Biology subjects

Ghosh, A.

Publications and source records attributed to Ghosh, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

p63 and PITX1 sustain a pre-invasive malignant keratinocyte population in squamous cell carcinoma precursors

BackgroundCutaneous squamous cell carcinoma (cSCC) is among the most common human cancers, yet the cellular identity and molecular programs of its preinvasive precursor, actinic keratosis (AK), remains poorly defined. MethodsWe applied CITE-seq to patient-matched AK, UV-exposed normal skin, and non-UV-exposed normal skin (n=5 patients, 12 biopsies) and performed spatial whole-transcriptome profiling in an independent cohort (n=4) to map pre-invasive keratinocyte states at single-cell resolution. ResultsWe identify AK-specific keratinocytes (ASK), a discrete population localized to the dysplastic basal epidermis and characterized by UV-associated mutational signatures (SBS7b), high mutational burden, and recurrent copy number alterations including 9p loss and 8q gain. ASK occupies a basal-like undifferentiated state sustained by a {Delta}Np63/PITX1 regulatory module that attenuates Notch/HES1-driven differentiation and activates glycolytic metabolism. Comparison with published cSCC data reveals that ASK share core tumor-propagating gene networks with tumor-specific keratinocytes (TSK), including IGFBP6, IGFBP2, and ITGA6, but lack invasion effectors MMP1, MMP10, and PTHLH. Functional experiments identify IGFBP6 as a pro-proliferative factor in AK-derived keratinocytes. The AK microenvironment shows expansion of inflammatory basal keratinocytes, barrier disruption, and early immunosuppressive T cell remodeling. ConclusionsThese findings define the molecular identity of a pre-invasive malignant keratinocyte population governed by p63/PITX1 and distinguish early oncogenic programs shared with invasive cSCC from later-acquired invasion effectors, identifying candidate targets for prevention or treatment of squamous cell carcinoma.

cancer biology↗

bioRxiv2026

A BRRF1-CCR4-NOT axis underlies conserved transcriptome-wide loss of splicing fidelity during gammaherpesvirus reactivation

Gammaherpesvirus reactivation drives a collapse of host mRNA splicing fidelity that extends across the transcriptome, with exon skipping affecting up to [~]57% of expressed genes, exceeding the effects of depletion of any of 186 splicing factors. Combining five Epstein-Barr virus (EBV) and Kaposis sarcoma-associated herpesvirus (KSHV) reactivation systems across B cell and epithelial models with deep poly(A)+ RNA sequencing of purified lytic cells, we find that most induced isoforms are predicted to undergo nonsense-mediated decay or to lose conserved protein domains, broadly compromising cell cycle, innate immune and RNA-processing pathways. The phenotype arises independently of viral DNA replication, indicating early host remodeling. A screen of EBV early genes identifies BRRF1 as a key driver: through a CIY(Y/E) motif conserved in KSHV ORF49, BRRF1 engages the nuclear CCR4-NOT complex through its CNOT9 and CNOT1 subunits, hijacking this canonically cytoplasmic deadenylation hub for nuclear disruption of host splicing.

pathology↗

bioRxiv2026

A conserved transcriptomic model defines metabolic resilience and vulnerability in obesity

