Biology subjects

Khan, S.

Publications and source records attributed to Khan, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Amino Acid Metabolic Signature Links Pediatric Environmental Enteric Dysfunction to Maternal-Fetal Growth Restriction Across Two Independent Cohorts

Environmental Enteric Dysfunction (EED) is a leading contributor to childhood stunting. Most EED literature derives from postnatal pediatric cohorts, leaving unclear how much of the metabolic signature reflects acquired intestinal pathology versus growth restriction originating earlier. We applied genome-scale metabolic modeling to explore whether metabolic features of pediatric EED overlap with those of maternal plasma proteomes associated with adverse early-life growth. Duodenal transcriptomics from the Study of Environmental Enteropathy and Malnutrition (SEEM; 52 children with EED, 24 controls) and maternal plasma proteomics from the Alliance for Maternal and Newborn Health Improvement (AMANHI; n = 2,485 pregnant women) were integrated with the Human1 model using Reaction Inclusion by Parsimony and Transcript Distribution (RIPTiDe), followed by flux sampling and Linear Discriminant Analysis, across five growth-related proxies (small-for-gestational-age, low birth weight, preterm birth, stunting, and wasting). Amino acid and nucleotide metabolism were prominent among the top discriminating reactions in EED and most proxies. Of the 50 reactions distinguishing EED from control, 24 (48%) were among the top reactions in at least one proxy, and 19 (38%) with low birth weight, the largest of any proxy. These exploratory findings suggest shared metabolic pathways across tissues and life stages and motivate longitudinal studies.

systems biology↗

bioRxiv2026

PepPr: De Novo peptide sequencing with peptide priors

Mass spectrometry-based peptide sequencing underpins proteomics. Database search confines to predefined candidates, whereas de novo peptide sequencing (DNPS) struggles with incomplete spectra. Existing hybrid methods use databases only for post hoc correction or retrieve previously identified spectra to guide decoding. We instead combine DNPS with a peptide prior: a language model fitted to a reference proteome, tolerating variants yet uncertain on strongly divergent sequences. Relative to prior-free DNPS, our implementation, PepPr, improved reference peptide identification and improved rather than suppressed variant identification. Using a related proteome as prior, it matched or outperformed homology-driven database search, and its gain over prior-free DNPS grew with relatedness. In antibody sequencing, it improved recovery of peptides spanning the variable-constant boundary, deamidation calls, and assembly, while preserving recall of hypervariable regions inaccessible to database search. Peptide priors thus bring reference knowledge into DNPS without limiting discovery.

bioinformatics↗

bioRxiv2026

Resistance-Mutant Rescue Establishes On-Target CHI3L1 Inhibition by CHI-DEL, a Brain-Penetrant Small Molecule with In Vivo Efficacy in Glioblastoma

CHI3L1 (YKL-40) drives glioblastoma progression and immunosuppressive neuroimmune signaling, but as a non-enzymatic secreted glycoprotein it has lacked a genetic tool to confirm that small molecule effects are truly on-target. From a DNA-encoded small molecule library we identify CHI-DEL, a potent CHI3L1 ligand, and solve a 2.81 [A] co-crystal structure (PDB 10JV) revealing a binding trajectory centered on Trp99. Structure-guided mutagenesis yields W99F, a compound-resistant CHI3L1 allele that retains native secretion, basal signaling, and thermal stability, unlike the destabilizing W99A control, establishing a clean chemical-genetic separation of biology from drug sensitivity. In isogenic knockout/rescue cells, wild-type rescue restores both phenotype and CHI-DEL sensitivity across invasion, proliferation, and a multi-node signaling program (pSTAT3 and NF-{kappa}B), while W99F rescue restores phenotype but confers resistance to CHI-DEL that is complete for some readouts and partial for others. This same epistasis was reproduced in human iPSC-derived microglia, where CHI-DEL reverses a GBM-conditioned-medium-induced phenotype in a CHI3L1- and Trp99-dependent manner. In vivo, CHI-DEL achieves brain and tumor exposure, engages its target and disrupts CHI3L1-CD44 signaling in a dose-dependent manner, remodels the tumor immune microenvironment, and confers a dose-dependent survival benefit that is specific to the active compound. Together, these data extend CHI3L1 small molecule inhibitor development beyond in vitro optimization, providing genetic proof of on-target pharmacology and a brain-penetrant therapeutic strategy for glioblastoma.

