Biology subjects

Chakraborty, S.

Publications and source records attributed to Chakraborty, S..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

A High-throughput Fluorescence Polarization Assay for Screening Sirtuin Inhibitors

Sirtuins (SIRTs), which remove protein lysine acyl modifications, play crucial roles in diverse cellular processes, including metabolism, gene transcription, DNA damage repair, cell survival, and stress response. Several sirtuins are considered non-oncogene addiction of cancer cells and promising targets for anticancer drug development. High-throughput screening (HTS) methods for sirtuins are critical for the development of potent and isoform-selective sirtuin inhibitors, which are needed to validate the therapeutic potential. Herein, we designed and synthesized a fluorescent polarization (FP) tracer, KP-SC-1. Using this high-affinity tracer, we developed a robust, high-throughput FP competition assay for screening SIRT1-3 inhibitors. The assay was validated by testing known SIRT1-3 inhibitors. The assay can detect NAD+-independent SIRT1-3 inhibitors, as well as NAD+-dependent inhibitors, such as Ex-527 and TM. Finally, our assay showed satisfactory stability and outstanding performance in a pilot library screening. Compared to previous assays, the FP assay uses much less SIRT1-3 enzymes, a feature important for high-throughput library screening. We believe that the FP assay developed here will accelerate the discovery and development of SIRT1-3 inhibitors.

biochemistry↗

bioRxiv2026

The association of extracellular vesicle (EV)-cargo miR-330-3p with postoperative delirium and a potential mechanism of tau phosphorylation and neuron toxicity

BackgroundPostoperative delirium (POD) is a frequent and severe neurocognitive complication following cardiac surgery, associated with poor long-term outcomes. The underlying mechanisms are unclear, and objective biomarkers are urgently needed. MethodsWe used pre- and post-operative plasma samples from 59 patients undergoing cardiac surgery in three separate studies with rigorous delirium assessment using the Confusion Assessment Method in a case-control design. Small extracellular vesicles (sEVs) were isolated from plasma, and their miRNA cargo was profiled using RNA sequencing. Target miRNAs were validated by qRT-PCR, and digital PCR (dPCR). The functional impact of the lead candidate miRNA was investigated in vitro by assessing tau phosphorylation and cell viability in HT22 neuronal cell line. ResultsThere were no differences in sEV morphology or numbers between patients with and without POD. While three candidate miRNAs were initially validated by qRT-PCR, subsequent dPCR analysis confirmed that only the perioperative change in plasma sEV-cargo miR-330-3p expression was significantly greater in patients who developed POD (n = 20) compared with those who did not (n = 20) (5.22 copies/L plasma; 95% Confidence Interval (CI), 1.187 to 9.256; p = 0.0139). Receiver operating characteristic curve analysis for this change yielded an area under the curve of 0.745 (95% CI, 0.589 to 0.901). In vitro overexpression of miR-330-3p in a neuronal cell line significantly increased the phosphorylation of tau at Ser199 (p < 0.0001) and Ser396 (p < 0.001) and reduced cell viability (p < 0.001). ConclusionsOur findings suggest that sEV-bound miR-330-3p increases in patients with POD after cardiac surgery. In vitro results suggest a potential pathogenic role for miR-330-3p, linking a systemic signal to tau-related neuronal injury. Clinical PerspectiveO_ST_ABSWhat Is New?C_ST_ABSO_LIThis study identifies a specific perioperative increase in small extracellular vesicle (sEV)-cargo miR-330-3p in patients with postoperative delirium (POD) following cardiac surgery. C_LIO_LIWe provide the first evidence that miR-330-3p directly induces tau hyperphosphorylation and reduces neuronal viability in vitro, establishing a potential mechanistic link between systemic sEV signaling and neurodegeneration. C_LI What Are the Clinical Implications?O_LIThe measurement of perioperative change in miR-330-3p could serve as an objective biological marker to assist in the early identification and risk stratification of patients at high risk for POD. C_LIO_LIThe identified miR-330-3p/tau pathway represents a potential new therapeutic target; future interventions aimed at inhibiting this specific miRNA might help prevent or mitigate POD-related neuronal injury. C_LIO_LIThese findings emphasize the importance of monitoring dynamic sEV-cargo changes to better understand and manage perioperative neurocognitive disorders. C_LI

molecular biology↗

bioRxiv2026

DOT1L-AF10-mediated H3K79me3 promotes NF-kB p65-dependent inflammatory activation in endothelial cells

