Biology subjects

Pandey, A.

Publications and source records attributed to Pandey, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Developmental control of DNA damage responses in α- and β-cells shapes the selective beta-cell susceptibility in diabetes

Accumulation of DNA damage drives {beta}-cell dysfunction, senescence, and death in Type 1 and Type 2 diabetes. While -cell dysfunction also contributes to disease pathology, they remain remarkably resistant to senescence and cell-death. The mechanisms underlying these differential responses to diabetogenic stress, particularly differences in their DNA damage vulnerability, remain unclear. We demonstrate that replication introduces a window of genomic vulnerability in both - and {beta}-cells during neonatal growth, with -cells exhibiting higher replication rates and DNA damage. We show that neonatal {beta}-cells resolve DNA damage more efficiently during mitosis and favor error-free repair, while -cells compensate for their higher DNA damage vulnerability through increased cellular turnover. Using mouse models of overnutrition and diabetes, we show that {beta}-cells exhibit greater vulnerability to terminal DNA damage and impaired repair capacity under diabetogenic stress, with compensatory replication amplifying this vulnerability. We demonstrate that developmental epigenetic programs shape the differential DNA damage vulnerability of postnatal {beta}- and -cells. Loss of de novo DNA methyltransferase Dnmt3a in pancreatic progenitors selectively increases the DNA damage vulnerability of {beta}-cells from neonatal growth through adulthood. Our findings uncover novel developmental mechanisms that shape the distinct DNA damage responses of postnatal {beta}- and -cells during growth and diabetes. Article HighlightsO_LIMechanisms underlying the differential susceptibility of pancreatic {beta}- and -cells to diabetogenic stress remain unclear. C_LIO_LIDo replication dynamics, repair fidelity, and developmental epigenetic programs determine the vulnerability of postnatal {beta}- and -cells to DNA damage, a key driver of {beta}-cell failure in diabetes? C_LIO_LIReplication introduces DNA damage vulnerability in both neonatal {beta}- and -cells, yet {beta}-cells resolve damage more efficiently. Loss of DNA methyltransferase 3a in pancreatic progenitors selectively heightens {beta}-cell DNA damage vulnerability that persists into adulthood. Moreover, diabetogenic-stress preferentially compromises {beta}-cell repair fidelity. C_LIO_LIThese findings reveal how developmental programs shape {beta}-cell resilience and may influence lifelong diabetes risk. C_LI

developmental biology↗

bioRxiv2025

SHORT DISORDERED PEPTIDES ARE SUFFICIENT TO CONVERT PROTEINS INTO MECHANOSENSORS THAT RESPOND TO PHYSIOLOGICAL CELLULAR FORCES

Mechanical forces regulate many biological processes and a handful of mechanosensor domains have been identified in proteins that respond to cellular forces. The Notch signaling pathway, a key regulator of cell communication processes ranging from animal development to cancer, is activated by mechanical forces generated by cell-cell interactions. The mechanosensing element of Notch is thought to be a 300 amino acid extracellular domain called negative regulatory region (NRR). Ligand binding exerts mechanical forces that are believed to partially unfold NRR, rendering it susceptible to cleavage by extracellular metalloproteases that leads to activation of signaling. However, some engineered notch-like receptors lacking the NRR can be activated upon ligand binding, although the mechanisms underlying this activation are not known. Here we observe that Notch molecules without the NRR, but with a 12 amino acid sequence present in the extracellular juxta-transmembrane domain (eJTMD) are also cleaved and activated upon interaction with their ligands in cultured cells and in transgenic animals. Furthermore, the [~]12 aa eJTMD from notch genes from other species (chicken, xenopus, zebrafish and Drosophila), from other unrelated transmembrane proteins (erbB4, N-CAM, and E-Cadherin), or multiple artificial sequences of [~]12 amino acids without any apparent structure or specific sequence can also convert proteins into ligand-dependent mechanosensors. These results indicate that short, disordered amino acid sequences that are commonly found in many proteins are capable of imparting mechanosensing capabilities into proteins, suggesting that mechanical force may regulate many more cellular processes than previously suspected.

cell biology↗

bioRxiv2025

Cold-responsive MtCBF4-MtJMJ13 positive feedback loop negatively regulates anthocyanin biosynthesis in Medicago truncatula