BackgroundObesity arises from a complex interplay of genetic and environmental factors, with alterations of transcriptional networks that integrate metabolic, immune, and regulatory pathways. Conventional measures such as body mass index (BMI) quantify body size but fail to capture the molecular heterogeneity underlying divergent metabolic outcomes. We therefore sought to construct a gene expression-based transcriptomic representation of obesity, using BMI as a practical training anchor, and to use this framework to delineate transcriptional programs associated with metabolically healthy and pathogenic obesity, with subsequent projection to mouse transcriptomic data for cross-species validation. MethodsTranscriptome data of human visceral adipose tissue (N= 1,298) were used to derive the transcriptomic BMI model, and genes contributing to the model were functionally annotated by gene set enrichment analysis. The human-trained model was subsequently applied to mouse selection lines (N = 18) with divergent obesity phenotypes. In the human cohort, post hoc stratification into metabolically healthy obesity (MHO) and metabolically unhealthy obesity (MUO) groups was performed using a downstream classification framework incorporating observed BMI together with predicted BMI, to assess whether model-derived predicted BMI reflected obesity-related pathophysiologic status. ResultsModel-selected genes were involved in coordinated regulation of lipid metabolism, immune activation, and growth signaling, extending to mitochondrial and translational pathways. Cross-species analyses uncovered conserved metabolic polarization: DU6 mice exhibited lipid-anabolic and inflammatory remodeling, whereas DU6P mice displayed oxidative, mitochondrial, and GH-axis-enriched transcriptional states. In human cohorts, MHO individuals showed upregulation of mitochondrial energetics and protein synthesis, while MUO individuals were characterized by increased autophagy, lipid catabolism, and stress-adaptive signaling on the transcriptional level. Together, these findings define a conserved molecular continuum linking oxidative efficiency to metabolic health and inflammation to metabolic vulnerability. ConclusionsThis integrative transcriptomic framework bridges human and mouse adipose biology to uncover conserved mechanisms underlying obesity phenotypes. By contrasting mitochondrial and translational programs with inflammatory and catabolic pathways, it provides mechanistic insight into metabolic resilience and a foundation for precision approaches to obesity management.

systems biology↗

bioRxiv2026

Purinergic signaling promotes gliomagenesis through nuclear calcium transients

Intracellular Ca2+ transients drive key developmental and physiological processes, yet their role in oncogenesis remains incompletely understood. In glioblastoma (GBM), an aggressive brain malignancy, tumor cellular networks exhibit self-sustaining Ca2+ transients that promote tumor growth through unclear mechanisms. Using patient-derived GBM models, we show that these transients depend primarily on intracellular Ca2+ stores and extend to the nucleus to drive tumorigenesis. A neuromodulator screen identified extracellular purines ATP and ADP as potent inducers of both nuclear and cytosolic Ca2+ transients via activation of metabotropic purinergic P2RY1 receptors, whose knockdown attenuates tumorigenicity in vitro and in vivo. Mechanistically, Ca2+ transients promote tumorigenesis via the nuclear Ca2+/calmodulin-dependent kinase CAMK4, which regulates transcriptional and epigenetic programs, as well as ribosomal DNA transcription. From the therapeutic perspective, pharmacologic P2RY1 inhibition suppresses tumor growth in vitro and in vivo. Collectively, these findings reveal a pharmacologically targetable oncogenic mechanism in GBM and possibly other malignancies.

cancer biology↗

bioRxiv2026

NO modulates human airway smooth muscle function by altering glucose-6-phosphate dehydrogenase effects on sGC function in asthma

Since NO can modulate mesenchymal cell function, we posit that NO can modulate gene expression associated with excitation-contraction coupling. Our study shows that treating asthma-derived HASMCs with a low dose of NO plus sGC stimulator BAY-41, in most cases sensitized smooth muscle sGC towards activation via an elevated sGC heterodimer and in some cases also improved sGC{beta}1, catalase, Cyb5r3 or Trx1 expression (n=24 non-asthma and n=25 asthma). Interestingly we found that majority of asthma HASMCs showed a marked downregulation of G6PD expression inducing a low GSH/GSSG ratio in asthma, and these findings were replicated in murine lungs of allergic asthma (OVA and CFA/HDM). Studies with HEK/COS-7 cells showed G6PD synergizing with hsp90 in enabling sGC heme-maturation. G6PD overexpression in HASMCs enhanced the sGC heterodimerization while silencing of endogenous G6PD abrogated it. Complementation of these cellular results with whole animal models of G6PD deficiency or overexpression provided verification to our findings. Mouse lung tissue from the humanized variant of G6PD deficiency, V68M (G6PD A-deficiency) showed significant downregulation in the sGC heterodimer, with a concomitant reduction in its NO heme-dependent activity, thereby showing that G6PD deficiency lowers sGC heme. Conversely, G6PD overexpressing mouse lung tissue displayed an elevated sGC heterodimer and also showed a robust G6PD-sGC{beta}1 interaction, suggesting G6PD to be involved in the heme-maturation of sGC{beta}1. While G6PD maintains the cell redox by generating NADPH, its new role in regulating sGC maturation links sGC dysfunction in asthma to G6PD deficiency and may potentially uncover new targets for asthma treatment.