DOT1L-catalyzed H3K79 methylation is a hallmark of actively transcribed genes and has been extensively studied in developmental and disease contexts. While DOT1L inhibition has emerged as a promising therapeutic strategy in cancer, its role in pro-atherogenic endothelial inflammation remains unclear. To investigate this, we utilized an in vivo partial carotid artery ligation model and observed increased DOT1L expression and H3K79me3 level. Consistently, in vitro studies employing a 3D-printed human coronary artery model and TNF- stimulation corroborated these results, showing elevated DOT1L expression and H3K79me3 deposition, while levels of H3K79me and me2 remained unchanged. Further analyses identified key DOT1L-containing complex (DotCom) components, AF10 and AF9 (upregulated) and AF17 (downregulated), as contributors to the enhanced H3K79me3 landscape. CUT&RUN sequencing showed prominent H3K79me3 enrichment at the RELA (NF-{kappa}B p65) promoter, corresponding with increased NF-{kappa}B p65 expression and activation. Notably, inhibition/knockdown of the methyltransferase DOT1L or overexpression of the demethylase FBXL10 significantly reduced H3K79me3 levels, thereby suppressing NF-{kappa}B p65 expression and attenuating endothelial inflammation, independent of canonical NF-{kappa}B p65 activation. These findings establish DOT1L-mediated H3K79me3 as a crucial epigenetic regulator of endothelial inflammation, highlighting a potential therapeutic avenue for mitigating NF-{kappa}B p65-driven pro-atherogenic endothelial dysfunction.

cell biology↗

bioRxiv2026

ATM functions as a rheostat of metabolic stress in small-cell lung cancer

ATM is best known as a guardian of genomic stability, yet its contributions to oncogenic signaling in aggressive malignancies like small-cell lung cancer (SCLC) remain poorly understood. Despite ATM being an established clinical vulnerability in SCLC, its influence on dysregulated tumorigenic circuits remains unclear. We demonstrate that inhibition of ATM disrupts the AKT-mTORC1-4EBP1 signaling axis, leading to attenuation of the master regulator of stress, ATF4. ATF4 and MYC appear to co-regulate one another in a feedback loop critical for redox homeostasis. ATM inhibition perturbs both the expression and function of MYC and ATF4, leading to increased intracellular reactive oxygen species, impaired glutathione recycling, and ferroptotic cell death, thereby exposing a crucial dependency of SCLC on stress-adaptive signaling. We uncover previously unrecognized metabolic vulnerability in SCLC, nominating ATM as a regulator of adaptive stress, expanding its role beyond canonical DNA damage repair (DDR) and highlighting therapeutically exploitable opportunities in aggressive tumors. Statement of SignificanceThe metabolic landscape of SCLC remains poorly characterized, particularly its interaction with dysregulated signaling networks, limiting the development of effective strategies to overcome therapeutic resistance. Our work reveals an expanded role for ATM beyond DNA repair, positioning it as a key regulator of metabolic rewiring and highlighting new therapeutic opportunities for SCLC.

cancer biology↗

bioRxiv2026

Decoding epitope immunodominance in HIV Env using cryoEM and machine learning

Viral surface glycoproteins, such as the HIV envelope protein (Env), present numerous antibody (Ab) epitopes, yet immune responses consistently focus on only a subset, a phenomenon known as immunodominance. Although structural studies have provided insights into Env antigenicity, our understanding of the molecular features that govern efficient Ab engagement remains incomplete, thereby limiting the predictive and rational design of vaccines. Here, we characterized the structural determinants of epitope immunodominance in HIV Env by integrating high-resolution cryoEM-based polyclonal epitope mapping (cryoEMPEM) across different clades with quantitative analyses of epitope topology, accessibility, and physicochemical properties. More than 70 new structures were resolved to assemble a library of >100 Env-antibody complexes. These data informed the development of a surface-centric, machine-learning model to predict relative Antigen Surface Immunodominance (ASI model). Comparison of ASI-predicted epitope sites with the specificities of Env-induced antibodies showed that the model accurately identifies immunodominant regions and highlights the structural features driving immune bias. Notably, immunogens redesigned based on model predictions successfully redirected Ab responses toward a normally subdominant epitope, demonstrating the potential of strategies coupling targeted assembly of focused structural libraries with machine learning to uncover complex molecular patterns and enable design of more effective vaccine antigens.