Legumes, being significant food sources for both humans and animals globally, experience several adverse conditions that considerably affect their crop yield. Medicago sp., an important forage crop, thrives under adverse conditions, such as drought, extreme temperatures (heat and cold), and salinity. Several studies have shed light on the regulatory pathways of cold/chilling stress tolerance in Medicago sp. in recent years. In the present study, we found that a cold-repressed transcription factor, MtCBF4, negatively regulates anthocyanin synthesis by directly repressing the expression of MtLAP1, a critical regulatory gene for anthocyanin synthesis in Medicago truncatula. It leads to the downregulation of anthocyanin biosynthesis genes, and reduced anthocyanin accumulation. Apart from the transcriptional cascade, MtCBF4 exerts its effect through histone H3K27 trimethylation. It directly binds to the promoter of MtJMJ13, an H3K27me3 demethylase, to activate its expression, resulting in decreased H3K27 trimethylation. Furthermore, MtJMJ13 demethylates the gene body of MtCBF4 to positively regulate its expression, forming a positive feedback loop that functions in a cold-responsive manner. MtJMJ13 also demethylates the gene body of MtMYB2, MtKFB1, and MtKFB2 genes, which are negative regulators of anthocyanin biosynthesis. Altogether, we have unveiled a new regulatory loop involving a transcriptional regulator and a histone demethylase, operating together to limit anthocyanin production. This regulatory module is repressed under cold stress, leading to increased anthocyanin production and enhanced cold stress tolerance in M. truncatula.

plant biology↗

bioRxiv2025

Cholesterol-mediated activation of VapC12 toxin modulates growth and drug susceptibility in Mycobacterium tuberculosis

Tuberculosis eradication efforts are severely hampered by antimicrobial resistance (AMR). We have previously reported that VapBC12 TA system in Mycobacterium tuberculosis (M. tuberculosis) regulates both disease and antibiotic persistence in tuberculosis. In this study, we developed a mechanistic understanding of the VapBC12-dependent modulation of growth and antibiotic susceptibility in M. tuberculosis. We identified a unique Cholesterol Recognition Amino acid Consensus (CRAC) motif in VapC12 toxin and demonstrated that its heterologous expression induces toxicity in M. smegmatis. We have solved the crystal structure of VapB12 antitoxin at a 1.6A0 wavelength and using molecular modeling predicted the structure of TA complex. Structure-function analysis revealed specific residues critical for the assembly and activity of the VapBC12 TA system. Our study suggests that cholesterol activates the VapC12 toxin by competitively displacing its cognate antitoxin at the CRAC motif which consequently restricts the growth of M. tuberculosis. Finally, we demonstrated that chemical inhibition of VapC12 prevents growth restriction and potentiates activity of anti-TB drugs.

microbiology↗

bioRxiv2025

Methionine metabolism shapes immune response against Mycobacterium tuberculosis

The methionine metabolism is central to epigenetic reprogramming to produce pro-inflammatory cytokines. Disruptions in methionine metabolism contribute to complex disorders, providing an important target for nutrient interventions. Here, Mycobacterium tuberculosis (Mtb) H37Rv-infected C57BL/6 mice showed functional heterogeneity between alveolar and non-alveolar macrophage (AMs/Non-AMs) with major metabolic reprogramming in Non-AMs. Global metabolite and proteome analysis of Mtb-infected bone marrow-derived macrophages (BMDMs) showed a diversion of flux from methionine metabolism toward increased nucleotide salvage and glutathione (GSH) production. Carbon units of 13C5-methionine via isotopomer analysis contributed to polyamine synthesis, fuelling the nucleotide salvage node in Mtb-infected BMDMs. Methionine supplementation increased mycobacterial clearance in C57BL/6 mice and in BMDMs by promoting a pro-inflammatory response, as evident by increased IL-1{beta} and IFN-{gamma}. Increased IL-1{beta} production is mainly contributed to by increased H3K4 trimethylation in macrophages. These findings reveal an important strategy by which methionine supplementation in macrophages and mice remodels host metabolism to enhance acute pro-inflammatory responses and exploit dietary supplementation to improve nutritional immunity in TB. HighlightsO_LIMycobacterium tuberculosis (Mtb) infection decreases intracellular methionine levels and increases purine levels in primary macrophages. C_LIO_LIMethionine carbon units contribute to nucleotide salvage, and their restriction lowers IL-1 response and mycobacterial clearance. C_LIO_LIEx vivo methionine supplementation in Mtb-infected macrophages increases H3K4me3 at the Il-1b gene promoter and gene body, leading to an increased pro-inflammatory response and improved mycobacterial clearance. C_LIO_LIIn vivo methionine supplementation improved pro-inflammatory response in lungs, spleen and bone marrow, leading to accelerated mycobacterial clearance upon Mtb-H37Rv infection. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=157 SRC="FIGDIR/small/680834v2_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@1bf5corg.highwire.dtl.DTLVardef@ba4dbdorg.highwire.dtl.DTLVardef@145f23dorg.highwire.dtl.DTLVardef@122b2a2_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