cell biology↗

bioRxiv2026

Targeting IL-6-STAT3/STAT4 Signaling Restores FOXP3 Expression in Pulmonary Arterial Endothelium and Reveals Novel Biomarkers for PAH

BackgroundInterleukin-6 (IL-6) is a central driver of pulmonary vascular remodeling in idiopathic, heritable, and connective tissue disease-associated pulmonary arterial hypertension (PAH). Elevated IL-6 correlates with right ventricular (RV) dysfunction and poor survival. However, the specific downstream mechanisms by which IL-6 drives pathogenesis remain poorly defined. We investigated the therapeutic impact of direct IL-6 neutralization and its regulation of a novel epigenetic signaling axis in PAH. Materials and MethodsWe evaluated species-specific IL-6-neutralizing antibodies in murine Sugen/hypoxia and rat monocrotaline models of PAH. RV structure and function were assessed using cardiac MRI and invasive hemodynamics. Lung transcriptomic profiling was performed by RNA sequencing mouse lung tissue. Key findings were validated in explanted human PAH lungs, serum, and peripheral blood mononuclear cells (PBMCs), and further interrogated through mechanistic in vitro studies in human pulmonary artery endothelial cells (PAECs). ResultsIL-6 neutralization significantly improved RV function, reduced pulmonary arterial pressures, and attenuated pulmonary vascular remodeling in both experimental models. Transcriptomic analysis identified a dysregulated FOXP3 signaling axis. Mechanistically, IL-6 induced cooperative binding of phosphorylated STAT3 and STAT4 to the FOXP3 promoter, facilitating DNMT1-mediated DNA methylation and stable gene silencing. IL-6 blockade restored downstream FOXP3 expression, rescued downstream BMPR2 signaling, and re-established endothelial homeostasis. In clinical PAH cohorts, FOXP3 expression was markedly reduced and inversely correlated with circulating IL-6 levels and indices of disease severity. ConclusionIL-6 drives pulmonary hypertension through STAT3/STAT4- and DNMT1-dependent epigenetic repression of FOXP3, linking chronic inflammation to BMPR2 dysfunction and pulmonary vascular remodeling. IL-6 neutralization reverses this pathogenic program in experimental PAH. FOXP3 emerges as a mechanistic biomarker of disease severity and a potential tool for precision stratification of patients likely to benefit from IL-6-targeted therapies. Clinical PerspectiveO_ST_ABSWhat Is New?C_ST_ABSO_LISynergistic Gene Repression: The study demonstrates that phosphorylated STAT3 functional transcriptional complex that binds directly to the FOXP3 promoter. Acting as a molecular scaffold, this complex actively represses FOXP3 expression within the pulmonary endothelium. C_LIO_LIEpigenetic Silencing Mechanism: IL-6 does not merely induce a transient suppression of FOXP3. Instead, IL-6/STAT3 signaling recruits DNMT1 to the FOXP3 promoter, leading to site-specific DNA methylation and long-term epigenetic silencing. This mechanism provides a direct molecular link between chronic systemic inflammation and sustained pulmonary vascular injury. C_LIO_LIThe FOXP3-BMPR2 Connection: The findings identify FOXP3 as a critical positive regulator of BMPR2 expression. Neutralization of IL-6 disrupts this pathological inhibitory loop, permitting restoration of BMPR2 signaling, the central gatekeeper of pulmonary vascular integrity and homeostasis. C_LIO_LITranslational Biomarkers: Importantly, the molecular changes within the lung are reflected systemically. Suppressed FOXP3 expression is readily detectable in PBMCs and serum, offering a non-invasive biomarker that correlates with pulmonary hemodynamic status and vascular health. C_LI Clinical ImplicationsO_LIPrecision Patient Stratification: FOXP3 expression in PBMCs and serum functions as a surrogate marker of pulmonary vascular epigenetic health. This could identify a specific inflammatory endotype of PAH patients most likely to respond to IL-6-targeted therapies. C_LIO_LIPrognostic Biomarker: Because FOXP3 levels integrate both systemic inflammatory burden and dysfunction of the RV-pulmonary vascular axis, they may provide a more sensitive tool for monitoring therapeutic response and predicting clinical worsening than current standard-of-care markers. C_LI

