localization

AO_SCPLOWBSTRACTC_SCPLOWThe cellular transcription factor BCL11b (B-cell CLL/lymphoma 11b) interacts with numerous cellular and viral factors to modulate gene expression positively or negatively. Post-translational modifications of BCL11b, such as SUMOylation and phosphorylation, have been documented to switch its transcriptional activity from a repressor to an activator state. In the present study, we investigated the acetylation of BCL11b and we identified the histone acetyltransferase p300 as able to acetylate BCL11b. Subsequently, we observed that the mutation of the lysine K686 residue of BCL11b (BCL11b K686R) influenced its global acetylation. Furthermore, the BCL11b K686R mutation also modulated the transcriptional regulation of BCL11b, including its activity in regulating the p21 and IL-2 promoters. This effect on transcriptional regulation was due to the importance of the lysine K686 residue for BCL11b nuclear localization. Our results underscore the critical role of the lysine K686 residue in BCL11b for its interaction with p300 and its nuclear localization, suggesting a possible function of p300 in the nuclear transport of BCL11b. Collectively, our findings contribute to a better understanding of BCL11b-mediated gene expression and of the interactions of BCL11b with cellular partners.

molecular biology↗

bioRxiv2026

THE HIV-1 SILENCER BCL11B/CTIP2 REGULATES THE TLR3-MEDIATED CELLULAR RESPONSE TO VIRAL INFECTIONS

HIV-1 latency remains a major barrier to viral eradication. The persistence of the latently infected reservoirs results from multifactorial mechanisms controlling gene transcription and cellular responses to viral reactivation. The transcriptional repressor BCL11B/CTIP2 is known to promote the establishment and persistence of the latently infected reservoirs. However, its contribution to the cellular response to viral infection has not been investigated before. Together with HEXIM1, paraspeckles contribute to cellular innate sensing of viral infections and to the production of type I interferons. Paraspeckles are nuclear membrane-less organelles composed of proteins, including SFPQ/PSF and NONO, wrapped around the long non-coding RNA NEAT1. Here, we show that HIV-1 infection promotes a TLR3-mediated CTIP2 overexpression delayed from a transitory NEAT1 overexpression, paraspeckles formation and type I IFN production. In response to this interferon production, CTIP2 is recruited to the NEAT1 promotor together with HEXIM1 and repressive histone marks to inhibit NEAT1 gene expression. The resulting depletion of the paraspeckles abrogated INF production, dampening TLR3 signalling and reinforcing HIV-1 latency. Our results demonstrate CTIP2 as a dual-function regulator that silences HIV-1 transcription and restricts antiviral innate immune response as part of a negative feedback loop limiting the interferon response to viral infection. O_FIG O_LINKSMALLFIG WIDTH=147 HEIGHT=200 SRC="FIGDIR/small/699245v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@7ab0b0org.highwire.dtl.DTLVardef@e60aa6org.highwire.dtl.DTLVardef@c5564corg.highwire.dtl.DTLVardef@1a4bbe0_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

Engineering a Multilayer Microfluidic Airway-On-A-Chip with Tunable GelMA Hydrogel for Physiologically Relevant Aerosol Exposure Studies

Climate change-driven increases in forest fires pose a major global health risk due to exposure to smoke containing hazardous gases and fine particulates, emphasizing the need for physiologically relevant in vitro airway models for studying smoke-induced responses. Microfluidic lung-on-a-chip technologies provide a strong foundation for in vitro airway modeling and ongoing developments are expanding their ability to incorporate multicellular organization, extracellular matrix complexity, and physiologically relevant exposure methods. This work presents the optimization and integration of a photopolymerizable gelatin methacrylate (GelMA)-based hydrogel into a microfluidic airway-on-a-chip that models the human small conducting airways and supports controlled aerosol exposure to wood smoke. The GelMA hydrogel was optimized to support fibroblast encapsulation, endothelial, and epithelial adhesion and robust mechanical stability. The device combines the hydrogel with a compartmentalized microchannel layout, and sacrificial molding to create a 3D organotypic airway culture featuring a multilayer architecture, 3D stromal matrix, and a perfusable vasculature-like lumen. Coupling the platform with a custom aerosol exposure system enables precise, biomimetic exposure to whole wood smoke. Proof-of-concept studies using transforming growth factor beta1 (TGF-{beta}1) and whole wood smoke elicited expected inflammatory and fibrotic responses, validating the platforms physiological relevance for inhalation studies and investigating smoke-induced airway remodeling and inflammation.

