Biology subjects

Amin, S.

Publications and source records attributed to Amin, S..

At least 19 recordsLinked to original sources

bioRxiv2026

COG5-mediated Golgi organization coordinates neural progenitor fate during human brain development

Apical radial glial cells (aRGs) are highly polarized epithelial cells that drive human cortical development through tightly regulated lineage progression. A distinctive feature of aRGs is their non-canonical Golgi organization, raising the possibility that specialized intracellular trafficking and secretory processes contribute to progenitor behaviour. However, how Golgi architecture contributes to human corticogenesis remains poorly understood. Here, we investigate this question in the context of COG5 deficiency, a rare congenital disorder of glycosylation associated with neurodevelopmental defects, using patient-derived fibroblasts and brain organoids, N-glycomics, glycolipidomics, and single-cell transcriptomics. We show that COG5 deficiency disrupts Golgi organization and impairs Golgi-to-ER retrograde trafficking. At the neurodevelopmental level, COG5-deficient organoids display altered ventricular organization and reduced basal progenitor abundance. Single-cell transcriptomic analysis reveals rewired developmental trajectories characterized by premature differentiation from apical progenitors with activation of neuronal pathways. Despite the absence of major abnormalities in plasma glycoproteins glycosylation, glycolipidomic analysis identified marked defects in glycosphingolipid maturation within patient-derived brain organoids, indicating selective impairment of neural lipid glycosylation. Transcriptomic and biochemical analyses further revealed dysregulation of developmental pathways, including reduced Notch signalling and altered localization of both cleaved Notch1 and the Golgi-associated protein ACBD3. Consistent with impaired progenitor maintenance, COG5-deficient organoids displayed altered cleavage plane orientation in apical progenitors. Together, our findings suggest a link between Golgi organization, intracellular trafficking, membrane glycosylation, and lineage progression in human neural progenitors, identifying Golgi architecture as an important regulator of apical radial glial cell biology and cortical development.

cell biology↗

bioRxiv2026

An improved CRISPR-LICHT screen of 120 Tdark genes illuminates new biologically relevant SOX2 targets in human brain organoids

SOX2 is a transcription factor and central regulator of neural progenitor identity, yet the downstream molecular networks through which it supports human brain development remain incompletely characterized. Here, we applied CRISPR-lineage tracing at cellular resolution in heterogeneous tissue (CRISPR-LICHT) to human cerebral organoids to functionally interrogate SOX2-dependent regulatory networks. Using a SOX2-focused library targeting SOX2 together with conserved neurodevelopmental regulators expressed in neural progenitor cells, we showed that CRISPR-LICHT detects reproducible lineage- depletion phenotypes across genes already known to be involved in progenitor maintenance, fate specification, glial differentiation and neuronal maturation. This extends the application of CRISPR-LICHT beyond the severe neural progenitor phenotypes previously characterized for microcephaly-associated genes and demonstrates its ability to detect perturbation effects across a broader set of neurodevelopmental regulators, involving SOX2 targets previously defined in mouse and now open to further understanding in a human model setting. We further screened 120 evolutionarily conserved, poorly characterized SOX2-dependent genes classified as Tdark within the Illuminating the Druggable Genome framework and identified 28 candidate hits whose disruption impaired neural progenitor lineage expansion and/or survival. These candidates included proteins associated with cytoskeletal organization, membrane dynamics and intracellular architecture, suggesting that SOX2-dependent developmental programmes may engage cellular processes beyond transcriptional regulation. Individual downregulation of CDC42EP4, a poorly characterized CDC42 effector linked to cytoskeletal organization, revealed altered distribution of targeted progenitors between ventricular- and subventricular- like compartments, with changes consistent with altered progenitor-state progression. Together, these findings expand the functional landscape of SOX2-dependent regulation in human neural progenitors and identify cellular architecture as a potential component of SOX2-associated developmental programs.

