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Biology subjects

Sinha, T.

Publications and source records attributed to Sinha, T..

At least 19 recordsLinked to original sources

Extracellular matrix proteoglycans lumican and biglycan promote innate immune signals and viral clearance in HSV-1 infections of mouse corneas

The extracellular matrix (ECM) regulates innate immunity, but its role in HSV-1 keratitis is unclear. Here, we identify the ECM proteoglycans lumican (Lum) and biglycan (Bgn) as key regulators of early antiviral defense in the cornea. Lum-/- and BgnKO mice showed impaired viral clearance, increased corneal opacity, and worse keratitis than wild-type controls. These defects were associated with reduced early recruitment of neutrophils, monocytes, and plasmacytoid dendritic cells, and blunted induction of pro-inflammatory cytokines, chemokines, and type I interferons. In infected wild-type corneas, Lum and Bgn were upregulated, including in the basal epithelium, where Ccl2 emerged as an early epithelial response that was diminished in knockout mice. In human corneal epithelial cells, recombinant LUM or BGN enhanced HSV-1-induced CCL2 secretion, and human corneal organoids recapitulated epithelial viral tropism and CCL2 induction. Together, these findings identify Lum and Bgn as regulators of epithelial-innate immune crosstalk that promote early antiviral immunity during corneal HSV-1 infection.

immunology↗

Comprehensive profiling of infant gut virome assembly reveals associations with eczema and wheeze

Infancy is a critical developmental window during which the gut ecosystem assembles and helps train the immune system, thereby setting trajectories for lifelong health. Bacteria and viruses are equally numerous in this early ecosystem, yet the gut viromes composition, dynamics, and health relevance remain poorly understood. Here, we show that the infant gut virome is diverse, dynamic, and linked to health outcomes. We performed comprehensive virome profiling of 1,110 longitudinal fecal samples from 314 mother-infant pairs from the Dutch birth cohort Lifelines NEXT using both virus-like particle enrichment (VLP) and total metagenomic sequencing (MGS). We find only 18.9% compositional overlap between the VLP- and MGS-metaviromes, with VLP recovering the active virome and most novel species and MGS predominantly capturing temperate phages. By combining both methods, we identified 8,348 novel virus species spanning diverse hosts, from bacteria to humans, and all major viral genome types (dsDNA, ssDNA, and RNA). We find that bacteriophages frequently encode metabolic functions, including genes related to B vitamin metabolism. We further observe that the development of the infant gut virome is shaped by both host factors, including delivery mode and feeding practices, and continuous switching of temperate phage lifecycles. Notably, the relative abundance of induced temperate phages is also associated with eczema development within the first year of life. Together, these findings establish the infant gut virome as a dynamic and clinically relevant component of early-life microbial development and highlight how comprehensive dual-method profiling is a necessary framework for future virome research.

microbiology↗

K9HeartCircDB: A circRNA Atlas of Tachypacing-Induced Canine Dilated Cardiomyopathy

Cardiovascular disease (CVD) remains a leading cause of death worldwide. Dilated cardiomyopathy (DCM), a major cause of heart failure (HF), exhibits ventricular dilation, impaired systolic/diastolic function, arrythmias, and adverse cardiac remodeling. While genetic causes of DCM have been extensively studied, non-genetic and acquired forms of DCM-like HF are less well characterized, especially with respect to non-coding RNA regulation. Circular RNAs (circRNAs) are stable, covalently closed non-coding RNAs that regulate cellular function via sequestering miRNAs, RNA-binding proteins, or translation. Their role in canine HF that recapitulates features of non-genetic DCM remains largely unexplored. To address this, we developed K9HeartCircDB (https://www.k9heartcircdb.com/), a publicly accessible database that catalogs circRNAs expressed in canine left ventricular (LV) tissues under tachypacing-induced HF, a model of non-genetic DCM-like disease, and healthy control conditions. The online interface enables users to query and explore circRNAs based on exon composition, predicted miRNA binding sites, protein-coding potential, siRNA targets, and primer design for experimental validation. By providing an integrated and user-friendly platform for canine heart circRNA exploration, K9HeartCircDB offers a valuable resource to facilitate mechanistic and advance translational studies on non-genetic DCM-like disease.

