Biology subjects

Ashok, A.

Publications and source records attributed to Ashok, A..

11 recordsLinked to original sources

bioRxiv2026

Developmental conversion of the nucleolus into an RNA Polymerase II transcriptional platform in Drosophila spermatocytes

The nucleolus is widely regarded as a specialized compartment for RNA polymerase I (Pol I)-driven ribosomal RNA transcription and ribosome biogenesis. Yet the presence of "atypical nucleoli", or nucleolus-like bodies (NLBs), which lack rRNA transcription despite containing canonical nucleolar components, has long been recognized, most notably during mammalian oogenesis and spermatogenesis. NLBs have been shown to have an essential function independent of rRNA transcription, but the nature of that function remained unclear. Here, we demonstrate that the nucleolus becomes an NLB during spermatocyte development in Drosophila melanogaster and, surprisingly, that this NLB serves as a platform for RNA polymerase II (Pol II)-mediated transcription. We find that the Y chromosome-linked fertility genes, which are heterochromatic in most cell types but highly expressed in spermatocytes, are transcribed at the spermatocyte NLB. We further show that the recruitment of active Pol II to the NLB requires known spermatocyte-specific transcriptional regulators. In their absence, the Y-linked fertility genes embedded within heterochromatin are not properly transcribed. Our findings reveal an active role for an NLB as a Pol II platform, and we propose that other NLBs may have similar functionality.

developmental biology↗

bioRxiv2026

Functional Equivalence of Heat-Inactivated (HI) and Live Probiotic RSB11 in Suppressing Inflammation: Expanding Formulation and Application Potential

The clinical potential of probiotics has been widely recognized, but their translation into reliable therapeutic products has been hindered by major limitations such as undesirable immunogenic responses, the need to maintain viability, instability during storage and transport, and concerns regarding safety in vulnerable populations. Postbiotics, defined as inanimate microbial cells or their components with pro-health activities, overcome many of these limitations by offering enhanced stability, reproducibility, and safety. However, it is very vital to understand if the heat inactivation (conversion of a probiotic to its postbiotic inert form) compromise its functional efficacy. Here, we systematically compared a novel probiotic-derived candidate, Lactiplantibacillus plantarum RSB11 strain, in its live (RSB11 Life, probiotic) and heat-inactivated (RSB11-HI, postbiotic) forms across multiple human epithelial and non-epithelial models relevant to inflammation driven pathologies. To investigate the gut-tissue(s)-axis concept we used gut (Caco-2), lung (HBE), ovary (BG1), bone (osteoblasts, MG-63), kidney (A-498) and liver (HepG2) cells exposed to E-coli or lipopolysaccharide (LPS), and quantified matrix metalloproteinase-9 (MMP-9), an inflammatory mediator, by qPCR and pro-inflammatory cytokines such as tumor necrosis factor- (TNF-), IL-6, and IL-1{beta} by ELISA. In addition, we assessed {beta}-glucuronidase activity and estrogen modulation to explore gut-ovarian axis signaling. Across all models, both RSB11 Life and RSB11-HI robustly suppressed MMP-9, TNF-, IL-6 and IL-1{beta} induction, with equivalent magnitude of effect. The inactivated form retained full cytokine-suppressive capacity and, notably, enhanced {beta}-glucuronidase activity, suggesting additional benefits in microbiome hormone cross-talk. Our findings demonstrate that heat inactivation does not compromise, and may even expand, the functional range of RSB11. By maintaining bioactivity while eliminating the drawbacks of live biotics, heat inactivated RSB11 emerges as a robust, scalable, and versatile postbiotic with potential applications in systemic inflammatory disorders. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/705228v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@7bb1e6org.highwire.dtl.DTLVardef@dc86c7org.highwire.dtl.DTLVardef@147448org.highwire.dtl.DTLVardef@de5232_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical abstract of RSB11-HI activityHeat-inactivated postbiotic RSB11-HI retains the anti-inflammatory efficacy of its live counterpart (RSB11Life) across diverse organ-relevant cell models. Upon LPS or E-coli stimulation, epithelial, immune, and tissue-specific cells (gut, lung, ovary, bone, kidney, liver) upregulate pro-inflammatory mediators including MMP-9, TNF-, IL-6, and IL-1{beta}. Both RSB11Life and RSB11-HI effectively suppress these inflammatory responses, with RSB11-HI exhibiting more consistent and robust reductions of inflammatory markers across models. Additionally, RSB11-HI uniquely enhances {beta}-glucuronidase activity, facilitating estrogen metabolism and signaling through the gut-ovary axis. Together, these findings highlight RSB11-HI as a stable, safe, and multifunctional postbiotic candidate suitable for therapeutic formulation. Image was designed using ChatGPT.

immunology↗

bioRxiv2025

12-Hydroxystearic acid induces epidermal keratinocytes to secrete antimicrobial peptides that are potent inhibitors of viral infection.

