Biology subjects

Tripathi, A.

Publications and source records attributed to Tripathi, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Sfh3 is a sterol-modulated PI/PI4P transfer protein that confers azole resistance in yeast by specifically mediating lanosterol/PI exchange

Lipid transfer proteins precisely distribute lipids within eukaryotic cells, supporting functions such as vesicular trafficking and cellular signaling. Here, we analyzed whether Sfh3 (Sec14 homolog 3) functions as a sterol/phosphatidylinositol (PI) exchanger to clarify its role in neutral lipid mobilization from lipid droplets and in azole resistance in yeast. Using real-time assays, we found that its ergosterol transfer capacity is not activated by PI and is inhibited by ergosterol biosynthesis intermediates, such as lanosterol. Next, we found that Sfh3 exhibits both PI and PI4P transfer activities, which sterols can modulate. Through kinetic, structure-function, and thermal stability analyses, we identified remarkable Sfh3 mutants and ranked Sfh3's relative affinity for its lipid ligands. This allowed us to show that Sfh3 performs selective lanosterol/PI exchange, provided it recognizes PI, in the presence of ergosterol, and that this activity is necessary for yeast resistance to miconazole. Collectively, our data show that Sfh3 is a sterol-regulated PI/PI4P transfer protein, potentially linking sterol metabolism and PI4P signaling during lipid droplet utilization. In azole-treated yeast, elevated lanosterol levels may shift Sfh3 into an exclusive PI/lanosterol exchange mode, promoting cellular detoxification and conferring drug resistance. By revealing unanticipated Sfh-mediated lipid transfer mechanisms, our study provides new insights into the Sec14 family.

biochemistry↗

bioRxiv2026

Isolation of oxygen-dependent nicotine- and pseudooxynicotine-metabolizing enzymes

NicA2 is a flavin-bound amine dehydrogenase from Pseudomonas putida S16 that converts nicotine to the pharmacologically inactive N-methylmyosmine. In animal models of nicotine addiction, injection of NicA2 can decrease nicotine-seeking behavior 10-fold. Accordingly, NicA2-related enzymes have been investigated as smoking-cessation therapeutics. However, efficient catalysis by NicA2 in Pseudomonas putida relies on electron transfer to CycN, a cytochrome c, and not directly to O2. Impractically high amounts of NicA2 are thus necessary to achieve a pharmacological effect in the absence of CycN. Directed evolution has improved the ambient-O2 value of kcat from 0.007 s-1 to 1 s-1 for NicA2, but further improvements have been challenging. Here, we identify a strain of Peribacillus frigoritolerans NIC8 which encodes two flavin amine oxidoreductases, Ncox and Pnox. In the presence of oxygen, Ncox and Pnox act on nicotine and pseudooxynicotine respectively with apparent kcat values of 7.7 s-1 and 3.9 s-1. Transient kinetics establishes bimolecular rate constants of 51100 M-1s-1 and 81000 M-1s-1 for the half-reactions between Ncox and O2 and between Pnox and O2 respectively, consistent with Ncox and Pnox being bona-fide oxidases. Transcriptomics shows enhanced expression of Ncox and Pnox under nicotine-dependent growth as well as supporting the identification of downstream enzymes. Phylogenetic analysis suggests that Ncox and Pnox arose out of repurposing of homologous enzymes found in Bacillus species. The enzymes we describe may be useful for the development of nicotine addiction therapeutics and for bioconversion of nicotine in waste streams.