immunology↗

bioRxiv2026

Tabular foundation model predicts alternative lengthening of telomeres (ALT) and identifies SMARCAL1 as a target in ALT-driven cancers

Alternative lengthening of telomeres (ALT) is a telomerase-independent pathway used by aggressive cancers to maintain their replicative immortality. Because ALT is absent from normal human cells, it is an appealing target for cancer therapy, but the lack of ability to determine ALT status at scale has hindered discovery. Here, we developed ALTitude, a machine learning method from a tabular foundation model that infers ALT from cell line whole genome sequencing data, without need for paired germline analysis. We deployed ALTitude across the DepMap, doubling the number of known ALT+ cancer models. Systematic integration of ALTitude with CRISPR-Cas9 screens yielded the selective dependency on SMARCAL1 in ALT+ cell lines, where we show it stabilizes the ALT phenotype. Acute depletion of SMARCAL1 leads to G2/M arrest, mitotic catastrophe, and cell death. These data provide a valuable resource for studying ALT-related genomic features and present SMARCAL1 as a therapeutic target for ALT+ malignancies.

cancer biology↗

bioRxiv2026

Regulatory network architecture constrains inflammatory responses in tissue-resident alveolar macrophages

Macrophages across different tissues exhibit remarkable functional diversity while maintaining core innate immune-cell programming. These complex programs are governed by gene regulatory networks, in which precise transcription factor activity tunes the expression of functionally relevant gene modules. Although the contributions of individual transcription factors have been well characterized, the higher-order regulatory interactions that coordinate tissue-resident macrophage identity and inflammatory response regulation remain poorly understood. Here, we integrate single-cell RNA-seq data with ATAC-seq profiling and deep-learning-based chromatin accessibility modeling to infer gene regulatory network architectures in tissue-resident versus recruited monocyte-derived alveolar macrophages under inflammatory stress. Our results suggest that inflammatory responses are more restrained in tissue-resident alveolar macrophages compared with recruited macrophages due to a stabilizing regulatory network architecture involving PU.1 and CEBP/{beta}. This work advances our understanding of functional plasticity in tissue-resident macrophages and their role in host defense.

immunology↗

bioRxiv2026

Modeling the organizational heterogeneity of lipid-enriched microdomains in the neuronal membranes of gray and white matter of Alzheimer brain: A computational lipidomics study

Alzheimers disease (AD) is a leading cause of death among the elderly, with no existing treatment. The development of therapy is further challenged by a limited understanding of molecular pathogenesis and the absence of reliable early-detection biomarkers. Neuroimaging and lipidomic studies reveal structural and biochemical alterations in both gray and white matter in AD patients, including disruptions in membrane organization and neuronal signaling pathways. In the present work, we employed lipidomics-guided modeling of membranes in gray and white matter regions in healthy and diseased (AD) conditions, and used all-atom molecular dynamics (MD) simulations to examine how AD-associated alterations in lipid composition influence the structure, spatial organization, and micro-heterogeneity of neuronal plasma membranes in different brain regions. Data suggest that Alzheimers disease-associated lipid alterations in gray matter (GM) and white matter (WM) impact membrane thickness and microdomain distribution, highlighting the critical role of lipid composition in maintaining neuronal membrane homeostasis and function. Higher-order cholesterol-ceramide- sphingomyelin-enriched domains are more abundant in the neuronal membranes of the GM region in diseased conditions. Under AD-mimicking conditions, lipidomic analyses demonstrate that neuronal membranes in GM experience more substantial compositional and structural remodeling than those in WM. Our results show significant changes in membrane microdomain distribution across the lipid bilayers, and, interestingly, these changes are more pronounced in the gray matter than in the white matter. This study establishes a framework for modeling the tissue-specific lipidomics data to understand how disease-driven compositional changes affect the structure, organization, and dynamics of biological membranes.