developmental biology↗

bioRxiv2026

Inferring ecDNA Evolution from Allele Frequency Spectra

Extrachromosomal DNA (ecDNA) can arise early in the development of aggressive tumors or later upon progression, but the impact of chronology on patient outcome is not known. Currently, it is not possible to determine when an ecDNA arose in the course of tumor development and progression, based on genome sequencing data. Here, we develop an analytic method, ecEvol, to infer ecDNA emergence time, selection strength, mutation rate, and clonal dominance from allele frequency spectra in bulk whole-genome sequencing. EcEvol outperforms other methods and predicts parameters with high accuracy across a wide range of parameter values. Applying ecEvol to primary, treatment-naive tumors, we find that ecDNA typically emerges early and undergoes strong positive selection, albeit with substantial variation across cancer types. EcDNAs carrying known oncogenes emerge earlier and reach greater clonal dominance than ecDNAs lacking known oncogenes. In advanced and predominantly treated tumors, ecDNA emerges substantially later than in matched primary tumors, consistent with the generation and selection of new ecDNA during tumor progression and therapy. Longitudinal samples further support continued expansion of ecDNA-bearing lineages. Finally, earlier ecDNA emergence is associated with poorer overall survival. These results provide insight into the chronology of ecDNA formation from a single tumor biopsy taken at any point during the course of the disease, revealing that allele-frequency spectra encode the evolutionary history of ecDNA and provide a quantitative framework for reconstructing its emergence and expansion.

bioinformatics↗

bioRxiv2026

TRAPPC8 Is an Endogenous Brake on UFMylation That Suppresses Tauopathy

UFMylation, a ubiquitin-like protein modification, drives tau spread through the brain, but what keeps this process in check has remained unclear. We show that TRAPPC8 acts as a natural brake on UFMylation, binding directly to the E1 enzyme UBA5 to dampen pathway activity. In Alzheimer's disease brain tissue, TRAPPC8 is reduced while UFMylation is elevated, suggesting this brake fails as disease progresses. Sustaining UFMylation in human iPSC-derived neurons increased tau aggregation and spread while disrupting lysosomal function and lipid balance. Restoring TRAPPC8-UBA5 binding reversed these defects through the lysosomal protein CLN8, which restored lysosomal function and reduced tau pathology. Notably, expressing just the UBA5-binding region of TRAPPC8 was enough to suppress tau pathology in vivo, marking it as a promising therapeutic target.

neuroscience↗

bioRxiv2026

Chromatin Landscape of Cancer Cell Lines Identifies Enhancer Subtypes

Epigenetic aberrations are a hallmark of cancer; however, systematic chromatin state maps of cancer cells are unavailable. We generated and analyzed 803 histone mark profiles in 142 cancer cell lines and 114 human tumors belonging to 9 solid tumor types. Irrespective of their cell-of-origin, cancer cells segregate from normal tissues based on their enhancer patterns, suggesting enhancer deregulation is a fundamental epigenetic feature in cancer. Enhancer based clustering defined 5 distinct subgroups of cancer cells (EpiC1-5) with unique developmental trajectories, molecular features and dependencies. Importantly, we define a set of core TFs that are critical for EpiC-specific enhancer patterns and survival. Notably, EpiC4 represented a predominantly epigenetic, pan-cancer subtype that displays poor survival, activation and dependence on a FN1-CAV1-SRC-PI3K-AKT signaling network. Together, these data uncover enhancer heterogeneity in pan-cancer systems with identification of a novel enhancer-based subtype and identify potential new therapeutic targets associated with unique epigenetic features.

cancer biology↗

bioRxiv2026

Chemoselective Halogenation of Premarineosin A for Next-Generation Antimalarial Development

Premarineosin A undergoes rapid, chemoselective C12 halogenation under mild conditions, providing brominated, chlorinated, fluorinated, and iodinated analogs. These derivatives retained potent antiplasmodial activity against both chloroquine-sensitive and -resistant Plasmodium falciparum strains and displayed smaller reductions in potency against the resistant strain than the parent compound.

