Biology subjects

Dasgupta, S.

Publications and source records attributed to Dasgupta, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Aryl Hydrocarbon Receptor (Ahr) Pathway Drives TBBPA Induced Cartilage Development Defects.

Tetrabromobisphenol A (TBBPA), is one the most widely produced brominated flame retardant, detected in human matrices including cord plasma, raising concern over its impact on embryonic development. Our previous work demonstrated that TBBPA disrupts craniofacial cartilage development in zebrafish; however, inhibition of bone morphogenetic protein (BMP) signaling did not rescue these defects, suggesting the involvement of alternative molecular mechanisms. Transcriptomic profiling revealed significant upregulation of aryl hydrocarbon receptor (Ahr) signaling genes, including cyp1a and cyp1c, as well as reactive oxygen species (ROS) responsive genes, such as nfe and gstp. Consistent with these findings, KEGG pathway enrichment analysis identified significant enrichment of pathways involved in xenobiotic metabolism, cytochrome P450-mediated metabolism, and molecular docking predicted stronger binding of TBBPA to Ahr2 than the Ahr2 agonist TCDD. Then we investigated the role of Ahr signaling and ROS in TBBPA-induced craniofacial cartilage defects using microinjection of Ahr2 translation-blocking morpholino and the antioxidant N-acetylcysteine (NAC), respectively. Immunohistochemistry confirmed concentration-dependent induction of Cyp1a and ROS at environmentally relevant concentrations (0.05;0.005 uM). Ahr2 knockdown using a translation-blocking morpholino rescued TBBPA-induced alterations in Cyp1a expression, ROS levels, DNA damage, the expression of chondrogenesis-related markers (Sox10 and Sox2), and epithelial to mesenchymal transition (EMT) markers (E-cadherin, N-cadherin, and Snail2). Furthermore, Ahr2 knockdown rescued several TBBPA-induced alterations in craniofacial cartilage parameters. Co-exposure of TBBPA with the antioxidant NAC rescued the ROS and DNA damage and rescued only ceratohyal cartilage length, whereas other cartilage parameters remained disrupted. These findings establish a causal role for the Ahr-Cyp1a axis in TBBPA-induced craniofacial cartilage developmental toxicity and identify ROS as an important downstream contributor, indicating that both ROS-dependent and ROS-independent Ahr mechanisms underlined the observed TBBPA induced craniofacial defects.

pharmacology and toxicology↗

bioRxiv2026

Cerebrovascular Single-Nucleus RNA-Seq Reveals Heat Shock Activation and Vascular Remodeling in Alzheimer's Disease and Primary Tauopathies

Cerebrovascular alterations are widely observed in both Alzheimers Disease (AD) and primary tauopathies. Here, we hypothesized that mechanisms of cerebrovascular alterations are shared between AD and primary tauopathies. We performed single-nucleus RNA sequencing of postmortem human inferior temporal gyrus to characterize transcriptomic changes across cerebrovascular cell types in AD and primary tauopathies (Corticobasal Degeneration, Picks disease, and Progressive Supranuclear Palsy). Differential gene expression analyses revealed disease-specific transcriptional programs across vascular cell populations. However, genes involved in the heat-shock response were consistently upregulated across all diseases, suggesting a conserved cerebrovascular stress response during neurodegeneration. We further identified marked cerebrovascular remodeling in AD relative to primary tauopathies, along with dysregulation of genes mapping to AD risk loci in endothelial cells. Transcriptomic findings were validated using tissue clearing, light-sheet microscopy, and immunofluorescence quantification of vascular markers. These results define a conserved vascular stress program alongside AD-specific remodeling, highlighting the vasculature as a therapeutic target in neurodegeneration.

neuroscience↗

bioRxiv2026

PFAS triggers a SpoT-associated metabolic switch that promotes persister-like phenotype in Salmonella Typhi

