Biology subjects

Dhawan, J.

Publications and source records attributed to Dhawan, J..

10 recordsLinked to original sources

bioRxiv2026

Sex-divergent trajectories of hippocampal and cortical NMDA receptor density across the Alzheimer 's disease continuum

While loss of NMDA receptors (NMDARs) is associated with Alzheimers disease (AD) severity, the effect of sex or the relationship between regional NMDAR density and antemortem cognitive status across the AD spectrum has not been examined. We performed quantitative in vitro autoradiography of hippocampus, entorhinal cortex (EC), and parietal cortex using NMDAR and tau radioligands. Relationships between regional NMDAR density and cognitive status assessed by the Mini Mental State Exam (MMSE), and between NMDAR and tau density, were examined by bivariate correlations. In both sexes, the largest AD-related decreases in NMDAR density were observed in the CA1 field. However, there was a significant diagnosis by sex interaction driven by sex-specific changes in the mild cognitive impairment (MCI) stage, with lower NMDAR density in MCI women, but not MCI men relative to same-sex controls. Within diagnosis analyses revealed positive correlations between NMDAR density and MMSE scores and significant negative correlations between EC NMDAR and tau density, which was significant only in AD men. Our data show that changes in hippocampal NMDAR density across the AD continuum are modulated by sex and may contribute to the known sex differences in the clinical trajectory of the disease.

neuroscience↗

bioRxiv2024

Sporophyte Directed Gametogenesis via the Ubiquitin Proteasome System

Plants alternate between diploid sporophyte and haploid gametophyte generations. In mosses which retain features of ancestral land plants, the gametophyte is dominant and has an independent existence. However, in flowering plants the gametophyte has undergone evolutionary reduction to just a few cells enclosed within the sporophyte. The gametophyte is thought to retain genetic control of its development even after reduction. Here we demonstrate that male gametophyte development in Arabidopsis, long considered to be autonomous, is also under genetic control of the sporophyte via a repressive mechanism involving large-scale regulation of protein turnover. We identify an Arabidopsis gene SHUKR as an inhibitor of male gametogenesis. SHUKR is unrelated to proteins of known function and acts sporophytically in meiosis to control gametophyte development by negatively regulating expression of a large set of ubiquitination genes specific to post-meiotic gametogenesis. This control is late-emerging as SHUKR homologs are found only in eudicots. We show that SHUKR is rapidly evolving under positive selection suggesting that variation in control of protein turnover during male gametogenesis has played an important role in evolution within eudicots.

plant biology↗

bioRxiv2021

PTPRU, a quiescence-induced receptor tyrosine phosphatase negatively regulates osteogenic differentiation of human mesenchymal stem cells

Bone marrow mesenchymal stem cells (MSCs) are heterogeneous osteo-progenitors that are mainly responsible for bone regeneration and homeostasis. In vivo, a subpopulation of bone marrow MSCs persists in a quiescent state, providing a source of new cells for repair. Previously, we reported that induction of quiescence in hMSCs in vitro skews their differentiation potential in favour of osteogenesis while suppressing adipogenesis. Here, we uncover a new role for a protein tyrosine phosphatase, receptor type U (PTPRU) in repressing osteogenesis during quiescence. A 75 kD PTPRU protein isoform was found to be specifically induced during quiescence and down-regulated during cell cycle reactivation. Using siRNA-mediated knockdown, we report that in proliferating hMSC, PTPRU preserves self-renewal, while in quiescent hMSC, PTPRU not only maintains reversibility of cell cycle arrest but also suppresses expression of osteogenic lineage genes. Knockdown of PTPRU in proliferating or quiescent hMSC de-represses osteogenic markers, and enhances induced osteogenic differentiation. We also show that PTPRU positively regulates a {beta}-catenin-TCF transcriptional reporter. Taken together, our study suggests a role for a quiescence-induced 75kD PTPRU isoform in modulating bone differentiation in hMSC, potentially involving the Wnt pathway.

cell biology↗

bioRxiv2021

Inducible expression of Oct-3/4 reveals synergy with Klf4 in targeting Cyclin A2 to enhance proliferation during early reprogramming