bioengineering↗

bioRxiv2025

Bactofilins are essential spatial organizers of peptidoglycan insertion in the Lyme disease spirochete Borrelia burgdorferi

The Lyme disease spirochete Borrelia burgdorferi has a distinctive pattern of growth. Newly-born cells elongate by primarily inserting peptidoglycan at mid-cell, while in longer cells, additional insertion sites form at the one-quarter and three-quarter positions along the cell length. It is not known how peptidoglycan insertion is concentrated at these locations in B. burgdorferi. In other bacteria, multi-protein complexes are known to synthesize new peptidoglycan and are often organized by cytoskeletal proteins. We show here that B. burgdorferis zonal concentration of peptidoglycan insertion requires BB0538 (BbbA) and BB0245 (BbbB), two members of the bactofilin class of cytoskeletal proteins. Bactofilin depletion redistributes peptidoglycan insertion along the cell length. Prolonged bactofilin depletion arrested growth in culture and induced extensive cell blebbing, indicating that B. burgdorferi bactofilins are essential for viability. Fluorescent protein fusions of BbbA and BbbB localized to areas of peptidoglycan insertion, with BbbB accumulation preceding peptidoglycan insertion at these sites. Similar to peptidoglycan insertion, BbbB localization was disrupted upon depletion of BbbA. Our results show that BbbB relies on BbbA for its localization, and that together, BbbA and BbbB direct the spatial patterning of new peptidoglycan insertion in B. burgdorferi. IMPORTANCEThe spirochetal bacterium Borrelia burgdorferi causes Lyme disease, the most prevalent vector-borne infection in North America and Europe. Cellular replication, which requires growth and division of the peptidoglycan cell wall, facilitates B. burgdorferi transmission to, and dissemination within, new hosts. Cellular replication is therefore essential for pathogenesis. Bactofilins regulate peptidoglycan-related processes in several bacteria. However, these functions are typically non-essential for cellular replication, as bactofilin-encoding genes can be readily deleted in multiple bacterial species. In contrast, we show that the B. burgdorferi bactofilins BbbA and BbbB are essential for cellular viability and direct zonal peptidoglycan insertion. Our findings broaden the spectrum of known bactofilin functions and advance our understanding of how peptidoglycan insertion is regulated in this unusual, medically important spirochete bacterium.

microbiology↗

bioRxiv2025

Characterization of Woodsmoke Generated in the Air Pollution Exposure Lab and Comparison to Diesel Exhaust

To address the increasing concern of woodsmoke (WS) and better understand its effects on human health, a woodsmoke generation system was built in the Air Pollution Exposure Laboratory to facilitate future controlled human exposure studies. Two different woodsmoke conditions, flaming (WSFL) and smoldering (WSSM), were generated, and PM2.5 concentrations of approximately 500 g/m3 were achieved. The woodsmoke produced using the system was characterized in this study and compared with diesel exhaust (DE) generated and collected at the same facility. Within the gas phase generated by the pollutants, WS showed slight increases in CO and CO2 compared to filtered air (FA), while DE contained significantly higher levels of NOx, CO2, and total volatile organic compounds compared to FA. The WS aerosols were comprised of approximately 98% organics, 0.6% NH4, 0.9% NO3, and 0.2% SO4. Among the organic species, the CHO1 and CHOgt1 families encompassed around 60%, which was higher than the fraction of oxygenated families in DE aerosols. Moreover, the WS aerosols had higher concentrations of Cd compared to the DE aerosols. Greater oxidative potentials were also observed for WSFL and WSSM compared to DE, with DTT consumption rates normalized to the PM mass being 0.0099 and 0.0090 nmol/min/g, respectively. The difference in the compositions and properties of WS and DE suggests that it is critical to conduct further studies on how these pollutants can affect health differently.

pharmacology and toxicology↗

bioRxiv2025

High-Resolution Proteomics Unveils Salivary Gland Disruption and Saliva-Hemolymph Protein Exchange in Plasmodium-Infected Mosquitoes