Per- and polyfluoroalkyl substances (PFAS) are new pollutants in the environment whose effects on bacterias physiology is not well understood. In this study, we show that exposure to PFAS causes membrane depolarization in Salmonella enterica serovar Typhi. This works as a metabolic uncoupler that breaks down proton motive force without immediately killing the cells. This disturbance results in a significant elevation of intracellular NADH and NAD levels while preserving redox equilibrium, signifying an augmented metabolic flux. At the same time, we see that {beta}-oxidation pathways are turned on, which suggests that the cells are shifting toward breaking down fats to make up for the lack of energy. Even though there are more reducing equivalents, ATP levels go down, which is what happens when respiration is uncoupled. This puts the cells in a state of "pseudo-starvation." This metabolic stress triggers the SpoT-dependent stringent response, leading to the accumulation of (p)ppGpp. Genetic analysis employing {Delta}relA and {Delta}relA{Delta}spoT mutants confirm that SpoT is necessary for this adaptive response. Functionally, PFAS-treated populations show an enhanced proportion of persister-like cells, which connects exposure to environmental pollutant in the environment to antibiotic tolerance. Our findings reveal a previously unidentified mechanism by which PFAS alters bacterial metabolism and stress responses, facilitating persistence through membrane depolarization, metabolic reconfiguration, and stringent response activation. This study underscores the potential influence of environmental pollutants on bacterial survival mechanisms and antibiotic resistance.

microbiology↗

bioRxiv2026

Emergence of a potentially ancestral ATP-synthesizing activity under prebiotic amino acid constraints

How amino acid composition shapes enzymatic function remains a central question in molecular evolution. Early proteins were likely composed of a limited set of amino acids, yet the catalytic properties of proteins under such compositional constraints are still poorly understood. Here we show that restricting amino acid repertoires can replace native enzymatic activity with an alternative phosphoryl-transfer reaction that disproportionates ADP into ATP and AMP. Using a reconstructed ancestral nucleoside diphosphate kinase (NDK) variant composed of a restricted amino acid set, we demonstrate this reaction, which is not observed in extant NDKs but is chemically analogous to that catalyzed by adenylate kinase. Although modest in catalytic rate, X-ray crystallography, molecular dynamics, and mutational analyses reveal a distinct active-site organization in which aspartate and arginine residues cooperatively coordinate Mg2+ and support phosphoryl transfer through a noncanonical mechanism. Lysine can substitute for arginine under these constraints while retaining activity. Together, these findings show that restricting amino acid diversity can remodel active sites and promote alternative phosphoryl-transfer reactions, illustrating how limitations in amino acid availability could influence catalytic functions in early enzyme evolution. Significant StatementThe first enzymes arose on early Earth, where only a limited set of amino acids was likely available. Whether such limitations reduce catalytic efficiency or reshape enzyme function is still unclear. We reconstructed a model of an ancestral enzyme using a simplified amino acid set approximating those available on early Earth and found that restricting amino acid diversity replaced its original catalytic activity with an alternative function that produces ATP from two ADP molecules. Structural and mutational analyses indicate that this shift involves a reorganization of the active site. These results provide experimental evidence that limiting amino acid diversity can reshape catalytic function and may have influenced the emergence of catalytic activities during enzyme evolution.

evolutionary biology↗

bioRxiv2025

Sparse, random sampling is sufficient for central tolerance

Negative selection in the thymus limits autoimmunity by eliminating T cells that react strongly to self. Individual T cells, however, are only exposed to a small fraction of all self peptides during their "training" in the thymus, and it is puzzling how tolerance can be generalized to the remaining "test" self peptides across peripheral tissues in the body. Using a machine learning perspective, we show that such generalization is possible because the immune system satisfies two conditions: first that peptide abundance levels in the human thymus and periphery are highly correlated (i.e., training distribution {approx} test distribution), and second that cross-reactivity allows T cells to effectively learn binding information of similar peptides without explicitly interacting with all of them. Together, we show that sparse, random sampling of only 10% of self peptides in the thymus is sufficient to avoid reactivity to 90% of peripheral self, and we support this result with diverse experimental data. We then validate two predictions by our model; the first is that only 200-250 antigen presenting cells need to be seen by a T cell to ensure its robust selection, and the second relates how peptides missing from the thymus can drive auto-immunity of peripheral tissues. Overall, we provide a plausible answer to a long-standing question underlying adaptive immunity, and we highlight how generalization, a fundamental challenge faced by nearly every learning algorithm, is uniquely tackled by the immune system.