biochemistry↗

bioRxiv2026

Coordinated immune architecture underlies durable survival in pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) is characterised by profound immune dysfunction and limited response to immunotherapy. Although tertiary lymphoid structures (TLSs) are associated with improved outcomes, most studies focus on their presence or density, providing limited insight into how their organisation contributes to tumour control. Here, we analyse a unique cohort of treatment-naive PDAC patients enriched for exceptionally rare long-term survivors (LTS, n = 23; >5-year survival) alongside more common short-term survivors (STS, n = 24), enabling direct interrogation of mechanisms underlying durable tumour control. We develop a multi-scale spatial framework integrating multiplex imaging, computational modelling, and transcriptomics to quantify TLS architecture. By modelling TLSs as higher-order immune assemblies, we define their structural states, spatial organisation, assembly rules and tissue context-dependency within the tumour microenvironment. We show that long-term survival is associated with organised, spatially integrated TLSs exhibiting coordinated B and T cell zoning, whereas short-term survival is characterised by disorganised, Treg-enriched, and spatially isolated TLSs, despite similar immune cell abundance. These architectural differences align with transcriptional programmes: LTS tumours display coordinated lymphoid and NF-{kappa}B-driven chemokine signalling, while STS tumours exhibit inflammation uncoupled from immune organisation. Together, these findings demonstrate that durable anti-tumour immunity in PDAC is defined by coordinated transcriptional, cellular, and spatial organisation, rather than immune presence alone. This study provides a blueprint for structure-informed strategies to reprogram the tumour microenvironment and improve outcomes in PDAC. Statement of significanceIntegrating multiplex imaging, computational modelling and transcriptomics in treatment-naive PDAC enriched for exceptional survivors shows that durable tumour control is associated with organised TLS architecture rather than immune abundance alone, providing a framework for immune-architecture-based biomarkers and therapeutic reprogramming.

cancer biology↗

bioRxiv2026

cGAS inhibition delays TDP-43-driven ALS Pathogenesis

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder marked by motor neuron loss and cytoplasmic mislocalization of TAR DNA-binding protein 43 (TDP-43), a key regulator of RNA splicing. However, the upstream modulators of this process remain poorly defined. Here we identify cyclic GMP-AMP synthase (cGAS) as a central mediator of TDP-43 pathology and associated mis-splicing. cGAS expression was elevated in ALS patient brains and enriched across activated microglia. In human iPSC-derived microglia-motor neuron co-cultures, neuronal TDP-43 pathology triggered microglial cGAS activation, whereas pharmacological inhibition with a potent human cGAS inhibitor reduced phosphorylated TDP-43, restored lysosomal and phagocytic programs, normalized microglial reactivity, and reversed TDP-43-associated RNA splicing defects. In vivo, cGAS inhibition in TDP-43 Q331K mice reversed widespread RNA splicing abnormalities across neurons and oligodendrocyte lineage cells, attenuated neurodegenerative pathology, and preserved motor function. Together, these findings identify cGAS as a druggable upstream regulator linking innate immune signaling to TDP-43-dependent RNA mis-splicing and neurodegeneration, and establish cGAS inhibition as a promising therapeutic strategy for ALS.

neuroscience↗

bioRxiv2026

cGAS-mediated IFN-I signaling contributes to disease progression in drug-refractory epilepsy

Epilepsy is a prevalent neurological disease with a third of patients becoming non-responsive to antiepileptic drugs and developing drug-refractory epilepsy (DRE). Here we report that DRE disease progression is contributed by overactive cyclic GMP-AMP synthase (cGAS), a double-stranded DNA sensor that induces type I interferon (IFN-I) signaling. In human DRE microglia, we observe a robust IFN-I signature and the activation of upstream cGAS-STING signaling. Further, in mouse models of Dravet syndrome, a genetic form of DRE, we observe the activation of the cGAS pathway. We show that microglial cGAS can be activated by DNA released from hyperexcitable neurons. Genetic reduction and pharmacological inhibition of cGAS reduces epileptic phenotypes, glial inflammatory signatures, and neuronal transcriptomic changes, underscoring the therapeutic potential of targeting cGAS for DRE treatment.

neuroscience↗

bioRxiv2025

Hallmarks of adaptive immunity in a metastatic clear cell renal cell carcinoma (ccRCC) long-term elite survivor

