Biology subjects

Kapoor, S.

Publications and source records attributed to Kapoor, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Tryptophan Restores Recovery Competence Following Starvation in the Absence of Lysosomal Amino Acid Sensing

How organisms recover from starvation to nutrient-replete physiology remains poorly understood. In C. elegans, we previously observed that transcription factor hlh-30 or a combination of glucose and linoleic acid in its absence are essential for survival with refeeding following starvation, i.e. recovery competence. A forward genetic screen to evaluate mechanisms identified depd-5, which encodes a GATOR1 subunit, loss of which is expected to impair amino acid sensing with unrestrained raga-1 and mTOR activation. Surprisingly, glucose refeeding reduced recovery competence in depd-5(lf, loss-of-function) animals, which was rescued by amino acids, specifically tryptophan. Increasing tryptophan levels in depd-5(lf) worms through supplementation, reduced tryptophan catabolism with tdo-2 ablation and prolonged starvation restored recovery competence. raga-1(gf, gain-of-function) recapitulated whereas raga-1(lf) rescued the impaired recovery competence in starved depd-5(lf) worms. An analogous DEPDC5 mutation in mammalian cells impaired starvation-induced mTOR inactivation. We conclude that tryptophan counters unrestrained mTOR activity to restore recovery competence following starvation.

cell biology↗

bioRxiv2026

The biophysical interaction network that couples zona occludens-1 to membrane proteins at tight junctions

Tight junctions are dynamic membrane-bound protein assemblies that maintain barrier function for tissues as cells divide, grow, and move through development and throughout life. Maintenance of tissue barriers requires spatially separated intracellular and extracellular signaling pathways to be linked through novel and dynamic protein interaction networks. Tight junction intracellular signaling is governed by zona occludens-1 (ZO-1), a Membrane-Associated GUanylate Kinase (MAGUK) family protein that recruits and assembles transmembrane proteins and scaffolds them to the actin cytoskeleton through its own oligomerization, localization to membranes, and phase separation. Here we report comprehensive quantitative studies that nearly completely maps the intracellular interaction network between ZO-1 and tight junction transmembrane proteins that elucidates the biophysical principles governing their binding and a mechanism for how stimuli transmit through membranes. We establish where, how, and with whom each protein interacts, and identify how membrane proteins enable ZO-1 and greater tight junction function through specific interactions or by phase separation. Our findings reveal the intracellular interactome that triggers and regulates tight junction assembly, the active and direct roles each membrane protein plays in these processes, and provide a mechanism for how intra/extracellular signaling is coupled to transmit mechanochemical signals between cells via tight junctions. These insights provide a prospective blueprint for how other MAGUK/membrane protein interaction networks form and function across biology.

biophysics↗

bioRxiv2026

Hypoxia drives asymmetric envelope remodelling to promote membrane adaptation and antibiotic tolerance in mycobacteria

Mycobacterium tuberculosis persists within the host by adapting to stressful microenvironments, with hypoxia representing a key clinically relevant challenge. However, how hypoxia alters mycobacterial membrane organization and function remains poorly understood. Using Mycobacterium smegmatis as a model, we combined membrane biophysics, layer-resolved lipidomics, and membrane-drug interaction analyses to characterize envelope adaptation under oxygen limitation. Hypoxia induced asymmetric remodelling of the cell envelope, with the inner membrane becoming more ordered and less hydrated, while the outer membrane exhibited increased fluidity and hydration. Lipidomic analyses revealed corresponding membrane-specific changes, including enrichment of saturated, tightly packed lipids in the inner membrane and unsaturated, inverted-conical lipids in the outer membrane. Functionally, hypoxic cells showed reduced envelope permeability and decreased susceptibility to rifampicin, while membrane partitioning studies suggested reduced rifampicin association with hypoxia-adapted inner membranes. We identify asymmetric envelope remodeling as a previously unrecognized principle of bacterial adaptation to environmental stress. Rather than responding as a uniform structure, the mycobacterial envelope undergoes coordinated but divergent remodeling in its constituent membrane layers during hypoxia. This spatially resolved response couples inner membrane rigidification with outer membrane fluidization, generating a functionally specialized envelope architecture that simultaneously preserves membrane integrity, modulates permeability, and reduces antibiotic association. These findings suggest that membrane asymmetry is not merely a structural feature of complex bacterial envelopes but an actively regulated adaptive strategy that links environmental sensing to stress resilience and antimicrobial tolerance

biophysics↗

bioRxiv2026

Principal Genes: A PCA-based approach to highly variable genes selection for scRNA-Seq analysis