Systems Biology↗

Genome-wide protein-protein interaction analysis between aquaporins and harpin (HrpZ2) through molecular docking and MD simulations to unravel its role in growth and stress management in tomato.

HrpZ2, a harpin protein produced by Pseudomonas syringae, a gram-negative plant pathogenic bacterium, elicits hypersensitive response and pathogen defense in non-host plants. Harpins from various bacterial sources elicit varying responses in different non-host plants, due to its structural variations, their precise mechanisms of action are not yet completely understood. As per previous reports, harpins from diverse bacterial sources interact with distinctive members of integral membrane proteins, known as aquaporins. For example, harpin (Hpa1Xoo) interacts with OsPIP1;3 in rice, whereas, in Arabidopsis the harpins Hpa1 and HrpZ interacts with AtPIP1;4 and AtPIP1;3 respectively. Here, we conducted the first genome-wide computational screening of protein-protein interactions between HrpZ2 and all 47 members of tomato aquaporins. Molecular docking identified nine interactors across five subfamilies of aquaporins, with HrpZ2 N-terminal residues mediating these interactions. We validated these via molecular dynamics (MD) simulations, principal component analysis, and free energy landscape analysis, assessing the stability (RMSD, RMSF, radius of gyration), dynamics, and affinity (MM-GMSA). PIP complexes, especially PIP2;1 (-460.46 kcal/mol) and PIP1;7 (-303.82 kcal/mol), exhibited superior stability, compactness, and defined energy minima, confirming PIPs as primary sensors of harpins. Non-PIP aquaporins like TIP1;1 and NIP4;1 showed moderate stability, outperforming weaker interactors (SIP2;1, XIP1;5, XIP1;3). These findings provide robust evidence that HrpZ2 preferentially targets PIPs in tomato, while engaging TIPs and NIPs as auxiliary partners. This multifaceted interaction profile of harpins suggests complex plant-pathogen recognition, modulating aquaporin-mediated cellular responses like growth and stress management in plants.

plant biology↗

TOCA-2 regulates gonad development in C. elegans

The development of C. elegans gonad involves the coordinated action of diverse biochemical factors and physical forces. The precise roles and interconnections of these diverse components remain poorly understood. TOCA-2, the C. elegans ortholog of mammalian TOCA-1 (Transducer of CDC42 Dependent Actin Assembly) is an F-BAR domain protein known to play important roles in oocyte maturation and embryogenesis through membrane remodelling and regulation of actin cytoskeleton. Here we demonstrate that TOCA-2 is actively involved in maintaining the structural integrity and function of the C. elegans gonad. toca-2(null) animals exhibit pronounced architectural defects with particularly strong perturbations on the dorsal side of the gonad. Phalloidin staining and cytoplasmic particle velocity analysis revealed that the actomyosin corset surrounding the common rachis in the syncytial germline is severely disorganized in the mutants. This disorganization leads to significant disruptions in cytoplasmic flow across different regions of the syncytium. Together, our findings quantitatively highlight mechanisms underlying gonad morphogenesis and maintenance, establishing TOCA-2 as a key regulator of these processes. This work also provides a framework for positioning TOCA-2 within broader biochemical pathways governing organogenesis and other developmental processes dependent on actomyosin dynamics in C. elegans.

developmental biology↗

Pregnancy and Early-Life Gut Virome in the Lifelines NEXT cohort:Origin, Persistence, Influencing Factors and Health Implications

The human gut virome is a key modulator of gut microbial ecology and function, yet its role in early gut ecosystem development remains poorly understood. Here, we profiled the DNA virome from 4,523 fecal and 91 breastmilk metagenomes from 714 mother-infant pairs in the Dutch birth cohort Lifelines NEXT. This analysis generated a catalog of 31,205 unique vOTUs, with 31,019 detected in fecal and 248 in breastmilk samples, including 16,540 not previously reported in other databases. We find that the maternal virome is largely stable, in contrast to the infant viromes rapid diversification over time. We also identify delivery and feeding modes as major drivers of infant virome developmental trajectories, with additional influences of maternal parity, infections during pregnancy, socioeconomic factors, gestational age and infant birth weight. Notably, increased viral diversity was associated with the infant developing a food allergy. Strain-level virome profiling confirmed the maternal gut as the primary source of viruses for the infant gut, with increased sharing rates in vaginally delivered infants and with breastmilk as a secondary reservoir. We demonstrate that temperate phages frequently co-transmit with their bacterial hosts and identify multiple protein families associated with anti-defense functions enriched among maternally shared viruses. Finally, we show that DNA adenine N6-methyltransferase hin1523, together with widely active diversity-generating retroelements, promote long-term viral persistence in the infant and maternal gut. Together, these findings establish the origin, dynamics and modulating factors of the infant gut virome, along with the genetic strategies supporting its persistence in the gut ecosystem.