neuroscience↗

bioRxiv2026

STAT3 dual role in sex-biased and differentiation-gated interferon gamma memory

The innate immune system possesses a unique form of memory, known as trained immunity. An initial stimulus induces cellular reprogramming for a non-specific amplified response to a subsequent challenge. This process can be achieved through gene priming, where exposure to a specific cue sensitizes future gene expression. Interferon-gamma (IFN{gamma}) memory is a specialized form of priming, where both the initial and recall signals are mediated by the same IFN{gamma} cytokine. The mechanisms governing IFN{gamma} memory in humans remain poorly understood. We investigated the mechanisms governing IFN{gamma} memory and characterized it in human primary macrophages. We discovered a dual role for the STAT3 transcription factor in IFN{gamma} memory. It acts as a repressor of memory establishment by indirectly inhibiting STAT1 Ser727 phosphorylation, while also being required for memory recall. Furthermore, we demonstrated that IFN{gamma} memory is sex-biased, with males exhibiting a more pronounced effect characterized by reduced variability in gene expression upon re-exposure to IFN{gamma}. This defines IFN{gamma} recall as a function of transcriptional precision. We also identified a novel family of chemokine genes that exhibit IFN{gamma} concentration dependent memory effects. Additionally, we established a model system to study this process and found that memory is critically dependent on the cellular phenotype. Specifically, our results show that for some genes, monocyte-to-macrophage differentiation is necessary, while for others, this differentiation step is sufficient for recall of the previous response. Our findings redefine the IFN{gamma} memory program, establishing it as a sex-biased phenomenon governed by a novel regulatory network involving differentiation and STAT3 function. These insights provide critical context for understanding immune heterogeneity and are essential for the rational design of personalized therapies that harness trained immunity.

molecular biology↗

bioRxiv2026

Integration of Neuroimaging and Histopathology in a Squirrel Monkey Model of Spontaneous Cerebral Amyloid Angiopathy and Amyloid-Related Imaging Abnormalities

Cerebral amyloid angiopathy (CAA) is a prevalent cerebrovascular pathology in AD and contributes to amyloid-related imaging abnormalities (ARIA), a major complication of current anti-amyloid immunotherapy. Despite its growing clinical importance, critical gaps remain in the development of reliable biomarkers for antemortem diagnosis of CAA. Squirrel monkeys (SQMs) are a valuable non-human primate model with translational relevance due to their universal propensity to develop abundant CAA and spontaneous ARIA in geriatric animals. The present study employed R2*, the apparent transverse relaxation rate, which is sensitive to susceptibility-related tissue properties, including iron content and blood oxygenation levels, to monitor age-related brain pathology in SQMs with varying CAA severity. Young, early geriatric, and late geriatric SQMs underwent 7T MRI using a dual-purpose T2*-w 3D multi-gradient-echo sequence for high-resolution anatomy and quantitative R2* mapping, alongside T2-w/FLAIR imaging. Whole-brain and gray matter R2* increased with age. In contrast, white matter R2* showed an initial increase followed by a late-life reversal, likely reflecting age-related changes in myelin integrity, tissue microstructure, and tissue water content. MRI-histopathology correlation linked T2*-w MRI hypointensities to CAA-positive iron-laden vessels associated with perivascular inflammation and, in some cases, hemosiderin deposits. Here we confirmed the occurrence of ARIA-H and ARIA-E events in geriatric animals. SQMs provided a valuable opportunity to examine the underlying pathology of spontaneous ARIA-E, revealing distinctive tissue signatures associated with its manifestation. ARIA-E hyperintensities were characterized by reactive gliosis and BBB disruption, whereas more advanced lesions exhibited perivascular lymphocytic infiltration and evidence of myelin and axonal injury. The current study presents compelling evidence linking R2* alterations with CAA severity and ARIA-related tissue injury, providing a foundation for further advancing early detection of CAA, ARIA risk assessment, and treatment strategies.

neuroscience↗

bioRxiv2026

Spatial proteomics identifies altered thick ascending limb cells as drivers of kidney disease through uromodulin retention