Single cell RNA-sequencing (scRNA-Seq) data are typically represented as cell-by-gene count matrices, which capture the expression of each gene as detected in the sampled cells; often a heterogeneous population of multiple different cell types or cell states. Almost all scRNA-Seq analysis workflows have a gene selection step prior to applying clustering algorithms which helps remove genes with low variability and hence reduce the high-dimensional gene space. A de-facto method for achieving selection of highly variable genes (HVG) uses dispersion and mean expression scores to evaluate the variability of each individual gene. However, methods based on direct mean-to-variance relationship for gene selection often suffer from susceptibility to variance instability and arbitrary determination of the optimal number of genes to use in downstream analysis tasks, additionally, they often prioritize genes with low abundance but high variance. Here, we propose an innovative method for selecting highly variable genes that is not based on mean to variance ratios: "Principal Genes (PG)" method; it utilizes the rotations (or loadings) from Principal Component Analysis (PCA) to calculate a novel variability score per gene that we name "Gene Principal Score (GPS)". GPS helps evaluate the genes based on their contribution in the PCA rotations and hence ranks the genes according to their variability from highest to lowest variable genes. For efficient implementation we utilize Augmented Implicitly Restarted Lanczos Bidiagonalization methods to efficiently obtain Principal Components (PCs) associated with the largest variance. Genes with the highest GPS score, i.e. Principal Genes, can then be used for downstream analysis tasks, especially the clustering step. To test the performance of our highly variable gene identification method, we use several validation strategies, including clustering of labeled single cell RNA-Seq data (i.e. data with known ground truth cell type labels). Furthermore, we measure the performance of our method against dispersion-based highly variable gene (HVG) selection approaches. We use several validation metrics, including sensitivity and adjusted rand index scores for clustering based on genes selected using our method against genes selected using HVG; and our validation datasets include six real labeled single cell RNA-Seq datasets. Our findings show that our new method, Principal Genes, is comparable and often favorable in performance in selecting highly variable genes and achieves ultra-fast gene selection from PCA results.

bioinformatics↗

bioRxiv2026

Mucus cell and ionocyte precursors migrate between epithelial cells to disperse through the zebrafish epidermis

Mucus-secreting cells and ionocytes play critical roles in many organs. Both cell types are usually distributed as scattered, solitary cells within an epithelium, a pattern presumably optimal for their function. To investigate how they attain their dispersed distributions, we imaged mucus cell and ionocyte precursors in the epidermis of developing zebrafish. Previous reports found that precursors of both cell types are first detected in the ventral epidermis (covering the yolk) before spreading dorsally, but the mechanism driving this progression was unknown. Photoconverting basal epidermal cells in the ventral embryo revealed that some cells actively migrate away from this area to populate the rest of the epidermis. These cells lose their basal cell identity when they start migrating and begin expressing markers of mature mucus cells or ionocytes during migration. These cells travel entirely between the two epithelial layers of the epidermis, occasionally pause migration to divide, and repel one another through contact inhibition of locomotion, behaviors that likely aid in their dispersal. After migrating for about a day, mucus cell and ionocyte precursors intercalate into the superficial epithelial layer of the epidermis, where they complete differentiation. These observations reveal how mucus cells and ionocytes achieve their scattered distributions in the zebrafish epidermis, suggesting that similar processes promote their distribution in other mucosal organs.

developmental biology↗

bioRxiv2026

Reversible hypervascularization drives cognitive decline and blood-brain barrier damage during aging

