Biology subjects

Shen, S.

Publications and source records attributed to Shen, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Coronavirus nucleocapsid proteins differentially antagonize RIG-I-like receptor signaling to shape pathogenicity

Coronaviruses cause human infections with divergent clinical outcomes. Viral proteins likely play important roles in the severity of human diseases but are poorly defined. In this study, we discovered that viral nucleocapsid (N) proteins from various human coronaviruses have distinct abilities to antagonize human innate immune responses. N proteins from more pathogenic coronaviruses, such as SARS-CoV and SARS-CoV-2, have more potent activities specifically against human RIG-I-like receptor (RLR) activation than less pathogenic coronaviruses including OC43 and HKU1. Mechanistically, the SARS-CoV-2 N protein interacts with RLR pathway viral RNA sensors MDA5 and RIG-I and inhibits their interaction with MAVS. The CTD of SARS-CoV-2 N protein is an important region for RLR antagonism. Consequently, N proteins from more pathogenic coronaviruses promote viral replication more effectively than N proteins from less pathogenic coronaviruses. Blocking N protein function may be a promising antiviral strategy.

microbiology↗

bioRxiv2026

Gut Microbiota Signatures of Brain and Peripheral gamma-amino butyric acid (GABA) in Healthy Adult Males

Gamma-aminobutyric acid (GABA), the principal inhibitory neurotransmitter in the mature human nervous system, plays a central role in neurodevelopment, emotion regulation, and sensory processing. Many psychiatric drugs act on the GABAergic system, highlighting its importance for healthy brain function. Individual differences in brain and circulating GABA levels have traditionally been attributed to genetic variation. However, several gut bacteria produce neuroactive compounds, including GABA, raising the possibility that microbial variation influences peripheral and central GABA levels and related measures in humans. This relationship remains largely unexplored. In a cross-sectional study of 251 healthy adults, we investigated associations between gut microbiota composition, central and peripheral GABA, and associated features. Brain GABA was quantified using magnetic resonance spectroscopy, blood GABA using enzyme-linked immunosorbent assays, and gut microbiota profiles using absolute and relative abundance measures derived from Flow Cytometry Fluorescent In Situ Hybridisation and 16S rRNA gene sequencing. Motor cortex GABA+ levels were positively associated with greater numbers of Bacteroides/Prevotella bacteria. A similar association was observed for blood GABA, which was additionally associated with greater numbers of lactic acid bacteria, Eubacterium rectale/Clostridium coccoides, and Clostridium histolyticum groups, and with predicted microbial gene pathways involved in GABA, propionate, and butyrate biosynthesis. No association was observed between brain and blood GABA concentrations. These findings provide new evidence for relationships between gut bacterial groups and central and peripheral GABA pools, supporting future longitudinal studies of causal links between gut microbiota and host GABA levels, as well as the potential for future intervention studies to influence GABAergic processing.

neuroscience↗

bioRxiv2026

Yck2 links mitochondrial function and pH homeostasis to cell wall remodeling and antifungal susceptibility in Cryptococcus neoformans

Invasive fungal infections are on the rise due to climate change, antifungal resistance, and increased usage of immunomodulating therapies. The antifungal arsenal is limited in number and in efficacy necessitating novel therapeutics. Deletion of the gene encoding the fungal yeast casein kinase, YCK2, has pleiotropic effects, impacting morphology, drug resistance, metabolism, cell wall, and virulence. Yck2 has recently been shown to be druggable, however the mechanisms by which Yck2 elicits its impacts are unknown. We show that C. neoformans Yck2 is a regulator of cell wall masking, thermotolerance, general stress, and drug resistance. Proximity labeling of Yck2-interacting proteins revealed that Yck2 interacts with proteins that function in the mitochondria as well as the essential plasma membrane H+ ATPase, Pma1. A role for Yck2 in mitochondrial regulation was supported by sensitivity to mitochondrial inhibitors and increased mitochondrial ROS production in the absence of Yck2, and presence of Yck2 in mitochondrial fractions. Using pHluorin-expressing cells we also found that intracellular pH is elevated in cells lacking Yck2 supporting a role in regulating Pma1 activity. Both mitochondria and cellular pH may contribute to cellular signaling and may explain the multitude of phenotypes associated with the yck2{Delta} mutant. Our results begin to identify the mechanisms by which Yck2 contributes to fungal cellular homeostasis which may support efforts to optimize Yck2 inhibitors.