microbiology↗

Circular Smad1-Encoded Polypeptide Regulates Myogenesis

The majority of RNAs transcribed from the genome are non-coding RNAs (ncRNAs) that are involved in regulating the expression of protein-coding genes. However, a growing body of research highlights several novel microproteins encoded by unconventional ncRNAs such as long non-coding RNAs and circular RNAs (circRNAs) as important regulators of disease and development. Although several circRNAs have recently been reported to translate into functional peptides in diverse tissues, their roles in skeletal muscle remain largely unexplored. In this study, polyribosome-associated RNA sequencing and publicly available translatable circRNAs from the riboCIRC database were curated to discover potential protein-coding circRNAs in mouse C2C12 skeletal muscle cells. We validated a few circRNAs with high potential of translating into proteins in mouse C2C12 cells, including circular Smad1 (circSmad1) that encodes a 194 amino acid peptide called circSmad1-194aa. Interestingly, silencing of circSmad1 in C2C12 cells resulted in loss of myotube fusion and maturation. CircSmad1-194aa was found to contain the DNA-binding SMAD1-MH1 domain that localized into the nucleus during myogenesis. Moreover, CircSmad1-194aa associates with the BMP-responsive element (BRE) in the Id1 promoter that is known to inhibit Myod1-driven myoblast differentiation. We propose that circSmad1-194aa promotes myogenesis by masking Id1-BRE from SMAD complex interaction, leading to suppression of ID1 expression and upregulation of MYOD1. Together, our findings identify circSmad1-194aa as a novel regulator of skeletal muscle differentiation and highlight the potential for the discovery of other functional circRNA-derived peptides in muscle pathophysiology. HIGHLIGHTSO_LIRNA-seq discovers hundreds of polysome-associated circRNAs in mouse C2C12 myoblasts C_LIO_LIProtein-coding circRNAs exhibit myogenesis-specific expression C_LIO_LICircSmad1 is abundant, methylated, and translated into a 194aa polypeptide C_LIO_LICircSmad1-encoded polypeptide promotes myogenesis C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=172 SRC="FIGDIR/small/708385v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@2074cforg.highwire.dtl.DTLVardef@d4fd98org.highwire.dtl.DTLVardef@1554735org.highwire.dtl.DTLVardef@1b6124a_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

Prophages of infant-derived Bifidobacterium longum subspecies employ antagonistic and synergistic strategies to persist in their host

Early colonisation by bifidobacteria is crucial for infant health, with Bifidobacterium longum subspecies (BL.) dominating the early gut microbiome. However, the interactions between these bacteria and their viruses remain poorly characterised. Here, we applied genomics-based approaches to examine BL. prophage composition and dynamics in infants, as well as their antagonistic and mutualistic evolutionary strategies. Across 213 metagenome-assembled genomes recovered from 139 infant faecal samples in the Dutch Lifelines NEXT cohort, 286 previously undescribed prophages were identified and analysed. Comparative genomics revealed extensive viral diversity, evidence of historical recombination, and widespread counter-defence, with [~]80% of prophages encoding anti-CRISPR or CRISPR-evasion proteins. Approximately half of prophages encoded metabolism altering genes. Notably, prophages and host CRISPR spacer arrays were highly stable across longitudinal samples, indicating stable phage-host associations during early life. Together, these findings show that BL. prophages employ antagonistic and synergistic strategies to maintain infectivity and long-term persistence in the infant gut.

microbiology↗

Sensorineural regulation of skull healing implicates FGF1 signaling in non-healing bone