A Rare Multipotent Peg-like Epithelial Cell is a Candidate Cell-of-Origin for High-Grade Serous Ovarian Cancer

To illuminate the origins of high-grade serous ovarian cancer (HGSOC), the most lethal and common form of ovarian cancer, we have created a comprehensive living organoid biobank of human fallopian tube tissue, which is thought to be the origin of this cancer. Through optimized culture protocols and integrated multi-omic profiling--including single-cell RNA sequencing, chromatin accessibility (ATAC) analysis, proteomics, and secretomics--we assembled the largest molecular atlas of the fallopian tube epithelium to date. This resource revealed diverse epithelial lineages and regulatory networks, including a rare, multipotent epithelial subpopulation with hybrid epithelial-mesenchymal features. Spatially localized to the basal epithelium and resembling mesonephric developmental precursors, these cells exhibit transcriptomic and proteomic similarities to the mesenchyme-like subtype of HGSOC, implicating them as potential cells-of-origin. Their molecular identity is preserved in organoid models, enabling future mechanistic and translational studies. This resource, which advances fundamental understanding of epithelial hierarchy and cancer susceptibility, provides a platform to inform early detection and prevention strategies for aggressive forms of ovarian cancer. HighlightsO_LIEstablishment of a clinically annotated fallopian tube organoid biobank enables delineation of epithelial lineage hierarchies and differentiation capacity. C_LIO_LIMulti-omics integration defines robust, lineage-specific transcriptional and regulatory networks in the fallopian tube epithelium. C_LIO_LIA rare basal epithelial subpopulation with mesenchymal features aligns with a mesenchyme-like subtype of high-grade serous ovarian cancer. C_LIO_LIRare basal peg cells exhibit fetal mesonephric developmental transcriptional programs and are maintained ex-vivo in fallopian tube organoids. C_LI

cancer biology↗

bioRxiv2025

Dietary α-Ketoglutarate delays lung adenocarcinoma in females and modulates TBX5-associated transcriptional programs and the immune microenvironment