Chronic kidney disease (CKD) is increasingly prevalent and is a leading cause of mortality. Recent transcriptomic studies have identified the persistence of injury-induced renal tubular epithelial cell states, yet the cell populations that drive CKD remain unresolved. Uromodulin (UMOD) is the most abundant urinary secreted protein expressed exclusively in thick ascending limb (TAL) epithelial cells in the kidney. UMOD is strongly associated with CKD risk in genome-wide association studies, suggesting a broader, yet unexplored role of UMOD and TAL cells in CKD pathogenesis. Here, using spatial proteomics, we identified an injury-induced TAL cell state marked by intracellular UMOD accumulation. Spatially resolved multimodal integration revealed that UMOD accumulation occurred without transcriptional upregulation. Impaired urinary UMOD secretion further supported pathological intracellular retention. These altered TAL cells with UMOD retention exhibited inflammatory signaling, formed profibrotic niches enriched with M2-like macrophages across renal compartments, and were associated with CKD progression in multiple experimental models. Reducing the burden of UMOD retention diminished altered TAL cells and their profibrotic microenvironments, and attenuated CKD development. A similar altered TAL state was identified in human kidney disease and was associated with worse kidney function. Together, we identify pathological UMOD retention and altered TAL cells as key drivers of CKD development and potential therapeutic targets. This study also highlights that protein-level alterations can redefine disease-associated cell states beyond transcript profiling.

cell biology↗

bioRxiv2026

AGROtools: A comprehensive modular cloning toolset for Agrobacterium strain engineering

Agrobacterium-mediated transformation is a cornerstone of plant genetic engineering, yet many crops remain recalcitrant to transformation and its efficiency is highly species- and genotype-dependent. The limited diversity of disarmed agrobacterial strains available for biotechnology, and the technically challenging workflows typically required for strain modification, constrain efforts to develop improved plant transformation platforms. Here, we describe the development of AGROtools-a versatile, expandable, and user-friendly modular cloning plasmid collection comprising more than 75 individual components, that is designed to simplify genetic engineering of agrobacteria. Constructs assembled with this toolkit couple visual reporters with selectable and counterselectable markers to facilitate identification of recombinant clones, thereby reducing reliance on PCR-based screening. We constructed and tested reporter cassettes that are functional across diverse agrobacterial strains and genomic contexts. By linking a visual reporter combinatorially with various antibiotic resistance markers and orthogonal site-specific recombinase recognition sequences, AGROtools can enable marker removal and recycling for up to four successive genomic modifications. We demonstrate the utility of AGROtools by disarming 10 novel wild-type strains, and accomplishing serial modifications within individual strain backgrounds. In addition to conventional recA-mediated homologous recombination, the collection incorporates components for applying contemporary strain engineering approaches, including CRISPR/dCas9 base editing, INTEGRATE-mediated targeted insertion, and phage-derived recombineering systems. Constructs can be assembled and deployed rapidly, enabling isolation of strains carrying an intended modification in less than two weeks. AGROtools provides a broadly applicable resource for accelerating strain development and genetic studies in agrobacteria, with potential to advance plant biotechnology by aiding improvement of disarmed strains.

plant biology↗

bioRxiv2026

Mitochondrial priming in human germ cell tumors is dependent on MCL1 and BCL2L1

Germ cell tumors (GCTs) are highly sensitized to cell death in response to DNA damaging agents, a property that underlies the success of current chemotherapeutic regimens. To address the molecular basis for this, known as apoptotic priming, we evaluated how different BCL2 family members modulate the heightened sensitivity of GCTs to therapy. Our analysis of human GCTs finds consistently high expression of the pro-survival factors MCL1 and BCL2L1 (BCLX) in a cohort of primary tumors and in their embryonic precursor cells, frequently accompanied by copy number gains of these loci and reciprocal losses of their pro-apoptotic interaction partners and inhibitors, PMAIP1 (NOXA) and BAD. We find that co-inhibition of MCL1 and BCLX using selective BH3 mimetics results in a potent synthetic lethality in multiple GCT embryonal carcinoma cell lines. When these cell lines were cultured with the DNA damaging agents cisplatin or etoposide, inhibition of MCL1 or BCLX potentiated their apoptotic effect in undifferentiated embryonal carcinoma cell lines, but not in retinoic acid-differentiated cells. The inhibition of MCL1 also heightened cisplatin sensitivity in p53-deficient or -mutant cell lines, which is associated with resistance to therapy. Employing an in ovo human xenograft model, we validate that the combination of cisplatin and MCL1 inhibition enhanced the therapeutic response by eliminating tumor cells. Our findings identify MCL1 and BCLX as critical factors to maintain GCT viability and as putative therapeutic targets to further augment GCT responsiveness to DNA damaging agents.