immunology↗

bioRxiv2025

Deciphering Membrane Pore Formation Mechanisms of Plasmodium falciparum Perforin-Like Protein 1 (PfPLP1)

Membrane Attack Complex/Perforin (MACPF) domain proteins are {beta}-pore forming toxins ({beta}-PFTs) involved in the pathogenesis of various organisms. Among them, Perforin-like proteins (PLPs), produced by Plasmodium species, play essential roles in parasite invasion and egress. Due to increasing drug resistance in Plasmodium, PLPs represent promising but underexplored therapeutic targets, largely due to the lack of structural and mechanistic data. This study investigates the binding and pore formation mechanism of the Plasmodium falciparum PLP1 (PfPLP1), which is expressed during the human life cycle of the parasite. We modeled PfPLP1 structure and performed both all-atom and coarse-grained molecular dynamics simulations in soluble and membrane-associated states. PfPLP1 comprises two domains, a canonical MACPF domain and a {beta}-pleated sheet domain-apicomplexan perforin {beta}-domain (APC{beta}). Initial membrane binding is mediated by cationic residues at the base of the APC{beta} domain, which interact with the polar headgroups of the lipids from the host cell membrane. We analyzed the membrane-inserted tetrameric form where water molecules were observed to penetrate between the tetramer and the lipid bilayer, initiating pore opening. During this process, lipids reorganize into a toroidal edge to shield their hydrophobic tails, while water mixes with lipid headgroups in a disordered, heterogeneous fashion. Larger oligomeric assemblies show lateral displacement of lipids and a clear tendency to form pore-like structures. This study provides molecular insights into PfPLP1s membrane binding and pore-forming behavior in both monomeric and oligomeric forms. The outcome of this study would be applicable in understanding pore formation mechanism in other PLPs and similar toxins. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=182 SRC="FIGDIR/small/682298v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@181ad3borg.highwire.dtl.DTLVardef@940471org.highwire.dtl.DTLVardef@1af9c23org.highwire.dtl.DTLVardef@33fd45_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIStructure of Plasmodium falciparum PLP 1 (PfPLP1) as soluble form and membrane-inserted form. C_LIO_LIPfPLP1 initiates pore formation by binding to the host cell membrane with the help of the APC-{beta} domain through cationic residues. C_LIO_LISmaller oligomers of membrane-inserted PfPLP1 form an arc-like structure by reorganizing membrane lipids into a toroidal edge. C_LIO_LIDecamer and higher oligomers of membrane-inserted PfPLP1 form a pore-like structure by lateral displacement of the membrane lipids. C_LI

biochemistry↗

bioRxiv2025

GLIS3 Marks a Neural-like Progenitor Cell State that Drives Metastasis in Pancreatic Ductal Adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) has a high rate of recurrence and metastasis despite intensive therapy. The neural-like progenitor (NRP) transcriptional program is enriched in residual disease after neoadjuvant chemotherapy and radiotherapy; however, the mechanisms for increased NRP expression in the post-treatment setting remain unclear. Here, we find that NRP signatures are strongly enriched in tissue injury and regeneration, and NRP cancer cells co-express transcription factors involved in pancreatic development. We identify both cell autonomous and ligand mediated mechanisms for inducing NRP expression in vitro. We establish and characterize isogenic mouse organoid overexpression models for transcription factors associated with the NRP, classical, and basal-like states. We discovered that Glis3 is a key NRP-associated transcription factor that drives malignant properties including greater clonogenicity, tumor growth, and metastasis compared to isogenic models for the classical and basal-like states. Our work highlights the emergence of clinically relevant developmental regeneration programs in the post-treatment context.