biochemistry↗

bioRxiv2026

Divergent evolution of the Wnt signaling system in flatworms

Regenerative capacity varies widely across flatworms (Platyhelminthes). Whereas catenulids, microstomids and planarians can regenerate a complete head de novo, other flatworms cannot. This striking diversity raises a longstanding evolutionary question: does whole-body regeneration represent an ancestral trait that was subsequently lost in multiple lineages, or did it evolve convergently? Addressing this question requires comparative analyses of the molecular mechanisms underlying regeneration across phylogenetically diverse flatworms. Here, we focus on Wnt signaling, a deeply conserved regulator of antero-posterior (A-P) patterning and a central determinant of head-versus-tail identity during planarian regeneration, to establish a mechanistic framework for such comparisons. Although Wnt signaling has been studied extensively in planarians and parasitic neodermatans, its evolution and deployment in other flatworm clades remain poorly characterized. To address this gap, we characterized the complement of Wnt signaling components in two early-diverging flatworm clades, Catenulida and Macrostomorpha, with particular emphasis on expression and function in the catenulid Stenostomum brevipharyngium. Phylogenetic analyses reveal the ancient loss of six Wnt families and one secreted Frizzled-related protein (sFRP) family in the last common ancestor of flatworms, followed by additional lineage-specific gene losses and expansions. Moreover, several Wnt pathway components display markedly divergent expression patterns between catenulids and other flatworms, while functional analyses indicate corresponding differences in their regenerative deployment. Together, our findings reveal a dynamic evolutionary history of the flatworm Wnt signaling toolkit and establish a comparative framework for testing whether the molecular circuitry underlying head regeneration is ancestrally conserved or has evolved independently in distinct flatworm lineages.

evolutionary biology↗

bioRxiv2026

E2F1 Drives Endothelial Arterial Programming in Pulmonary Arterial Hypertension

BackgroundPulmonary arterial hypertension (PAH) is driven by maladaptive endothelial remodeling, but the transcriptional regulators that couple proliferative stress to arterialized endothelial states remain incompletely defined. E2F transcription factor 1 (E2F1) is classically viewed as a cell-cycle regulator; whether E2F1 functions as a disease-driving node that promotes endothelial arterial programming in PAH remains unknown. MethodsWe integrated human PAH lung transcriptomic analyses, deconvolution-based endothelial-state scoring, and complementary mouse and rat PH models with bulk RNA-seq, single-cell RNA-seq, pseudotime analysis, and CellChat inference. E2F1 function was tested using adenoviral E2F1 overexpression, pharmacological pan-E2F inhibition with HLM006474, and genetic E2f1 loss on a tamoxifen-inducible endothelial Egln1-deletion background. ResultsIn PAH lungs, E2F1 was increased and arterial endothelial cell (AEC) fraction and expanded arterial program scores were elevated. Similarly, Egln1Tie2Cre lungs showed increased E2F1, induction of arterial remodeling genes, and activation of an E2F target program. Genetic loss of E2f1 reduced right ventricle systolic pressure, right ventricle hypertrophy, vascular remodeling, and distal muscularization in Egln1-driven PH mice model. Bulk RNA-seq showed suppression of E2F, mitotic, epithelial mesenchymal transition, and extracellular matrix-remodeling programs. Single-cell RNA-seq showed reduced AEC accumulation, normalized CAP1/CAP2 distribution, and reduced progression along the CAP1-AEC trajectory. CellChat analysis identified loss of an arterial communication hub, including reduced ECM, VEGF, and Notch signaling when E2F1 is loss. Conversely, E2F1 overexpression in human lung microvascular ECs increased proliferation, activated E2F/cell-cycle and Notch/arterial programs. Pharmacological inhibition of E2F via HLM006474 suppressed endothelial proliferation and attenuated Egln1-driven and MCT-induced PH, including reversal of established MCT-PH. ConclusionsE2F1 acts as a disease-relevant transcriptional factor linking endothelial cell-cycle activation to arterial programming, matrix and angiogenic communication programs, and pulmonary vascular remodeling. Genetic or pharmacological E2F inhibition mitigates experimental PH, supporting E2F1 as a therapeutic target in PAH. Clinical Perspective What is new?1. This study identifies E2F1 as a previously unrecognized driver of PAH rather than only a downstream marker of cell-cycle activation. 2. Genetic loss of E2f1 rescues hemodynamic and structural features of Egln1-driven PAH, and pharmacological E2F inhibition attenuates both Egln1-driven and monocrotaline-induced PH. 3. Mechanistically, E2F1 links endothelial proliferation to Notch-associated arterial programming, AEC accumulation, and CAP1-to-iAEC-to-AEC trajectory progression. What are the clinical implications?1. E2F1 defines a tractable transcriptional node that integrates proliferative stress with arterial endothelial reprogramming, a core pathological feature of PAH vascular remodeling. 2. Pan-E2F small-molecule inhibitors, several of which are in development for oncology, may be repurposable for PAH if E2F1-dependent endothelial arterial-programming signatures identify responsive disease states. 3. Plasma- or tissue-based readouts of E2F1 activity may identify PAH patients most likely to benefit from E2F-directed therapy.

