Biology subjects

Arora, R.

Publications and source records attributed to Arora, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Inferring somatic copy number aberrations from spatial transcriptomics data to study early cancer development

Understanding the spatial organisation of cells undergoing early transformation and their interactions with the local microenvironment is critical to studying the earliest stages of cancer development. Somatic copy number aberrations (SCNAs) are among the earliest genomic alterations observed in many cancers, but their spatial context remains difficult to study using conventional sequencing approaches. We developed a computational framework to infer SCNAs directly from Xenium spatial transcriptomics data, enabling the identification and spatial mapping of cell populations sharing common SCNA profiles. Applying this approach to ovarian, cervical and breast cancer datasets identified spatially coherent SCNA-defined populations that recapitulated known tumour-associated copy number aberrations and pathological states. In high-grade serous ovarian cancer, we identified an intermediate epithelial population within the fallopian tube exhibiting features of early transformation accompanied by immune remodelling. Together, our pipeline establishes a scalable framework for reconstructing the spatial architecture of SCNA-defined clones, providing new opportunities to identify and characterise candidate early transforming cell populations in situ.

cancer biology↗

bioRxiv2026

Dynamic Changes in Endometrial Folding and Secretory Activity Across the Menstrual Cycle

Embryo implantation remains a major limitation of assisted reproductive technology, with failure occurring in approximately 30% of euploid embryo transfers. Implantation requires a synchronized dialogue between the blastocyst and receptive endometrium during the window of implantation (WOI), yet minimally invasive approaches to characterize the structural and molecular features of receptivity remain limited. We analyzed paired sonohysterogram images and uterine lavage samples collected during the proliferative and mid-secretory phases from subjects with regular ovulatory cycles and proven fertility. Endometrial folds were quantified, and lavage samples were analyzed by Luminex multiplex immunoassay. Folds were present in both phases but were significantly more abundant during the mid-secretory WOI, independent of imaging view and endometrial thickness. Folding correlated strongly with circulating estradiol level during the proliferative phase but not the mid-secretory phase, and folding patterns between phases were not correlated, suggesting distinct regulatory mechanisms. Consistent with these structural patterns, uterine lavage demonstrated phase-specific differences in expression of factors associated with endometrial receptivity and implantation, with glandular epithelium, and myeloid-lineage cells emerging as major contributors. Together, these findings identify coordinated structural and secretory processes during the WOI and support further evaluation of endometrial folding and uterine lavage as complementary, minimally invasive markers of endometrial receptivity.

developmental biology↗

bioRxiv2026

PIAS1 loss and INHBA gain define a TGFβ-driven EMT state in OSCC progression

Oral squamous cell carcinoma (OSCC), a highly aggressive subtype of head and neck cancer, remains a major clinical challenge with limited therapeutic options and poor survival outcomes. The Protein Inhibitor of Activated STAT1 (PIAS1), a SUMO E3 ligase involved in transcriptional regulation, DNA repair, and epithelial-mesenchymal transition (EMT), exhibits cancer type-specific roles, but its function in OSCC has not been well characterized. Here, we investigated the molecular and functional role of PIAS1 in OSCC progression and prognosis. All patient cohorts analysed here comprise HPV-negative disease. Analysis across multiple cohorts revealed that PIAS1 mRNA expression is significantly lower in tumor tissues than in normal oral cavity squamous epithelium, including in a cohort of 60 patient-matched tumor and normal pairs. Within the tumor compartment, protein abundance of PIAS1 correlated positively with patient survival. Functional assays using OSCC cell lines demonstrated that PIAS1 acts in a SUMO E3-dependent manner to suppress TGF{beta}-induced migration and invasion. Transcriptomic profiling of PIAS1-depleted cells revealed alterations in expression of genes with relevance in TGF{beta} signaling and pro-invasive cellular responses. Further analyses showed that 46 of these differentially altered hits intersected with The Cancer Genome Atlas (TCGA)-OSCC datasets, where four of these genes, including INHBA, associated with cell stemness-pathway. Spatial analysis of the mRNA abundance of INHBA within OSCC-derived surgical specimens showed increased abundance at the invasive front, and positively associated with aggressive tumor phenotypes, poor patients' outcomes, and resistance to immunotherapy. Single-cell RNA-seq analyses of INHBA revealed increased levels within tumor cells and cancer-associated fibroblasts (CAFs), suggesting potential tumor-intrinsic and extrinsic (tumor microenvironment) sources and hence actions. Collectively, our findings establish PIAS1 as a tumor suppressor in OSCC that restrains TGF{beta}-driven aggressive behaviour. Furthermore, we identify INHBA as a potential therapeutic target, among other genes characterized by spatially restricted, invasive tumor phenotypes.