Plasmodium sporozoites, the stage that initiates a malaria infection, must invade the mosquito salivary glands (SGs) before transmitting to a vertebrate host. However, the effects of sporozoite invasion on salivary gland physiology and saliva composition remain largely unexplored. We examined the impact of Plasmodium infection on Anopheles gambiae salivary glands using high-resolution proteomics, gene expression, and morphological analysis. The data revealed differential expression of various proteins, including the enrichment of humoral proteins in infected salivary glands originating from the hemolymph. These proteins diffused into the SGs due to structural damage caused by the sporozoites during invasion. Conversely, saliva proteins diffused out into the circulation of infected mosquitoes. Moreover, infection altered saliva protein composition, as shown by proteomes from saliva collected from mosquitoes infected by P. berghei or P. falciparum, revealing a significant reduction of immune proteins compared to uninfected mosquitoes. This reduction is likely due to the association of these proteins with the surface of sporozoites within the mosquito salivary secretory cavities. The saliva protein profiles from mosquitoes infected with both Plasmodium species were remarkably similar, suggesting a conserved interaction between sporozoites and salivary glands. Our results provide a foundation for understanding the molecular interactions between Plasmodium sporozoites and mosquito salivary glands.

microbiology↗

bioRxiv2023

Ultrastructural identification and molecular characterization of two new parabasalid species that naturally colonize laboratory mice, Tritrichomonas musculus and Tritrichomonas casperi

Tritrichomonas muris is a flagellated protist isolated from the cecum of wild mice in the Czech Republic. This commensal protist has been shown previously to alter immune phenotypes in laboratory mice. Other trichomonads, previously referred to as Tritrichomonas musculis and Tritrichomonas rainier, also naturally colonize laboratory mice and cause immune alterations. This report formally describes two new trichomonads, Tritrichomonas musculus n. sp., and Tritrichomonas casperi n. sp., at the ultrastructural and molecular level. These two protists were isolated from laboratory mice, and were differentiated by their size and the structure of their undulating membrane and posterior flagellum. Analysis at the 18S rRNA and trans-ITS genetic loci supported their designation as distinct species, related to T. muris. To further assess the true extent of parabasalid diversity infecting laboratory mice, 135 mice were screened at the NIH using pan-parabasalid primers that amplify the trans-ITS region. Forty-four percent of mice were positive for parabasalids, encompassing a total of 8 distinct sequence types. Tritrichomonas casperi and Trichomitus-like protists were dominant. T. musculus and T. rainier were also detected, but T. muris was not. Our work establishes a previously underappreciated diversity of commensal trichomonad protists that naturally colonize the enteric cavity of laboratory mice.

microbiology↗

bioRxiv2022

Network topology in brain tumor patients with and without structural epilepsy- a prospective MEG-study

It has been proposed that functional connectivity (FC) and network topology (NT) are altered in patients with glial brain tumors. So far there is no consensus on the pattern of these changes, furthermore data on FC in patients with brain metastases (BMs) as well as on the presence and absence of tumor-related epilepsy is lacking. We aimed to analyze preoperative NT of newly diagnosed, singular, supratentorial glial brain tumors (GBTs) and BMs with and without structural epilepsy. FC and NT derived from resting state magnetoencephalography (MEG) were compared between patients (PAs) and matched healthy controls (HCs), between GBTs and BMs as well as between patients with and without structural epilepsy. We investigated all patients, who met our inclusion criteria from February 2019 to March 2021. Clinical data was collected from patients electronic medical charts. We analyzed whole brain (wb) connectivity in six frequency bands, calculated three different network topological parameters (node degree (ND), shortest path length (L), clustering coefficient (CC)) and performed a stratification, where differences in the power were to be found. For data analysis we used Fieldtrip, Brain Connectivity Matlab toolboxes and in-house built scripts. We consecutively included 41 patients (21 men), mean age 60.1ys (range 23-82), who were operated on at our institution. Tumor histology included high-grade gliomas (n=18), low-grade gliomas (n=4), dysembryoplastic neuroepithelial tumor (DNET, n=1), BMs (n=14) and others (n=4). Statistical analysis revealed a significant decrease for wb ND in patients compared to healthy controls in every frequency range analyzed at the descriptive and corrected level (p1-30Hz=0.002, p{gamma}=0.002, p{beta}=0.002, p=0.002, p{theta}=0.024, p{delta}=0.002). Furthermore, at the descriptive level, we found a significant augmentation for wb CC (p1-30Hz=0.031, p{delta}=0.013) in PAs compared to HCs, which did not persist the false discovery rate (FDR) correction. There were no differences in the networks of glial brain tumors and metastases identified. However, we found a significant increase in wb CC in patients with structural epilepsy (p{theta}= 0.048), and significantly lower wb ND (p= 0.039) at the uncorrected level. Our data suggests that network topology is altered in brain tumor patients, which is in line with previous studies. Tumor histology per se might not influence the brains functional network, however, tumor-related epilepsy seems to do so. Longitudinal studies and in-depth analysis of possible factors and confounders might be helpful to further substantiate these findings.