Clear cell renal cell carcinoma (ccRCC) presents with metastatic disease in nearly one-third of patients, with a 5-year survival of only [~]10%. Although anti-angiogenic therapies and immune checkpoint inhibitors (ICIs) have improved outcomes, therapeutic resistance and immune-related adverse events limit durable responses. Exceptional long-term survivors provide a unique opportunity to uncover mechanisms of sustained anti-tumour immunity and guide therapeutic strategies. Here, we present a spatial and temporal dissection of adaptive immunity in an extraordinary 16-year ccRCC survivor, integrating single-cell sequencing, multiplex immunofluorescence, B and T cell receptor (BCR/TCR) repertoire analysis, and antibody profiling. We reveal persistent and spatially coordinated B and T cell clones over 16 years, indicating long-term immune memory and surveillance throughout tumour evolution. B cell analysis identified pronounced clonal expansions involving intrinsically autoreactive IGHV4-34 B cells undergoing ongoing germinal centre (GC) maturation in tumour-draining lymph nodes (dLNs) and spleen. These clones progressively lost autoreactivity while acquiring tumour-specificity through somatic hypermutation (SHM), consistent with clonal redemption. Redeemed B cells displayed enhanced antigen-presenting functions and localised to tertiary lymphoid structures (TLS), where they interacted with CD8 T cells, as inferred from doublet analysis. In parallel, persistent CD8+ effector T cell clones highlighted the contribution of long-lived lymphocytes to tumour control. Comparison of the primary tumour and pancreatic metastatic with paired tumour-free dLNs showed that TLS mirrored GC functionality, particularly for PD-1+ CD8+ T cells, while TLS maturation was stroma-dependent and impaired at the metastatic site. Finally, tumour-derived BCRs revealed antibody binding to tumour specific "public" antigens without cross-reactivity to normal tissue. Together, these findings establish clonal persistence, TLS engagement, and coordinated B-T cell immune surveillance as hallmarks of durable tumour control, providing a framework for next-generation antibody therapeutics and patient stratification in metastatic ccRCC. What is already known on this topic.Tertiary lymphoid structures within the tumour microenvironment (TME) and clonal expansions of CD8+ T cells are associated with better survival and improved response to immunotherapies in ccRCC. However, identifying markers of prolonged survival is challenging due to the rarity of long-term survivors (LTS), and the predominance of studies focused on T cell immunity, leaving B cell contribution almost unexplored. What this study adds.This study provides an integrated analysis of B and T cell responses in an exceptional 16-year LTS with metastatic ccRCC, revealing key immunologic features of sustained anti-tumour immunity. Beyond T cell dynamics, it highlights the multifaceted role of B cells as antigen presenting cells, antibody producers, and modulators of CD8+ T cell effector functions through direct interactions within TLS. Importantly, it reveals potential tumour-specific antigens driving humoral responses. How this study might affect research, practice or policy.By uncovering mechanisms of sustained tumour control, this work establishes a framework for identifying adaptive immune biomarkers of long-term survival and refining patient stratification in metastatic ccRCC. Multimodal assessment of B cell specificity and spatial interactions between re-educated B cells and CD8+ T cells within TLS introduces a new paradigm for understanding coordinated B and T cell responses. These insights have direct implications for antibody-based drug discovery and development of immunotherapies that harness the B-T cell axis.

cancer biology↗

bioRxiv2025

Sex Differences in Low-dose Ethanol Effects on Motivated Behavior and Limbic Corticostriatal Activity