Epidermal keratinocytes produce antimicrobial peptides (AMPs) that serve as a crucial component of the skins innate immune barrier. These peptides effectively target a broad spectrum of pathogenic microorganisms while preserving commensal microbiota essential for skin barrier homeostasis and overall skin health. Regulating the release of these AMPs presents a promising approach to enhancing the skin barriers defense mechanisms with minimal side effects. We have identified 12-hydroxystearic acid (12-HSA) as a potent stimulator of AMP secretion from primary epidermal keratinocytes. Mechanistic investigations revealed that, akin to bacterial stimulation, 12-HSA induces AMP release through the downregulation of caspase-8, which subsequently activates the inflammasome. Notably, we discovered that 12-HSA mediates caspase-8 downregulation via the acute activation of DNA methyltransferase 3A (DNMT3A), leading to transcriptional silencing of the caspase-8 locus. Importantly, 12-HSA is widely utilized in the cosmetic industry for its several skin beneficial properties including hydration and emolliency. Our findings suggest that this compound can be leveraged to enhance innate immune defenses in the skin, effectively mobilizing stored AMPs from keratinocytes to counteract microbial threats. This discovery highlights the potential for 12-HSA as a novel agent in dermatological applications aimed at fortifying skin barrier immunity.

cell biology↗

bioRxiv2024

Reduced SH3RF3 may protect against Alzheimer disease by lowering microglial pro-inflammatory responses via modulation of JNK and NFkB signaling

Understanding how high-risk individuals are protected from Alzheimers disease (AD) may illuminate potential therapeutic targets. We identified protective genetic variants in SH3RF3/POSH2 that delayed the onset of AD among individuals carrying the PSEN1G206A mutation. SH3RF3 acts as a JNK pathway scaffold and activates NF{kappa}B signaling. While effects of SH3RF3 knockdown in human neurons were subtle, including decreased ptau S422, knockdown in human microglia significantly reduced inflammatory cytokines in response to either a viral mimic or oA{beta}42. This was associated with reduced activation of JNK and NF{kappa}B pathways in response to these stimuli. Pharmacological inhibition of JNK or NF{kappa}B signaling phenocopied SH3RF3 knockdown. We also found PSEN1G206A microglia had reduced inflammatory response to oA{beta}42. Thus, further reduction of microglial inflammatory responses in PSEN1G206A mutant carriers by protective variants in SH3RF3 might reduce the link between amyloid and neuroinflammation to subsequently delay the onset of AD. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=174 SRC="FIGDIR/small/600281v2_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@46f29org.highwire.dtl.DTLVardef@11e1dfeorg.highwire.dtl.DTLVardef@43311eorg.highwire.dtl.DTLVardef@14de11f_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2024

Inhibition of Proteasome Activity Facilitates Definitive Endodermal Specification of pluripotent Stem Cells by influencing YAP signaling

Understanding the molecular players that control the specification of definitive endoderm is imperative to obtain the homogenous population of pancreatic {beta}-cells from stem cells. Though the Ubiquitin proteasome system (UPS) has been envisaged as a crucial intracellular protein degradation system, its role in germ layer specification remains elusive. In this study, using a mouse embryonic stem cells model system (mESCs) we observed decreased proteasomal activity specifically during endoderm, but not in meso- or ecto-derm differentiation. Extraneous inhibition of proteasomal activity during differentiation enhanced the expression of endodermal genes specifically. Enhancing proteasomal activity by including the activator IU1 in the induction culture, inhibited definitive endodermal differentiation. Further, inhibiting proteasomal activity at the definitive endodermal stage resulted in enhanced generation of insulin-positive cells. A similar increase in endodermal gene expression by inhibiting proteasomal activity was observed in miPSC and hiPSC differentiated towards endodermal lineage. Mechanistic insight showed no contribution of endoplasmic reticulum unfolded protein response but revealed the involvement of the YAP signaling pathway in proteasome-inhibited enhanced endodermal differentiation. Unravelling the specific involvement of UPS in endodermal cell fate specification in pluripotent stem cells paves the way for obtaining better qualitative and quantitative definitive endodermal cells for plausible cellular therapy in the future.

cell biology↗

bioRxiv2023

Suppressing DNMT3a Alleviates the Intrinsic Epigenetic Barrier for Optic Nerve Regeneration and Restores Vision in Adult Mice