cancer biology↗

bioRxiv2026

Time-Resolved Single-Cell Atlas Reveals Early Endothelial Activation and Stage-Dependent Immune-Stromal Communication in HFpEF

BackgroundHeart failure with preserved ejection fraction (HFpEF) is a heterogeneous syndrome associated with metabolic stress, hypertension, systemic inflammation, and microvascular dysfunction. Early cell-type-specific events and intercellular communication programs that accompany disease onset and progression remain poorly defined. MethodsWe performed a longitudinal study of HFpEF progression in high-fat diet (HFD)+L-NAME mice at control/baseline (0 weeks, 0w/Ctrl), early (1w), intermediate (4w), and established (8w) stages. Metabolic, hemodynamic, exercise, echocardiographic, and single-cardiomyocyte function were assessed. Cardiac non-cardiomyocytes (non-CMs) were profiled by single-cell RNA sequencing (scRNA-seq), with bulk RNA-seq for tissue-level comparison. Endothelial remodeling was assessed in an L-NAME-independent HFD plus mild transverse aortic constriction model (HFD+mTAC) and a published human HFpEF single-nucleus RNA-seq cohort. An endothelial-macrophage adhesion assay tested whether HFpEF-mimic stress promotes endothelial activation and macrophage adhesion. ResultsIn the HFD+L-NAME model, metabolic dysfunction, hypertension, reduced exercise tolerance, abnormal diastolic filling with preserved ejection fraction, and altered cardiomyocyte calcium handling were detected by 1w and persisted through 8w. Bulk RNA-seq showed progressive remodeling, with limited change between 8w and 12w, guiding scRNA-seq timepoint selection. scRNA-seq of 94,848 cardiac non-CMs identified nine major populations with stage-dependent remodeling. Endothelial cells (ECs) were recovered in high proportion and showed an early, pronounced transcriptional response, with inflammatory, adhesion, interferon-response, migratory, and vascular-remodeling programs emerging by 1w. Related EC activation signatures were observed in HFD+mTAC and human HFpEF data. Functionally, HFpEF-mimic stress increased adhesion and chemokine expression in human ECs and enhanced macrophage adhesion. Fibroblast matrix remodeling occurred at later stages, while macrophages progressively shifted toward inflammatory states. CellChat suggested stage-dependent communication remodeling from early endothelial-immune interactions toward later macrophage-fibroblast crosstalk. ConclusionTime-resolved scRNA-seq reveals coordinated, stage-dependent remodeling of the cardiac microvascular and interstitial microenvironment during HFpEF progression. Early endothelial activation emerges before later fibroblast matrix remodeling and inflammatory macrophage remodeling, identifying candidate cell states and signaling pathways for future mechanistic investigation. Clinical PerspectiveO_ST_ABSWhat Is New?C_ST_ABSO_LIThis study provides a time-resolved single-cell atlas of the cardiac non-cardiomyocyte compartment across baseline, early, intermediate, and established stages of HFpEF progression, rather than a single late-stage snapshot. C_LIO_LIEndothelial cells exhibit early inflammatory, adhesion, interferon-response, and vascular-remodeling programs within the first week of disease, preceding the later predominance of fibroblast matrix remodeling and inflammatory macrophage remodeling. C_LIO_LIThis endothelial activation signature is supported across two mechanistically distinct HFpEF mouse models and aligns with endothelial inflammatory and vascular-remodeling programs in human HFpEF myocardium, supporting its translational relevance. C_LI What Are the Clinical Implications?O_LIEarly endothelial activation may represent a targetable stage of HFpEF pathogenesis that arises before more established structural and fibrotic remodeling. C_LIO_LITherapeutic strategies aimed at limiting endothelial inflammatory activation or endothelial-immune interactions may help attenuate downstream vascular, immune, and stromal remodeling in HFpEF. C_LIO_LIThese findings provide a preclinical foundation for future longitudinal human studies testing whether early endothelial activation can serve as a biomarker, therapeutic target, or disease-staging feature in HFpEF. C_LI

cell biology↗

bioRxiv2026

MTB-LysB1: A Novel Endolysin Against Multidrug-resistant Mycobacterium tuberculosis