Structured abstractO_ST_ABSBackgroundC_ST_ABSEven at lower doses, ethanol exposure impacts both the brain and behavior. Emerging work has shown that chronic exposure to lower doses of ethanol may lead to inflexible behaviors and promote aberrant reward seeking. This study investigated the impact of chronic, low-dose ethanol exposure on neural substrates of reward and on motivated behavior. MethodsAdult C57BL/6J mice were trained to self-administer sucrose. Throughout training, mice received an injection of low-dose ethanol (0.5g/kg) or saline, 1 hour after each session. Mice did not receive ethanol during testing. Mice were then tested in a PR task in which the reward magnitude of reinforcer was reduced (small or large) or increased (small or large). A subset of mice expressed a retrograde tracer in the nucleus accumbens (NAc), and cFos expression within NAc circuits was analyzed following a sucrose self-administration session. ResultsChronic low-dose ethanol exposure altered behavioral responding in female mice following small changes in reward magnitude. Female mice showed divergent response patterns when there was a small reduction in reward magnitude, with greater proportions of ethanol-exposed female mice either increasing or decreasing responding versus controls. Following a small increase, low-dose ethanol female mice significantly increased responding versus controls. Female - but not male - mice exposed to chronic low-dose ethanol shifted behavioral strategy with a reduction in magazine checking behavior. Low-dose ethanol exposure altered cFos expression within the prelimbic cortex and its projections to the NAc during reward seeking. ConclusionsChronic, low-dose ethanol altered behavioral responding and strategy in female mice in response to changes in reward value. Low-dose ethanol exposure impacted cFos induction in prelimbic cortex and its projections to NAc in both female and male mice. Future studies should investigate the consequences of chronic, low-dose ethanol on the brain and behavior to understand what underlying processes drive aberrant reward-seeking behaviors.

animal behavior and cognition↗

bioRxiv2025

Ionic modulation of interpenetrating network formation, structure and recovery in low-polymeric, supramolecular hyaluronic acid based-hydrogel

The formation of interpenetrating polymer networks (IPNs) in polysaccharide-based hydrogels is influenced by ion valency and coordination chemistry. In this work, hyaluronic acid (HA) and kappa-carrageenan ({kappa}-CG) were combined at low polymer concentrations suitable for injectable hydrogel applications and enriched with monovalent (K+), divalent (Ca2+), and trivalent (Al3+) ions to investigate ion-specific contributions to network formation, structure and recovery. FTIR spectroscopy showed that K+ did not produce detectable sulfate or carboxylate shifts, consistent with a predominantly physical mixture and the absence of IPN formation. Ca2+ induced concentration-dependent shifts in both the amide/carboxylate region and the sulfate band (1232 [->] 1236 cm-1), absent at a low concentration but reemerging at higher concentrations, consistent with local chain compaction, complexation of HA carboxylates and bridging between{kappa} -CG helices, indicating promotion of a semi-interpenetrated network structure above a thresh-old concentration. Al3+ induced a distinct shoulder in the HA carboxylate region, confirming HA coordination and co-crosslinking with{kappa} -CG, yielding a semi-IPN. Microrheology showed progressively stronger local confinement with increasing ion valency corroborating insights from spectroscopy, while recovery tests showed Ca2+ attained the highest recovery potential possibly due to more robust network formation, Al3+ systems displayed moderate recovery but overscreening at high concentrations resulted in network collapse, and K+ systems displayed poor recovery.Importantly, these ion-specific outcomes must be interpreted in the context of combined electrostatic screening effects, which contribute to charge neutralization and polymer chain association independent of coordination chemistry. Collectively, these findings highlight ion charge as critical design levers which may be leveraged in tailoring mechanical properties of interpenetrating network hydrogels for injectable applications. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=124 SRC="FIGDIR/small/675661v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@1924ee2org.highwire.dtl.DTLVardef@7916cforg.highwire.dtl.DTLVardef@1c89221org.highwire.dtl.DTLVardef@f1c2c7_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIIncorporation of{kappa} -carrageenan ({kappa}CG) into a chemically unmodified hyaluronic-acid (HA) based hydrogel even at low concentrations is a potentially viable route for more efficient structuring. C_LIO_LIInterpenetrating network formation, structure and recovery of HA-{kappa} CG networks can be tuned by charge density and coordination behavior of the crosslinking ion. C_LIO_LICa2+ reinforces{kappa} CG junction zones, yielding the highest elastic moduli and recovery capacity, with evidence of semi-IPN formation pointing to more robust network formation relative to Al3+ and K+. C_LI

biochemistry↗

bioRxiv2025

SpatioEv: Spatial evolution of protein and morphological features reveals development dynamics of cells and spatial neighbourhoods