molecular biology↗

bioRxiv2026

Unique nasal cell states induced by common pediatric respiratory viruses

Respiratory viral infections in early childhood are major drivers of acute morbidity and long-term airway disease, yet how distinct viruses remodel the pediatric nasal mucosa at cellular resolution remains unresolved. Here, we generated a single-cell RNA sequencing atlas of 335,174 nasal epithelial and immune cells from 132 children under five years of age with SARS-CoV-2, rhinovirus, or respiratory syncytial virus (RSV) infection, alongside uninfected controls. Mapping viral transcripts to individual cells revealed virus-specific infected epithelial states: an NF-kB-responsive ciliated subset in SARS-CoV-2 and a previously undescribed KRT17+ squamous-like subset in RSV. We delineated divergent mucosal response programs, including a robust interferon (IFN) response in SARS-CoV-2, an IL-13-responsive secretory program in rhinovirus, and heightened inflammatory and cytotoxic immune activation in RSV. In RSV, specific immune subsets and elevated IFN-response signatures were associated with disease severity, whereas rhinovirus-induced wheeze was marked by expansion of a CST1+ goblet cell subset. Integration of asthma genome-wide association data with our atlas revealed a KRT13+ hillock-like squamous epithelial subset enriched for expression of childhood-onset asthma risk loci. Finally, we demonstrate that this resource enables high-resolution annotation of independent pediatric cohorts in Kolkata, India and rural Bangladesh. Together, this atlas establishes a comprehensive view of antiviral immunity in the pediatric nasal mucosa and defines virus-specific mucosal immune programs relevant to disease severity and asthma risk in early life.

immunology↗

bioRxiv2026

An INF2-dependent actin-mediated step in Inositol 1,4,5-trisphosphate receptor cluster formation and activity

Intracellular calcium signaling plays a vital role in regulating various cellular processes including gene regulation, motility, metabolism and cell death. Inositol 1,4,5-trisphosphate receptors (IP3R) on the Endoplasmic Reticulum (ER) are a major cation channel that regulates stimulus-induced calcium release from the ER. While several molecular players regulate activity of IP3R, its regulation by actin filaments were uncharacterized. Here we show that actin filaments polymerized by a specific actin nucleator INF2 facilitates agonist-induced IP3R activity. Our results demonstrate that INF2-mediated actin filaments regulate formation and/or stability of IP3R clusters on the ER that have been previously shown to be hotspots of ER calcium release. Using cell-biological and biochemical techniques we further show that INF2 physically interacts with IP3R isoforms, often at IP3R clusters. While INF2-IP3R interaction is independent of INF2-activity, the ability of INF2 to mediate IP3R clusters is dependent on its actin polymerization activity. Finally, we demonstrate that in addition to its calcium mobilization activity, INF2 on ER specifically regulates IP3R cluster positioning to mediate ER-mitochondrial contacts and facilitate ER to mitochondrial calcium transfer. Overall, these results reveal an actin-dependent step in regulation of IP3R activity both in terms of ER calcium release and modulation of ER-mitochondrial contacts. HighlightsO_LIINF2-mediated actin filaments potentiate agonist-induced IP3R-mediated ER calcium release without affecting the ER calcium stores per se. C_LIO_LIER-localization of INF2 is dispensable for its role on IP3R activity. Moreover INF2-mediated actin filaments affect the activity of all IP3R isoforms. C_LIO_LIINF2 interacts with IP3R in an activity and actin filament independent manner through its C-terminal region. C_LIO_LIINF2 regulates IP3R cluster formation in actin-filament dependent manner and thereby regulates IP3R activity. C_LIO_LIFurther we show that ER-localized INF2 specifically regulate IP3R cluster positioning thereby promoting ER to mitochondrial contact and calcium transfer. C_LI