Bone injuries demonstrate rapid peripheral nerve ingrowth followed by nerve pruning as healing ensues. However, in non-healing bone injuries, peripheral innervation remains elevated, the implications of which remain unknown. Therefore, we investigated the neuroskeletal microenvironment in subcritical-and critical-sized calvarial defects using quantitative 3D fluorescence imaging. We identified elevated densities of peripheral nerves and Osterix positive (Osx+) osteoprogenitors in critical-sized defects, while osteogenic differentiation markers were severely diminished. Moreover, Osx+ osteoprogenitors in critical-sized defects exhibited enhanced proximity to peripheral nerves, which in turn was associated with increased osteoprogenitor cell proliferation. Using retrograde tracing in conjunction with single cell RNA-sequencing of sensory nerves from the innervating trigeminal ganglia, genes encoding for nerve-secreted proliferative and anti-differentiation factors were identified. Specifically, FGF-1/FGFR-1 signaling was identified as a significant neuroskeletal interaction with critical-sized defects demonstrating higher FGF-1 expression in fluorescence imaging. Presence of FGF-1 in neurons innervating the calvarial was confirmed, and neural conditioned media depleted for FGF1 showed enhanced induction of osteogenesis when placed on parietal bone cells. Collectively, we identify a sensorineural-skeletal signaling interaction elevated in critical-sized defects that can be leveraged as a potential therapeutic target for enhancing bone healing.

bioengineering↗

P. aeruginosa disrupts CDC-42/ARP-2/3 mediated F-actin organization to induce intestinal deformation in C. elegans

Apico-basal polarity is crucial for maintaining cortical actin organization and regulating secretory functions in intestinal epithelium. The opportunistic pathogen, Pseudomonas aeruginosa, exploits the interplay between cell polarity and cytoskeletal machineries to subvert host defenses. Mechanistic insights into such pathogen-induced cytoskeletal alterations have largely been derived from in-vitro epithelial monolayers, which may not capture the influences of multicellular physiology such as tissue mechanics, and innate immunity. Here, we show that the extracellular P. aeruginosa disrupts apical polarity in C. elegans enterocytes, leading to fragmentation of ARP-2/3 clusters and disorganization of apical F-actin. This disruption causes shedding of actin-rich vesicles into lumen and a pronounced apical deformation. Inhibition of CDC-42-ARP-2/3-mediated actin polymerization or PI3K-AKT signalling attenuated enterocyte deformation and extended the lifespan of C. elegans upon P. aeruginosa exposure. Our findings reveal a conserved strategy by which P. aeruginosa exploits cellular polarity machinery to disrupt host actin organization during extracellular infection of the intestinal epithelium.

cell biology↗

Lineage Tracing Reveals a Shared Cellular Origin for Supraclavicular Brown and Inguinal Beige Adipocytes

The metabolic importance of brown adipose tissue (BAT) has been recognized, but the origins of BAT, particularly supraclavicular BAT (scBAT), are less clear. Here, we traced the origin of scBAT to Mef2c-anterior heart field (AHF)-marked cells. Mef2c-AHF-marked cells isolated from scBAT can spontaneously differentiate into brown adipocytes, express mesenchymal stem cell markers, and can be isolated from the stromal-vascular fraction (SVF) of wild-type scBAT as [CD31-CD45-SCA-1+CD29+CD34-CD24-] (CD34-) cells. Mef2c-AHF-marked cells substantially overlap with Prrx1-marked cells in scBAT, which also contribute to beige adipocytes in inguinal white adipose tissue (iWAT) during development. Similarly, CD34- cells isolated from the SVF of iWAT can spontaneously differentiate into beige adipocytes in vitro. Using intersectional tracing, we revealed that common progenitors of Mef2c-AHF- and Prrx1-marked cells in scBAT emerge from the developing heart. Thus, these studies reveal a common origin for scBAT and cardiac tissue and a close lineage relationship between scBAT and beige adipocytes of the iWAT.

developmental biology↗

Bifidobacterium longum subsp. nexus nov., a novel subspecies isolated from infant stool