microbiology↗

bioRxiv2026

Destabilization of intratumor Tregs by CTLA-4 engagement confers anti-CTLA-4-driven immunotherapy

Immune checkpoint inhibitors (ICI) that are antibodies against CTLA-4 have achieved therapeutic effects on multiple types of cancers 1-4, but the mechanisms underlying the therapy remain incompletely understood. In contrast to the initial theory that the antibody blockades CTLA-4 on T cells is of central importance, it has recently been demonstrated that selective reduction of CD4+Foxp3+ regulatory T cells (Tregs) in the tumor microenvironment by the antibody plays a key role in the anti-tumor effects5-8, although this phenomenon remains under debate in human patients9-12. We show here that anti-CTLA-4 antibody engages CTLA-4 in Tregs specifically in the tumor tissues to reduce their stability and survival and weaken their suppressive function through upregulating TGF-{beta} signaling. This leads to the antibody-mediated - upregulation of CD4+ and CD8+ effector T cell anti-tumor immunity and consequently cancer immunotherapy. Specifically, anti-CTLA-4 antibody directly stimulates CTLA-4 in intratumor Tregs to enhance their TGF-{beta} receptor I (T{beta}RI)-mediated TGF-{beta} signaling13. This results in reduction of IL-2 receptor CD25 expression and downregulation of lactate metabolism in intratumor Tregs to reduce their stability and survival 14-16, and also compromises their suppressive function by inhibiting Foxp3 expression. This activity requires high levels of CTLA-4 expression in the intratumor Tregs and the presence of antibody Fc receptors in the tumor tissues. Strikingly, deletion of T{beta}RI specifically in Tregs completely prevents the reduction of intratumor Tregs and abrogates the anti-CTLA-4-mediated cancer immunotherapy. In contrast to intratumor Tregs, anti-CTLA-4 antibody treatment blocks CTLA-4 in the intratumor CD4+ Foxp3- and CD8+ T effector cells and in the peripheral Tregs to decrease their T{beta}RI expression and increase their expansion due to their relatively low levels of CTLA-4 in the same tumor bearing mice. Significantly, the engagement of CTLA-4 by anti-human CTLA-4 antibody (ipilimumab) also upregulates TGFBR1 but decreases Il2RA expression and lactate metabolism in human Tregs in vitro and in humanized mice in vivo, leading to suppression of tumor progression. We have provided additional mechanism underlying anti-CTLA-4-mediated anti-tumor effects through destabilizing intratumor Tregs by CTLA-4 engagement-mediated TGF-{beta} signaling. This could lay a theoretical foundation for designing optimal immunotherapy based on anti-CTLA-4 antibody in cancer patients.

immunology↗

bioRxiv2026

Colon-to-hind paw cross-organ sensitization is partially mediated by TrkB.T1-facilitated spinal neuroinflammation to activate lumbar DRG neurons

Patients with bowel disease can develop referred somatic pain at a later time with unknown molecular mechanisms. Using experimental mice with colitis induced by intracolonic installation of 2,4,6-Trinitrobenzenesulfonic acid (TNBS), we find an increase in the percentage of hind paw primary afferent neurons expressing Piezo2 or calcitonin gene-related peptide (CGRP), which are attenuated by TrkB.T1 knockout (KO). Concomitantly, TrkB.T1 KO also attenuates colitis-induced hind paw mechanical hypersensitivity and pain. Next, we find that TrkB.T1 is expressed in spinal cord astrocytes and its expression level is increased by colitis. TrkB.T1 KO reduces colitis-induced upregulation of Tumor necrosis factor-alpha (TNF-) mRNA but not upregulation of interleukin (IL)-6 mRNA in the spinal cord. Using calcium (Ca2+) imaging and ex vivo approaches, we find that TNF- elicits Ca2+ transients in capsaicin-sensitive as well as capsaicin-insensitive DRG neurons, and increases Piezo2 and CGRP expression in DRG neurons via distinct signaling pathways. Notably, TNF-or colitis-induced Piezo2 upregulation in L4 DRG neurons is mediated by or associated with the PI3K/Akt pathway that does not participate in CGRP upregulation. In contrast, CGRP upregulation in hind paw primary afferent neurons is associated with an upregulation of phosphorylated cAMP response element binding protein (p-CREB). Finally, we find that TrkB.T1 KO does not change the expression level of transient receptor potential cation channel subfamily V member 1 (TrpV1) in L4 DRG in colitis, explaining the ineffectiveness of TrkB.T1 KO on colitis-induced hind paw thermal hyperalgesia. These results suggest complex and distinct molecular pathways in colitis-induced somatic pain modalities and provide information for specific pain modality management.