neuroscience↗

bioRxiv2022

acCRISPR: An activity-correction method for improving the accuracy of CRISPR screens

High throughput CRISPR screens are revolutionizing the way scientists unravel the genetic underpinnings of novel and evolved phenotypes. One of the critical challenges in accurately assessing screening outcomes is accounting for the variability in sgRNA cutting efficiency. Poorly active guides targeting genes essential to screening conditions obscure the growth defects that are expected from disrupting them. Here, we develop acCRISPR, an end-to-end pipeline that identifies essential genes in pooled CRISPR screens using sgRNA read counts obtained from next-generation sequencing. acCRISPR uses experimentally determined cutting efficiencies for each guide in the library to provide an activity correction to the screening outcomes, thus determining the fitness effect of disrupted genes. This is accomplished by calculating an optimization metric that quantifies the tradeoff between guide activity and library coverage, which is maximized to accurately classify genes essential to screening conditions. CRISPR-Cas9 and -Cas12a screens were carried out in the non-conventional oleaginous yeast Yarrowia lipolytica to determine a high-confidence set of essential genes for growth under glucose, a common carbon source used for the industrial production of oleochemicals. acCRISPR was also used in gain-and loss-of-function screens under high salt and low pH conditions to identify known and novel genes that were related to stress tolerance. Collectively, this work presents an experimental-computational framework for CRISPR-based functional genomics studies that may be expanded to other non-conventional organisms of interest.

synthetic biology↗

bioRxiv2022

Concomitant AD and DLB pathologies shape subfield microglia responses in the hippocampus

Hippocampal alteration is at the centre of memory decline in the most common age-related neurodegenerative diseases: Alzheimers disease (AD) and Dementia with Lewy Bodies (DLB). However, the subregional deterioration of the hippocampus differs between both diseases with more severe atrophy in the CA1 subfield of the AD patients. How AD and DLB-typical pathologies compose the various local microenvironment of the hippocampus across AD and DLB needs to be further explored to understand this process. Additionally, microglia responses could further impact the atrophy rate. Some studies suggest that microglia react differently according to the underlying neurodegenerative disorder. How microglia are transformed across hippocampal subfields in AD and DLB, and how their changes are associated with disease-typical pathologies remains to be determined. To these purposes, we performed a volumetric analysis of phospho-Tau (P-Tau), Amyloid-{beta} (A{beta}), and phospho--Synuclein (P-Syn) loads, quantified and classified microglia according to distinct morphological phenotypes using high-resolution confocal 3D microscopy of hippocampal CA1, CA3 and DG/CA4 subfields of late-onset AD (n=10) and DLB (n=8) as well as age-matched control samples (n=11). We found that each of the Tau, A{beta} and Synuclein pathologies followed a specific subregional distribution, relatively preserved across AD and DLB. P-Tau, A{beta} and P-Syn burdens were significantly exacerbated in AD, with Tau pathology being particularly severe in the AD CA1. P-Tau and P-Syn burdens were highly correlated across subfields and conditions (R2Spear = 0.79; P < 0.001) and result from a local co-distribution of P-Tau and P-Syn inclusions in neighbouring neurons, with only a low proportion of double-positive cells. In parallel, we assessed the changes of the microglia responses by measuring 16 morphological features of more than 35,000 individual microglial cells and classifying them into seven-distinct morphological clusters. We found microglia features- and clusters-variations subfield- and condition-dependent. Two of the seven morphological clusters, with more amoeboid and less branched forms, were identified as disease-enriched and found to be further increased in AD. Interestingly, some microglial features or clusters were associated with one but more often with a combination of two pathologies in a subfield-dependent manner. In conclusion, our study shows a multimodal association of the hippocampal microglia responses with the co-occurrence, distribution and severity of AD and DLB pathologies. In DLB hippocampi, pathological imprint and microglia responses follow AD trends but with lesser severity. Our study suggests that the increased pathological burdens of P-Tau and P-Syn and associated microglia alterations are involved in a more severe deterioration of the CA1 in AD as compared to DLB.

neuroscience↗

bioRxiv2021

Genome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and -Cas12a guides in Yarrowia lipolytica