Bifidobacterium longum is a foundational, genetically diverse member of the infant gut microbiome, yet resolving its subspecies in metagenomic data remains challenging. Here, we performed a deep phylogenetic characterization of the B. longum species utilizing 4,577 fecal metagenomes from the LLNEXT mother-infant cohort alongside a global dataset of 1,220 genomes and metagenome-assembled genomes (MAGs). We identified a novel, geographically widespread lineage: Bifidobacterium longum subsp. nexti. Using a polyphasic taxonomic analysis, including average nucleotide identity and digital DNA-DNA hybridization, confirms subspecies-level divergence. Distinct from other members of the B. longum species, BL. nexti harbors -amylopullulanase and grows on soluble starch and often pullulan, consistent with -glucan utilization. Within the LLNEXT cohort, BL. nexti is enriched in formula-fed infants and shows evidence consistent with vertical transmission. Globally, while BL. nexti is geographically widespread, it usually persists at low relative abundance across diverse populations. By resolving a major fraction of previously unclassified B. longum diversity, this study provides new insights into the specialized lineages and ecological dynamics driving the assembly of the developing infant microbiome.

microbiology↗

Heart tube morphogenesis is regulated by segment-specific gene regulatory networks controlled by MEF2C

The gene regulatory networks (GRNs) that control early heart formation are beginning to be understood, but lineage-specific GRNs remain largely undefined. We investigated networks controlled by the vital transcription factor MEF2C, with a time course of single-nucleus RNA- and ATAC-sequencing in wild-type and Mef2c-null embryos. We identified a "posteriorized" cardiac gene signature and chromatin landscape in the absence of MEF2C. Integrating our multiomics data in a deep learning-based model, we constructed developmental trajectories for each of the outflow tract, ventricular, and inflow tract segments, and alterations of these in Mef2c-null embryos. We computationally identified segment-specific MEF2C-dependent enhancers, with activity in the developing zebrafish heart. Finally, using inferred GRNs we discovered that the Mef2c-null heart malformations are partly driven by increased activity of the nuclear hormone receptor NR2F2. Our results delineate lineage-specific GRNs in the early heart tube and provide a generalizable framework for dissecting transcriptional networks governing developmental processes.

developmental biology↗

Dynamics and determinants of the gut mobilome in early life

As mobile genetic elements (MGE) are critical yet understudied determinants of gut microbiome composition, we characterized the gut virome and plasmidome in 195 samples from 28 mother-infant dyads delivered by caesarean section. Infant mobilome increased in richness over the first 6 postnatal weeks, demonstrating high individual-specificity and temporal stability, establishing a personal persistent mobilome. Formula-fed infants exhibited greater mobilome richness than breastfed infants, with plasmid composition influenced by antibiotic exposure and birth weight. Plasmids constituted a significant reservoir of antibiotic resistance genes (ARG), with around 5% of infant gut plasmid taxonomic units carrying ARG. Notably, ARG profiles did not differ with antibiotic exposure at birth. We found that mother-infant sharing of viral and plasmid strains primarily occurred after 6 months of age. Overall, our integrative analysis offers novel insights into the dynamics, modulation, origin, and clinical implications of MGE in the developing gut microbiome.

genomics↗

Single-nucleus multiomics reveals the disrupted regulatory programs in three brain regions of sporadic early-onset Alzheimer's disease

Sporadic early-onset Alzheimers disease (sEOAD) represents a significant but less-studied subtype of Alzheimers disease (AD). Here, we generated a single-nucleus multiome atlas derived from the postmortem prefrontal cortex, entorhinal cortex, and hippocampus of nine individuals with or without sEOAD. Comprehensive analyses were conducted to delineate cell type-specific transcriptomic changes and linked candidate cis-regulatory elements (cCREs) across brain regions. We prioritized seven conservative transcription factors in glial cells in multiple brain regions, including RFX4 in astrocytes and IKZF1 in microglia, which are implicated in regulating sEOAD-associated genes. Moreover, we identified the top 25 altered intercellular signaling between glial cells and neurons, highlighting their regulatory potential on gene expression in receiver cells. We reported 38 cCREs linked to sEOAD-associated genes overlapped with late-onset AD risk loci, and sEOAD cCREs enriched in neuropsychiatric disorder risk loci. This atlas helps dissect transcriptional and chromatin dynamics in sEOAD, providing a key resource for AD research.