cancer biology↗

bioRxiv2025

Comparative genome analysis of tea rhizosphere dwelling Paenarthrobacter nicotinovorans AB444: Uncovering Physiological Resilience and Ecological Adaptability

Plant growth-promoting rhizobacteria (PGPR) can be considered a promising tool for sustainable agriculture. The recent scenario of growing demand for higher crop yields, with declining soil fertility and impacts of climate change, promotes the global shift towards eco-friendly agricultural practices, emphasising the significance of PGPR as a sustainable solution. In this study, a PGPR Paenarthrobacter sp. AB444 was isolated from the rhizosphere of tea plants at the Longview and Makaibari tea estates in the Darjeeling District of West Bengal. Based on the draft genome sequence along with comprehensive chemotaxonomic analyses, strain AB444 was identified as Paenarthrobacter nicotinovorans. The pangenomic analysis with phylogenetically close strains revealed the gene clusters that are common and unique to the isolate. The plant growth-promoting attributes of AB444 were explored with different assays like phosphate solubilisation, IAA and siderophore production, ACC deaminase, nitrogen fixation, and protease activity. The colonization of the isolate to the plant root and in-planta growth were also assessed. The presence of biosynthetic gene clusters of AB444 related to plant growth was also extensively studied, highlighting the unmapped disposition of Paenarthrobacter nicotinovorans.

microbiology↗

bioRxiv2025

Nuclear Fetuin-A Drives Adipocyte Senescence via HIF-1 α During Obesity

Fetuin-A (FetA), a liver derived glycoprotein, has emerged from genome-wide association studies and epidemiological surveillance as a serum biomarker linked to obesity-driven type 2 diabetes mellitus (T2D), primarily due to its contribution to adipose tissue dysfunction. Here, we uncovered an eccentric role of nuclear FetA in visceral white adipocytes of obese T2D conditions. Hypoxia-inducible factor-1 (HIF-1) facilitates the nuclear translocation of FetA via direct interaction, a process that promotes the emergence of a senescence-associated secretory phenotype (SASP). While nuclear co-localization of FetA and HIF-1 strongly promotes adipocyte senescence, silencing FetA alone is sufficient to prevent senescence, even in conditions of HIF-1 overexpression or lipid-rich hypoxic stress. Although nuclear FetA does not directly bind to DNA, it enhances HIF-1 transcriptional activity, potentiating the activation of senescence markers such as {beta}-galactosidase and p53. Selective knockdown of FetA in obese mice notably reduced adipocyte senescence in visceral white adipose tissue (vWAT) and improved fasting glycemic control. Collectively, our findings reveal a previously unrecognized nuclear function for FetA in orchestrating adipocyte senescence in obesity, establishing nuclear FetA as a potential therapeutic target for obesity related metabolic diseases.

cell biology↗

bioRxiv2024

Embryonic exposures to flame retardant tetrabromobisphenol A (TBBPA) disrupts dorsoventral patterning in zebrafish

Tetrabromobisphenol A (TBBPA), a widely used flame retardant in commercial products such as synthetic textiles, plastics, and electronics poses potential toxicity risks through indoor exposure. This study aims to leverage zebrafish as a model to study TBBPA impacts on zebrafish dorsoventral patterning--a process that lays the foundation of an embryos axial determination and localization of specific tissues and organs. Zebrafish embryos were exposed to varying concentrations of TBBPA (0-10 {micro}M) at either 0.75- or 6-hours post-fertilization (hpf) and phenotyped at 8 or 24 hpf. Following this, whole-mount immunohistochemistry (IHC) was conducted out to quantify various proteins important in the BMP signaling pathway, epithelial-to-mesenchymal transition (EMT) and ectoderm and mesoderm germ layers. Importantly, these assessments were done at environmentally relevant concentrations ranging down to nM and pM levels. Our data showed a significant concentration-dependent increase in ventralization phenotypes, marked by enlarged blood island area, coupled with a disruption of the ventral-to-dorsal gradient of pSMAD protein levels, indicating BMP signaling disruptions. Perturbations in epithelial-to-mesenchymal transition (EMT), as evidenced by changes in E- and N-cadherin expression and Snail2 transcription factor levels, indicated impaired cell migration on TBBPA exposures. We then interrogated if TBBPA impacts germ layers and structures derived from specific germ layers. We observed significant concentration-dependent changes in levels of Sox2 and Sox10- both indicators of neural crest cell formation and differentiation from the ectoderm. We also observed a significant reduction of Tbx16- a marker of paraxial mesodermal cells. Collectively, both these data show TBBPA-induced impact on germ layers. Finally, we examined specific cell types derived from ectoderm and mesoderm and showed TBBPA-induced inhibition of cartilage development (derived from ectodermal neural crest cells) and blood cell development (derived from mesodermal cells). Our findings collectively demonstrate that TBBPA-induced disruptions in early developmental signaling and dorsoventral patterning may contribute to systemic toxicity in zebrafish embryos. Importantly, we see these disruptions at environmentally relevant concentrations, reinforcing the importance of continued interrogation of TBBPA in targeting early embryogenesis.