bioinformatics↗

bioRxiv2026

Drought tolerance of Aedes aegypti mosquito eggs is influenced by adaptation to local climate conditions and associations with humans

Urbanization is intensifying human interactions with mosquitoes, exacerbating public health challenges. Densely populated areas provide ideal conditions for container-dwelling mosquitoes, with increased host availability and the presence of artificial breeding sites. These anthropophilic mosquitoes often exhibit distinct ecological adaptations compared to their rural counterparts. Since mosquito eggs are immobile and remain at the site of oviposition, they provide a valuable lens for assessing how urbanization, climate-driven shifts in temperature, and drought affect mosquito reproductive success. This study examined Ae. aegypti egg viability under varying temperature and dry conditions over five months, focusing on lineages with distinct ancestries from West African populations. Mosquitoes collected from urban habitats with a high human preference demonstrated higher egg survival under prolonged arid conditions. Analysis of climatic factors revealed that dry season temperature and precipitation during wet periods are significant predictors of egg drought tolerance. Modeling future climate scenarios based on input from our egg viability results suggests a projected shift and expansion in the seasonal survival window for Ae. aegypti by the end of the century. This study highlights the importance of understanding environmental constraints on the drought tolerance of mosquito eggs to predict and mitigate future mosquito outbreaks.

physiology↗

bioRxiv2026

miRNA Sensor HuR Compartmentalizes Ago2-Uncoupled miRNAs to Lipid Droplets to Buffer miRNA Activity in Mammalian Cells

miRNA activity must be optimized to ensure target gene expression in mammalian cells in response to specific needs. How and when miRNA activity is regulated remains an open question in gene expression regulation, with limited information on how cellular machinery senses miRNA levels to regulate miRNA expression and activity. Because miRNAs are stable molecules that can be reversibly used, the existence of a miRNA-sensing mechanism in mammalian cells has been anticipated. With ectopic expression of miRNAs in mammalian cells, we found a dose-dependent miRNA buffering mechanism in which miRNA export and its storage on lipid droplets are essential for miRNA activity optimization in mammalian cells. We found that the miRNA-binding protein HuR, known for its role in miRNA export, has a dual function in mammalian cells. HuR uncouples miRNAs from Ago2 to facilitate association of lipid droplets with nonfunctional miRNAs, a process that gets augmented in cells with high lipid droplet content and restricted extracellular export. Thus, HuR acts as a miRNA sensor, and the optimal activity and abundance of HuR regulate miRNA storage on lipid droplets or its export to maintain cellular miRNA homeostasis, thereby preventing detrimental effects of an excess miRNA pool in mammalian cells. Thus, targeting miRNA export or lipid droplet association is an important strategy for buffering cellular miRNA levels. ImportanceTo ensure that target gene expression in mammalian cells is appropriately regulated, miRNA activity needs to be carefully fine-tuned. Although miRNAs are stable and can be reused, the precise mechanisms by which their levels are sensed and regulated remain unclear. Our research uncovered a fascinating dose-dependent miRNA buffering process that involves export and storage of miRNAs on lipid droplets--essential steps for precise regulation. We also found that HuR, a protein that facilitates miRNA export, plays a key role by uncoupling miRNAs from Ago2 and promoting their association with lipid droplets in cells with abundant lipid droplets and limited extracellular export capacity. Overall, HuR acts as a miRNA sensor, helping to balance miRNA storage and export to maintain cellular homeostasis and prevent the harmful effects of miRNA overactivity.