During reprogramming of somatic cells, heightened proliferation is one of the earliest changes observed. While other early events such as mesenchymal-to-epithelial transition have been well studied, the mechanisms by which the cell cycle switches from a slow cycling state to a faster cycling state are still incompletely understood. To investigate the role of Oct-3/4 in this early feature of reprogramming, we created a 4-Hydroxytamoxifen dependent Oct-3/4 Estrogen Receptor fusion (OctER). We show that OctER can substitute for Oct-3/4 to reprogram mouse embryonic fibroblasts to induced pluripotent stem cells. While over-expression of OctER or Klf4 individually did not affect cell proliferation, in combination, these factors hasten the cell cycle, in a tamoxifen dose-dependent manner, supporting a key role for OctER. Oct-3/4 + Klf4 increased proliferation by enhancing expression of Cyclin A2. We verified occupancy of endogenous Oct-3/4 and Klf4 at bioinformatically identified binding sites in the Cyclin A2 promoter in mouse embryonic stem cells (mESC). Using inducible OctER along with Klf4, we show dose-dependent induction of Cyclin A2 promoter-reporter activity and mRNA levels. Taken together, our results provide further evidence of the interdependence of pluripotency and the rapid cell cycle seen in mESC, and identify CyclinA2 as a key early target.

cell biology↗

bioRxiv2020

An Inexpensive RT-PCR Endpoint Diagnostic Assay for SARS-CoV-2 Using Nested PCR: Direct Assessment of Detection Efficiency of RT-qPCR Tests and Suitability for Surveillance

With a view to extending testing capabilities for the ongoing SARS-CoV-2 pandemic we have developed a test that lowers cost and does not require real time quantitative reverse transcription polymerase chain reaction (RT-qPCR). We developed a reverse transcription nested PCR endpoint assay (RT-nPCR) and showed that RT-nPCR has comparable performance to the standard RT-qPCR test. In the course of comparing the results of both tests, we found that the standard RT-qPCR test can have low detection efficiency (less than 50%) in a real testing scenario which may be only partly explained by low viral representation in many samples. This finding points to the importance of directly monitoring detection efficiency in test environments. We also suggest measures that would improve detection efficiency.

molecular biology↗

bioRxiv2019

The primary cilium dampens proliferative signaling and represses a G2/M transcriptional network in quiescent myoblasts

Reversible cell cycle arrest (quiescence/G0) is characteristic of adult stem cells and is actively controlled at multiple levels. G0 cells extend a primary cilium, which functions as a signaling hub, but how it controls the quiescence program is not clear. Here, we report that primary cilia distinguish different states of cell cycle exit: quiescent myoblasts elaborate a primary cilium in vivo and in vitro, but terminally differentiated myofibers do not. Myoblasts where ciliogenesis is ablated using RNAi against a key ciliary assembly protein (IFT88) can exit the cell cycle but display an altered quiescence program and impaired self-renewal. Specifically, the G0 transcriptome in IFT88 knockdown cells is aberrantly enriched for G2/M regulators, suggesting a focused repression of this network by the cilium. Cilium-ablated cells also exhibit features of activation including enhanced activity of Wnt and mitogen signaling, and elevated protein synthesis via inactivation of the translational repressor 4EBP1. Taken together, our results show that the primary cilium integrates and dampens proliferative signaling, represses translation and G2/M genes, and is integral to the establishment of the quiescence program.\n\nSummary statementThe primary cilium contributes to reversible arrest (quiescence) in skeletal muscle myoblasts, by coordinating and dampening mitogenic signaling focused on a G2/M transcriptional program and protein synthesis.

cell biology↗

bioRxiv2018

Cytoplasmic sequestration of the RhoA effector mDiaphanous1 by Prohibitin2 promotes muscle differentiation

Adhesion and growth factor dependent signalling control muscle gene expression through common effectors, coupling cytoskeletal dynamics to transcriptional activation. Earlier, we showed that mDiaphanous1, an effector of adhesion-dependent RhoA-signalling promotes MyoD expression in myoblasts, linking contractility to lineage determination. Here, we report that paradoxically, mDia1 negatively regulates MyoD function in myotubes. Knockdown of endogenous mDia1 during differentiation enhances MyoD and Myogenin expression, while over-expression of mDia1{Delta}N3, a RhoA-independent mutant, suppresses Myogenin promoter activity and expression. We investigated mechanisms that may counteract mDia1 to promote Myogenin expression and timely differentiation by analysing mDia1-interacting proteins. We report that mDia1 has a stage-specific interactome, including Prohibitin2, MyoD, Akt2, and {beta}-Catenin, of which Prohibitin2 colocalises with mDia1 in cytoplasmic punctae and opposes mDia1 function in myotubes. Co-expression of mDia1-binding domains of Prohibitin2 reverses the anti-myogenic effects of mDia1{Delta}N3. Our results suggest that Prohibitin2 sequesters mDiaphanous1 to dampen its activity and finetune RhoA-mDiaphanous1 signalling to promote differentiation. Overall, we report that mDia1 is multi-functional signaling effector with opposing functions in different cellular stages, but is modulated by a differentiation-dependent interactome.\n\nSummary statementmDia1 has common and stage-specific functions in muscle cells. In myotubes, mDia1 is sequestered by an interacting protein Prohibitin2, which promotes Myogenin expression and mitigates mDia1s inhibitory effects on differentiation.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC=\"FIGDIR/small/283044v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (28K):\norg.highwire.dtl.DTLVardef@1b1578eorg.highwire.dtl.DTLVardef@1eb6b13org.highwire.dtl.DTLVardef@c2c913org.highwire.dtl.DTLVardef@1f1f9c_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2018