Understanding cellular function in tissues demands sophisticated tools to decode complex microenvironmental interactions. Current spatial analysis methods often lack the comprehensive framework needed to systematically analyse cell morphology, dynamics, interactions, and extracellular matrix (ECM) architecture. We introduce SpatioEv, a unified computational framework for highly multiplexed tissue imaging that addresses these critical gaps. SpatioEv integrates automated quality control, cell phenotyping, neighbourhood identification, multi-scale spatial characterization, niche boundary analysis, ECM fiber-cell interaction mapping, and spatiotemporal trajectory inference. This pipeline enables reproducible cell annotation, reveals novel ECM-cell interactions, characterizes tissue neighbourhood boundaries, and infers developmental progressions directly from spatial data. Using this, we can identify disease-specific spatial signatures distinguishing rheumatoid arthritis from osteoarthritis, characterize diverse tumour boundary phenotypes in cancer metastases in liver, and map evolutionary trajectories in pancreatic ductal adenocarcinoma (PDAC) at single-niche resolution. Our findings highlight the significance of spatial context in shaping cell behaviour and underscore its potential to uncover emergent tissue architecture and cellular dynamics. By addressing major analytical challenges, SpatioEv provides a scalable, adaptable platform for advancing spatial biology and translational research.

systems biology↗

bioRxiv2025

Early Indirect Neurogenesis transitions to late Direct Neurogenesis in mouse cerebral cortex development

The cerebral cortex must contain the appropriate numbers of neurons in each layer to acquire its proper functional organization. Accordingly, neurogenesis requires precise regulation along development. Cortical neurons are made either directly by Radial Glia Cells (RGCs) that self- consume, or indirectly from RGCs via Intermediate Progenitor Cells (IPCs) and largely preserving the RGC pool. According to the standing model of cortical development, Direct Neurogenesis predominates at early stages of development, and progressively shifts to Indirect Neurogenesis, which predominates at late stages. However, neurogenesis at early stages should be compatible with RGC amplification, and neurogenesis at late stages needs to involve RGC consumption, which seems in conflict with the standing model. Here we studied the modes of neurogenesis along cortical development using multiple approaches, including birthdating, live imaging and MADM clone labeling. Contrary to the established dogma, our data show that Indirect Neurogenesis clearly predominates at early developmental stages, gradually shifting to Direct Neurogenesis at late stages. These findings challenge the current model of cortical neurogenesis, and prompt a re-evaluation of previous and ongoing work about the genetic and molecular mechanisms regulating this process.

neuroscience↗

bioRxiv2025

Temperature and Excipient Mediated Modulation of Monoclonal Antibody Interactions Revealed by kD, Rheology, and Raman Spectroscopy

High-concentration monoclonal antibody (mAb) formulations are frequently constrained by elevated viscosity and colloidal instability, stemming from enhanced intermolecular interactions under crowded conditions. This study delineates the thermodynamic and rheological consequences of modulating protein-protein interactions through excipient-mediated and temperature-dependent mechanisms. Using an orthogonal analytical framework comprising diffusion interaction parameter (kD) measurements, high-shear rheometry, and Raman spectroscopic profiling, we interrogated mAb solutions at [~]80 and 160 mg/mL across a physiologically and industrially relevant thermal window (5-45 {degrees}C). In the absence of ionic additives, high kD values ([~]60 mL/g) indicated dominant long-range electrostatic repulsions, resulting in suppressed self-association and lower viscosity. Incorporation of NaCl (0.05% w/v) markedly decreased kD ([~]16-20 mL/g), consistent with Debye screening of surface charges and a shift toward short-range hydrophobic and van der Waals attractions, particularly impactful at elevated protein concentrations and low temperatures. Polysorbate 20 (0.05% v/v) mitigated these interactions via preferential surface adsorption, while sucrose exhibited a dualistic, concentration-dependent influence on viscosity via preferential exclusion and entropic crowding. The combination of NaCl and PS20 yielded the most pronounced rheological suppression, reflecting synergistic attenuation of both long-range repulsion and short-range association. Raman spectral analysis of Amide I/III regions confirmed structural invariance under thermal and shear stress, attributing viscosity modulation to colloidal rather than conformational perturbations. Collectively, these data elucidate the multivariate control of interparticle potentials in mAb solutions and provide a predictive basis for engineering subcutaneous formulations that optimize manufacturability, physical stability, and injectability through strategic manipulation of colloidal interaction landscapes.