Lung adenocarcinoma (LUAD) is the most common form of lung cancer and a leading cause of cancer-related mortality, underscoring the need for new chemopreventive strategies. -Ketoglutarate (-KG), a tricarboxylic acid cycle metabolite and dioxygenase cofactor, links cellular metabolism to chromatin regulation. Here, we show that dietary -KG remodels LUAD in a sex-dependent manner. In female mice, -KG reduced tumor area, decreased repressive histone marks (H3K27me3, H3K9me3), and upregulated TBX5 and myogenesis-associated genes. In male mice, -KG-treated male mice exhibited increased tumor area, elevated H3K27me3, and immune remodeling characterized by CD8 T cell expansion and transcriptomic signatures of T cell exhaustion. Analysis of human LUAD revealed that TBX5 expression is enriched in female tumors and associated with improved survival, suggesting it may serve as a marker of favorable outcome. Together, these findings support -KG as an epigenetic modulator with potential chemopreventive activity in lung cancer and highlight the importance of incorporating sex as a biological variable in preclinical studies. SummaryOral -Ketoglutarate (-KG) has a known anti-aging effect and has been suggested to inhibit cancer development. However, the role of -KG in lung cancer is not known. Here, we investigated the effect of oral -KG on the development of lung adenocarcinoma in a KrasG12D-driven murine model. In females, -KG reduced lung tumor growth, accompanied by TBX5 induction, activation of a myogenesis transcriptional program, and loss of repressive histone methylation. In males, -KG increased tumor growth, coinciding with TBX5 repression, suppression of myogenesis programs, and accumulation of repressive histone methylation. -Ketoglutarate also remodeled the tumor immune microenvironment in a sex-dependent manner, with divergent effects on T cell infiltration. HIGHLIGHTSO_LIOral -Ketoglutarate reduces lung adenocarcinoma development in a genetically engineered murine model in a sex-dependent manner C_LIO_LIIn females, -Ketoglutarate reduces repressive histone marks and induces TBX5/myogenesis C_LIO_LIIn males, -Ketoglutarate increases repressive histone marks and suppresses TBX5/myogenesis C_LIO_LI-Ketoglutarate remodels the tumor immune microenvironment with sex-specific effects C_LIO_LITBX5 is enriched in female LUAD patients and predicts improved survival in human datasets C_LI CONTEXT AND SIGNIFICANCELung adenocarcinoma (LUAD) is the most common form of lung cancer and a leading cause of cancer mortality worldwide. Preventive strategies are limited, highlighting the need for safe approaches that can intercept tumor progression. Metabolic cofactors are increasingly recognized as modulators of the cancer epigenome. Among these, -Ketoglutarate (-KG), a central metabolite of the tricarboxylic acid cycle, functions as a cofactor for chromatin-modifying enzymes. Here, we demonstrate that dietary -KG supplementation limits LUAD progression in female mice, reduces repressive histone methylation, and activates TBX5-associated transcriptional programs. These effects are sex dependent, underscoring the importance of biological context in shaping metabolic responses. In human LUAD, TBX5 is enriched in females and predicts improved survival, suggesting that it may serve as a marker of favorable outcome and help guide future studies of -KG. Together, this work identifies -KG as an epigenetically active metabolite with translational promise for lung cancer chemoprevention. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=154 SRC="FIGDIR/small/677388v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@1615a31org.highwire.dtl.DTLVardef@68884corg.highwire.dtl.DTLVardef@cc5ed1org.highwire.dtl.DTLVardef@1652c60_HPS_FORMAT_FIGEXP M_FIG C_FIG One-sentence summary-Ketoglutarate remodels lung adenocarcinoma through sex-dependent epigenetic, transcriptional, and immune reprogramming.

cancer biology↗

bioRxiv2025

Mono-allelic p.R37H Dehydrodolichyl Diphosphate Synthase variants lead to protein glycosylation defects, aberrant lipid profiles and interneuron scarcity in a novel mouse model of progressive epileptic encephalopathy.

Developmental delay and seizures with or without movement abnormalities (OMIM 617836) caused by heterozygous pathogenic variants in the DHDDS gene (DHDDS-CDG) is a rare genetic disease that belongs to the progressive encephalopathy spectrum. It results in cognitive delay in affected children, accompanied by myoclonus, seizures, ataxia and tremor, which worsens over time. DHDDS encodes a subunit of a DHDDS/NUS1 cis-prenyltransferase (cis-PTase), a branch point enzyme of the mevalonate pathway essential for N-linked glycosylation. We describe the first mouse model of this disease, DhddsR37H+/-strain, heterozygous for the human recurrent de novo c.110G>A:p.R37H pathogenic variant. DhddsR37H+/- mice present with seizures, myoclonus and memory deficits associated with reduced density or/and maturity of inhibitory interneurons in the cortex. Multiomics analyses of mouse CNS tissues, together with the enzymatic/structural characterization of the R37H DHDDS mutant protein, reveal that the variant produces a catalytically inactive enzyme and results in a brain dolichol deficit, aberrant glycosylation of brain glycoproteins, including those involved in synaptic transmission and major perturbations in the CNS proteome and lipidome. Acetazolamide, a carbonic anhydrase inhibitor clinically approved for treatment of glaucoma, epilepsy, and intracranial hypertension, and successfully used "off-label" to treat genetic movement disorders, reduces seizure susceptibility to pentylenetetrazol in DhddsR37H+/- mice, suggesting potential therapeutic value of using this drug in human DHDDS-CDG patients. Together, our results define cis-PTase as a master regulator of CNS development and function and establish that its monoallelic debilitating variants cause a novel congenital disorder of glycosylation associated with aberrant levels of neuronal proteins and lipids.

neuroscience↗

bioRxiv2025

Chromosome-Scale, Telomere-to-Telomere Assembly of Winged Bean (Psophocarpus tetragonolobus (L.) DC.) Genome Reveals Lipid Biosynthetic Hotspots and Gene Family Dynamics