physiology↗

bioRxiv2026

Cereal grafting in rice and pearl millet preserves photosynthetic performance and stomatal dynamics, establishing a platform for root-shoot communication studies

O_LICereal grafting using embryonic tissues has recently become technically feasible; however, the physiological consequences of cereal grafting remain uncharacterized. C_LIO_LIWe systematically evaluate photosynthetic performance and stomatal dynamics across different graft combinations in two photosynthetically distinct species, rice (C3) and pearl millet (C4). We first assessed steady-state photosynthetic performance and dynamic stomatal responses in five-week-old rice and pearl millet grafts grown under a saturated water regime, to establish whether cereal grafting alters physiology at early stages. Next, we assessed same traits at the onset of optimal water regime, and after five days to determine whether any graft-induced effects on photosynthesis or growth persisted over time. C_LIO_LIWe observed that across contrasting water regimes and at different plant developmental stages, cereal grafting did not alter growth, photosynthesis or stomatal kinetics in either species, while revealing modest early stage C4-specific adjustments in stomatal dynamics without affecting photosynthetic capacity or biochemical parameters. C_LIO_LIWe demonstrate that cereal grafting does not alter core physiological traits in rice or pearl millet and can be deployed without long-term impact on photosynthesis. These findings establish cereal grafting as a tractable platform for mechanistic dissection of root-shoot signaling and trait combination across different C3 and C4 cereals. C_LI

Plant Biology↗

bioRxiv2026

Inorganic sulfate transport by the Mycobacterium tuberculosis PE22/PPE36 complex

Mycobacterium tuberculosis (Mtb) encodes two multigene families with 169 members that are exclusive to mycobacteria, the pe and ppe genes. These genes have unusual sequences including low-complexity repeat regions, but their functions--and whether they share a common function--have long been unclear. Recently, several members of the pe/ppe family were shown to transport nutrients across the outer Mtb membrane, a role for which no other proteins have yet been identified. Whether nutrient transport is a family-wide function and the range of nutrients transported by the PE/PPEs remains unclear. Sulfur is an essential nutrient for Mtb physiology and pathogenesis. To test whether PE/PPE transporters contribute to sulfur acquisition, we analyzed the transcriptional response of Mtb to sulfate by RNA sequencing. The pe22/ppe36 genes were induced in sulfate-limiting conditions. Deletion of pe22/ppe36 impaired growth in low-sulfate media and reduced intracellular sulfate levels, effects that were reversed by heterologous expression of the Mycobacterium smegmatis porin MspA. The response of sulfur-responsive genes to sulfur was muted in the pe22/ppe36 deletion strain, and mass spectrometry showed lower sulfolipid and sulfur metabolite levels in the deletion strain. These findings identify PE22/PPE36 as a specific sulfate uptake system and supports the emerging idea of PE/PPE proteins as nutrient uptake systems across the Mtb outer membrane. Significance statementThe mechanism of nutrient transport across the porin-less mycobacterial outer membrane and the function of the large pe/ppe gene family have been longstanding questions in mycobacterial biology. This study shows that the Mycobacterium tuberculosis PE22/PPE36 complex serves as a selective conduit for inorganic sulfate. Deletion of this complex disrupts intracellular sulfur homeostasis and triggers a metabolic seesaw that depletes cell-surface sulfolipids. Our findings expand the PE/PPE transport paradigm and suggest a direct link between nutrient acquisition and TB transmission.