pharmacology and toxicology↗

bioRxiv2024

Complementation of a human disease phenotype in vitro by intercellular mRNA transfer

There is growing evidence that full-length mRNAs undergo intercellular transfer through long, thin cytoplasmic connections called tunneling nanotubes (TNTs), but whether transferred mRNAs are translated and effect cellular changes post-transfer is unknown. Using multiple lines of evidence, we show that transferred mRNAs undergo translation and can fully complement the phenotype of genetic mutations in vitro. For example, the human peroxisome biogenesis disorder, Zellweger Syndrome, results from mutations in genes like PEX5 and PEX6. We demonstrate that the co-culture of patient-derived PEX6 mutant fibroblasts or PEX5 knock-out cells with wild-type cells leads to de novo peroxisome biogenesis. Complementation occurs by TNT-mediated mRNA transfer and translation in acceptor cells and not by peroxisome transfer. We provide additional examples of genetic complementation via transfer of mRNAs encoding the HSF1 transcription factor or CRE recombinase. Our study provides evidence for the physiological significance of mRNA transfer and suggests a new approach for mRNA therapeutics. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=128 SRC="FIGDIR/small/622258v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@fe4563org.highwire.dtl.DTLVardef@17d6d3forg.highwire.dtl.DTLVardef@18f47f7org.highwire.dtl.DTLVardef@1bdae08_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2024

Examining perfluorohexane sulfonate (PFHxS) impacts on sensorimotor and circadian rhythm development

Perfluorohexane sulfonate (PFHxS) is a ubiquitous perfluoroalkyl substance known for its environmental persistence and potential toxicity. This study investigated PFHxSs impact on zebrafish embryos, focusing on sensorimotor behavior, circadian rhythm disruption, and underlying molecular mechanisms. Under 24 hr dark incubations, PFHxS exposure induced concentration-dependent hyperactivity within larval photomotor response, characterized by the distinctive "O-bend" response, strong light-phase hyperactive movement and seizure-like movements. It appears that PFHxS-treated embryos cannot sense light cues in a normal manner. Similar hyperactivity was seen for acoustic startle response assay, suggesting that the response is not merely visual, but sensorimotor. LC-MS studies confirmed detectable uptake of PFHxS into embryos. We then conducted mRNA-sequencing across multiple time points (48 and 120 hpf) and concentrations (0.00025, 0.0025 and 25 {micro}M). Data at the 25 {micro}M (2-120 hpf) exposure showed disrupted pathways associated with DNA and cell cycle. Interestingly, data at 0.00025 {micro}M - an environmentally relevant concentration- at 48 hpf showed disruption of MAPK and other signaling pathways. Immunohistochemistry of eyes showed reduced retinal stem cell proliferation, consistent with observed DNA replication pathway disruptions. To assess if these impacts were driven by circadian rhythm development, we manipulated light/dark cycles during PFHxS incubation; this manipulation altered behavioral patterns, implicating circadian rhythm modulation as a target of PFHxS. Since circadian rhythm is modulated by the pineal gland, we ablated the gland using metronidazole; this ablation partially rescued hyperactivity, indicating the glands role in driving the phenotype. Collectively, these findings underscore proclivity of PFHxS to cause neurodevelopmental toxicity, necessitating further mechanistic exploration and environmental health assessments.