biophysics↗

bioRxiv2025

Advancing (-)-Premarineosin A as a Potent Antimalarial Therapeutic via Metabolic Engineering and Late-Stage Derivatization

Diversification of structurally complex natural products remains a key challenge in the discovery of next-generation therapeutics. Premarineosin A, a potent and selective antimalarial natural product, is a promising yet underexplored scaffold due to limited availability and synthetic complexity. In this work, we overcome both barriers by coupling metabolic engineering with late-stage derivatization, enabling the first systematic exploration of the premarineosin A scaffold. Rational engineering of Streptomyces eitanensis, encoding a (-)-premarineosin A biosynthetic gene cluster, increased titers over 200-fold. Sustainable production of (-)-premarineosin A enabled a unique semi-synthetic and biocatalytic derivatization campaign. In this first structure-activity relationship study of premarineosin A, we accessed a suite of novel analogs, including a C12-brominated derivative with nanomolar potency (EC50 < 5 nM). This work establishes (-)-premarineosin A as a tractable and evolvable antimalarial scaffold, demonstrating how chemical biology approaches can unlock new structural and pharmacological space from complex microbial metabolites.

microbiology↗

bioRxiv2024

A resource for extracellular vesicles from activated CD4 T cells that relay pro-inflammatory signals

CD4 T helper cells (TH cells) play a vital role in coordinating and amplifying the immune response to specific pathogens. They constitutively produce different kinds of extracellular vesicles (EVs), which mediate cell-to cell communication and play diverse roles in immune regulation and inflammatory processes. Here we provide a resource documenting the composition of activated TH cell EVs and demonstrating their ability to instigate pro-inflammatory response in antigen-presenting cells (APCs). EVs were characterized by lipidomics, proteomics, and NanoFCM. The activated TH cells derived EVs (act-EVs) were found to be enriched in TH cell-specific proteins, transmembrane and cytosolic EV marker proteins, and HLA proteins relative to resting CD4 T cells EVs (rest-EVs). The pro-inflammatory effect of act-EVs vs rest-EVs on donor matched APCs were characterized by chemokine and cytokine profiling and flow cytometry analysis. There was no discernible contrast in endotoxin levels between act-EVs and rest-EVs. Functional distinctions were seen to arise from variations in the content and composition of these EVs. Moreover, we validated our findings with an in-vivo investigation in mice, demonstrating the recruitment of monocytes, dendritic cells (DCs), neutrophils, and NK cells in the spleen, accompanied by the release of pro-inflammatory cytokines in the serum after administering act-EVs. In summary, this study sheds light on the role of TH cell released EVs in modulating the immune response during pro-inflammatory responses and this resource provides a foundation for development of novel therapeutics on EV based scaffolds.

immunology↗

bioRxiv2024

Alzheimer's disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model

The strongest risk factors for Alzheimers disease (AD) include the {chi}4 allele of apolipoprotein E (APOE), the R47H variant of triggering receptor expressed on myeloid cells 2 (TREM2), and female sex. Here, we combine APOE4 and TREM2R47H (R47H) in female P301S tauopathy mice to identify the pathways activated when AD risk is the strongest, thereby highlighting disease-causing mechanisms. We find that the R47H variant induces neurodegeneration in female APOE4 mice without impacting hippocampal tau load. The combination of APOE4 and R47H amplified tauopathy-induced cell-autonomous microglial cGAS-STING signaling and type-I interferon response, and interferon signaling converged across glial cell types in the hippocampus. APOE4-R47H microglia displayed cGAS- and BAX-dependent upregulation of senescence, showing association between neurotoxic signatures and implicating mitochondrial permeabilization in pathogenesis. By uncovering pathways enhanced by the strongest AD risk factors, our study points to cGAS-STING signaling and associated microglial senescence as potential drivers of AD risk.

neuroscience↗