The phenotypic plasticity, slow replication, and complex, hydrophobic cell envelope of Mycobacterium tuberculosis contribute to its successful survival as a pathogen and its drug tolerance. Consequently, the global threat of multidrug-resistant Tuberculosis (MDR-TB), coupled with lengthy and highly toxic treatment regimens, necessitates the development of innovative treatment solutions. Mycobacteriophages are natural viruses of mycobacteria that typically encode two endolysins, which cooperatively facilitate host cell lysis at the end of the lytic life cycle: LysA, a peptidoglycan hydrolase, and LysB, a lipolytic enzyme, targeting the mycolylarabinogalactan-peptidoglycan complex. Their precise and efficient lytic activity, along with their low propensity to induce resistance, make them, particularly LysBs, promising candidates for new treatment solutions. In this study, we report MTB-LysB1, a novel LysB enzyme from an F1 sub-cluster mycobacteriophage isolated from our laboratory collection. While studying its structural features by comparing the modelled structure with representative mycobacteriophage LysB homologues, we found that the /{beta}-hydrolase fold and key motifs are conserved. Also, we identified putative membrane-interaction motifs that may play a role in LysB1s cell permeation. Significantly, we found MTB-LysB1 to be active against both drug-susceptible and multidrug-resistant (MDR) M. tuberculosis strains at nanomolar concentrations, comparable to the well-characterised D29 LysB reference enzyme. Beyond its standalone activity, MTB-LysB1 exhibits an additive effect when combined with the TB drugs rifampicin and moxifloxacin, and co-administration reduces the drugs minimum inhibitory concentrations (MICs), which holds clinical significance. By structurally damaging the mycobacterial cell wall, the enzyme appears to act as a permeability enhancer for the chemotherapeutic drugs, thereby improving antibiotic efficacy. Collectively, our findings position the enzyme not only as a novel antimycobacterial agent but also provide a structural framework for its rational engineering as a promising next-generation adjunct to TB drug regimens. HighlightsO_LIA novel F1 sub-cluster phage-derived LysB is discovered and characterised using integrated computational, biochemical and microbiological methods. C_LIO_LIAlphaFold2 modelling, molecular dynamics simulations and comparative structural analyses revealed an /{beta}-hydrolase fold with conserved catalytic and membrane-interaction features. C_LIO_LIThe enzyme exhibited high esterase activity, thermal stability and potent lytic activity against Mycobacterium tuberculosis. C_LIO_LIAn additive effect with TB drugs rifampicin and moxifloxacin highlights MTB-LysB1s potential as an adjunct therapeutic. C_LI

microbiology↗

bioRxiv2026

Aberrations in stromal signaling, muscle contractility and epithelial architecture underlie poor embryo-implantation outcomes after murine ovarian stimulation

Ovarian stimulation is widely used in assisted reproductive technologies, yet its effects on uterine architecture and embryo implantation remain poorly understood. Using a mouse model, we show that ovarian stimulation or superovulation disrupts pre-implantation luminal epithelial folding and induces aberrant smooth muscle structure and contractile function. These structural defects result in embryo trapping within aberrant longitudinal folds, impaired implantation chamber formation, misalignment of the embryo-uterine axis, and subsequent embryo loss. These ovarian stimulation effects were reversible after rest and restoration of normal estrus cycling. Transcriptomic analysis suggests widespread disruption in the stroma and immune compartments of the stimulated uteri. Pathway analysis revealed significant disruption of stromal extracellular matrix and enhanced probability of stroma-immune communication via collagen signaling. Platelet derived growth factor receptor A (PDGFRA) expression was elevated in both the stroma and smooth muscle of the stimulated uteri. Short-term pharmacological inhibition of PDGFRA in the stimulated uteri prior to implantation fully restored epithelial fold transition and implantation chamber formation and partially restored smooth muscle architecture and contractility. Importantly, PDGFRA protein was also elevated in endometrial biopsies from women undergoing ovarian stimulation when compared to natural cycle biopsies. Together, this study establishes muscle contractions and stromal and smooth muscle PDGFRA signaling as novel non-cell autonomous regulators of uterine epithelial architecture critical for embryo implantation.