Winged bean (Psophocarpus tetragonolobus) is a nutritionally rich but cytologically and genomically underexplored legume with potential for climate-resilient agriculture. We report a telomere-to-telomere, chromosome-scale genome assembly ([~]697.69 Mb; N50 = 85.98 Mb; [~]98.25% of the cytometric estimate) of the cultivar AKWB1 using a combination of PacBio HiFi, Illumina, BioNano, and Hi-C technologies. Cytogenetics revealed a diploid karyotype (2n = 18) with exclusively metacentric chromosomes, establishing the first chromosomal ideotype map for the species. The high-quality assembly anchors 98.28% of bases to nine pseudochromosomes and includes 53,745 annotated protein-coding genes, with 97.6% BUSCO completeness. Repeat elements comprise [~]60% of the genome, dominated by LINEs, LTRs, and DNA transposons. KEGG and GO annotations reveal diverse biosynthetic capabilities across metabolic and stress-response pathways. Comparative genomics with nine legumes demonstrates conserved chromosomal synteny with Glycine max, absence of recent whole-genome duplication, and a contraction-dominated gene family history. Lipid metabolism analysis identified 750+ genes across 12 KEGG pathways, including fatty acid biosynthesis, elongation, and triacylglycerol assembly. Chromosomes 2, 3, and 5 showed enrichment of lipid biosynthetic loci, suggesting evolutionary hotspots. This reference genome positions P. tetragonolobus as a valuable model for studying genome evolution and engineering underutilized legumes for oil yield, protein enrichment, and climate adaptability.

genomics↗

bioRxiv2025

Multi-Model LLM Architectures for Personalized Summarization and Relevance Ranking in Biomedical Literature

ObjectiveTo develop and evaluate a personalized literature review system that efficiently processes and summarizes biomedical literature to provide timely, relevant insights for researchers. MethodsThe system integrates ontology-aware keyword extraction (MeSH/ACM constrained TF-IDF from CV/Research Statement), citation-informed retrieval (PubMed and NIH iCite API), and dual-model large language model (LLM) summarization (Google Gemini 2.0 flash, OpenAI GPT-4o-mini). These LLMs leverage advanced Transformer architectures, building on foundations such as BERT, BART, and BioBERT. A two-stage ranking algorithm combines Relative Citation Ratio (RCR) with cosine similarity. Summary quality was evaluated using ROGUE-1/2/L and BERTScore. The system is deployed as a Streamlit web application. ResultsAcross 20 biomedical queries, the system demonstrated strong average performance (BERT-F1{approx} 0.86), with cosine similarity strongly correlating with summary quality. Human evaluation involving 10 users yielded average scores above 4.5/5 across summary fidelity and keyword relevance. ConclusionHybrid ranking and ensemble LLM summarization significantly accelerate scientific sense-making. These findings suggest broad applicability to various domains beyond biomedicine.

bioinformatics↗

bioRxiv2025

A lateralized sensory signaling pathway mediates context-dependent olfactory plasticity in C. elegans

Lateralization of neuronal functions plays a critical role in regulating behavioral flexibility, but the underlying molecular mechanisms are challenging to establish at a single-neuron level. We previously showed that attraction of C. elegans to a medium-chain alcohol switches to avoidance in a uniform background of a second attractive odorant. This context-dependent behavioral plasticity is mediated by symmetric inversion of the odor-evoked response sign in the bilateral AWC olfactory neurons. Here we show that this symmetric response plasticity is driven by asymmetric molecular mechanisms in the AWC neuron pair. Mutations in the gcy-12 receptor guanylyl cyclase abolish odor response plasticity only in AWCOFF; the opposing odor-evoked response signs in AWCOFF and AWCON in gcy-12 mutants results in these animals being behaviorally indifferent to this chemical. We find that gcy-12 is expressed, and required, in both AWC neurons to regulate odor response plasticity only in AWCOFF. We further show that disruption of AWC fate lateralization results in loss of asymmetry in the response plasticity in gcy-12 mutants. Our results indicate that symmetric neuronal response plasticity can arise from asymmetry in underlying molecular mechanisms, and suggest that lateralization of signaling pathways in defined conditions may enhance neuronal and behavioral flexibility.

neuroscience↗

bioRxiv2025

Triple-Negative Breast Cancer Cells Activate Sensory Neurons via TRPV1 to Drive Nerve Outgrowth and Tumor Progression