neuroscience↗

bioRxiv2026

Open-source robotic chip-to-plate interface for high-throughput microfluidic generation of materials libraries

Data-driven materials development requires large, well-characterized libraries of precisely defined formulations. While microfluidic platforms excel at generating highly controlled materials, their throughput is often limited by the challenge of efficiently interfacing device outputs with standard well plates. This bottleneck frequently necessitates manual transfer or non-microfluidic workflows, constraining both throughput and reproducibility. Here, we present LMNOP-bot (Libraries of Micro- and Nano-materials, OPen-source bot), an open-source robotic platform for the automated generation and collection of micro- and nanomaterial libraries from serial microfluidic outputs. Using synchronized, pressure-driven flow, LMNOP-bot enables continuous formulation and direct deposition into standard well plates. The system is low-cost (<$700, excluding pressure regulators), constructed from readily available or easily fabricated components, and designed for broad accessibility. LMNOP-bot collects [≥]30 {micro}L per formulation at a rate of one sample every four seconds, representing an approximately 50x increase in throughput over existing serial microfluidic workflows, and operates robustly for over 10,000 runs without maintenance. We demonstrate compatibility with both PDMS/glass and commercial polycarbonate devices, with seamless interfacing to 96- and 384-well plates. Repeated sampling confirms high precision and reproducibility. By removing a key bottleneck in microfluidic library generation, LMNOP-bot enables rapid, scalable, and accessible exploration of material design spaces.

bioengineering↗

bioRxiv2026

Combinatorial epigenomic patterns define regulatory programs underlying disease heterogeneity

Complex diseases exhibit substantial variation in clinical presentation and outcome despite shared diagnoses. Current genetic models typically represent inherited risk as a single additive liability, obscuring the diverse biological mechanisms through which variants influence disease. Here, we show that disease-associated variants are organized into recurrent regulatory programs that reveal latent disease mechanisms. Using genome-scale epigenomic maps across human tissues and cell states, we identify regulatory programs that partition disease-associated variants without phenotypic or disease-specific priors. Variants assigned to different programs exert distinct biological effects that translate into divergent clinical outcomes. In type 2 diabetes, these programs reveal previously unrecognized disease subtypes with opposing cardiometabolic profiles that stratify future risk of myocardial infarction and non-alcoholic fatty liver disease. Together, our findings establish that inherited disease risk is organized into latent regulatory programs, revealing a fundamental layer of biological heterogeneity underlying complex disease.

genomics↗

bioRxiv2026

SCIMETAR-seq tracks immunophenotype, demethylation, mutations, and transcriptomes in single cells undergoing HMA therapy

5-azacytidine improves haematopoiesis and delays leukaemic progression in myelodysplastic neoplasms, but responses vary and are complicated by clonal mosaicism and heterogenous demethylation. Using a novel single-cell pipeline ("SCIMETAR-seq"), we found 5-azacytidine induced clonally distinct differentiation responses, with nuclear DNA demethylation occurring primarily in cycling progenitors. Despite the absence of significant nuclear DNA demethylation, quiescent stem cells underwent transcriptional remodelling in vivo, accompanied by 5-azacytidine-induced C*G-to-G*C mutations in mitochondria.

cancer biology↗

bioRxiv2026

A luminal proteome of the endoplasmic reticulum and Golgi apparatus reveals a novel modulator of ER stress tolerance in African trypanosomes