cancer biology↗

bioRxiv2026

WHAT IS NORMAL? MULTIMODAL CHARACTERIZATION OF NON-DISEASED PEDIATRIC DUODENAL BIOPSIES USING MACHINE LEARNING IMAGE ANALYSIS AND TRANSCRIPTOMICS

Pediatric endoscopy is performed only when clinically indicated, limiting access to healthy duodenal tissue. Biopsies with duodenal no pathologic abnormality (NPA) are often used as controls despite the presence of symptoms or inflammatory disease found elsewhere in the gastrointestinal (GI) tract. We characterized pediatric duodenal NPA tissue across clinical, histologic, cellular, and transcriptomic domains. Methods Archival duodenal NPA biopsies were obtained with clinical metadata and hematoxylin-and-eosin whole-slide images (WSIs). Duodenal mRNA-seq data were analyzed from a subset of patients with duodenal NPA. Clinical metadata and WSIs underwent machine-learning analysis, cell populations were quantified from WSIs, and RNA-seq data underwent differential expression and pathway-enrichment analyses. Results The primary cohort included 195 patients with duodenal NPA. Comparisons between patients with non-duodenal GI disease and those with no GI disease showed differences in inflammatory biomarkers and follow-up utilization. Unsupervised clinical clustering identified three clusters with partial enrichment for IBD with colonic inflammation and Eosinophilic Esophagitis (EoE) with esophageal inflammation. Supervised clinical classification showed modest discrimination. WSI clustering showed limited disease-status discrimination, and cell quantification showed no significant group differences. In the separate RNA-seq cohort of 43 patients, differential-expression and pathway-enrichment analyses identified transcriptional and pathway-level differences between disease-status groups. Conclusions This multi-level characterization indicates that pediatric duodenal NPA tissue should not be treated as a uniform control category. Clinical metadata and transcriptomics revealed clinical and molecular heterogeneity, while histologic and cell analyses showed limited disease-status separation, supporting a refined definition of control tissue.

physiology↗

bioRxiv2026

Isoleucine and asparagine influence the growth of staphylococcal strains in atopic dermatitis

Atopic dermatitis (AD) is a multifactorial, chronic skin disease associated with microbial factors. It is known that staphylococcal skin microbes play a role in the pathophysiology of AD, notably S. aureus. However, how staphylococcal strain variation affects disease aetiology and progression remains unclear. Using a culture-dependent approach, we analyzed the genomic and phenotypic profile of staphylococcal strains isolated from a Hong Kong children cohort (n = 70). Presence of S. aureus was positively associated with AD skin, whilst S. epidermidis and S. hominis were positively associated with healthy skin, but no overall strain type was associated with AD. In vitro experimentation revealed that there is demarcation in S. aureus strain growth, biofilm biomass formation, and metabolite production by disease severity. While isoleucine and asparagine promoted S. aureus growth, these amino acids suppressed S. hominis growth. These collective findings highlight the importance of strain-level and metabolic interactions of staphylococci in AD pathophysiology.

microbiology↗

bioRxiv2026

Single-cell proteomics reveals cell-type-specific functional coordination in PBMCs

The coordination of molecular networks defines cellular functions. This is reflected in molecular covariation within a cell type, which is more subtle than the differences separating cell types and has therefore been difficult to quantify. To achieve the depth, consistency and accuracy required to resolve such covariation, we leveraged single-cell proteomics (plexDIA) and transcriptomics (Smart-seq3xpress) to analyze the proteomes and transcriptomes of thousands of single peripheral blood mononuclear cells (PBMCs). plexDIA quantified more protein-coding gene products per cell with higher data completeness while Smart-seq3xpress quantified more gene products across all cells. The protein measurements revealed cell-type-specific proteome architecture -- shaped in part by protein stability, and complex coordination -- that was undetectable in our mRNA data. Specifically, protein covariation within a cell type suggests cell-type-specific protein-protein interactions and functional rewiring of biological pathways independent of previously characterized abundance differences. Covariation analysis within cell types resolves a B cell-specific axis of translational states inversely covarying with GDF6 cytokine abundance. Our framework captures cell-type-specific functional coordination representing a distinct information layer accessible via single-cell proteomics.