cell biology↗

bioRxiv2026

Emergent smartphone temporal structures reflect cognitive constraints

Fine-grained temporal structures emerge in smartphone behavioral recordings over multi-day periods. Complex systems research suggests that emergent temporal structures reflect underlying resource constraints of the system. Here we test whether cognitive abilities measured through speeded tasks (spanning fractions of a second) are reflected in emergent smartphone temporal structures spanning days, revealing how cognitive resource limitations shape naturalistic behavior. We analyzed smartphone tap interval patterns accumulated over several days and used decision tree regression models to predict performance in simple and choice reaction time tasks from these patterns. Simple reaction time was poorly predicted (R2 = 0.003), indicating that basic sensorimotor constraints play only a marginal role in shaping real-world behavioral timing. In contrast, choice reaction time was moderately predictable (R2 = 0.4), demonstrating that higher-order cognitive constraints prominently influence naturalistic temporal organization. Notably, while task performance operates at sub-second timescales, predictive temporal patterns in smartphone behavior spanned milliseconds to several seconds and was accumulated over days, revealing the broad, multi-scale influence of cognitive resource constraints on everyday behavior. Both predicted and measured choice reaction times showed age-related decline, but the decline was more pronounced in predicted values, suggesting that age-related cognitive changes may be amplified in naturalistic contexts. These findings demonstrate that emergent temporal structures in smartphone use can reveal how cognitive processes measured using speeded tasks manifest, or fail to manifest, in real-world behavior. Complex-systems approaches can bridge laboratory and naturalistic assessments of cognition, revealing which cognitive processes meaningfully constrain real-world behavior.

animal behavior and cognition↗

bioRxiv2026

Evaluating codon optimization strategies for mammalian glycoprotein production with an open-source expression vector

Efficient production of human proteins for the development of tool compounds and biologics depends on a detailed understanding of the protein expression machinery in mammalian cells. Codon optimization is widely believed to enhance protein yield, yet its impact in homologous mammalian systems remains poorly defined. Here, we systematically compare five codon usage strategies reflecting common assumptions about rare codons, RNA stability, and synthesis efficiency. We developed pTipi, an efficient open-source mammalian expression vector, and evaluated its performance in antibody production. We generated plasmids for common epitope tag antibodies such as V5, anti-biotin and anti-His for distribution by Addgene. To compare codon usage schemes, we performed a bake-off of 18 human and murine Wnt pathway glycoproteins in mammalian cells. Small-scale expression screens revealed that codon optimization did not provide a general advantage over native coding sequences, while strategies prioritizing RNA stability consistently reduced expression. Interestingly, a skewed codon scheme using the most abundant codons produced yields comparable to native sequences and occasionally enhanced protein output. To enable flexible evaluation of codon strategies, we implemented a Golden Gate-compatible pTipi platform for efficient synthetic gene incorporation. We conclude that native codons are sufficient for robust homologous mammalian expression of glycoproteins, while selective codon skewing can be beneficial for some targets.

molecular biology↗

bioRxiv2026

RSTG: Robust Generation of High Quality Spatial Transcriptomics Data using Beta Divergence Based AutoEncoder