African trypanosomes employ specialised mechanisms of membrane trafficking as a key strategy to persist in both the mammalian host and insect vector. Their survival and pathogenicity rely on the continuous synthesis and surface delivery of extremely abundant surface coat proteins, imposing an extraordinary biosynthetic burden on the secretory pathway. Despite this, the luminal proteome of the T. brucei endoplasmic reticulum (ER) and Golgi apparatus remains incompletely characterised. Here, we exploit TurboID proximity biotinylation, using the abundant ER chaperone BiP (Binding-immunoglobulin protein) as luminal bait to map the ER proteome in bloodstream and procyclic lifecycle stages of Trypanosoma brucei. Comparison with BiPN, a truncated secretory form of BiP that transits the Golgi, provides differential compartmental labelling, together identifying 366 (BiP) and 428 (BiPN) proximity partners respectively and encompassing established ER quality control machinery, secretory cargo, and Golgi proteins. Quantitative ranking of BiP labelling intensity identifies a cohort of candidate BiP interactors: the most strongly enriched is Tb927.5.1160, a protein sharing structural homology with the mammalian BiP nucleotide exchange inhibitor MANF (mesencephalic astrocyte-derived neurotrophic factor). Endogenous mNeonGreen tagging confirms ER localisation of TbMANF in both life cycle stages, and reciprocal manipulation of its abundance by RNAi and inducible expression produces opposing shifts in cellular sensitivity to ER stress. These data are consistent with a role in regulating BiP ATPase cycling in an organism that, unlike yeast and mammals, lacks a canonical unfolded protein response, making TbMANF the first candidate regulator of BiP activity identified in kinetoplastids. Finally, TurboID proximity labelling anchored at the inner face of the nuclear pore via NUP65 extends our endomembrane map to the inner nuclear membrane, identifying candidate proteins of this specialised ER-continuous domain. AUTHOR SUMMARYAfrican sleeping sickness is caused by Trypanosoma brucei, a parasite that survives in the mammalian bloodstream by constantly renewing its protective protein coat. To synthesise and export this surface coat, the parasite relies on two intracellular compartments, the endoplasmic reticulum (ER) and the Golgi apparatus, which function as a quality control and sorting factory for proteins entering the secretory pathway. However, the identity of the proteins that populate these compartments in blood-stage parasites, and that maintain functioning under stress conditions, has remained poorly mapped. Here, we used an enzyme-based proximity labelling strategy that identifies neighbouring proteins in live cells without disturbing their targeting signals, generating a comprehensive protein inventory of both compartments across the two main T. brucei lifecycle stages. Among the most strongly labelled proteins was Tb927.5.1160, a protein structurally related to a mammalian regulator of the master ER chaperone BiP. Reducing or increasing the abundance of Tb927.5.1160 in parasites produced opposite changes in ER stress tolerance, identifying it as a candidate modulator of ER homeostasis in a lineage that regulates protein quality control through mechanisms distinct from those operating in yeast or human cells. Together, our findings provide a new molecular resource for understanding how T. brucei sustains secretory pathway function under the biosynthetic demands of mammalian and insect host infection.

biochemistry↗

bioRxiv2026

Protocol-dependent cardiomyocyte states determine disease modelling capacity of human iPSCs

Human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) are widely used to model cardiovascular disease, yet numerous differentiation protocols generate cardiomyocytes with heterogeneous molecular and functional properties, complicating experimental design. Here we systematically compare sixteen commonly used cardiomyocyte differentiation protocols and characterize their resulting cell states using single-nucleus RNA sequencing, functional phenotyping and computational integration with human genetic data. Despite similar cardiomyocyte yields, protocols produced distinct transcriptional programs, subtype compositions and physiological properties. By integrating protocol-specific gene expression signatures with genome-wide association studies of cardiovascular traits, we identify cardiomyocyte states enriched for genetic architectures underlying specific diseases. These analyses accurately predict protocols most suitable for modelling particular disease contexts, including electrophysiological defects associated with Brugada syndrome and metabolic vulnerability relevant to myocardial infarction. Our results demonstrate that differentiation protocols encode biologically distinct cardiomyocyte states with differential disease relevance and establish a framework for aligning stem-cell differentiation strategies with human complex trait genetics to guide model selection. This approach enables rational design of iPSC-based disease models and highlights how population-scale genetic data can inform experimental systems in stem cell biology.