Genome-wide functional genetic screens have been successful in discovering genotype-phenotype relationships and in engineering new phenotypes. While broadly applied in mammalian cell lines and in E. coli, use in non-conventional microorganisms has been limited, in part, due to the inability to accurately design high activity CRISPR guides in such species. Here, we develop an experimental-computational approach to sgRNA design that is specific to an organism of choice, in this case the oleaginous yeast Yarrowia lipolytica. A negative selection screen in the absence of non-homologous end-joining, the dominant DNA repair mechanism, was used to generate single guide RNA (sgRNA) activity profiles for both SpCas9 and LbCas12a. This genome-wide data served as input to a deep learning algorithm, DeepGuide, that is able to accurately predict guide activity. DeepGuide uses unsupervised learning to obtain a compressed representation of the genome, followed by supervised learning to map sgRNA sequence, genomic context, and epigenetic features with guide activity. Experimental validation, both genome-wide and with a subset of selected genes, confirms DeepGuides ability to accurately predict high activity sgRNAs. DeepGuide provides an organism specific predictor of CRISPR guide activity that could be broadly applied to fungal species, prokaryotes, and other non-conventional organisms.

synthetic biology↗

bioRxiv2021

Novel Role of UHRF1 in DNA methylation-mediated repression of latent HIV-1

The multiplicity, heterogeneity and dynamic nature of HIV-1 latency mechanisms are reflected in the current lack of functional cure for HIV-1 and in the various reported ex vivo potencies of latency- reversing agents. Here, we investigated the molecular mechanisms underlying the potency of the DNA methylation inhibitor 5-aza-2-deoxycytidine (5-AzadC) in HIV-1 latency reversal. Doing so, we uncovered specific demethylation CpG signatures induced by 5-AzadC in the HIV-1 promoter. By analyzing the binding modalities to these CpG, we revealed the recruitment of the epigenetic integrator UHRF1 to the HIV-1 promoter. We further demonstrated the role of UHRF1 in DNA methylation- mediated silencing of the latent HIV-1 promoter. As a proof-of-concept to this molecular characterization, we showed that pharmacological downregulation of UHRF1 in ex vivo HIV+ patient cell cultures resulted in potent reactivation of latent HIV-1. Together, we identify UHRF1 as a novel actor in HIV-1 gene silencing and highlight that it constitutes a new molecular target for HIV-1 curative strategies.

microbiology↗

bioRxiv2021

Structure of an infectious mammalian prion

Classical mammalian prions are assemblies of prion protein molecules that are extraordinarily transmissible, with a microgram of protein containing up to 108 lethal doses of infectivity1,2. Unlike most other pathologic and amyloidogenic proteins, prions typically contain glycolipid anchors 3 and abundant asparagine-linked glycans4-6. The infectious nature, complexity, and biophysical properties of prions have complicated structural analyses and stymied any prior elucidation of 3D conformation at the polypeptide backbone level7. Here we have determined the structure of the core of a fully infectious, brain-derived prion by cryo-electron microscopy with [~]3.1 [A] resolution. The purified prions are amyloid fibrils comprised of monomers assembled with parallel in-register intermolecular beta sheets and connecting chains. Residues [~]95-227 of each monomer provide one rung of the ordered fibril core, with the glycans and glycolipid anchor projecting from the lateral surfaces of the fibril. The fibril ends, where prion growth occurs, are formed by single monomers in an extended serpentine combination of {beta}- arches, a Greek key, and loops that presumably template the refolding of incoming monomers. Our results describe an atomic model to underpin detailed molecular hypotheses of how pathologic prion proteins can propagate as infectious agents, and how such propagation and associated pathogenesis might be impeded.

biochemistry↗

bioRxiv2021

Mitophagy antagonism by Zika virus reveals Ajuba as a regulator of PINK1-Parkin signaling, PKR-dependent inflammation, and viral invasion of tissues.

Dysregulated inflammation dominated by chemokine expression is a key feature of disease following infection with the globally important human pathogens, Zika virus (ZIKV) and dengue virus, but a mechanistic understanding of how pro-inflammatory responses are initiated is lacking. Mitophagy is a quality control mechanism that regulates innate immune signaling and cytokine production through selective degradation of damaged mitochondria. Here, we demonstrate that ZIKV NS5 antagonizes mitophagy by binding to the host protein Ajuba and preventing its translocation to depolarized mitochondria where it is required for PINK1 activation and downstream signaling. Consequent mitophagy suppression amplified the production of pro-inflammatory chemokines through PKR sensing of mitochondrial RNA. In Ajuba-/- mice, ZIKV induced early expression of pro-inflammatory chemokines associated with significantly enhanced dissemination to tissues. This work identifies Ajuba as a critical regulator of mitophagy, and demonstrates a role for mitophagy in limiting systemic inflammation following infection by globally important human viruses.

microbiology↗