One of the key challenges in spatial transcriptomics data analysis is the lack of sufficient data to train models. To address this shortcoming, multiple generative models have been developed to generate synthetic spatial transcriptomics samples in a controlled environment. However, these models often fail in out-of-the-box generation in the presence of noise (such as outliers). To tackle this challenge, we propose RSTG (Robust Spatial Transcriptomic Generator), an autoencoder that incorporates the {beta}-ELBO loss, to generate realistic and high-quality spatial transcriptomic sequences. Our model uncovers data intrinsic structure by approximating its underlying distribution through variational inference, resulting in more interpretable and robust density estimation. We validate the effectiveness of RSTG across multiple tasks, including the recovery of cellular positions in both the 2D spatial and location domains. Our method shows improved performance, both qualitatively and quantitatively, across multiple datasets, including brain and liver samples generated using MERFISH, MERSCOPE, and Visium technologies. We further illustrate the robustness of RSTG to outliers by contaminating a portion of the data with anomalies (such as white noise, batch effects, and dropouts) as well as on a reallife degraded sample. The results show that our proposal maintains high quality and stability even when the training data are contaminated, across a variety of experimental settings and in comparison with existing approaches.

bioinformatics↗

bioRxiv2026

Candida albicans Snf2 modulates the response to DNA damage by regulating gene expression and uptake of the genotoxic stressors

The SWI/SNF complex comprising of the catalytic subunit, Snf2, is a key regulator of gene expression and DNA damage repair in eukaryotic cell. Candida albicans Snf2 is known to regulate hyphal formation. In this paper, we have investigated the role of this protein in DNA damage response. We show that CaSnf2 is required for cell division as deletion of both copies of SNF2 leads to increased duplication time. The mutant cells form clumps with increased chitin and {beta}-glucan deposition on the cell wall. The altered cell wall phenotype leads to reduced uptake of genotoxic stressors leading to increased resistance to both methyl methane sulfonate (MMS) and hydroxyurea (HU). In addition, resistance of Casnf2{Delta} cells to MMS also appears to be mediated by upregulation of CaRAD9 expression by CaFun30, an ATP-dependent chromatin remodeling protein, and CaRtt109, a fungal-specific histone acetyltransferase. The response of Casnf2{Delta} to genotoxic stressors is at variance with the response of Scsnf2{Delta} mutant, highlighting the differences in DNA damage response/repair pathway between the two organisms. Finally, we show that Casnf2{Delta} mutants are extremely sensitive to azoles due to downregulation of multi-drug resistance pumps leading to reduced efflux of the drug.

microbiology↗

bioRxiv2026

S1PR1 signaling biases neutrophils toward long-lived low-inflammatory functional states

Sphingosine 1-phosphate (S1P), a lipid mediator that signals through five G protein-coupled S1P receptors (S1PRs), regulates T cell trafficking, tissue residency, and inflammatory processes. In contrast to the established roles of S1P signaling in T cell trafficking, its role in neutrophil biology remains poorly understood. Here, we demonstrate that S1PR1, one of the two S1PRs expressed in neutrophils, promotes mitochondrial fitness, enhances survival, and reduces inflammatory output. Using myeloid- and neutrophil-selective S1PR1 overexpression (S1PR1hi) mouse models, we show that elevated S1PR1 signaling promotes redistribution of neutrophils from the bone marrow to peripheral tissues under steady-state conditions, without inducing overt inflammation or tissue injury. S1PR1hi neutrophils display altered surface marker profiles consistent with a less mature state. These cells also exhibit reduced in vivo turnover, increased mitochondrial membrane potential and oxidative phosphorylation, and transcriptional programs linked to survival and dampened inflammatory signaling. Functionally, S1PR1hi neutrophils exhibit a reduced oxidative burst while preserving phagocytic capacity. However, in vivo bacterial challenge revealed impaired bacterial clearance in the lung. In contrast, in a model of influenza A virus infection of the lung, enhanced neutrophil-intrinsic S1PR1 signaling conferred reduced lung injury, decreased inflammatory output, and improved survival. Together, these findings support a model in which S1PR1 reprograms neutrophils, enabling their survival and dampening inflammatory potential in a context-dependent manner, thereby differentially shaping host defense and tissue protection during microbial infections.