systems biology↗

bioRxiv2026

Protonation- and substrate-regulated dimer opening couples brain-type creatine kinase to vesicular and actin-remodeling membranes

Brain-type creatine kinase (CK-BB) buffers local ATP demand through reversible phosphotransfer between ATP and phosphocreatine, yet how this soluble metabolic enzyme engages membrane compartments is unknown. Here, we combine fluorescence microscopy, DEER spectroscopy, hydrogen-deuterium exchange and native mass spectrometry, DEER- and AlphaFold-guided modeling, and long-timescale molecular dynamics to define the pH- and substrate-regulated conformational landscape governing CK-BB membrane association. Acidification promotes curvature-sensitive membrane binding and redistributes endogenous and recombinant CK-BB from diffuse cytosolic pools to punctate vesicular structures and membrane ruffles. Substrates independently promote curvature-sensitive association at neutral pH. DEER and modeling reveal an asymmetric dimer in which the convex surface remains restrained, whereas the concave catalytic-regulatory surface samples pH- and substrate-dependent intermediates. We identify progressive dimer opening as a novel regulatory mechanism whereby acidification and substrate binding increase dynamics across the convex surface and N-terminal dimer interface, generating membrane-competent conformations that facilitate curvature sensing and membrane association. Substrate binding buffers acid-induced deprotection while preserving dynamics near the His191/Ser199 regulatory interface. These findings establish CK-BB as a previously unrecognized curvature-sensitive metabolic enzyme and define dimer dynamics as a molecular switch coupling protonation and substrate occupancy to curved-membrane recognition and localized ATP regeneration, with potential relevance to neurodegeneration and cellular stress.

biophysics↗

bioRxiv2026

Interplay between ferroptosis and guttae in an early-onset murine model of Fuchs endothelial corneal dystrophy (FECD)

Col8a2Q455K/Q455K (Q455K) mice exhibit features of early-onset Fuchs endothelial corneal dystrophy (FECD), including decreased endothelial cell density (ECD) and guttae formation. Within the context of these clinical features, this study longitudinally evaluates ferroptosis in Q455K and wild-type (WT) mice using in vivo imaging, PCR and immunohistochemistry. Fifty-six Q455K and 56 WT mice were evaluated from 3 to 24 months of age with in vivo confocal microscopy; ECD and guttae were measured. Ferroptosis marker expression was determined with PCR and immunohistochemistry (IHC). Data were analyzed using two-way ANOVA with Tukeys post hoc test, Chi-square test and a paired t-test. The ECD significantly decreased in both groups from 3 to 24 months of age, but more markedly in Q455K (2285 {+/-} 317 to 1012 {+/-} 58 cells/mm{superscript 2}) versus WT mice (2714 {+/-} 139 to 2057 {+/-} 149 cells/mm{superscript 2}, P<0.0001). Guttae were observed exclusively in Q455K mice beginning at 3 months of age and increased over time (P=0.0003). The Q455K mice demonstrate guttae at the vertices of corneal endothelial cells rather than their centers (74.3% vs. 25.7%P<0.001). Expression of ferroptosis-related genes (Tfrc, Slc40a1, Ftl1, Gpx4) were significantly increased in the Q455K versus WT mice (P<0.05). Furthermore, corresponding protein expression (transferrin receptor 1, ferroportin, ferritin and glutathione peroxidase 4) was significantly elevated adjacent to guttae in Q455K versus WT mice (P<0.05). These findings implicate guttae in the initiation of ferroptosis as it relates to the pathophysiology of FECD and provide an optimal window for testing novel FECD therapies using this murine model, particularly those that target ferroptosis. Significance StatementFuchs endothelial corneal dystrophy (FECD) is a major cause of corneal blindness, yet the mechanisms driving endothelial cell loss remain unclear. Using an early-onset Q455K murine model, we show that disease onset occurs by 3 months of age and progresses with characteristic corneal guttae, endothelial cell loss, and morphological abnormalities replicating human FECD. By identifying ferroptosis adjacent to guttae in the Q455K, we demonstrate this mechanism is not specific to genetic mutations, but rather a conserved driver of corneal endothelial loss within the context of guttae formation. These findings establish an FECD progression timeline and reveal a mechanistic link between ferroptosis and guttae, validating this model as a critical tool for evaluating targeted therapeutic strategies.