Developmental Biology↗

bioRxiv2025

Murine implantation chamber formation precedes natural and artificial decidualization

During pregnancy uterine stromal cells undergo a mesenchymal to epithelial cell transition termed decidualization. In humans initiation of decidualization occurs in the absence of an embryo resulting in a need to identify embryo-independent molecular cues that can initiate decidualization. Although, similar to humans, decidualization in the mouse can be induced in the absence of an embryo, whether an implantation event is prerequisite for such decidualization is not known. In this study using different models of estrogen-dependent implantation, including natural (embryo) and artificial (sesame oil, agarose only beads, and Concanavalin A coated agarose beads) we determined that implantation chamber formation precedes decidualization. We show that focal stimuli, including the embryo, Concanavalin A coated bead, and oil droplets, induce V-shaped implantation chambers that lead to sub-epithelial PTGS2 expression and decidualization. Unfertilized eggs and uncoated agarose blue beads fail to form an implantation chamber and do not initiate decidualization. Further, we show that lectins that share sugar binding properties with Concanavalin A can also induce a V-shaped implantation chamber. Finally, using second harmonic generation we show that during decidualization collagen fibers spread radially away from the implantation chamber irrespective of the focal signal used for inducing the chamber. Thus, in the mouse artificial decidualization also initiates at the site of implantation chamber formation. These findings are critical when separating physical stimulus-dependent, embryo-dependent and embryo-independent mechanisms of decidualization that underlie a successful pregnancy.

developmental biology↗

bioRxiv2025

Pre-implantation non-steroidal anti-inflammatory drug treatment disrupts mouse embryo spacing and post-implantation chamber morphogenesis

Non-steroidal anti-inflammatory drugs (NSAIDs), which inhibit the prostaglandin synthase (PTGS) enzymes PTGS1 and PTGS2, may present a risk when consumed during early pregnancy. The impact of PTGS enzyme inhibition by NSAIDS on the three-dimensional organization and function of uterine compartments in context of implantation success is not well known. Here we show that pre-implantation treatment of mouse pregnancy with indomethacin, an NSAID that inhibits both PTGS1 and PTGS2, results in embryo crowding, delayed embryo implantation, defective implantation chamber formation that eventually results in significant pregnancy loss. These effects are dose dependent as lower doses of indomethacin do not show these effects on pregnancy. When embryo spacing defects were observed, a significant proportion of embryos that showed delayed growth or resorption were located in distinct decidual sites, suggesting that additional mechanisms beyond spatial distribution are at play. These findings highlight the potential risks associated with NSAID use during early pregnancy and underscore the need for further research into the underlying molecular mechanisms and the development of safer pain management strategies during pregnancy.

physiology↗

bioRxiv2025

Magnetically Controlled Microrobots for In Vivo Non-Invasive Embryo Transfer

Infertility affects millions worldwide and is often linked to factors such as poor sperm quality and female reproductive organ disorders. Despite significant advancements in in vitro fertilization (IVF) and intracytoplasmic sperm injection (ICSI), implantation rates remain low, ranging from 17 to 21% after three days of incubation, mainly due to stress, lifestyle factors, and uterine conditions. Extended embryo culture techniques have shown promise in improving pregnancy rates. However, the availability of high-quality blastocysts remains a major challenge. Intrafallopian transfer techniques, such as gamete/zygote intrafallopian transfer (GIFT/ZIFT), were introduced to improve fertilization and early embryo development, particularly for patients with repeated embryo implantation failure (10-30% of assisted reproduction technology (ART) cases, particularly in women >35). However, these methods have declined due to advancements in IVF and the variability in laparoscopy procedures used for GIFT/ZIFT. To address these challenges, we propose a non-invasive microrobotic embryo transfer ({micro}ET) technique using remotely controlled microcarriers comparable in size to embryos. We demonstrate the capabilities of magnetically actuated spiral microrobots, fabricated using laser direct writing for capturing, transporting, and releasing embryos into murine uteri. Additionally, we characterize their motion performance and implement image-guided closed-loop control and dual ultrasound (US)/photoacoustic (PA) tracking for deep-tissue interventions. Recognizing the importance of clinical translation, we present preliminary studies on gelatin-based microrobots, a biodegradable alternative, and explore endometrial remodeling after the in vivo transfer of microrobots carrying embryo-like structures. Our findings show that these microrobots can effectively transport embryos, support their development, and enable minimally invasive delivery, providing a more natural, targeted, and non-invasive strategy for in vivo assisted reproduction. One-Sentence SummaryWe propose a non-invasive {micro}ET technique using magnetically actuated microcarriers to improve embryo cargo-delivery in assisted reproduction, addressing challenges in infertility treatments by enabling precise, image-guided embryo delivery with minimal invasiveness.