pharmacology and toxicology↗

bioRxiv2024

Segregation, Finite Time Elastic Singularities and Coarsening in Renewable Active Matter

Material renewability in active living systems, such as in cells and tissues, can drive the large-scale patterning of forces, with distinctive phenotypic consequences. This is especially significant in the cell cytoskeleton, where multiple species of myosin bound to actin, apply differential contractile stresses and undergo differential turnover, giving rise to patterned force channeling. Here we study the dynamical patterning of stresses that emerge in a hydrodynamic description of a renewable active actomyosin elastomer comprising two myosin species. Our analytical framework also holds for an actomyosin elastomer with a single myosin species. We find that a uniform active contractile elastomer spontaneously segregates into spinodal stress patterns, followed by a finite-time collapse into tension carrying singular structures that display self-similar scaling and caustics. Our numerical analysis carried out in 1D, shows that these singular structures move and merge, and gradually result in a slow coarsening dynamics. We discuss the implications of our findings to the emergence of stress fibers and the spatial patterning of actomyosin. Our study suggests, that with state-dependent turnover of crosslinkers and myosin, the in vivo cytoskeleton can navigate through the space of material parameters to achieve a variety of functional phenotypes.

biophysics↗

bioRxiv2024

Faster amylin aggregation on fibrillar collagen hastens diabetic progression through β cell death and loss of function

Amyloid deposition of the neuroendocrine peptide amylin in islet tissues is a hallmark of type 2 diabetes (T2DM), leading to {beta}-cell toxicity through nutrient deprivation, membrane rupture and apoptosis. Though accumulation of toxic amylin aggregates in islet matrices is well documented, the role of the islet extracellular matrix in mediating amylin aggregation and its pathological consequences remains elusive. Here, we address this question by probing amylin interaction with collagen I (Col I)--whose expression in the islet tissue increases during diabetes progression. By combining multiple biophysical techniques, we show that hydrophobic, hydrophilic & cation-{pi} interactions regulate amylin binding to Col I, with fibrillar collagen driving faster amylin aggregation. Amylin-entangled Col I matrices containing high amounts of amylin induce death and loss of function of INS1E {beta}-cells. Together, our results illustrate how amylin incorporation in islet matrices through amylin-Col interactions drives T2DM progression by impacting {beta}-cell viability and insulin secretion.

biophysics↗

bioRxiv2024

Satellite glial contact enhances differentiation and maturation of human induced sensory neurons

Sensory neurons generated from induced pluripotent stem cells (iSNs) are used to model human peripheral neuropathies, however current differentiation protocols produce sensory neurons with an embryonic phenotype. Peripheral glial cells contact sensory neurons early in development and contribute to formation of the canonical pseudounipolar morphology, but these signals are not encompassed in current iSN differentiation protocols. Here, we show that terminal differentiation of iSNs in co-culture with rodent Dorsal Root Ganglion satellite glia (rSG) advances their differentiation and maturation. Co-cultured iSNs develop a pseudounipolar morphology through contact with rSGs. This transition depends on semaphorin-plexin guidance cues and on glial gap junction signaling. In addition to morphological changes, iSNs terminally differentiated in co-culture exhibit enhanced spontaneous action potential firing, more mature gene expression, and increased susceptibility to paclitaxel induced axonal degeneration. Thus, iSNs differentiated in coculture with rSGs provide a better model for investigating human peripheral neuropathies.

neuroscience↗

bioRxiv2024

DNA methylation database for gynecological cancer detection, classification and assay development