cell biology↗

bioRxiv2025

Improved Bayesian inference of hybrids using genome sequences

A Bayesian hybrid inference method is developed which infers hybrids and back-crosses across two generations using sampled genomes from two populations. The method improves on that of Chakraborty and Rannala (2023) by accounting for uncertainty of population haplotype frequencies and correctly marginalizing over haplotypes while still modeling linkage and recombination across the genome. In analyses of simulated data the new method produced posterior probabilities nearly identical to the method of Chakraborty and Rannala (2023) when sample sizes were large. For small sample sizes, posterior probabilities produced by the new method tended to be lower as expected since it accounts for additional uncertainties of population haplotype frequencies. Statistical performance of the new method as measured by the ROC (Receiver Operation Characteristic) curve, appears equivalent to that of Chakraborty and Rannala (2023). The new method is applied to three recently published datasets for populations of kiwifruit (genus Actinidia), plateau fence lizard (Sceloporus tristichus) and puma (Puma concolor).

genetics↗

bioRxiv2025

Organelle distribution and protein translation defects in radial glia cells with mutations in Eml1

Cerebral cortical development is a finely regulated process, depending on key neuronal progenitors, giving rise to post-mitotic neurons that migrate to superficial regions in the developing brain. Disruptions can give rise to severe cortical malformations that are associated with intellectual disability and intractable epilepsy. Mutations in EML1/Eml1, coding for a microtubule (MT)-associated protein, lead to subcortical heterotopia (SH) in both humans and mice. In developing mutant mouse brains, ectopic apical radial glia (aRG) progenitors were found outside the normal proliferative ventricular zone (VZ). The normal role of Eml1 in these cells remains to be precisely determined. Using proteomics and imaging approaches, we compared brain tissue from control and mutant mice and identified microtubule and organelle dysregulation. Eml1 influences the trafficking of organelles to different compartments of aRG, where they may be involved in local functions. Thus, we find that mitochondrial and polysome distribution are altered in mutant conditions. Indeed, Eml1 interacts with translational machinery, and an overall downregulation of translation is observed when analysing the translatome of Eml1 mutant aRG. Paradoxically, an upregulation of translation-related mRNAs is also observed. These new data uncover an unprecedented function of Eml1, as well as associating novel subcellular patho-mechanisms with severe heterotopia formation.

neuroscience↗

bioRxiv2025

Romaciclib, a CDK8/CDK19 inhibitor, can overcome venetoclax resistance through a combinatorial strategy

The combination of venetoclax (VEN) and hypomethylating agents (HMA) is the standard of care in acute myeloid leukemia (AML) for elderly patients unfit for intensive chemotherapy. Despite its clinical success, most patients eventually relapse, creating an urgent need for effective therapeutic alternatives. In this study, we aimed to evaluate the potential of romaciclib, a first-in-class CDK8/CDK19 inhibitor, in combination with VEN to overcome stroma-mediated and primary/acquired VEN-resistance. We assessed the efficacy of RVU120+VEN combination in both sensitive and resistant AML cell lines and primary patient-derived models. Our finding demonstrated that romaciclib synergizes with VEN in AML cell lines and in 8 out of 11 patient-derived cell samples. The proteomic and functional studies demonstrated that combination induced apoptosis through caspase-dependent cleavage of MCL-1. In vivo studies confirmed the efficacy of RVU120+VEN, showing eradication of leukemic cells and bone marrow recovery. Importantly, the combination effectively overcame both stroma-mediated and transcriptionally dependent VEN-resistance. Mechanistic studies, focusing on transcriptomic analyses, identified key resistance-associated pathways, including IL6/JAK/STAT3, TGF-{beta}, PI3K/AKT/MTOR, and inflammatory signaling, being suppressed by combination treatment. Furthermore, an in vivo study using a VEN-resistant patient-derived xenograft (PDX) model confirmed the efficacy of the combination, demonstrating a significant reduction in leukemia burden and a decreased proportion of leukemia initiating cells (LIC) following treatment. These findings prove the highly synergistic mechanism of action of RVU120+VEN combination and the potential to overcome primary/acquired VEN resistance in relapse/refractory AML disease. Altogether, the presented results support ongoing clinical studies evaluating romaciclib and VEN in VEN/HMA-refractory patients (NCT06191263) and provide a basis for future exploration as a frontline therapy in VEN-naive patients.

cancer biology↗

bioRxiv2025

RAF isoform selectivity of MEK inhibitors and rational design of a covalent ARAF-MEK inhibitor