bioengineering↗

bioRxiv2025

HRDPath: An Explainable Multi-Model Deep Learning Architecture for Predicting Homologous Recombination Deficiency from Histopathology Images

Homologous recombination deficiency (HRD) is a critical biomarker for guiding treatment decisions in high-grade serous tubo-ovarian carcinoma (HGSOC), a cancer with few reliable biomarkers. However, existing genomic-based tests for HRD are variable, expensive, and time-consuming. To this end, we developed HRDPath, a novel patient-level deep learning architecture that combines the strengths of two complementary models with a multi-task design, to predict genomically derived HRD status from whole slide images in HGSOC. HRDPath was comprehensively validated across three datasets and benchmarked against leading deep learning models. It achieved an AUC of 0.846, surpassing previously reported H&E-based HRD prediction results for HGSOC images by 0.09, and for the first time, reporting a specificity of 0.938, where accuracy significantly increased when multiple slides per patient were used. Our proposed patient-level approach and interpretability pipeline enhance model trustworthiness and reveal important clinical and biological insights into HRD-positive cancers, highlighting the associated morphological and pathological changes at the cellular and tissue levels. HRDPath is a potentially accessible and scalable digital biomarker that could improve ovarian cancer diagnosis and therapy selection.

bioinformatics↗

bioRxiv2025

RNAGym: Large-scale Benchmarks for RNA Fitness and Structure Prediction

Understanding RNA structure and predicting the functional consequences of mutations are fundamental challenges in computational biology with broad implications for therapeutic development and synthetic biology. Current evaluation of machine learning-based RNA models suffers from disparate experimental datasets and inconsistent performance assessments across different RNA families. To address these challenges, we introduce RNAGym, a large-scale benchmarking framework specifically designed for three core tasks-RNA fitness, secondary structure, and tertiary structure prediction. The framework integrates extensive datasets, including 70 standardized deep mutational scanning assays covering over a million mutations across diverse RNA types; 901k chemical-mapping reactivity profiles for secondary structure; and 215 diverse tertiary structures curated from the PDB. RNAGym is designed to facilitate a systematic comparison of RNA models, offering an essential resource to enhance the understanding and development of these models.

synthetic biology↗

bioRxiv2025

Single cell mapping of the human endometrium and first trimester decidua identifies distinct epithelial and stromal cell contributions to fertility

The human endometrium undergoes dynamic changes across the menstrual cycle to establish a receptive state for embryo implantation. Using bulk and single-cell RNA sequencing, we characterized gene expression dynamics in the cycling endometrium and the decidua from early pregnancy. We are the first to demonstrate that during the mid-secretory phase--the period encompassing the window of implantation--secretory glandular epithelial cells undergo notable transcriptional changes in cell-cell communication. Through comprehensive analyses, we identified the Glandular Epithelium Receptivity Module (GERM) signature, comprising 556 genes associated with endometrial receptivity. This GERM signature was consistently perturbed across multiple datasets of endometrial samples from women with impaired fertility, validating its relevance as a marker of receptivity. In addition to epithelial changes, we observed shifts in stromal cell populations, notably involving decidual and senescent subsets, which also play key roles in modulating implantation. Together, these findings provide a high-resolution transcriptomic atlas of the receptive and early pregnant endometrium and shed light on key molecular pathways underlying successful implantation.

molecular biology↗

bioRxiv2025

Excessive Postnatal Smooth Muscle Differentiation in a Lung Specific Model of TBX4-related Pulmonary Hypertension