microbiology↗

bioRxiv2026

The CCCH-type zinc-finger PfMD3 promotes translation for malaria parasite transmission

Sexual maturation and fertility of the malaria causing parasite, Plasmodium spp., is critical to transmission between hosts. This developmental process involves an intricate gene expression regulatory network that drives gametocyte commitment, development, and the production of male and female gametes. Here, we characterized the role of the CCCH-type zinc-finger protein Plasmodium falciparum Male Development 3 (PfMD3) in the formation of gametes. Genetic disruption of PfMD3 revealed a male fertility defect that decreased infectivity to mosquitoes. Molecular characterization of PfMD3 revealed its binding to mRNA transcripts associated with male gamete development through a specific RNA sequence. Gametocyte proteins encoded by these PfMD3-bound transcripts decreased significantly in PfMD3 knockout parasites, suggesting that PfMD3 impacts translation. In addition to RNA-binding, PfMD3 also interacts with proteins involved in mRNA processing and nuclear export that influence translational regulation. This study establishes PfMD3 as an RNA-binding protein that impacts lineage-specific translation and male gamete fertility.

molecular biology↗

bioRxiv2026

A Plasmodium falciparum PX1 haplotype is associated with reduced susceptibility to artemisinin and lumefantrine

Effective control of falciparum malaria depends on the sustained efficacy of frontline antimalarial drugs, particularly artemether-lumefantrine (AL), the most widely used therapy in Africa. However, the emergence of artemisinin partial resistance and reduced lumefantrine susceptibility in eastern Africa threaten malaria control and elimination. Robust genetic markers of decreased susceptibility to lumefantrine remain elusive, and our understanding of artemisinin resistance is incomplete. We report results of a Plasmodium falciparum genetic cross between a drug-sensitive line and a Ugandan strain exhibiting reduced susceptibility to dihydroartemisinin and lumefantrine. Targeted deep sequencing of progeny pools and 460 recombinant progeny clones derived under drug pressures revealed distinct haplotypic signatures. Drug-selection experiments identified genetic polymorphisms in Plasmodium falciparum px1, encoding a phosphoinositide-binding protein, as the strongest correlates of reduced susceptibility to dihydroartemisinin and lumefantrine. The PX1 PIN haplotype (L1222P, M1701I, D1705N) recently discovered in Ugandan parasites was highly enriched following dihydroartemisinin or lumefantrine treatment of pooled mixtures of genetically diverse Ugandan clinical isolates. This haplotype was associated with reduced susceptibility to dihydroartemisinin and lumefantrine, compared to wild-type sequence, in culture-adapted Ugandan P. falciparum lines. These results confirm that PX1 mutations were selected across geographically distinct Ugandan parasite backgrounds. Long-term competitive fitness assays demonstrated that PX1 mutations confer asexual blood-stage parasites with a growth advantage, potentially explaining a rapid rise of PX1 PIN alleles over the last two decades in Uganda. Overall, our data suggest the PX1 PIN haplotype is a robust marker of reduced AL susceptibility in African P. falciparum, enabling surveillance of emerging drug resistance.

microbiology↗

bioRxiv2025

Lipid droplets promote the aberrant liquid-liquid phase separation of alpha-synuclein leading to impaired energy homeostasis