immunology↗

bioRxiv2026

Sotatercept Reverses SIN3a Deficiency-Driven PAH by Reprogramming BMPR2/TGF-β-HIF-1α Signaling Pathways

BackgroundPulmonary arterial hypertension is a progressive and fatal cardiopulmonary disease marked by excessive proliferation of pulmonary artery smooth muscle cells (PASMCs), pathological vascular remodeling, and ultimately right heart failure. Dysregulated BMPR2 signaling is a central molecular hallmark of PAH and is often associated with epigenetic suppression of BMPR2 expression. Switch-independent 3a (SIN3a), a transcriptional co-regulator and chromatin-modifying scaffold protein, has emerged as a key regulator of BMPR2 expression, yet its role in PAH pathogenesis remains poorly defined. MethodsWe generated smooth muscle cell-specific SIN3a knockout mice (SIN3aSMC-/-) and subjected them to the Sugen/hypoxia protocol to induce PAH. A cohort received Sotatercept treatment. In parallel, human PASMCs engineered to overexpress SIN3a were exposed to TGF{beta}1 or hypoxia (1% O2) in vitro. Comprehensive transcriptomic profiling and pathway analyses identified molecular networks regulated by SIN3a and Sotatercept. Hemodynamic measurements and detailed morphometric analyses were used to assess disease severity and treatment response. ResultsSIN3a overexpression in PASMCs suppressed hypoxia-inducible factor-1 and TGF-{beta}/SMAD2/3 signaling, restored BMPR2 expression, and activated canonical BMP signaling through SMAD1/5/9 phosphorylation, while reducing pro-inflammatory, oxidative, and fibrotic gene programs. Transcriptomic analyses revealed that SIN3a and Sotatercept converge on gene networks that regulate BMPR2 signaling, ID isoforms, extracellular matrix remodeling, oxidative stress, and inflammation. In vivo, smooth muscle-specific SIN3a deletion exacerbated Sugen/hypoxia-induced PAH, increasing right ventricular systolic pressure, right ventricular hypertrophy, pulmonary vascular remodeling, and fibrosis. Sotatercept treatment reversed these pathological features, restored SIN3a and BMPR2 expression, reactivated BMP signaling, and attenuated HIF-1 and TGF-{beta} signaling in SIN3a-deficient mice. ConclusionsSIN3a is a central epigenetic regulator of PASMC homeostasis that integrates oxidative stress, inflammation, and fibrotic signaling. Loss of SIN3a accelerates PAH progression, whereas Sotatercept restores SIN3a expression, rebalances BMPR2 and TGF-{beta} signaling, and attenuates pulmonary vascular remodeling and right ventricular dysfunction. Together, these findings identify SIN3a as a disease-relevant therapeutic target and support the use of Sotatercept as a disease-modifying approach for pulmonary vascular disease.

molecular biology↗

bioRxiv2026

Early microglial priming in Alzheimer's disease revealed by ME-seq

Epigenetic modifications, particularly DNA methylation, change dynamically with aging and are implicated in Alzheimers Disease (AD), yet how methylation interfaces with transcriptional and chromatin regulation at single-cell resolution remains poorly understood. Progress has been limited by a lack of scalable technologies capable of jointly profiling these regulatory layers. Here, we present ME-seq, a highly scalable technologies capable of simultaneously profiling DNA methylation, gene expression, and chromatin accessibility, while achieving a 100-fold reduction in cost. We generated over 400,000 single-nucleus trimodal profiles from the aging and AD mouse brain across ages, producing the first such atlas of neurodegeneration. We found AD progression triggers pronounced, disease-specific shifts in cellular composition, characterized by accelerated epigenetic aging and the expansion of disease-associated microglia (DAM). Integrative analyses, including aging clocks, revealed that DNA methylation acts as an early priming layer preceding transcriptional activation with IRF1 identified as a methylation-sensitive transcription factor serving as a gatekeeper for DAM activation. Our results establish ME-seq as a transformative tool for large-scale epigenomic dissection, revealing DNA methylation as a primary coordinator of cell-state transitions in the aging brain. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=195 HEIGHT=200 SRC="FIGDIR/small/702946v1_ufig1.gif" ALT="Figure 1"> View larger version (70K): org.highwire.dtl.DTLVardef@67435dorg.highwire.dtl.DTLVardef@177c22aorg.highwire.dtl.DTLVardef@16c6fd9org.highwire.dtl.DTLVardef@231b92_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2026