Heterozygous TBX4 variants are the second most common genetic cause of pediatric pulmonary hypertension (PH), yet the mechanisms underlying the pathophysiology of TBX4-related lung disease remain poorly understood. We developed a lung mesenchyme-specific Tbx4 loss of function (Tbx4cKO) mouse model that bypasses embryonic lethality to investigate TBX4-related lung disease. Echocardiography of adult Tbx4cKO mice demonstrated significant hemodynamic changes consistent with PH. Three-dimensional whole-mount analysis of embryonic day 18.5 lungs revealed reduced lobe volumes and decreased distance between pleural edges and muscularized vessels. In adult Tbx4cKO lungs, high-resolution spatial quantitation identified extensive vascular remodeling characterized by significant medial thickening, distal muscularization of small diameter arteries, and extension of muscularized vessels into normally non-muscularized subpleural zones. Contrary to previous reports suggesting vascular simplification with Tbx4 loss, our comprehensive three-dimensional approach demonstrated an elaborated arterial tree with pathologic muscularization. Additional heterozygous loss of Tbx5 (Tbx4cKO;Tbx5het) exacerbated vascular phenotypes without worsening hemodynamic parameters. We also documented dysregulated airway smooth muscle patterning and prominent subpleural smooth muscle bands that share molecular features with myofibroblasts and airway smooth muscle cells, echoing pathologic findings in human TBX4 syndrome lung tissue. Collectively, our findings identify TBX4 as a critical suppressor of smooth muscle differentiation across multiple pulmonary compartments. This model recapitulates key features of human TBX4 syndrome and reveals mild developmental underpinnings with subsequent progressive postnatal smooth muscle dysregulation, highlighting a postnatal window during which therapeutic regulation of mesenchymal differentiation may be beneficial.

genetics↗

bioRxiv2025

Turning blood to brain cells: a plasma mediated reprograming model

The lack of effective stem cell protocols for generating personalized neurovascular niches poses a critical challenge in precision medicine. While iPSC-based methods are explored, their clinical use is hindered by high costs, long timelines, and cancer risks. Recent advancements in plasma-driven differentiation, using circulating monocytes, offer a promising solution as they can be reprogrammed into neuron-like, endothelial-like, and hematopoietic cells without genetic manipulation, by inducing growth factors mediated transdifferentiation. Vasculature is integral to neurodevelopment, with early blood supply transitioning from the perineural to intrinsic vascular plexus, driven by neuro-hematovascular signaling. The choroid plexus selectively transports proteins and growth factors from blood to CSF, supporting neural proliferation and differentiation. Building on these insights, we leveraged the innate reprograming potential of blood-derived cells to generate neuro-hematovascular niches using a novel PITTRep methodology, devoid of transgene and growth factor mediated transdifferentiation opening new avenues for regenerative and investigative neurovascular studies.

cell biology↗

bioRxiv2024

Human skin rejuvenation via mRNA

Aging is characterized by a gradual decline in function, partly due to accumulated molecular damage. Human skin undergoes both chronological aging and environmental degradation, particularly UV-induced photoaging. Detrimental structural and physiological changes caused by aging include epidermal thinning due to stem cell depletion and dermal atrophy associated with decreased collagen production. Here, we present a comprehensive single-cell atlas of skin aging, analyzing samples from young, middle-aged, and elderly individuals, including both sun-exposed and sun-protected areas. This atlas reveals age-related changes in cellular composition and function across various skin cell types, including epidermal stem cells, fibroblasts, hair follicles, and endothelial cells. Using our atlas, we have uncovered basal stem cells as a highly variable population across aging, more so than other skin cell populations, such as fibroblasts. In basal stem cells, we identified ATF3 as a novel regulator of skin aging. ATF3 is a transcriptional factor for genes involved in the aging process, with its expression reduced by 20% during aging. Based on this discovery, we developed an innovative mRNA-based treatment to mitigate the effects of skin aging. After treatment with ATF3 mRNA, cell senescence decreased 25%, and we observed an over 20% increase in proliferation in treated basal stem cells. Importantly, we also found communication between keratinocytes and fibroblasts as a critical component of therapeutic interventions, with ATF3 mRNA rescue of basal cells significantly enhancing fibroblast collagen production by approximately 200%. Furthermore, we validated the efficacy of ATF3 mRNA treatment in ex vivo human skin and in vivo mouse models. In ex vivo human skin, microneedle-mediated delivery of ATF3 mRNA induced robust rejuvenation, expanding the basal stem-cell population and enhancing dermal ECM reconstruction. In a wound healing mouse model, ATF3 mRNA reduced scarring, demonstrating strong regenerative potential for reversing age-related skin decline. We conclude that ATF3 mRNA treatment effectively reverses the effects of skin aging by modulating specific cellular mechanisms, offering a novel, targeted approach to human skin rejuvenation.