Alpha-synuclein (Syn) inclusions, termed Lewy bodies, are the characteristic neuropathological feature of Parkinsons disease. Growing evidence points towards a role of aberrant liquid-liquid phase separation in the dysregulation of Syn and sequence of events that lead to the formation of Lewy bodies. However, the triggers leading to aberrant phase separation are unknown, as is the relevance of this phenomenon to the neurodegeneration process. In this study, we showed that Syn spontaneously phase separates into condensates in the presence of lipid droplets. These lipid droplet-rich condensates represent a toxic species of Syn that prevents the turnover of the entrapped lipid droplets; they are also toxic to neighbouring mitochondria which are depolarized and undergo increased mitophagy. These findings underscore the increasing importance of lipid droplets in the pathogenesis of neurodegenerative diseases, and Parkinsons disease in particular. The lipid droplets are significantly enriched within the neuromelanin in midbrain dopaminergic neurons in the substantia nigra and could therefore uniquely facilitate the early Syn-associated neurodegeneration of this region in PD. Our findings reveal a novel pathway implicated in the dysregulation of Syn that connects aberrant liquid-liquid phase separation, lipid droplets and mitochondrial toxicity.

neuroscience↗

bioRxiv2025

The anti-retroviral therapy emtricitabine affects skeletal muscle DNA methylation and transcriptome patterns in a male HIV mouse model

BackgroundAlthough antiretroviral therapies (ART) have substantially reduced HIV-associated mortality, the increased lifespan achieved by widespread ART deployment has revealed that HIV infection is linked to an unexplained earlier onset and increased incidence of aging-associated conditions like sarcopenia. Complex syndromes, like sarcopenia, often arise from a combination of genetic and environmental factors, so in this study, we investigated effects of short-term treatment with emtricitabine (2,3-dideoxy-5-fluoro-3-thiacytidine; FTC), an FDA approved ART, on skeletal muscle DNA methylation patterns and transcriptome-wide responses in a male murine model of HIV phenotypic biology (Tg26 mice). MethodsWe treated 6 month old male Tg26 (+/-) mice or wildtype (WT) littermates on a C57BL/6 genetic background with FTC in the drinking water for one month; control groups received drinking water vehicle alone (VEH). Muscle function and body composition were measured longitudinally. Skeletal muscle methylation patterns, transcriptional changes, and histological features were quantified at sacrifice. ResultsAlthough neither gross structural nor functional muscle deficits were observed in this short-term study with ART usage, relative decreases in muscle endurance measured by hang time over the study were 2-fold more severe in the Tg26 as compared to WT mice (p=0.0453), and markers of myogenic cell maturation (Myf5, Myf6) were disrupted in the Tg26 HIV model as compared to WT littermates in a manner exacerbated by FTC treatment. Fat mass, measured by DXA, also tended (p=0.085) to be uniquely increased by FTC treatment in the Tg26 mice over the study. Differential methylation patterns and pathway enrichment data suggested that the presence of an HIV phenotype and exposure to an ART regimen altered the methylation status in skeletal muscle genes such as Camk2B, Pcolce2 and Lima1 in a manner consistent with promoting eventual functional impairment in muscle. Additionally, RNAseq revealed differential gene expression profiles and key regulatory pathways including cellular differentiation, regulation of lipid metabolism, and neuroactive ligand-receptor interactions. Lipodystrophy-related genes including LEP, ADIPOQ and PPAR involved in fat distribution and metabolism along with skeletal genes related to regulation of muscle strength were affected by the presence of an HIV phenotype and ART treatment. ConclusionsThe current study provides insights into mechanisms by which a clinically relevant ART may influence DNA methylation and transcriptome changes in skeletal muscle in the context of HIV biology. The differentially regulated pathways suggest novel targets for understanding, and eventually abrogating, the harmful effects of long-term ART use in PLWH on skeletal muscle mass and function.