Aberrant activation of the RAS/RAF/MEK/ERK pathway is a frequent cause of cancer. Allosteric MEK inhibitors block this pathway by binding RAF-MEK complexes to prevent activation of MEK by RAF. However, how MEK inhibitor potency varies across the three RAF isoforms remains poorly understood. We profiled seven allosteric MEK inhibitors and observed a striking hierarchy of sensitivity: all most potently inhibited CRAF-driven MEK activation while relatively sparing ARAF-driven activation. We identified point mutations in ARAF and CRAF proximate to the MEK inhibitor binding site that markedly altered inhibitor sensitivity. Using a rational design approach, we developed a more potent inhibitor of ARAF-driven MEK signaling, TWG-07-148. Our cryo-EM structure shows how this acrylamide-containing analog of MEK inhibitor trametinib covalently targets Cys514, a residue unique to ARAF. Our studies highlight the importance of the activating RAF isoform as a determinant of MEK inhibitor sensitivity and provide proof-of-concept for development of MEK inhibitors that more effectively block ARAF-driven MEK signaling via covalent targeting of Cys514.

biochemistry↗

bioRxiv2025

Organelles harbour pH gradients

Organelle pH is critical to organelle identity and function. Resident proteins that define each organelle modify transiting cargo proteins, with both retention and trafficking between organelles governed by pH-dependent mechanisms. For example, lysosomal enzymes bind mannose-6-phosphate receptors at the higher pH ([~]6.5) of the Golgi and dissociate at the lower pH ([~]5.5) of late endosomes1. Proteins that stray from the endoplasmic reticulum (ER) are captured by KDEL receptors in the acidic Golgi and returned into the neutral ER2,3. This pH-tuned trafficking system compartmentalizes organelle function and prevents mis-localization of critical enzymes4. Dysregulated organelle pH disrupts their function and leads to various diseases. Because protons move rapidly in water, the pH within a single organelle is currently assumed to be spatially uniform5. Here, using a reporter sensitive from pH 5.5 - 10.5 to map a spectrum of organelles at high resolution, we discovered that pH gradients exist within single, large or long organelles such as the ER and mitochondria, and in membrane-less organelles without ion-transporting proteins such as the nucleolus. These new findings upend our understanding of organellar pH, prompting new questions about proton diffusion within the cell, and its potential consequences on organelle function.

cell biology↗

bioRxiv2025

Metataxonomic insights into the effects of enhanced nitrogen addition on the bacterial communities in the tropical paddy soil of West Bengal, India

In relation to global rice cultivation, nitrogen (N) is fundamental for paddy soil and crop productivity; however, the exploitation of synthetic N fertilisation in the global agri-food system has emerged as a major environmental concern. In this study, the effects of various synthetic N-compounds on paddy soil bacterial communities, including species abundance, diversity, and interactions, were investigated under four different N-amended [NO2-, NO3-, NH4+, and urea] conditions using a microcosm-based culturomics approach. The N-amendments altered soil properties, adversely impacting microbial abundance, diversity, and community composition. The 16S rRNA gene qPCR and amplicon sequencing indicated a negative effect of N on bacterial and archaeal abundance, species diversity, and richness. Our analyses revealed the predominance and cosmopolitan distribution of Proteobacteria, Bacilli, Anaerolineae, and Bacteroidota, their extensive adaptability and metabolic versatility under different N-amended conditions. Soil microbial community exhibited distinct responses to added N-substrates, with some bacterial taxa (Sphingomonadales) showing enhanced abundances while others were inhibited (Thermodesulfovibrionia and Clostridiales). The core-community across N-amended sets exhibited 68% taxonomic variation from its native counterpart, with two most abundant members of native soil, Nitrosomonadaceae and Beijerinckiaceae, diminishing, while Bacillaceae, Pseudomonadaceae, and Sphingomonadaceae became more prominent and resilient under N-amended conditions. The co-occurrence network highlighted that though total and core soil communities responded to N-amendments with an increased abundance of copiotroph bacteria, oligotrophs thrived under nutrient-limited conditions, serving as keystone taxa during prolonged fertilisation. These findings elucidate how synthetic N inputs restructure paddy soil microbiomes and alter their ecological functioning.