synthetic biology↗

bioRxiv2024

Uterine stromal but not epithelial PTGS2 is critical for murine pregnancy success

Use of non-steroidal anti-inflammatory drugs that target prostaglandin synthase (PTGS) enzymes have been implicated in miscarriage. Further, PTGS2-derived prostaglandins are reduced in the endometrium of patients with a history of implantation failure. However, in the mouse model of pregnancy, peri-implantation PTGS2 function is controversial. Some studies suggest that Ptgs2-/- mice display deficits in ovulation, fertilization, and implantation, while other studies suggest a role for PTGS2 only in ovulation but not implantation. Further, the uterine cell type responsible for PTGS2 function and role of PTGS2 in regulating implantation chamber formation is not known. To address this we generated tissue-specific deletion models of Ptgs2. We observed that PTGS2 ablation from the epithelium alone in Ltfcre/+; Ptgs2f/f mice and in both the epithelium and endothelium of the Pax2cre/+; Ptgs2f/f mice does not affect embryo implantation. Further, deletion of PTGS2 in the ovary, oviduct, and the uterus using Pgrcre/+; Ptgs2f/f does not disrupt pre-implantation events but instead interferes with post-implantation chamber formation, vascular remodeling and decidualization. While all embryos initiate chamber formation, more than half of the embryos fail to transition from blastocyst to epiblast stage, resulting in embryo death and resorbing decidual sites at mid-gestation. Thus, our results suggest no role for uterine epithelial PTGS2 in early pregnancy but instead highlight a role for uterine stromal PTGS2 in modulating post-implantation embryo and implantation chamber growth. Overall, our study provides clarity on the compartment-specific role of PTGS2 and provides a valuable model for further investigating the role of stromal PTGS2 in post-implantation embryo development.

developmental biology↗

bioRxiv2024

Building neurovascular tissue from autologous blood for modeling brain-activity

There are no faithful individualized stem cell-based bioengineered neuro-vascularized models that can recapitulate the physiological hemodynamic phenomenon of neuro-vascular coupling (NVC)-the principal behind BOLD (blood oxygen level-dependent) signal in functional neuroimaging, thereby dissuading the research in exploring the brain activity-based investigative studies in neurological/neurosensory diseases. This encouraged us to establish a preclinical optoacoustic (Hb/dHb hemoglobin/deoxyhemoglobin) imaging-competent in vitro neuro-vascularized model by employing a novel cellular reprograming PITTRep (Plasma Induced Transcriptomics/ epi-Transcriptomics Reprograming) approach. The current reprograming approach is based on coaxing autologous blood components to ecto-mesodermal lineage intermediates that can subsequently self-pattern into neurovascular tissue by harnessing the hemorheological properties of RBCs. The nature of blood flow is non-Newtonian and is a function of RBC concentration /haematocrit when they flow through the regions of low shear rates as seen in cerebral microcirculation. The current reprograming approach is a modification of our previous cellular reprograming approach that employed a Newtonian plasma fluid. The autologous blood-derived neurovascular tissue is free from exogenous genetic modification, external growth factors, and induced pluripotent stem cell (iPSC) derivation. This model uniquely integrates functional vasculature and neurogenesis. The current reprogramming approach resulted (in part) serendipitously while testing a potential (yet completely unexplored) hypothesis of haemodynamic reprograming by leveraging the fluid mechanic feature of blood erythrocytes as seen in thrombus formation during cerebral ischemic stroke, that is characterized by physiologically intriguing yet clinically meaningful neurological recovery (neuroplasticity) during an early time window. The current study attempted to induce "a post stroke-like model" of adult neurogenesis with functional synaptogenesis by instructing autologous blood components into thrombus formation through incorporation of erythrocytes in varying concentrations. We tried to instruct adult neurogenesis and neuroplasticity (a relatively non-resilient phenomenon under in vitro conditions) by co-induction of a neuro-vascular niche (NVN). These NVNs are marked by dendrites, synapses, astrogliosis, microglia activation, and growth factor signaling, thus phenocopying molecular and cellular aspects of post-stroke recovery window. The induction of neuro-vascularized niches and functional neuro-vascular coupling (NVC) was characterized by confocal microscopy, scanning electron microscopy, proteomic profiling, and Hb/dHb spectra based optoacoustic imaging. The blood thrombus formation was checked by rotational thromboelastometry (ROTEM), and switching of adult-to-embryonic hemoglobin was confirmed by routine hemoglobin typing. We also attempted to establish patient-specific neuro-vascularized niches from autologous blood of sensorineural hearing loss (SNHL) patients. The individualized neovascularised tissues are intended to be employed for investigating deregulated synaptic plasticity/ long term potentiation underlying poor auditory comprehension outcomes in school going kids suffering from SNHL that greatly compromises their academic performance and socio-behavioural-cognitive development. The attendant multiomics of patient-specific NVNs may have potential implications in developing stem-cell based therapies for neurosensory and cerebrovascular diseases.