cell biology↗

bioRxiv2025

Anatomical input-output streams within mouse orbitofrontal cortex subdivisions

The orbitofrontal cortex (OFC) supports flexible value representation and decision making in primates, where different OFC subdivisions encode rewarding or aversive stimuli, and OFC dysfunction is implicated in depression. Recent anatomical and functional investigations have been performed in mice, but species differences in reward and value encoding physiology calls for deeper investigation of mouse OFC connectivity to better support translational research. Here, we compared density of retrograde inputs, axonal outputs and inter-subdivision connectivity, focusing on MO (medial-orbital), VO (ventral-orbital), (D)LO ((dorso)lateral-orbital) and AI (agranular insula). Central subdivisions (LO,VO) received dominant inputs from mediodorsal and submedius thalamic nuclei and projected respectively to medial prefrontal areas and sensory cortices. The striatal output was directed towards dorsal striatum, with reciprocal brainstem dopaminergic innervation. Input sources were more distributed for MO and AI, with reciprocal outputs to medial prefrontal cortices and amygdala, respectively. Striatal output was mainly to ventral striatum, and AI also received strong serotoninergic innervation. Cluster analysis revealed that VO/LO, and to lesser extent MO/DLO, shared strong similar input distributions, distinct from AI. Output clustering separated VO targeting sensory areas and AI targeting amygdala. Intra-OFC connectivity suggested information flow preferentially from (D)LO (entry nodes), to VO, MO and finally AI (output node). Together these data suggest a model that integrates in-series, information on sensory-motor plans (at (D)LO)), motivational state and cue uncertainty (at VO/LO) and current goals (at MO), via AI modulating the amygdaloidal and ventral striatal outputs, thus proposing an experimentally testable circuit to control emotional reactivity and decision-making in mouse OFC.

neuroscience↗

bioRxiv2025

Satiation is associated with OGT-dependent regulation of excitatory synapses.

Satiation is essential for energy homeostasis and is dysregulated in metabolic disorders like obesity and eating disorders such as anorexia nervosa. While satiation engages a large neural network across brain regions, how the communication within this network depends on metabolic fluctuations is unclear. This study shows that nutrient access can affect neuron-to-neuron communication in this network by regulating excitatory synaptic plasticity through O-GlcNAc transferase (OGT) in CaMKII satiation neurons in the paraventricular nucleus (PVN). Using cell-specific knockout mice and electrophysiological recordings, we demonstrate that OGT deletion in PVNCaMKII neurons increases input resistance and neuronal excitability while preserving basic membrane electrical properties. Strikingly, feeding triggered a robust 3.8-fold increase in the excitatory synaptic input in wild-type neurons, whereas OGT-knockout neurons failed to exhibit this feeding-induced synaptic activation, instead displayed a paradoxical trend towards increases in synaptic activity during hungry conditions. Furthermore, OGT deletion destabilized glucose-dependent synaptic responses, with knockout neurons displaying maladaptive depression of excitatory transmission in conditions where stability is normally preserved. These findings establish OGT as a nutrient-sensitive modulator of synaptic plasticity that ensures appropriate satiation signalling by coupling metabolic state to synaptic plasticity.

neuroscience↗

bioRxiv2025

Mitochondrial Response to Psychological Stress and Its Medial Prefrontal Biomarker Correlates

BackgroundStress response obligates increased mitochondrial activities to meet stress-induced high energy requirement. This stress-mitochondrial response process involves glucocorticoid but also multiple alternative pathways that are top-down regulated by the medial prefrontal cortex (mPFC). These pathways are important for many neuropsychiatric conditions that are sensitive to stress. However, the field lacks a reliable, clinically accessible stress-mitochondrial response paradigm to study the process in humans. MethodWe used an established psychological stress challenge combined with assaying salivary cell-free mitochondrial DNA (cf-mtDNA), thought to reflect heightened mitochondrial changes or disruptions, in 35 healthy individuals (21 males). We also explored if these stress-induced cf-mtDNA marker elevations were associated brain metabolites as measured by magnetic resonance spectroscopy (MRS), as well as high-resolution brain imaging based cortical thickness focusing on the mPFC. ResultsWe found that salivary cf-mtDNA was significant elevated immediately after the stress challenge (p=2.0x10-7) and gradually declined after. Exploratory causal analysis showed that this cf-mtDNA response was not primarily driven by cortisol response. Instead, individuals with higher baseline dACC lactate+ levels, thought to in part reflect mitochondrial dysfunctions, was significantly associated with the cf-mtDNA response (r=0.80, p<0.001). Higher mtDNA response was also significantly associated with thinner dorsomedial prefrontal cortex (r=-0.52, p=0.01). Age had a U-shape effect such that cf-mtDNA response trended lower in earlier adulthood but higher in older people, explaining 33.8% of the ct-mtDNA response variance (p=0.003). ConclusionThis stress challenge-salivary cf-mtDNA assay paradigm may offer a new, non-invasive approach to evaluate the stress-mitochondrial pathway functioning in aging, psychopharmacology, and neuropsychiatric conditions where psychological stress plays a role.