Cerebrovascular dysfunction emerges early in neurodegeneration, yet how vascular structure, blood-brain barrier (BBB) failure, and cognition are linked remains undefined. Using VesselPro, a whole-brain pipeline integrating perfusion-resolved 3D imaging with spatial proteomics, we mapped vascular aging across the mouse lifespan. We identify two discrete trajectories: a hypovascular state and a previously unrecognized hyper-vascular, BBB-compromised state, defined relative to a young-adult vascular baseline. The hyper-vascular trajectory, concentrated in the cortex and hippocampus, was associated with marked spatial memory impairment and pervasive BBB leakage. Spatial proteomics revealed a coordinated program involving angiogenic activation, endothelial stress, cytoskeletal remodeling, and inflammatory signaling. Cross-species comparison with human proteomic biomarkers from the UK Biobank showed strong alignment between the mouse hypervascular signature and vascular dementia risk, but minimal concordance with Alzheimers disease, defining a vascular-specific dementia endotype. Transient Tie2 activation with AKB-9778 attenuated this trajectory, improving vessel organization, BBB integrity, and memory performance. Our findings show that endothelial instability is a key mechanistic driver of this heterogeneous vascular aging state. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/720441v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@39494aorg.highwire.dtl.DTLVardef@faa4acorg.highwire.dtl.DTLVardef@1511dd5org.highwire.dtl.DTLVardef@7db29b_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIVesselPro: we developed a pipeline for capturing perfused blood vessels in the brain: unexpected bifurcation in vascular aging: traditional hypovascular state and a novel, hypervascular, BBB-compromised state. C_LIO_LIHypervascular pathology: Linked the hypervascular profile in the cortex and hippocampus to spatial memory impairment, pervasive BBB leakage, and angiogenic inflammatory signaling. C_LIO_LIClinical endotype: Cross-species analysis via the UK Biobank confirms this hypervascular signature aligns with vascular dementia risk rather than Alzheimers disease. C_LIO_LIPharmacological stabilization: Demonstrated that Tie2 signaling activation (AKB-9778) improves the vessel organization, BBB integrity, and memory performance. C_LI

neuroscience↗

bioRxiv2025

Remote Host Manipulation by Pathogenic Bacterial Extracellular Vesicles

Bacterial extracellular vesicles (BEVs) are known to enhance infection susceptibility in vivo, yet the mechanistic basis for this remote preconditioning of host cells is unknown. Here, we discover an evolutionarily conserved, lipid-driven physical mechanism by which pathogenic bacterial EVs systemically arrest phagosome maturation in bystander host cells. Using live-cell fluorescence lifetime imaging, in vitro reconstitution and micromanipulation, we show that EVs from diverse pathogens - Mycobacterium tuberculosis, Klebsiella pneumoniae, and Staphylococcus aureus - fuse with host plasma, phagosomal, and lysosomal membranes. This fusion increase membrane order and perturbs early phagosomal maturation. Transcriptomic profiling confirms a broad downregulation of phagosome maturation genes while upregulation of lysosomal stress responsive genes. Crucially, in vitro reconstitution shows that EVs, and their purified lipids alone, are sufficient to induce phase separation and increase membrane order, directly inhibiting phago-lysosomal fusion. Our findings establish a paradigm in which pathogens exploit EVs not merely as delivery vehicles, but as tools to remotely rewire host cell membrane mechanics to hijack phagosome maturation and promote infection - a strategy that moves beyond canonical effector-based models of pathogenesis.

cell biology↗

bioRxiv2025

IGF2BP3 remodels the microRNA targeting landscape in MLL-AF4 leukemia

Insulin-like growth factor 2 mRNA binding protein 3 (IGF2BP3/I3) is a multi-domain RNA-binding protein required for MLL-AF4-driven leukemogenesis, but its mechanism of action remains enigmatic. We hypothesized from our previous work that I3 amplifies oncogenic gene expression by modulating RNA induced silencing complex (RISC) mRNA interactions. To test this, we performed miR-eCLIP of AGO2, the catalytic RISC subunit, in I3 knock-out (I3KO) as well as control B-cell acute lymphoblastic cell lines (B-ALL) and identified I3-dependent AGO2 binding sites on 111 3'UTRs. Analyzing chimeric miRNA-mRNA reads, we observed differential miRNA occupancy in the I3KO compared to control, including increased targeting by miR-181a, a regulator of leukocyte differentiation. Notably, miR-181a overexpression phenocopied I3 loss, implicating I3 in restricting miR-181a-mediated repression. Biochemical assays confirmed direct competition between I3 and AGO2-miRNA complexes for 3'-UTR binding. Taken together, our results provide a model for how I3 promotes leukemogenesis by antagonizing RISC-mediated repression of oncogenic mRNAs.

cancer biology↗

bioRxiv2025

In Vivo AGO-APP For Cell-Type- and Compartment-Specific miRNA Profiling in the Mouse Brain