systems biology↗

bioRxiv2026

Arginine synthesis pathway and ASS1 play a critical role in mRNA translation reprogramming and ICI resistance in cutaneous melanoma

Immune checkpoint inhibitors (ICI) have revolutionized cancer treatment, but their efficacy has now reached a plateau. ICIs are the first class of treatment targeting the crosstalk between immune and tumor cells, making it crucial to understand the complex interactions within the tumor microenvironment (TME) to enhance therapeutic responses. The elevated consumption of resources by cancer cells, coupled with limited vascularization, often results in a TME that is deficient in nutrients, leading to competition for resources between cancer and stromal cells. Consequently, targeting tumor metabolism has emerged as a promising strategy to improve the efficacy of ICIs. Through metabolomic analysis, we have identified metabolic alterations in melanoma cells that are resistant to ICIs, specifically an increase in arginine synthesis and upregulation of ASS1, the rate-limiting enzyme in this pathway. By using gain and loss of function models, as well as a pharmacological inhibitor specific for ASS1, we demonstrated that modulations in the expression or activity of ASS1 is associated with translational reprogramming, characterized by an inhibition of the cap-dependent mRNA translation mediated through mTORC1/4EBP1 axis. We also demonstrated that targeting ASS1 in vivo, resensitize tumors initially resistant to ICI. Taken together, our results highlight the interaction between modulations of arginine synthesis pathway, mRNA translation reprogramming, antitumor immunity, and restauration of sensitivity to anti-PD-1. Our work also demonstrates the therapeutic potential of targeting arginine synthesis pathway, and especially ASS1, to offer new treatments to patients suffering from cutaneous melanoma resistant to ICIs.

cancer biology↗

bioRxiv2026

Hierarchical control of cardiomyocyte maturation and ischaemia sensitivity by metabolic culture conditions

Ischaemic heart disease remains the leading cause of mortality worldwide, yet no therapies prevent cardiomyocyte death during acute ischaemia-reperfusion injury (IRI). Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) provide a platform for modelling cardiac injury, but their immature phenotype limits the physiological fidelity of in vitro models. Here, we systematically evaluated how experimental variables used during preparation of hiPSC-CM endpoint assays influence cardiomyocyte maturation and susceptibility to IRI. Integrating literature mining, molecular profiling, statistical genetics, and functional assays, we examined the effects of replating conditions, backbone media, metabolic substrates, and signalling modulators. We define the relationship between culture conditions and metabolic supplements in determining contractile maturation and sensitivity to IRI. Notably, we show that metabolic composition of the backbone medium establishes the baseline maturation state and determines responsiveness to additional maturation cues. These findings identify metabolic environment as a dominant regulator of injury susceptibility and provide a framework for improving the physiological fidelity of hiPSC-CM models of cardiac ischaemia.

cell biology↗

bioRxiv2026

MYRF drives heterochronic miRNAs and LIN-42, and amplifies oscillatory programs for stage transitions

Larval development in C. elegans proceeds through discrete stages, yet the mechanisms that drive stage transitions remain incompletely defined. Here, we identify the transmembrane transcription factor MYRF as a master temporal regulator essential for larval progression. MYRF cleavage and nuclear accumulation oscillate across larval stages, peaking during mid-to-late intermolt phases. MYRF directly activates key heterochronic microRNAs--including lin-4, mir-48/241/84, and let-7--and amplifies the oscillatory gene network by promoting central regulators such as nhr-23. MYRF loss-of-function or acute depletion suppresses and flattens this network, causing developmental arrest during the late intermolt phase of each larval cycle and stalling molting, seam cell division, and vulval morphogenesis. Notably, MYRF oscillations precede and induce activation of lin-42/Period, which feeds back to repress myrf, sharpening oscillatory precision. Together, these findings establish MYRF as a central driver of larval stage transitions, coupling microRNA-conferred temporal identity with an amplifier-based logic that executes stage- and phase-specific developmental programs.