neuroscience↗

Mother-Infant Gut Viruses and their Bacterial Hosts: Transmission Patterns and Dynamics during Pregnancy and Early Life

Early development of the gut ecosystem is crucial for lifelong health. While infant gut bacterial communities have been studied extensively, the infant gut virome remains under-explored. We longitudinally assessed the composition of gut viruses and their bacterial hosts in 322 total metagenomes and 205 metaviromes from 30 mothers during and after pregnancy and from their 32 infants during their first year of life. While the maternal gut virome composition remained stable during late pregnancy and after birth, the infant gut virome was dynamic in the first year of life and contained a higher abundance of active temperate phages compared to the maternal gut viromes. The infant gut virome composition was also influenced by infant feeding mode and place of delivery. Lastly, we provide evidence of viral-bacterial strains co-transmission from mothers to infants, demonstrating that infants acquire some of their virome from their mothers gut. Highlights- Longitudinal characterisation of the gut microbiome and virome in 30 mothers during pregnancy, at birth and 3 months after birth and in 32 infants from birth across the first year of life. - The maternal gut bacteriome changes from the first to the second trimester and then remains stable through birth and the first 3 months after birth. - The maternal gut virome remains stable during late pregnancy, birth and the first 3 months after birth. - The infant gut virome is highly dynamic during the first year of life and is shaped by infant feeding mode and place of delivery. - The infant gut harbours more temperate bacteriophages than the maternal gut, but their relative abundance decreases with increasing infant age. - Gut viral strains and their bacterial host strains are co-transmitted from mothers to their infants. - Gut viral strains are transferred from mother to infant around birth directly or via transfer of their bacterial hosts followed by the induction of prophages.

microbiology↗

Mechanistic insights into the role of Ca2+-stimulated AMPK in the secretion of cellulases during carbon stress

The response of filamentous fungi towards recalcitrant carbohydrates is majorly governed by transcriptional activators of cellulase genes; however, little is known about the downstream events beyond transcription. We show here in Penicillium funiculosum that increasing the expression of a transcriptional activator CLR-2 in the catabolically derepressed strain, {Delta}Mig1, didnt exhibit a synergistic effect on cellulase production unless Ca2+ was simultaneously increased. The RNA-seq screen for Ca2+-activated kinases identified SNF1-AMPK and SSP1-AMPKK as being specific to cellulose induction. Deletion of snf1 led to negligible secretion of cellulase upon induction. Quantitative whole-cell proteomics followed by chemical-genetic experiments with snf1-deleted strain showed that Ca2+-signaling channelizes carbon, nitrogen and energy sources towards cellulase production. Further, Ca2+-signaling phosphorylates SNF1-AMPK via SSP1, which in turn downregulates the phospho-HOG1 levels, leading to stimulus for cellulase secretion during carbon stress. The findings reported here are significant for understanding fungal pathology and developing second-generation biorefineries.

cell biology↗

A Mesp1-dependent developmental breakpoint in transcriptional and epigenomic specification of early cardiac precursors

Transcriptional networks governing cardiac precursor cell (CPC) specification are incompletely understood due in part to limitations in distinguishing CPCs from non-cardiac mesoderm in early gastrulation. We leveraged detection of early cardiac lineage transgenes within a granular single cell transcriptomic time course of mouse embryos to identify emerging CPCs and describe their transcriptional profiles. Mesp1, a transiently-expressed mesodermal transcription factor (TF), is canonically described as an early regulator of cardiac specification. However, we observed perdurance of CPC transgene-expressing cells in Mesp1 mutants, albeit mis-localized, prompting us to investigate the scope of Mesp1s role in CPC emergence and differentiation. Mesp1 mutant CPCs failed to robustly activate markers of cardiomyocyte maturity and critical cardiac TFs, yet they exhibited transcriptional profiles resembling cardiac mesoderm progressing towards cardiomyocyte fates. Single cell chromatin accessibility analysis defined a Mesp1-dependent developmental breakpoint in cardiac lineage progression at a shift from mesendoderm transcriptional networks to those necessary for cardiac patterning and morphogenesis. These results reveal Mesp1-independent aspects of early CPC specification and underscore a Mesp1-dependent regulatory landscape required for progression through cardiogenesis.

developmental biology↗