The tumor microenvironment in triple-negative breast cancer (TNBC) is characterized by increased sensory nerve density, which contributes to cancer progression by promoting migration and metastasis. However, the origin of tumor-innervating nerves and the mechanisms driving sensory innervation into tumors remain poorly understood. Using in vivo retrograde labeling techniques, we show that mammary tumors are associated with an increase in nerves originating from the dorsal root ganglia. Additionally, we find that TNBC cells trigger stress and activation markers and induce neuronal firing in a transient receptor potential anilloid subtype 1 (TRPV1)-dependent manner. In both 2D and 3D cell culture models, TNBC cells promote outgrowth of sensory nerves that is abrogated with Trpv1 knockout. We identified c-Jun and IL-6 as an effector of neurite outgrowth that acts downstream of TRPV1 to promote outgrowth in vitro. Finally, in Trpv1 knockout mice, TNBC tumors exhibit delayed growth and reduced lung metastasis. These findings suggest that a critical role for TRPV1 in tumor-nerve crosstalk, offering a potential target to reduce metastatic disease.

cancer biology↗

bioRxiv2025

Receptor Tyrosine Kinase Profiling Identifies Chronic Constitutive Floodgate Oxidative Signaling in Glutathione-Independent Human Mammary Luminal Progenitor Cells

The human mammary epithelium contains a subset of luminal progenitor (LP) cells that are distinct from basal cells in both lineage potential and redox biology. LPs are uniquely equipped to tolerate oxidative stress through glutathione-independent mechanisms and have been implicated as candidate cells of origin in basal-like breast cancers. In this study, we identify the receptor tyrosine kinase (RTK) cKIT (CD117), as a defining feature of LPs and a key mediator of their expansion. cKIT is developmentally restricted to the LP compartment via Polycomb-mediated epigenetic repression in basal and luminal-committed cells. It is expressed in scattered epithelial cells within both ductal and alveolar regions of resting human mammary glands. Using RTK-engineered MCF10A models, we demonstrate that cKIT ligand/stem cell factor (SCF)-activated wildtype cKIT signaling is sufficient to drive proliferation in the absence of epidermal growth factor (EGF) and that cKIT is responsive not only to canonical ligands but also to hydrogen peroxide (H2O2). In primary human LPs, cKIT is rapidly phosphorylated upon exposure to SCF and H2O2, with concomitant AKT activation. These responses are enhanced when cKIT and EGFR signaling are co-engaged, suggesting a cooperative mitogenic program. In mammary gland, phosphorylation of the antioxidant enzyme PRDX1 is selectively detected in LPs, consistent with a floodgate model of redox signaling in which transient oxidative inactivation of peroxiredoxins (PRDXs) facilitates RTK signaling under elevated intracellular reactive oxygen species conditions. Clinically, elevated cKIT expression is associated with shorter progression-free survival in certain basal-like breast cancer, supporting a link between LP-like redox signaling states and aggressive tumor behavior. Together, these findings define a redox-integrated RTK signaling axis centered on cKIT that drives LP expansion and is associated with poor outcomes in a subset of basal breast cancers. This work establishes a mechanistic framework for targeting redox-responsive progenitor populations in both regenerative and oncologic context.

cancer biology↗

bioRxiv2025

ALG13 loss-of-function alters glycosylation, impairs neuronal maturation, and drives network hypoactivity in a cortical organoid model of CDG

BackgroundCongenital disorders of glycosylation (CDGs) are a group of rare metabolic diseases recognized for their neurological presentations, including developmental delay and seizures. However, the link between glycosylation defects and cortical brain network pathology remains elusive. MethodsTo address this unmet need, we generated iPSC derived human cortical organoids (hCOs) for ALG13-CDG, which is the second most common CDG that is also X-linked. To comprehensively understand the impact of glycosylation defects on cortical pathology in CDG, we combined electrophysiological recordings using multi-electrode arrays (MEA) with comprehensive molecular profiling via multiomics, including scRNA-seq, proteomics, glycoproteomics, N-glycan imaging, lipidomics, and metabolomics. X-inactivation status was also evaluated in both iPSCs and organoids. ResultsALG13-CDG hCOs revealed reduced glycosylation of proteins critical for extracellular matrix (ECM), neuronal migration, lipid metabolism, calcium ion homeostasis, and neuronal excitability. Dysregulation in related pathways was corroborated by proteomics and scRNA-seq, which also showed altered communication patterns in these pathways. Trajectory analysis revealed an inversion in neuronal development, with early inhibitory and delayed excitatory development, indicating an excitatory and inhibitory (E/I) imbalance. MEA recordings demonstrated early network hypoactivity with reduced firing rates, immature burst dynamics, and shorter axonal extensions. Despite this, transcriptomic and proteomic data revealed upregulation of excitatory receptors suggesting latent hyperexcitability. Altered lipid and sugar (GlcNAc) metabolism and skewed X-inactivation were also observed. ConclusionsOur study provides the first evidence of glycosylation defects in an ALG13-CDG human cortical organoid (hCO) model and links these defects to disrupted neuronal developmental trajectories and dysregulation of key pathways essential for brain function. We identify mistimed neuronal maturation and an excitatory/inhibitory (E/I) imbalance as early drivers of network hypoactivity and immature burst dynamics, with downstream compensatory hyperexcitability that may contribute to seizure susceptibility. While specific to ALG13-CDG, these mechanisms likely extend to other glycosylation disorders with overlapping neurological features. This work offers new mechanistic insight into cortical dysfunction associated with impaired protein glycosylation and highlights potential targets for therapeutic intervention.