developmental biology↗

bioRxiv2025

Discovery of Abundant Nano-scale Lymphatic-like Vessels in Brains

As one of the most metabolically active organs, the brain requires an exceptionally efficient system for waste clearance to sustain its high metabolic demands. However, whether such a system exists--and, if so, what structural features enable its efficiency--remains incompletely understood. More than a decade ago, the "glymphatic system" was proposed to describe neurofluid transport through cerebrospinal fluid (CSF) and perivascular spaces (PVS), in conjunction with dural and meningeal lymphatic pathways. Nevertheless, it remains unresolved whether neurofluid transport is organized as a structured, vessel-like flow network. Moreover, in stark contrast to the dense network of blood capillaries in the brain, only a sparse population of lymphatic vessels has been identified, raising doubts as to whether the currently recognized lymphatic architecture alone can support efficient metabolic waste clearance. By combining expansion microscopy with CRANAD-3, a pan-{beta}-amyloid fluorescent probe, we discovered abundant nanoscale lymphatic-like vessels (NLVs) within the brain parenchyma of both mice and humans. The majority of these structures have diameters below 1,000 nm and exhibit moderate positivity for multiple lymphatic markers, including LYVE-1, Prox-1, PDPN, and VEGFR3. NLVs frequently coil around blood vessels, and putative connections between vascular structures were observed. Notably, some NLVs traverse multiple cortical layers and display distinct orientation patterns that vary across cortical laminae. This discovery reveals a previously "hidden" vascular network in the brain parenchyma and raises the possibility that an abundant, highly organized system of nanoscale tubular structures may provide an efficient conduit for metabolic waste clearance. Such a system could represent a critical, previously unrecognized component supporting the brains extraordinary metabolic demands.

neuroscience↗

bioRxiv2025

RNA secondary structures modulate hnRNPH1-mediated alternative splicing of cold-shock protein RBM3

Alternative splicing is regulated not only by sequence-specific RNA-protein interactions, but also by dynamic RNA secondary structures that remodel under varying cellular conditions. hnRNPH1, a G-rich motif-binding protein, promotes exon skipping across numerous transcripts, yet how RNA structure shapes its regulatory activity remains unclear. Building on our previous work showing that cooler temperature enhances hnRNPH1 binding to RBM3 pre-mRNA and drives poison exon (PE) skipping, we now identify RNA G-quadruplex (rG4) remodelling as the principal cis-acting mechanism underlying this temperature-sensitive regulation. Using small-molecule stabilizers and destabilizers, we show that rG4 folding reduces PE skipping, whereas rG4 destabilization enhances hnRNPH1-mediated PE exclusion. These effects are conserved across neuronal and non-neuronal cells. Integrating proteomics, phosphoproteomics, kinase perturbation assays, and candidates emerging from our prior genome-wide CRISPR screen, we further uncover contributions from temperature-sensitive CDC2-like kinase signalling and the RNA helicase DDX5, a known rG4 resolver and an hnRNPH1/hnRNPF co-factor. Together, our findings establish rG4 remodelling as the dominant driver of hnRNPH1-dependent RBM3 splicing, while implicating helicase activity and kinase signalling as modulatory layers that fine-tune this response. More broadly, this work illustrates how environmentally driven RNA structural transitions interface with enzymatic regulators to achieve temperature-responsive control of alternative splicing.

molecular biology↗

bioRxiv2025

Anaerobic gut fungi Caecomyces communis, Neocallimastix frontalis and Piromyces spp. nov., have distinct effects on plant fibres during digestion.

Anaerobic gut fungi are the first colonizers of plant material that enters the digestive system of ruminants. However, it is unclear how different fungal species contribute to the ability of the rumen microbiome to convert feed to nutrients. Here we isolated three species of anaerobic fungi, including a novel Piromyces species. We investigated if these species have distinct roles in the digestion of fibrous feed components, via assessment of changes caused to plant material itself. We found Neocallimastix frontalis isolate CoB3 and Piromyces isolate SHC digested plant materials more effectively than Caecomyces communis isolate SHB. The three fungi had distinct effects on feed composition. N. frontalis CoB3 degraded hemicelluloses and cellulose to a similar extent, Piromyces spp. SHC preferentially degraded hemicellulose, while C. communis SHB preference depended on the substrate. From the panel of monosaccharides that may result from such degradative activity, all fungi consumed only glucose, suggesting involvement of mechanisms more complex than only fungal carbon source usage. Overall, this indicates that each of these fungal species have distinct roles in the degradation of plant material, and different niches in the rumen. Exploring these roles creates functional understanding of the rumen microbiome, critical for developing more sustainable agriculture.