The limited regenerative potential of the optic nerve in adult mammals presents a major challenge for restoring vision after optic nerve trauma or disease. The mechanisms of this regenerative failure are not fully understood1,2. Here, through small-molecule and genetic screening for epigenetic modulators3, we identify DNA methyltransferase 3a (DNMT3a) as a potent inhibitor of axon regeneration in mouse and human retinal explants. Selective suppression of DNMT3a in retinal ganglion cells (RGCs) by gene targeting or delivery of shRNA leads to robust, full-length regeneration of RGC axons through the optic nerve and restoration of vision in adult mice after nerve crush injury. Genome-wide bisulfite and transcriptome profiling in combination with single nucleus RNA-sequencing of RGCs revealed selective DNA demethylation and reactivation of genetic programs supporting neuronal survival and axonal growth/regeneration by DNMT3a deficiency. This was accompanied by the suppression of gene networks associated with apoptosis and inflammation. Our results identify DNMT3a as the central orchestrator of an RGC-intrinsic mechanism that limits optic nerve regeneration. Suppressing DNMT3a expression in RGCs unlocks the epigenetic switch for optic nerve regeneration and presents a promising therapeutic avenue for effectively reversing vision loss resulted from optic nerve trauma or diseases.

neuroscience↗

bioRxiv2023

ZCCHC17 modulates neuronal RNA splicing and supports cognitive resilience in Alzheimer's disease

ZCCHC17 is a putative master regulator of synaptic gene dysfunction in Alzheimers Disease (AD), and ZCCHC17 protein declines early in AD brain tissue, before significant gliosis or neuronal loss. Here, we investigate the function of ZCCHC17 and its role in AD pathogenesis. Co-immunoprecipitation of ZCCHC17 followed by mass spectrometry analysis in human iPSC-derived neurons reveals that ZCCHC17s binding partners are enriched for RNA splicing proteins. ZCCHC17 knockdown results in widespread RNA splicing changes that significantly overlap with splicing changes found in AD brain tissue, with synaptic genes commonly affected. ZCCHC17 expression correlates with cognitive resilience in AD patients, and we uncover an APOE4 dependent negative correlation of ZCCHC17 expression with tangle burden. Furthermore, a majority of ZCCHC17 interactors also co-IP with known tau interactors, and we find significant overlap between alternatively spliced genes in ZCCHC17 knockdown and tau overexpression neurons. These results demonstrate ZCCHC17s role in neuronal RNA processing and its interaction with pathology and cognitive resilience in AD, and suggest that maintenance of ZCCHC17 function may be a therapeutic strategy for preserving cognitive function in the setting of AD pathology. SignificanceAbnormal RNA processing is an important component of AD pathophysiology. We show here that ZCCHC17, a previously identified putative master regulator of synaptic dysfunction in AD, plays a role in neuronal RNA processing, and illustrate that ZCCHC17 dysfunction is sufficient to explain some of the splicing abnormalities seen in AD brain tissue, including synaptic gene splicing abnormalities. Using data from human patients, we demonstrate that ZCCHC17 mRNA levels correlate with cognitive resilience in the setting of AD pathology. These results suggest that maintenance of ZCCHC17 function may be a therapeutic strategy for supporting cognitive function in AD patients, and motivate future work examining a possible role of abnormal RNA processing in AD-related cognitive decline.

neuroscience↗

bioRxiv2022

Ter-Seq: A high-throughput method to stabilize transient ternary complexes and measure associated kinetics

Regulation of biological processes by proteins often involves the formation of transient, multimeric complexes whose characterisation is mechanistically important but challenging. The bacterial toxin CcdB binds and poisons DNA Gyrase. The corresponding antitoxin CcdA extracts CcdB from its complex with Gyrase through formation of a transient ternary complex, thus rejuvenating Gyrase. We describe a high throughput methodology called Ter-Seq to stabilize probable ternary complexes and measure associated kinetics using the CcdA-CcdB-GyrA14 ternary complex as a model system. The method involves screening a YSD saturation mutagenesis library of one partner (CcdB) for mutants that show enhanced ternary complex formation. We also isolated CcdB mutants that were either resistant or sensitive to rejuvenation, and used SPR with purified proteins to validate the kinetics measured using surface display. Positions where CcdB mutations lead to slower rejuvenation rates are largely involved in CcdA-binding, though there were several notable exceptions. Mutations at these positions reduce the affinity towards CcdA, thereby slowing down the rejuvenation process. Mutations at GyrA14-interacting positions significantly enhanced rejuvenation rates, either due to reduced affinity or complete loss of CcdB binding to GyrA14. We examined the effect of different parameters (CcdA affinity, GyrA14 affinity, surface accessibilities, evolutionary conservation) on the rate of rejuvenation. Finally, we further validated the Ter-Seq results by monitoring kinetics of ternary complex formation for individual CcdB mutants in solution by FRET studies.