neuroscience↗

bioRxiv2024

Loss of PRICKLE1 leads to abnormal endometrial epithelial architecture, decreased embryo implantation, and reduced fertility in mice.

Successful embryo implantation requires coordinated changes in the uterine luminal epithelium, including structural adaptations, apical-basal polarity shifts, intrauterine fluid resorption, and cellular communication. Planar cell polarity (PCP) proteins, essential for cell organization, are understudied in the context of uterine physiology and implantation. PRICKLE proteins, components of PCP, are suggested to play critical roles in epithelial polarization and tissue morphogenesis. However, their function in the polarized unicellular layer of endometrial epithelium, which supports embryo implantation, is unknown. We developed an endometrial epithelial-specific knockout (cKO) of mouse Prickle1 using Lactoferrin-iCre to investigate itss role in uterine physiology. Prickle1 ablation in the endometrial epithelium of mice resulted in decreased embryo implantation by gestational day 4.5 leading to lower fertility. Three-dimensional imaging of the uterus revealed abnormal luminal folding, impaired luminal closure, and altered glandular length in mutant uteri. Additionally, we observed decreased aquaporin-2 expression, disrupted cellular architecture, and altered E-Cadherin expression and localization in the mutant uterine epithelium. Evidence of epithelial-mesenchymal transition (EMT) was found within luminal epithelial cells, further linking PRICKLE1 loss to uterine pathologies. Furthermore, altered polarity of cell division leading to incomplete cytokinesis and increase in binuclear or multinucleated cells suggests a crucial role for PRICKLE1 in the maintenance of epithelial architecture. Our findings highlight PRICKLE1s critical role in the PCP pathway within the uterus, revealing its importance in the molecular and cellular responses essential for successful pregnancy and fertility. Significance StatementConservative cell division is essential to maintain apical-basal polarity and proper epithelial function in the uterus. Wnt/ Planar cell polarity signaling molecules are hypothesized to provide the spatial cues to organize unicellular, 2-dimensional sheet of epithelium in a plane orthogonal to the apical-basal polarity. Conditional ablation of Prickle1, a crucial Wnt/ PCP gene, in mouse uterine epithelium results in aberrant expression of epithelial cadherin, altered plane of cell division, incomplete cytokinesis leading to binucleated/ multinucleated cells, epithelial - mesenchymal transition, and defective implantation. Role of Prickle1 in maintaining symmetric uterine epithelial cell division and tissue architecture is unique among Wnt/PCP genes, including previously described mouse models for Vangl2, Ror2, and Wnt5a. Classification: Biological Sciences (Major) Cell Biology (Minor), Physiology (Minor) Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=86 SRC="FIGDIR/small/605120v2_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@cfd16corg.highwire.dtl.DTLVardef@1be29aborg.highwire.dtl.DTLVardef@1a1b938org.highwire.dtl.DTLVardef@87138c_HPS_FORMAT_FIGEXP M_FIG Conditional ablation of Prickle1, a crucial Wnt/ PCP gene, in mouse uterine epithelium results in altered plane of cell division and incomplete cytokinesis leading to binucleated/multinucleated cells, epithelial - mesenchymal transition, altered gland length, and defective implantation. Some images adapted from BioRender.com (2024). C_FIG

physiology↗