AGO-APP through the expression of the T6B peptide permits the isolation of Ago-bound miRNAs. Here we present the generation and characterization of two transgenic mouse lines allowing to perform AGO-APP in vivo. First, we generated mice for CRE-dependent expression of T6B in the cytoplasm. Using this line we performed Ago-APP in olfactory bulb (OB) inhibitory interneurons and cerebral cortex excitatory neurons. Bioinformatic analysis validated the high reproducibility of the approach. It also demonstrated that, despite global miRNome conservation between the two cell types, a set of miRNAs including the miR-200 family and the miR-183/96/182 cluster, is massively enriched in OB interneurons which is consistent with previous observations. In the second mouse line T6B is fused to the postsynaptic protein PSD95. Isolation of T6B-PSD95 fractions from OB and cortical neurons identified specific sets of post-synapse enriched miRNAs. Gene ontology analyses confirmed that these miRNAs preferentially target mRNAs related to synaptic functions. MotivationCollectively, miRNAs are required for all biological processes in eukaryotes. However, due to a lack of appropriate methodological tools, the actual mode of action of individual miRNAs in a given cell is currently poorly understood. In this article, we describe a novel approach to study the specific expression of miRNAs in vivo, at the level of cell type and in a specific cell compartment.

neuroscience↗

bioRxiv2024

Biophysical Basis of Paracellular Barrier Modulation by a Pan-Claudin-Binding Molecule

Claudins are a 27-member protein family that form and fortify specialized cell contacts in endothelium and epithelium called tight junctions. Tight junctions restrict paracellular transport across tissues by forming molecular barriers between cells. Claudin-binding molecules thus hold promise for modulating tight junction permeability to deliver drugs or as therapeutics to treat tight junction-linked disease. The development of claudin-binding molecules, however, is hindered by their intractability and small targetable surfaces. Here, we determine that a synthetic antibody fragment (sFab) we developed binds directly to 10 claudin subtypes with nanomolar affinity by targeting claudins paracellular-exposed surface. Application of this sFab to cells that model intestinal epithelium show that it opens the paracellular barrier comparable to a known, but application limited, tight junction modulator. This novel pan-claudin-binding molecule can probe claudin or tight junction structure and holds potential as a broad modulator of tight junction permeability for basic or translational applications.

biophysics↗

bioRxiv2024

Mast cells are not essential for pubertal mammary gland branching.

Mast cells are long-lived, tissue-resident immune cells of the myeloid lineage with cardinal functions in allergy and atopic disease. They are now increasingly recognized also for protective roles e.g. against infections and venoms. Other functions originally assigned to mast cells in development and physiology, however, have been refuted, and for yet others, their true contribution remains uncertain. Mast cells have been implicated in promoting ductal branching in the pubertal mammary gland, the organ that produces and secretes milk in mammals, but these findings are based on mouse models that are not mast cell-specific. In this study, we therefore re-addressed the impact of mast cells on mammary gland branching using several complementary genetic models, including a new transgenic line. We report that neither constitutive deficiency of mast cells, nor their conditional ablation induced at puberty affected mammary gland branching. Our results thus dispute that mast cells promote this process in mice, at least in a unique and non-redundant manner. This study adds to a growing body of work clarifying the biological roles of mast cells, and further expands the toolbox available to the field of mast cell research.

developmental biology↗

bioRxiv2024

Deep Learning and 3D Imaging Reveal Whole-Body Alterations in Obesity

Many diseases, such as obesity, have systemic effects that impact multiple organ systems throughout the body. However, tools for comprehensive, high-resolution analysis of disease-associated changes at the whole-body scale have been lacking. Here, we developed a suite of deep learning-based image analysis algorithms (MouseMapper) and integrated it with tissue clearing and light-sheet microscopy to enable a comprehensive analysis of diseases impacting diverse systems across the mouse body. This approach enables the quantitative analysis of cellular and structural changes across the entire mouse body at unprecedented resolution and scale, including tracking nerves over several centimeters in whole animal bodies. To demonstrate its power, we applied MouseMapper to study nervous and immune systems in high-fat diet induced obesity. We uncovered widespread changes in both immune cell distribution and nerve structures, including alterations in the trigeminal nerve characterized by a reduced number of nerve endings in obese mice. These structural abnormalities were associated with functional deficits of whisker sensing and proteomic changes in the trigeminal ganglion, primarily affecting pathways related to axon growth and the complement system. Additionally, we found heterogeneity in obesity-induced whole-body inflammation across different tissues and organs. Our study demonstrates MouseMappers capability to discover and quantify pathological alterations at the whole-body level, offering a powerful approach for investigating the systemic impacts of various diseases. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=187 SRC="FIGDIR/small/608300v1_ufig1.gif" ALT="Figure 1"> View larger version (74K): org.highwire.dtl.DTLVardef@17d2601org.highwire.dtl.DTLVardef@14a2d3dorg.highwire.dtl.DTLVardef@e04114org.highwire.dtl.DTLVardef@d0b8b5_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIWe developed MouseMapper: AI-driven pipeline for whole-body structural analysis in mice C_LIO_LIMouseMapper revealed obesity-induced changes in nerves and immune cells across multiple organs C_LIO_LIMouseMapper identified facial nerve alterations in obesity linked to impaired whisker sensitivity C_LIO_LIMouseMapper has the potential for holistic 3D analysis of systemic diseases C_LI Supplementary Videos can be seen at: http://discotechnologies.org/MouseMapper/