biophysics↗

bioRxiv2019

Aβ42 oligomers trigger synaptic loss through CAMKK2-AMPK-dependent effectors coordinating mitochondrial fission and mitophagy

During the early stages of Alzheimers disease (AD) in both mouse models and human patients, soluble forms of Amyloid-{beta}1-42 oligomers (A{beta}42o) trigger loss of excitatory synapses (synaptotoxicity) in cortical and hippocampal pyramidal neurons (PNs) prior to the formation of insoluble A{beta} plaques. We observed a spatially restricted structural remodeling of mitochondria in the apical tufts of CA1 PNs dendrites in the hAPPSWE,IND transgenic AD mouse model (J20), corresponding to the dendritic domain receiving presynaptic inputs from the entorhinal cortex and where the earliest synaptic loss is detected in vivo. We also observed significant loss of mitochondrial biomass in human neurons derived from a new model of human ES cells where CRISPR-Cas9-mediated genome engineering was used to introduce the Swedish mutation bi-allelically (APPSWE/SWE). Recent work uncovered that A{beta}42o mediates synaptic loss by over-activating the CAMKK2-AMPK kinase dyad, and that AMPK is a central regulator of mitochondria homeostasis in non-neuronal cells. Here, we demonstrate that A{beta}42o-dependent over-activation of CAMKK2-AMPK mediates synaptic loss through coordinated MFF-dependent mitochondrial fission and ULK2-dependent mitophagy in dendrites of PNs. We also found that the ability of A{beta}42o-dependent mitochondrial remodeling to trigger synaptic loss requires the ability of AMPK to phosphorylate Tau on Serine 262. Our results uncover a unifying stress-response pathway triggered by A{beta}o and causally linking structural remodeling of dendritic mitochondria to synaptic loss.

neuroscience↗

bioRxiv2019

New factors for protein transport identified by a genome-wide CRISPRi screen in mammalian cells

Protein and membrane trafficking pathways are critical for cell and tissue homeostasis. Traditional genetic and biochemical approaches have shed light on basic principles underlying these processes. However, the list of factors required for secretory pathways function remains incomplete, and mechanisms involved in their adaptation poorly understood. Here, we present a powerful strategy based on a pooled genome-wide CRISPRi screen that allowed the identification of new factors involved in protein transport. Two newly identified factors, TTC17 and CCDC157, localized along the secretory pathway and were found to interact with resident proteins of ER-Golgi membranes. In addition, we uncovered that upon TTC17 knockdown, the polarized organization of Golgi cisternae was altered, creating glycosylation defects, and that CCDC157 is an important factor for the fusion of transport carriers to the Golgi complex. In conclusion, our work identified and characterized new actors in the mechanisms of protein transport and secretion, and opens stimulating perspectives for the use of our platform in physiological and pathological contexts.

cell biology↗

bioRxiv2018

APOE4 is Associated with Differential Regional Vulnerability to Bioenergetic Deficits in Aged APOE Mice

The {varepsilon}4 allele of apolipoprotein E (APOE) is the dominant genetic risk factor for late-onset Alzheimers disease (AD). However, the reason for the association between APOE4 and AD remains unclear. While much of the research has focused on the ability of the apoE4 protein to increase the aggregation and decrease the clearance of A{beta}, there is also an abundance of data showing that APOE4 negatively impacts many additional processes in the brain, including bioenergetics. In order to gain a more comprehensive understanding of the APOE4s role in AD pathogenesis, we performed a multi-omic analysis of APOE4 vs. APOE3 expression in the entorhinal cortex (EC) and primary visual cortex (PVC) of aged APOE mice. These studies revealed region-specific alterations in several bioenergetic pathways, including oxidative phosphorylation (OxPhos), the TCA-cycle and fatty acid metabolism. Follow-up analysis utilizing the Seahorse platform revealed decreased mitochondrial respiration in the hippocampus and cortex of aged APOE4 vs. APOE3 mice, but not in the EC of these mice. Additional studies, as well as the original multi-omic data suggest that bioernergetic pathways in the EC of aged APOE mice may be differentially regulated by APOE4 expression. Given the importance of the EC as one of the first regions to be affected by AD pathology in humans, this differential bionenergetic regulation observed in the EC vs. other brain regions of aged APOE4 mice may play an important role in the pathogenesis of AD, particularly among APOE4 carriers.

neuroscience↗