microbiology↗

bioRxiv2025

Splicing factor proline- and glutamine-rich (SFPQ) protein causes transcriptional repression of SNAIL to counteract TGF-β signaling

TGF-{beta} is known to regulate several embryonic and adult signaling pathways. Moreover, this signaling pathway regulates several cellular functions including differentiation, cell division, angiogenesis, hematopoiesis, and cell migration. However, studies suggest that an uncontrolled activation of TGF-{beta} signaling may contribute to many human diseases. Therefore, counter-regulatory mechanism(s) to restrain abrupt TGF-{beta} activation during cellular homeostasis is necessary to maintain an adequate balance of TGF-{beta} downstream signaling. TGF-{beta} through Smad complex activation causes transcriptional regulation of many transcription factors including Snail which act as an immediate-early response gene in TGF-{beta} signaling. Herein, for the first time, we report that Splicing factor proline- and glutamine-rich (SFPQ), an RNA binding paraspeckles-associated protein works as a transcriptional repressor of Snail. We first confirmed a significant reduction in the expression level of SFPQ in the kidney glomeruli of rats that underwent subtotal nephrectomy. Endothelial cells (EC) treated with TGF-{beta} exhibited loss of SFPQ protein level without altering its transcript level. Inhibition of proteasomal or autophagosome-lysosome pathway revealed ubiquitination-dependent proteasomal degradation of SFPQ upon TGF-{beta} challenge. Prior to degradation, TGF-{beta} treatment resulted in the cytosolic export of SFPQ thereby diminishing nuclear SFPQ level. Knockdown of SFPQ augmented TGF-{beta}-dependent increase in Snail level while overexpression of SFPQ reversed TGF-{beta} induced Snail expression. Although SFPQ exhibited association with many transcription factors including Smad2/3, Smad4, and N1-ICD which regulate Snail gene expression, TGF-{beta} failed to alter the association of SFPQ with these transcription factors. Instead, through ChIP-qPCR analysis, we confirmed the enrichment of SFPQ in E-box promoter region and coding region proximal to TSS of the Snail gene. This study is the first to report SFPQ as a transcriptional repressor of Snail thereby regulating TGF-{beta} signaling during cellular homeostasis.

biochemistry↗

bioRxiv2025

Characterization of a water-soluble formulation of Passiflora incarnata and its effect on sperm motility: A novel male-centric contraceptive formulation

Passiflora incarnata (Passionflower) has a long history of use in traditional medicine across South America and Europe, primarily for its sedative and hypnotic effects. Recent evidence suggests that its bioactive constituents can modulate cellular signaling pathways. However, its impact on reproductive physiology, particularly sperm motility, remains underexplored. This study aimed to investigate the effects of an aqueous P. incarnata formulation on sperm motility and viability, with the goal of evaluating its potential as a plant-based, non-hormonal contraceptive agent. An aqueous extract of P. incarnata was prepared and subjected to phytochemical analysis to quantify polyphenols, flavonoids, and carbohydrate content using standard assays. Antioxidant activity was assessed via free radical scavenging assays. The presence of bioactive macromolecules was confirmed by liquid chromatography-mass spectrometry (LC-MS). Goat spermatozoa, isolated from the caudal epididymis, were treated with the formulation. Sperm motility (horizontal and vertical) was evaluated microscopically and spectrophotometrically, respectively. Sperm viability was assessed using standard viability staining. Phytochemical screening revealed high polyphenol (16.85 mg gallic acid equivalent/g) and flavonoid (2.5 mg quercetin equivalent/g) content, along with notable antioxidant activity (87.25%). LC-MS confirmed the presence of diverse plant macromolecules. Treatment with the P. incarnata formulation significantly reduced both horizontal (28.5%) and vertical (20%) sperm motility (both p < 0.0001), while sperm viability remained unaffected. The water solubility of the formulation supports its development as a topical contraceptive gel. The aqueous P. incarnata formulation modulates sperm motility without compromising cell viability, likely via biochemical pathway regulation. These findings highlight its potential as a novel, non-hormonal, plant-based contraceptive.

physiology↗