systems biology↗

bioRxiv2024

Optimization of an improved, time-saving, and scalable, protocol for the extraction of DNA from diverse viromes

IntroductionThe virome, composed of viruses inhabiting diverse ecosystems, significantly influences microbial community dynamics and host health. The phenol-chloroform DNA extraction protocol for viromes, though effective, is time-intensive and requires the use of multiple toxic chemicals. MethodsThis study introduces a streamlined, scalable protocol for DNA extraction using a commercially-available kit as an alternative, assessing its performance against the phenol-chloroform method across human fecal, mouse fecal, and soil samples. ResultsNo significant differences in virome diversity or community composition were seen between methods. Most viral operational taxonomic units (vOTUs) were common to both methods, with only a small percentage unique to either approach. Alpha- and beta-diversity analyses showed no significant impact of the extraction method on virome composition, confirming the kits efficacy and versatility. ConclusionsWhile the kit approach offers benefits like reduced toxicity and increased throughput, it has limitations such as higher costs and potential issues reliably capturing low-abundance taxa. This protocol provides a viable option for large-scale virome studies, although the phenol-chloroform approach may still be preferable for specific sample types.

microbiology↗

bioRxiv2023

Adenosine Kinase regulates Sleep Timing and the Homeostatic Sleep Response through Distinct Molecular Pathways

Sleep behaviour is broadly regulated by two drives, the circadian (Process C), which is orchestrated by the suprachiasmatic nuclei (SCN), and controls sleep timing, and the homeostatic (Process S), which controls sleep amount and the response to sleep deprivation (Borbely et al., 2016). However, the molecular pathways that mediate their independent effects, and their interactions remain unclear. Adenosine is an important integrator of both processes (Bjorness & Greene, 2009; Jagannath et al., 2021, 2022), such that adenosine levels track and modulate wakefulness, whilst adenosine signalling inhibits the circadian response to light. Therefore, we studied the sleep/circadian behaviour, and cortical and SCN transcriptomic profiles of a mouse model overexpressing Adenosine Kinase (Adk-Tg) (Fedele et al., 2005), (Palchykova et al., 2010). We found that overall, the Adk-Tg mouse slept less and showed lower amplitude circadian rhythms with an altered sleep/wake distribution across the 24h day, which correlated with changes in transcription of synaptic signalling genes that would shift the excitatory/inhibitory balance. In addition, the Adk-Tg mouse showed a reduced level of ERK phosphorylation, and attenuation of DNA repair related pathways. After sleep deprivation, however, the Adk-Tg mouse significantly increased relative to wildtype, immediate early gene expression levels including of Arc, but paradoxically reduced ERK phosphorylation. Thus, baseline sleep levels and timing are regulated by ERK signalling, whereas the response to sleep loss is mediated by the alteration of the transcriptomic landscape independently of ERK.

molecular biology↗

bioRxiv2023

PP2A-B55SUR-6 promotes nuclear envelope breakdown in C. elegans embryos

Nuclear envelope (NE) disassembly during mitosis is critical to ensure faithful segregation of the genetic material. NE disassembly is a phosphorylation-dependent process wherein mitotic kinases hyper-phosphorylate lamina and nucleoporins to initiate nuclear envelope breakdown (NEBD). In this study, we uncover an unexpected role of the PP2A phosphatase B55SUR-6 in NEBD during the first embryonic division of Caenorhabditis elegans embryo. B55SUR-6 depletion delays NE permeabilization and stabilizes lamina and nucleoporins. As a result, the merging of parental genomes and chromosome segregation is impaired. This NEBD defect upon B55SUR-6 depletion is not due to delayed mitotic onset or mislocalization of mitotic kinases. Importantly, we demonstrate that microtubule-dependent mechanical forces synergize with B55SUR-6 for efficient NE disassembly. Finally, our data suggest that the lamin LMN-1 is likely a bona fide target of PP2A-B55SUR-6. These findings establish a model highlighting biochemical cross-talk between kinases, PP2A-B55SUR-6 phosphatase, and microtubule-generated mechanical forces in timely NE dissolution.