neuroscience↗

bioRxiv2025

Dynamic extracellular interactions with AMPA receptors

Synaptic plasticity in the central nervous system enables the encoding, storing, and integrating new information. AMPA-type glutamate receptors (AMPARs) are ligand-gated ion channels that mediate most fast excitatory synaptic transmission in the brain, and plasticity of AMPARs signaling underlies the long-lasting changes in synaptic efficacy and strength important for learning and memory.1,2 Recent work has indicated that the enigmatic N-terminal domain (NTD) of AMPARs may be a critical regulator of synaptic targeting and plasticity of AMPARs. However, few synaptic proteins have been identified that regulate AMPAR plasticity through interactions with AMPAR NTDs. Moreover, the scope of AMPAR NTD interactors that are important for synaptic plasticity remains unknown. Here, we present the dynamic, extracellular interactome for AMPARs during synaptic plasticity. Using surface-restricted proximity labeling and BioSITe-based proteomics, we identified 70 proteins that were differentially labeled by APEX2-tagged AMPARs after induction of chemical Long-term potentiation of synapses (cLTP) in cultured neurons. Included in this list, were four members of the IgLON family of GPI-anchored proteins (Ntm, OBCAM/Opcml, Negr1, Lsamp). We show OBCAM and NTM directly interact with the extracellular domains of AMPARs. Moreover, overexpression of NTM significantly attenuates the mobility of surface AMPARs in dendritic spines. These data represent a significant first step at uncovering the unexplored extracellular regulation of AMPARs, with broad implications for synapse function and synaptic plasticity. Significance StatementOver the past 30 years, significant effort has been focused on understanding the mechanisms that induce long-lasting changes in synapse strength (synaptic plasticity) that drive learning and memory. While many studies have investigated intracellular mechanisms that enable plasticity, especially those acting on AMPA-type glutamate receptors (AMPARs), significantly less is known regarding extracellular mechanisms that shape changes in synapse function. Here, we identified 70 proteins that differentially associate with the extracellular region of AMPARs during chemically-induced synaptic plasticity. We show that OBCAM and NTM directly interact with the NTD of AMPARs and regulate their mobility on the surface of neurons. These data advance our understanding of extracellular AMPAR regulation, with broad implications for synapse function and synaptic plasticity.

neuroscience↗

bioRxiv2025

Resolving Emergent Oscillations in Gene Circuits with a Growth-Coupled Model

Synthetic gene circuits often behave unpredictably in batch cultures, where shifting physiological states are rarely accounted for in conventional models. Here, we find that degradation-tagged protein reporters could exhibit transient oscillatory expression, which standard single-scale models do not capture. We resolve this discrepancy by developing Gene Expression Across Growth Stages (GEAGS), a dual-scale modeling framework that explicitly couples intracellular gene expression to logistic population growth. Using a chemical reaction network (CRN) model with growth-phase-dependent rate-modifying functions, GEAGS accurately reproduces the observed transient oscillations and identifies amino acid recycling and growth-phase transition as key drivers. We reduce the model to an effective form for practical use and demonstrate its adaptability by applying it to layered feedback circuits, resolving long-standing mismatches between model predictions and measured dynamics. These results establish GEAGS as a generalizable platform for predicting emergent behaviors in synthetic gene circuits and underscore the importance of multiscale modeling for robust circuit design in dynamic environments. TeaserMultiscale modeling reveals how growth and proteolysis-linked recycling cause transient oscillations in synthetic gene circuits.

synthetic biology↗

bioRxiv2025

Coordinated regulation of trichome morphogenesis and flavonoid pathway by a MYB HDZIP JAZ module in banana (Musa sp.)