microbiology↗

bioRxiv2025

Sex-specific exploration accounts for differences in valence learning in male and female mice

Valence, the quality by which something is perceived as good or bad, appetitive or aversive, is a fundamental building block of emotional experience and a primary driver of adaptive behavior. Pavlovian fear and reward learning paradigms are widely used in preclinical research to probe mechanisms of valence learning but with limited consideration of sex as a biological variable despite known sex differences in neuropsychiatric disorders associated with impaired valence. Here, we compare appetitive-only, aversive-only and mixed-valence cue-outcome Pavlovian conditioning paradigms in male and female mice to dissociate effects of context, valence and salience in a sex-specific manner. Using a data-driven approach to identify behaviors indicative of valence learning in an unbiased manner, we compare task performance between paradigms in male and female mice. We show that while male and female mice acquire appetitive and aversive associations in both single- and mixed-valence paradigms, sex differences emerge in single-valence paradigms. Ultimately, we show that these apparent sex differences in valence learning are driven by non-specific baseline differences in exploratory behavior. Males explore more at baseline, altering their trajectory of cue-reward association acquisition whereas females explore less at baseline, increasing shock facilitated freezing in aversive-only contexts, masking cue discrimination. Overall, our findings illustrate how task design differentially impacts behavioral expression in male and female mice and demonstrate that mixed-valence paradigms afford a more accurate assessment of valence learning in both sexes.

neuroscience↗

bioRxiv2025

GFAP Proteolysis in TBI: Linking Novel Modified Cleavage Products to Astrocyte Pathology and Patient Outcomes

Glial fibrillary acidic protein (GFAP) is a significant clinical biomarker of traumatic brain injury (TBI), yet understanding the nature, timing, and impact of its degraded and modified products would inform clinical utility. We report novel GFAP breakdown products (BDPs) and post-translational modifications (PTMs) that are unique to TBI including fragment- and patient-specific citrullination signatures that destabilize GFAP filaments. GFAP and its fragments were sequenced by mass spectrometry (MS) from severe TBI patients cerebrospinal fluid (CSF) and sera, identifying two distinct TBI-specific jointly generated product sets within the rod-domain covering coil1 (20-26kDa) and coil2 (15-19kDa). Their endings differed from GFAP fragments described in Alzheimers and Alexander disease. Label-free quantification showed biofluid co-product abundance differences with coil1-BDPs enriched over coil2-BDPs. Coil imbalance was independently confirmed by immunoblot densitometry in twenty-three TBI patients. Measurements over ten days showed injury day peaks of full-length and end-clipped GFAP fragments, while proteolytic 37/39kDa and small fragments remained elevated. Six-month outcome (Extended Glasgow Outcome Scale) correlated with GFAP fragments, whereas levels of uncleaved and end-clipped GFAP did not. A human astrocyte culture trauma model provided mechanistic insights linking fluid GFAP levels, subcellular localization, and injury-induced astrocytopathy. A new cleavage site between the two coils was identified through selective epitope loss. Coil1-BDPs were fluid-released post-injury, while coil2-BDPs remained intracellular. Their cellular retention was explained by non-filamentous aggregation of citrulline-modified coil2-BDPs in pathological astrocytes. Trauma-triggered proteolysis involved calpains and caspases in specific astrocyte injury states using protease inhibitors and live-dye-reporter imaging. These novel data link TBI biofluid GFAP fragments with assembly-defective GFAP aggregation in pathological astrocytes. Clinical TBI outcome correlated with GFAP degradation rather than with overall GFAP release. These translational findings indicate that TBI biomarker GFAP undergoes degradation and modification alongside astrocyte pathology, providing a new conceptual framework for investigating biomarker-associated astrocyte proteinopathy potentially linked to post-traumatic neurodegeneration.

neuroscience↗