developmental biology↗

bioRxiv2026

Kinome-wide CRISPR/Cas9-knockout screening reveals critical protein kinases in vasopressin V2-receptor signaling

Identification of signaling networks is an essential goal in systems biology. Here, we use CRISPR/Cas9 knockout screening (employing a whole kinome sgRNA library) to identify functionally critical protein kinases in a well-studied Gs-dependent G-protein coupled receptor (GPCR)-signaling model, namely the vasopressin V2 receptor (V2R) pathway. Screening was done using a specially-designed fluorescence-based reporter cell line with green-fluorescent protein (GFP) co-transcribed with Aqp2, a gene whose transcription is dependent on vasopressin-mediated activation of protein kinase A (PKA). Positive regulators (n=14) included PKA-catalytic subunit (Prkaca) and Dyrk1a (minibrain homolog). Negative regulators (n=12) included PKA-regulatory subunit type I, Stk11 (catalytic subunit of liver kinase B1 [LKB1] complex), and three TGF-{beta} receptor subunits (Tgfbr1, Tgfbr2, Tgfbr3) (see https://esbl.nhlbi.nih.gov/Databases/Kinome-CRISPR-screen/ for full list). Dyrk1a knockout cell lines failed to express AQP2 protein and exhibited a profound decrease in AQP2 mRNA. RNA-sequencing demonstrated widespread increases in cell-cycle transcripts, with a general defect in cell differentiation, accounting for AQP2 loss. TGF-{beta} exposure to un-transformed cells results in a profound decrease in V2R and AQP2 mRNA abundance along with multiple additional transcriptional targets of V2R-PKA signaling, consistent with prior findings in TGF-{beta}-mediated vasopressin escape. Stk11/LKB1 knockout lines displayed marked increases in AQP2 protein and mRNA, even in the absence of vasopressin. RNA-sequencing showed a marked similarity between the responses to Stk11/LKB1 deletion and vasopressin exposure in untransformed cells. Phospho-proteomic data point to opposing roles of Stk11/LKB1 and PKA in the regulation of cAMP-responsive transcriptional coactivator (CRTC) proteins in the transcriptional response to V2R-PKA signaling. Significance StatementCells throughout the body are regulated by extracellular signals like the hormone, vasopressin. Hormonal effects on cellular function are mediated by membrane receptors that trigger biochemical changes, often by inducing chemical modification of the amino acids making up individual proteins, such as addition of function-altering phosphate groups (phosphorylation). Protein phosphorylation is mediated by enzymes known as "protein kinases". Here, we have screened all known protein kinases using modern CRISPR/Cas9 technology to identify those involved in vasopressin action in the kidney. As expected from prior knowledge, the screen identified protein kinase A and one of its regulatory subunits, but also identified several protein kinases not previously implicated in vasopressin action in the kidney.

systems biology↗

bioRxiv2026

Borrelia burgdorferi infection-enhanced Ixodes scapularis serpins S12c5 and S13c5, target MASP1/3 to inhibit MBL-pathway complement activation and promote spirochete survival

Tick serine protease inhibitors (serpins) are critical for tick feeding success and pathogen transmission. We previously demonstrated that two unique serpins, S12c5 and S13c5, are tandemly duplicated on Ixodes scapularis chromosome 5 and are injected into the host at heightened levels during feeding by Borrelia burgdorferi (Bb)-infected nymphs. Here, we characterize the biochemical properties and immunomodulatory functions of these serpins and investigate their roles in promoting Bb transmission. Despite their response to Bb infection, S12c5 and S13c5 share less than 20% overall amino acid identity and differ critically at their reactive center loop (RCL) P1 site, which determines substrate specificity: S13c5 contains a basic arginine residue, while S12c5 contains a polar serine residue. Consistent with these differences, recombinant S13c5 efficiently inhibited innate immune proteases including fXa, plasmin, and trypsin IV (SI: 2.5, 1.9, and 1.0; ka: 8.56 x 103, 3.97 x 10, and 1.08 x 10 M-{superscript 1}s-{superscript 1}, respectively), and consequently delayed plasma clotting via the common pathway, whereas rS12c5 did not inhibit these proteases. However, despite molecular modeling predicting stronger interactions between S13c5 and complement proteases, both serpins inhibited MBL-pathway complement activation by targeting MASP1/3. Deletion of the RCL domain abolished this inhibitory activity, confirming both proteins function as typical inhibitory serpins. Functionally, rS13c5 enhanced Bb colonization in C3H mouse organs. Interestingly, immune response assays revealed a trade-off: S13c5, despite its broader inhibitory activity, was less immunogenic than S12c5. Collectively, these findings establish S12c5 and S13c5 as Bb transmission factors that promote spirochete survival through disruption of host innate immunity.