RNA polymerase II pausing regulates a quiescence-dependent transcriptional program, priming cells for cell cycle reentry

Adult stem cells persist in mammalian tissues by entering a state of reversible arrest or quiescence associated with low transcription. Using cultured myoblasts and primary muscle stem cells, we show that RNA synthesis is strongly repressed in G0, returning within minutes of activation. We investigate the underlying mechanism and reveal a role for promoter-proximal RNAPol II pausing: by mapping global Pol II occupancy using ChIP-seq, in conjunction with RNA-seq to identify repressed transcriptional networks unique to G0. Strikingly, Pol II pausing is enhanced in G0 on genes encoding regulators of RNA biogenesis (Ncl, Rps24, Ctdp1), and release of pausing is critical for cell cycle re-entry. Finally, we uncover a novel, unexpected repressive role of the super-elongation complex component Aff4 in G0-specific stalling. We propose a model wherein Pol II pausing restrains transcription to maintain G0, preconfigures gene networks required for the G0-G1 transition, and sets the timing of their transcriptional activation.

developmental biology↗

bioRxiv2017

PDGFRα signaling in cardiac stem and stromal cells modulates quiescence, metabolism and self-renewal, and promotes anatomical and functional repair

The interstitial and perivascular spaces of the mammalian heart contain a highly interactive tissue community essential for cardiac homeostasis, repair and regeneration. Mesenchymal cells (fibroblasts) are one of the most abundant cell types, playing key roles as sentinels, tissue architects, paracrine signaling hubs and lineage precursors, and are linked to heart disease through their roles in inflammation and fibrosis. Platelet-derived growth factors (PDGFs) are secreted by several cell types involved in cardiac injury and repair, and are recognized mitogens for cardiac fibroblasts and mesenchymal stem cells. However, their roles are complex and investigations of their impact on heart repair have produced contrasting outcomes, leaving therapeutic potential uncertain. Here, we use new approaches and tools, including single cell RNA sequencing, to explore cardiac fibroblast heterogeneity and how PDGF receptor (PDGFR) signaling impacts fibroblasts during heart repair. Short-term systemic delivery of PDGF-AB to mice from the time of myocardial infarction (MI) led to enhanced anatomical and functional recovery. Underpinning these benefits was a priming effect, in which PDGF-AB accelerated exit of fibroblasts from quiescence and induced a higher translational biosynthetic capacity in both fibroblasts and macrophages without triggering fibrosis. Our study highlights the significant biosynthetic heterogeneity and plasticity in cardiac fibroblast populations, and suggests a rationale for a novel therapeutic approach to cardiac injury involving controlled stimulation of fibroblast activation.

cell biology↗

bioRxiv2017

C-State: An interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search

BackgroundComparative epigenomic analysis across multiple genes presents a bottleneck for bench biologists working with NGS data. Despite the development of standardized peak analysis algorithms, the identification of novel epigenetic patterns and their visualization across gene subsets remains a challenge.\n\nResultsWe developed a fast and interactive web app, C-State (Chromatin-State), to query and plot chromatin landscapes across multiple loci and cell types. C-State has an interactive, JavaScript- based graphical user interface and runs locally in modern web browsers that are pre-installed on all computers, thus eliminating the need for cumbersome data transfer, pre-processing and prior programming knowledge.\n\nConclusionsC-State is unique in its ability to extract and analyze multi-gene epigenetic information. It allows for powerful GUI-based pattern searching and visualization. We include a case study to demonstrate its potential for identifying user-defined epigenetic trends in context of gene expression profiles.

bioinformatics↗