neuroscience↗

bioRxiv2025

Blood and Neuronal Extracellular Vesicle Mitochondrial Disruptions in Schizophrenia

The high energy demand of the human brain obligates robust mitochondrial energy metabolism, while mitochondrial dysfunctions have been linked to neuropsychiatric disorders including schizophrenia spectrum disorders (SSD). However, in vivo assessments that can directly inform brain mitochondrial functioning and its etiopathophysiological path to SSD remain difficult to obtain. We hypothesized that system and brain mitochondrial dysfunctions in SSD may be indexed by elevated cell-free mitochondrial DNA (cf-mtDNA) levels in the blood and in neuronal extracellular vesicles (nEVs). We also explored if these mtDNA marker elevations were associated brain metabolites as measured by magnetic resonance spectroscopy (MRS). We examined blood cf-mtDNA in 58 SSD patients and 33 healthy controls, followed by assessing nEV mtDNA and metabolite levels using MRS in a subgroup of patients and controls. We found that people with SSD had significantly elevated cf-mtDNA levels in both the blood (p=0.0002) and neuronal EVs (p=0.003) compared to controls. These mtDNA abnormalities can be linked back to brain lactate+ levels such that higher blood and nEV mtDNA levels were significantly associated with higher lactate+ levels measured at the anterior cingulate cortex (r=0.53, 0.53; p=0.008, 0.03, respectively) in SSD patients. Furthermore, higher developmental stress and trauma were significantly associated with higher cf-mtDNA levels in both the blood and neuronal EVs in SSD patients (r=0.29, 0.49; p=0.01, 0.03, respectively). In conclusion, if replicated and fully developed, blood and neuronal EV-based cell free mtDNA may provide a clinically accessible biomarker to more directly evaluate the mitochondrial hypothesis and the abnormal bioenergetics pathways in schizophrenia.

neuroscience↗

bioRxiv2025

Foundation Model Attributions Reveal Shared Inflammatory Program Across Diseases

Determining a genes functional significance within a cellular context has long been a challenge, as absolute expression level is an unreliable indicator. We introduce SIGnature, a framework for scoring gene importance by leveraging attributions derived from single-cell RNA-sequencing (scRNA-seq) foundation models. Attribution scores reduce technical noise, emphasize regulatory genes, and facilitate cross-dataset comparison - a core challenge for scRNA-seq analyses. We developed the SIGnature package as a tool for generating and querying attributions, enabling rapid gene set searches across massive scRNA-seq atlases. We demonstrated its utility using the MS1 monocyte signature, a poorly understood gene program activated in severe COVID-19 and sepsis. Searching 400 studies revealed novel associations between the MS1 signature and multiple hyperinflammatory conditions, including Kawasaki disease. Experimental validation confirmed Kawasaki disease patient serum induces the MS1 phenotype. These findings highlight that SIGnature can uncover shared mechanisms across conditions, demonstrating its power for large-scale signature scoring and cross-disease analysis.

bioinformatics↗

bioRxiv2025

The representation of facial emotion expands from sensory to prefrontal cortex with development