Molecular Biology↗

bioRxiv2026

Cortical Excitation-Inhibition Balance in Autism Varies by Brain Region and Age

Autism spectrum disorder (ASD) is characterized by differences in social communication, interaction, and restricted and repetitive behaviors. The hypothesis that ASD involves altered cortical excitation-inhibition (EI) balance has been extensively investigated, yet evidence remains mixed, partly because EI balance changes substantially during typical maturation. We used resting-state magnetoencephalography (MEG) to examine developmental trajectories of cortical EI alterations with regional specificity in a large cross-sectional cohort (N = 172; 92 typically developing, 80 ASD; ages 6-32). Functional EI (fEI), derived from critical brain dynamics, was estimated across 500 cortical parcellations. Group-averaged fEI maps revealed broadly similar large-scale topographic patterns across groups. Age-stratified analyses revealed increased global fEI in childhood and decreased fEI in adolescence in ASD, with no evidence of a group difference in adulthood. Parcel-wise regressions identified a significant main effect of diagnosis in right dorsolateral prefrontal cortex, where typically developing individuals showed higher fEI across all ages. A significant group-by-age interaction in left inferior parietal cortex indicated diverging developmental trajectories. Finally, fEI in paracentral and precuneus regions was associated with the magnitude of ASD symptoms. These findings indicate that EI imbalance in ASD is neither globally distributed nor static, but expressed through regionally and developmentally specific differences, with relevance for ASD heterogeneity.

neuroscience↗

bioRxiv2026

Inducible lipid storage and steatosis in the human choroid plexus associated with age and adiposity

Cells that store lipids for other cells or organs can contain "giant" or large lipid droplets (LLDs) greater than 2 {micro}m in diameter. In this study, human postmortem choroid plexus was evaluated for lipid droplets. Staining with hematoxylin and eosin (H&E), the lipophilic dye Oil red O, and anti-adipophilin antibodies established the presence of LLDs exceeding 10 {micro}m in diameter in choroid plexus epithelial cells (CPECs). Manual annotation of H&E stains from 105 cases revealed a significant association between age and the percentage of CPECs containing LLDs (reaching up to 69%) and involving LLDs in our largest annotated category (>5 {micro}m in diameter). The LLD association with age was replicated and extended to a total of 245 cases using a trained convolutional neural network, which further showed significant associations with body mass index at time of death (increasing with BMI), sex (higher in females >65 years old), and a near-significant association with Alzheimers Disease (lower in AD). Like HepG2 and derived hepatocytes, excess fatty acids in culture media readily induced LLDs and steatosis in human embryonic stem cell-derived CPECs. Akin to hepatocytes for the human body, we propose that CPECs store lipids for the human brain and become steatotic in the setting of excess adiposity.

pathology↗

bioRxiv2026

Population-specific drivers of reproductive phenology in a widespread large carnivore, the gray wolf

Animals often rely on cues from the environment to time reproduction with optimal conditions. However, for most species, which environmental cues are used and how their use varies across a species distribution remains poorly understood. The gray wolf (Canis lupus) is found across a broad latitudinal range (12{degrees}N to 83{degrees}N) and diverse natural habitats, making them an ideal study species to explore these questions. Using 1,261 estimated birth dates of wild and captive wolves across their global range, we investigated how environmental variables influence reproductive phenology in this widespread large carnivore. Birth dates for wild wolves ranged from November 22nd for Indian wolves (18{degrees}N) to June 15th for Arctic wolves (80{degrees}N). The best predictor of timing of birth was increasing daylength during the mating season, followed by precipitation variability during the year. The timing of birth in captive wolves was highly similar to wild wolves at same latitudes, suggesting they use similar environmental cues to time reproduction. Near the equator where photoperiod is more stable, wolves remained seasonal and likely use climatic cues to time reproduction. Our work reveals populations may use different environmental cues to time reproduction, a characteristic that likely facilitates adaptation to diverse environments.

ecology↗