Changes in the genome wide DNA methylation landscape are hallmarks of cancer cells and precursor lesions of cancers. To capitalize on utilizing DNA methylation for detection and classification of cancer, we generated a DNA methylation database of gynecological cancers and associated healthy tissues using Methylated DNA sequencing (MeD-seq). We show that target cell enrichment to generate the database is crucial for marker discovery and report a wide range of novel biomarkers for classification and tissue of origin determination of gynecological cancers. We developed a subset of these novel biomarkers, both intragenic and intergenic, into a qMSP assays that detect all gynecological cancers at once or specific gynecological cancer subtypes, as well as cancers that are not part of our database. The database generated in this study not only provides the foundation for cancer detection, classification and biomarker discovery, but also for treatment monitoring of cancers using MeD-seq on liquid biopsies.

cancer biology↗

bioRxiv2024

Assessing mechanisms driving phenol isopropylated phosphate (IPP)- induced larval photomotor response deficits in zebrafish

Phenol isopropylated phosphates (IPP) are an additive organophosphate flame retardant (OPFR) which has been extensively used in furniture, electronics, automobiles, plastics, and childrens products to slow down the spread of fire. The processing and distribution of IPP-containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP-induced developmental toxicity using zebrafish embryos. We first conducted range finding experiments with embryonic zebrafish exposures to 0-200 M IPP from 6 to 120 h post fertilization and found significant morphological impacts like pericardial edema, yolk sac edema and spinal curvature at higher concentrations. For behavioral readouts, we performed larval photomotor response (LPR) assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Following this, relying on secondary analyses of our whole embryo mRNA-seq data, we conducted-1) retinoic acid receptor (RAR) signaling assay and 2) DNA methylation assays. In vitro assay for RA receptors indicate that IPP significantly inhibits RAR, but not RAR{beta} and RAR{gamma}. Whole-mount immunohistochemistry for 5-methylcytosine and global DNA methylation assay showed significant IPP-induced hypermethylation in situ. We conducted IPP co-exposure studies with a methylome modifier 5-azacytidine (Aza-c a methylation inhibitor) or retinoic acid signaling activators to assess if LPR phenotypes were mitigated by co-exposures. Data showed that Aza-c co-exposures partially reversed IPP-induced LPR hypoactivity and DNA hypermethylation, co-exposure with retinoic acid as well as AM580 (an RAR activator) were not able to reverse IPP-induced hypoactivity. Finally, based on RNA-seq data, we hypothesized that IPP affects the development of brain and eyes. Firstly, we performed global DNA methylation in brain and eyes, but did not find any significant effects. Then, we conducted mRNA sequencing on dissected brains and eyes, and found 2 and 135 differentially expressed genes, respectively. Gene ontology revealed that IPP affect phototransduction, voltage gated ion channels, synaptic and neurotransmitter signaling. Collectively, our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response, potentially through methylomic regulation. Finally, we observed that IPP affects gene expression within the developing eye, establishing synaptic transmission, vision and muscle contraction as a potential causative factor for LPR responses.

pharmacology and toxicology↗

bioRxiv2024

A mouse model of TB-associated lung fibrosis reveals persistent inflammatory macrophage populations during treatment

Post-TB lung disease (PTLD) causes a significant burden of global disease. Fibrosis is a central component of many clinical features of PTLD. To date, we have a limited understanding of the mechanisms of TB-associated fibrosis and how these mechanisms are similar to or dissimilar from other fibrotic lung pathologies. We have adapted a mouse model of TB infection to facilitate the mechanistic study of TB-associated lung fibrosis. We find that the morphologies of fibrosis that develop in the mouse model are similar to the morphologies of fibrosis observed in human tissue samples. Using Second Harmonic Generation (SHG) microscopy, we are able to quantify a major component of fibrosis, fibrillar collagen, over time and with treatment. Inflammatory macrophage subpopulations persist during treatment; matrix remodeling enzymes and inflammatory gene signatures remain elevated. Our mouse model suggests that there is a therapeutic window during which adjunctive therapies could change matrix remodeling or inflammatory drivers of tissue pathology to improve functional outcomes after treatment for TB infection.

microbiology↗