Facial expression recognition develops rapidly during infancy and improves from childhood to adulthood. As a critical component of social communication, this skill enables individuals to interpret others emotions and intentions. However, the brain mechanisms driving the development of this skill remain largely unclear due to the difficulty of obtaining data with both high spatial and temporal resolution from young children. By analyzing intracranial EEG data collected from childhood (5-10 years old) and post-childhood groups (13-55 years old), we find differential involvement of high-level brain area in processing facial expression information. For the post-childhood group, both the posterior superior temporal cortex (pSTC) and the dorsolateral prefrontal cortex (DLPFC) encode facial emotion features from a high-dimensional space. However, in children, the facial expression information is only significantly represented in the pSTC, not in the DLPFC. Further, the encoding of complex emotions in pSTC is shown to increase with age. Taken together, young children rely more on low-level sensory area than on the prefrontal cortex for facial emotion processing, suggesting that the prefrontal cortex matures with development to enable a full understanding of facial emotions, especially complex emotions that require social and life experience to comprehend.

neuroscience↗

bioRxiv2025

End-product inhibition of the LRRK2-counteracting PPM1H phosphatase

PPM1H phosphatase reverses Parkinsons disease-associated, Leucine Rich Repeat Kinase 2-mediated, Rab GTPase phosphorylation. We showed previously that PPM1H relies on an N-terminal amphipathic helix for Golgi membrane localization and this helix enables PPM1H to associate with liposomes in vitro; binding to highly curved liposomes activates PPM1Hs phosphatase activity. We show here that PPM1H also contains an allosteric binding site for its non-phosphorylated reaction products, Rab8A and Rab10. Microscale thermophoresis revealed that PPM1H binds thio-phosphorylated Rab8A at the active site with a KD of [~]1{micro}M; binding of Rab8A and Rab10 to an alternative site is of similar affinity and is not detected for another LRRK2 substrate, Rab12. Non-phosphorylated Rab8A or Rab10 inhibit PPM1H phosphatase reactions at concentrations consistent with their measured binding affinities and fail to inhibit PPM1H L66R phosphatase reactions. Independent confirmation of non-phosphorylated Rab binding to PPM1H was obtained by sucrose gradient co-flotation of non-phosphorylated Rabs with liposome-bound PPM1H. Finally, Rab8A or Rab10 binding also requires PPM1Hs amphipathic helix, without which the interaction affinity is decreased about 6-fold. These experiments indicate that Golgi associated Rab proteins contribute to the localization of PPM1H and non-phosphorylated Rabs regulate PPM1H phosphatase activity via an allosteric site. Targeting this site could represent a strategy to enhance PPM1H-mediated dephosphorylation of LRRK2 substrates, offering a potential therapeutic approach to counteract LRRK2-driven Parkinsons disease.

biochemistry↗

bioRxiv2025

A systems biology investigation to identify potential bi-omarkers in leprosy-affected host cells.

M. leprae adapts to the host cell environment and disrupts protein-protein interactions inside the host cell for its own survival and proliferation. This study is attempts to comprehend these host-pathogen interactions at the systems level. We utilised RNA-Seq data set of leprosy-resistant and leprosy-susceptible armadillos and investigated how five different human signaling pathways get hijacked by M. leprae. We also identified the corresponding human homolog proteins. By applying graph theory on these protein networks, we predicted 25 proteins which play important role in these pathways related to leprosy pathogenesis and/progression. The study is also supported by wet lab experiments identifying 69 proteins in armadillos upon leprosy progression after experimental infection which get differentially expressed. Our study found that 69.5% of these experimentally identified proteins are part of either M. leprae-affected signaling pathways or possibly contribute to leprosy pathogenesis based on their GO terms. This study identified three human proteins: LC3-II, PI3K and IDO1 which have been implicated in M. leprae pathogenesis in other studies also leprosy patients. Thus, upon further experimentally validation, such markers can be potentially useful to diagnose leprosy in patients at an early stage .

systems biology↗