O_LITrichomes are epidermal structures that function in defence against biotic and abiotic stresses. The developmental and metabolic aspects of trichomes have not been studied in banana (Musa acuminata). In the present study, we report that banana cultivars with AAA genome contain trichomes on inflorescence stalk. C_LIO_LITranscriptome analysis of epidermal tissues of trichome-rich and trichome-free banana cultivars suggested that genes concerning defence response and specialized metabolism are differentially regulated. Based on the gene expression and phylogenetic analysis, two transcription factors, MaTFR (trichome and flavonol related R2R3-MYB) and MaHDZIV6 (HDZIP-IV), were identified as candidate regulators of trichome development. C_LIO_LIBoth genes partially complemented the glabrous phenotype of trichome-related mutants of Arabidopsis. Transient overexpression and silencing in banana embryogenic cells (ECS) suggested that both MaTFR and MaHDZIV6 regulate the transcription of flavonol biosynthesis genes and modulate flavonoids content. Furthermore, MaTFR was found to directly activate the expression of MaHDZIV6. C_LIO_LITrichome-enriched cultivars have enhanced active JA content compared to trichome-free cultivar suggesting the involvement of JA signalling in regulating trichome development. Two JAZ repressors, MaJAZ5 and MaJAZ8 interacted with MaTFR and attenuated the flavonoid biosynthesis. Our study concludes that the MYB, HDZIP-IV, and JAZ module fine-tunes the flavonoid biosynthesis and the trichome development in banana. C_LI

plant biology↗

bioRxiv2025

PGM1 deficiency disrupts sarcomere and mitochondrial function in a stem-cell cardiomyocyte model

BackgroundPhosphoglucomutase-1 (PGM1) plays a pivotal role in glycolysis, glycogen metabolism, and glycosylation. Pathogenic variants in PGM1 cause PGM1-congenital disorder of glycosylation (PGM1-CDG), a multisystem disorder with cardiac involvement. While glycosylation abnormalities in PGM1-CDG are treatable with galactose, cardiomyopathy does not improve suggesting a glycosylation-independent pathomechanism. Recently, mitochondrial abnormalities have been shown in a heart of a PGM1-deficicient patient and PGM1-mouse model. In addition, PGM1 has been associated with LDB3 (ZASP/Cypher), a sarcomeric Z-disk protein also associated with cardiomyopathy. However, the cardiac-specific role of PGM1 remains poorly understood, and targeted therapies for PGM1-related cardiomyopathy are currently lacking. MethodsInduced pluripotent stem cell-derived cardiomyocytes (iCMs) were generated from PGM1-deficient patient fibroblasts. Multielectrode array (MEA) recordings, untargeted (glyco)proteomics, and pathway analysis were performed to assess functional and molecular changes. Key findings were validated using tracer metabolomics and mitochondrial respiration assays. ResultsPGM1-deficient iCMs exhibited reduced beating frequency, impaired contractility, and prolonged contraction kinetics. Proteomic analyses revealed depletion of Z-disk components, including LDB3. AlphaFold3 structural modeling predicted a direct interaction between PGM1 and LDB3, implicating PGM1 in Z-disk integrity, which was confirmed in vitro. In addition, mitochondrial proteins were severely depleted, prompting us to investigate mitochondrial function. Functional validation confirmed extensive metabolic rewiring, energy depletion, and severely impaired mitochondrial respiration. Finally, the in silico drug repurposing identified possible therapeutic options that could target PGM1-deficient cardiomyopathy. ConclusionPGM1 is a key regulator of cardiomyocyte function, linking sarcomeric Z-disk integrity with mitochondrial metabolism. These mechanistic insights offer a foundation for developing targeted therapies for PGM1-CDG and potentially other cardiomyopathies involving Z-disk dysfunction. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=175 HEIGHT=200 SRC="FIGDIR/small/662580v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@17da449org.highwire.dtl.DTLVardef@1acb669org.highwire.dtl.DTLVardef@1fbbeecorg.highwire.dtl.DTLVardef@b38b6f_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