Constraint Network Analysis of Global and Local Rigidity in Wild-Type EGFR: Apo vs Gefitinib-Bound States

The mechanical rigidity-flexibility architecture of protein kinases play a critical role in regulating conformational stability and inhibitor response, yet remains insufficiently quantified for Epidermal Growth Factor Receptor (EGFR). Here, we apply Constraint Network Analysis (CNA) to systematically characterize the global and local mechanical properties of wild-type EGFR in its apo state and when bound to the ATP-competitive inhibitor gefitinib. Analysis of multiple global rigidity indices reveal a well-defined rigidity percolation transition in apo EGFR at an energy cutoff of approximately -2.0 kcal mol-1, indicative of an intrinsically stable mechanical framework. Gefitinib binding shifts this transition slightly to higher energies and sharpens the percolation behavior, accompanied by enhanced long-range mechanical coupling, increased rigidity order parameters, and reduced configurational entropy. Importantly, residue-level rigidity and percolation profiles remain largely conserved between the two states, demonstrating that ligand binding does not induce large-scale reorganization of the EGFR mechanical network. Instead, inhibition arises from subtle, localized rigidification within functionally relevant regions, consistent with stabilization of an inactive conformational ensemble. Collectively, this work establishes the first CNA-based mechanical reference state for wild-type EGFR and underscores the utility of network rigidity analysis for resolving ligand-induced effects that are structurally subtle yet mechanistically significant. This framework provides a quantitative baseline for future studies of oncogenic mutations and drug-resistant EGFR variants.

biophysics↗

bioRxiv2026

Distinct CA1 inputs support shifts in neural dimensionality and memory resolution

Event-based memories may be encoded with high (e.g., episodic) or low (e.g., gist) mnemonic resolution. While the CA1 region of the hippocampus encodes events at both scales, it is unclear how such dual coding emerges. Consistent with theoretical predictions1,2, here we show that trisynaptic (from CA3) and monosynaptic (from the medial entorhinal cortex) projections to CA1 encode high- and low-resolution event-based memories, respectively. Recruitment of the trisynaptic pathway during contextual fear conditioning promotes feedforward inhibition of CA1 via activation of parvalbumin-positive (PV+) interneurons. This allows sparse encoding of event-based memories in high-dimensional neural states that support high-resolution contextual fear memories, where mice exhibit conditioned fear only in the training context and not similar contexts. Inhibiting this input during training reduces activation of CA1 PV+ interneurons and feedforward inhibition, shifting neural dynamics to low-dimensional states that support low-resolution contextual fear memories where mice freeze in the training context and similar contexts. These experiments identify a circuit-based mechanism that causally links the dimensionality of CA1 neural dynamics to mnemonic resolution.

neuroscience↗

bioRxiv2026

Inferring the genetic basis of sleep states in Drosophila melanogaster using hidden Markov models

Multiple lines of evidence suggest that sleep in flies is not a unitary state but has lighter and deeper stages similar to mammals. A hidden Markov model applied to activity count data revealed lighter and deeper sleep states in a wild-derived population of flies. Fitting the data to a range of possible sleep states enabled us to determine the optimal number of sleep states for each fly. Four sleep and waking states were optimal across the population. We verified physiological differences among states experimentally using an arousal threshold paradigm. We then calculated the time spent in each sleep state for each fly. The time spent in each sleep state was heritable and therefore mappable to the genome. We mapped these parameters to the genome, identifying state-specific genes. Additionally, we provide software, FlyDreamR, that users can apply to activity count data.

genomics↗