cell biology↗

bioRxiv2023

SARS-CoV-2 Spike Protein Accumulation in the Skull-Meninges-Brain Axis: Potential Implications for Long-Term Neurological Complications in post-COVID-19

Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), has been associated mainly with a range of neurological symptoms, including brain fog and brain tissue loss, raising concerns about the viruss acute and potential chronic impact on the central nervous system. In this study, we utilized mouse models and human post-mortem tissues to investigate the presence and distribution of the SARS-CoV-2 spike protein in the skull-meninges-brain axis. Our results revealed the accumulation of the spike protein in the skull marrow, brain meninges, and brain parenchyma. The injection of the spike protein alone caused cell death in the brain, highlighting a direct effect on brain tissue. Furthermore, we observed the presence of spike protein in the skull of deceased long after their COVID-19 infection, suggesting that the spikes persistence may contribute to long-term neurological symptoms. The spike protein was associated with neutrophil-related pathways and dysregulation of the proteins involved in the PI3K-AKT as well as complement and coagulation pathway. Overall, our findings suggest that SARS-CoV-2 spike protein trafficking from CNS borders into the brain parenchyma and identified differentially regulated pathways may present insights into mechanisms underlying immediate and long-term consequences of SARS-CoV-2 and present diagnostic and therapeutic opportunities. Graphical Summary O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/535604v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@b223eforg.highwire.dtl.DTLVardef@15539e9org.highwire.dtl.DTLVardef@4d17a9org.highwire.dtl.DTLVardef@14c63af_HPS_FORMAT_FIGEXP M_FIG C_FIG Short SummaryThe accumulation of SARS-CoV-2 spike protein in the skull-meninges-brain axis presents potential molecular mechanisms and therapeutic targets for neurological complications in long-COVID-19 patients.

neuroscience↗

bioRxiv2022

Lipid remodeling by hypoxia aggravates migratory potential in pancreatic cancer while maintaining membrane homeostasis

Membranes are crucial cell components underlying optimal cellular functioning under diverse conditions including cancer. The membrane physiology requires acute maintenance of biophysical properties and a regulation of cellular lipidome. Homeostatic adaptation of membranes to temperature, pressure and anti-cancer drugs is a well-recognized. However, how the same is regulated under the influence of oxygen deprivation in pancreatic cancers-highly hypoxic cancer- is not known. Here, we report robust lipidomic remodelling in response to HIF-1 induction in pancreatic cancer cells and significant accumulation of lipid droplets. The lipidome rewiring span changes across various lipid classes, levels of unsaturation and acyl chain lengths. Interestingly, despite extensive lipidome alteration, cellular membrane homeostatic response ensures no major modulation of membrane biophysical properties underlying enhanced migratory potential. The correlation of lipidome changes, with pathway analysis and proteomics provide the basis for mutually exclusive regulation of lipidome and membrane properties. These findings help to understand the hypoxic regulation of pancreatic membrane homeostasis.

biophysics↗

bioRxiv2022

miR-29 is an important driver of aging-related phenotypes

Aging is a consequence of complex molecular changes, but the roles of individual microRNAs (miRNAs) in aging remain unclear. One of the few miRNAs that are upregulated during both normal and premature aging is miR-29. We confirmed this finding in our study in both mouse and monkey models. Follow-up analysis of the transcriptomic changes during normal aging revealed that miR-29 is among the top miRNAs predicted to drive the aging-related gene expression changes. We also showed that partial loss of miR-29 extends the lifespan of Zmpste24-/- mice, an established model of progeria, which indicates that miR-29 is functionally important in this accelerated aging model. To examine whether miR-29 upregulation alone is sufficient to promote aging-related phenotypes in vivo, we generated mice in which miR-29 can be conditionally overexpressed (miR-29TG). We found that miR-29 overexpression in mice is sufficient to drive aging-related phenotypes including alopecia, kyphosis, osteoporosis, senescence, and leads to early lethality. Transcriptomic analysis of both young miR-29TG and old WT mice revealed shared downregulation of genes enriched in extracellular matrix and fatty acid metabolism, and shared upregulation of genes in pathways linked to inflammation. Together, these results highlight the functional importance of miR-29 in controlling a gene expression program that drives agingrelated phenotypes.

physiology↗