Biology subjects

Hirani, N.

Publications and source records attributed to Hirani, N..

10 recordsLinked to original sources

bioRxiv2026

Solid-like PAR protein assemblies encode long-term spatial memory of cell polarity during suspended animation

During suspended animation, organisms must preserve cellular organization despite the collapse of the active biochemical processes that normally maintain it. Here we show that anoxia-induced suspended animation drives cell polarity proteins into a poised, memory-like state that preserves spatial information and templates rapid resumption of morphogenesis upon reanimation. In C. elegans embryos, anoxia drives progressive assembly of the polarity protein PAR-3 into solid-like clusters that preserve the polarity axis during metabolic arrest despite inactivation of patterning reactions normally required to maintain PAR asymmetry. Embryos expressing cluster-defective PAR-3 fail to maintain asymmetry during arrest and consequently exhibit polarity axis defects upon reanimation, demonstrating that arrested PAR-3 clusters function as physical templates for re-establishment of polarity. Our data suggest that cells cope with transient metabolic arrest by reversibly converting actively maintained biochemical patterns into stable physical templates that preserve spatial information for later reactivation.

cell biology↗

bioRxiv2025

Cell cycle oscillations in a polarity network facilitate state switching by morphogenetic cues

The proper establishment of cell form, fate, and function during morphogenesis requires precise coordination between cell polarity and developmental cues. To achieve this, cells must establish polarity domains that are stable yet sensitive to guiding cues. Here we show that C. elegans germline blastomeres resolve this trade-off by creating a time-varying polarization landscape. Specifically, coupling the PAR polarity network to the cell-cycle kinase CDK-1 ensures that newborn cells operate in a low-feedback regime that lowers barriers to polarity state switching, allowing spatial cues to induce and orient PAR protein asymmetries. As CDK-1 activity rises at mitotic entry, increasing molecular feedback reinforces cue-induced asymmetries to yield robust and stable patterning of PAR domains. Consistent with this model, optogenetic and chemical perturbations show that low-CDK/low-feedback regimes destabilize PAR domains but are required for both de novo polarization and the reorientation of polarity in response to inductive cues. We propose that mitotic oscillations in cell polarity circuits dynamically optimize the polarization landscape to enable coordination of polarity with morphogenesis. Such temporal control of developmental networks is likely a general mechanism to balance robustness of cellular states with sensitivity to signal-induced state switching. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/681824v1_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@18b39f3org.highwire.dtl.DTLVardef@1898670org.highwire.dtl.DTLVardef@1d95517org.highwire.dtl.DTLVardef@1615f14_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2023

Nonlinear readout of spatial cues underlies robustness of asymmetric cell division

A key challenge in the development of an organism is to maintain robust phenotypic outcomes in the face of perturbation. Yet, how such robust outcomes are encoded by developmental networks remains poorly explored. Here we use the C. elegans zygote as a model to understand sources of developmental robustness during PAR polarity-dependent asymmetric cell division. By quantitatively linking alterations in protein dosage to phenotype in individual embryos, we show that spatial information in the zygote is read out in a highly nonlinear fashion and, as a result, phenotypes are highly canalized against substantial variation in input signals. Specifically, our data point towards an intrinsic robustness of the conserved PAR polarity network that renders polarity axis specification resistant to variations in both the strength of upstream symmetry-breaking cues and PAR protein dosage. At the same time, we find that downstream pathways involved in cell size and fate asymmetry are similarly robust to dosage-dependent changes in the local concentrations of PAR proteins, implying non-trivial complexity in translating PAR signals into pathway outputs. We propose that "quantitative decoupling" of symmetry-breaking, polarity, and asymmetric division modules acts to suppress the accumulation of error as embryos move along this developmental trajectory, thereby ensuring that asymmetric division is robust to perturbation. Such modular organization of developmental networks is likely to be a general mechanism to achieve robust developmental outcomes.

developmental biology↗

bioRxiv2023

Optimized dimerization of the PAR-2 RING domain drives cooperative and selective membrane recruitment for robust feedback-driven cell polarization

The behavior of cell polarity networks is defined by the quantitative features of their constituent feedback circuits, which must be tuned to enable robust and stable polarization, while also ensuring that networks remain responsive to dynamically changing cellular states and/or spatial cues that arise during development. Using the PAR polarity network as a model, we demonstrate that these features are enabled by dimerisation of the polarity protein PAR-2 via ubiquitin-independent function of its N-terminal RING domain. Specifically, we combine theory and experiment to show that dimer affinity is optimized to achieve dynamic, selective, and cooperative recruitment of PAR-2 to the plasma membrane during polarization. Reducing dimerization results in loss of positive feedback and compromises robustness of symmetry-breaking, while enhanced dimerization renders the network less responsive due to kinetic trapping of PAR-2 on internal membranes and reduced sensitivity of PAR-2 to membrane displacement by the polarity kinase, aPKC/PKC-3. Thus, our data reveal how a dynamically oligomeric RING domain results in a cell polarity network that is both robust and responsive and highlight how tuning of oligomerization kinetics can serve as a general strategy for optimizing dynamic and cooperative intracellular targeting.

cell biology↗

bioRxiv2022

Cleavage furrow-directed cortical flows bias mechanochemical pathways for PAR polarization in the C. elegans germ lineage

During development, the conserved PAR polarity network is continuously redeployed, requiring that it adapts to changing cellular contexts and environmental cues. How it does so and the degree to which these adaptations reflect changes in its fundamental design principles remain unclear. Here, we investigate the process of PAR polarization within the highly tractable C. elegans germline P lineage, which undergoes a series of iterative asymmetric stem cell-like divisions. Compared to the zygote, we observe significant differences in the pattern of polarity emergence, including an inversion of the initial unpolarized state, changes in symmetry breaking cues, and the timings with which anterior and posterior PARs segregate. Beneath these differences, however, polarity establishment remains reliant on the same core pathways identified in the zygote, including conserved roles for cortical actin flows and PAR-dependent self-organization. Intriguingly, we find that cleavage furrow-directed cortical actin flows play a similar symmetry-breaking role for the germline cell P1 as centrosome-induced cortical flows in the zygote. Through their ability to induce asymmetric accumulation of PAR-3 clusters, these furrow-directed flows directly couple the geometry of polarization to cell division, which could be a general strategy for cells to ensure proper organization within dynamically growing systems, such as embryos. In summary, our data suggest that coupling of novel symmetry-breaking cues with highly adaptable core mechanochemical circuits enable robust PAR polarity in response to changing developmental contexts.

cell biology↗

bioRxiv2022

Design principles for selective polarization of PAR proteins by cortical flows

Clustering of membrane-associated molecules is thought to promote interactions with the actomyosin cortex, enabling size-dependent transport by actin flows. Consistent with this model, in the C. elegans zygote, anterior segregation of the polarity protein PAR-3 requires oligomerization. However, through direct assessment of advection of PAR proteins, we not only find no links between PAR-3 advection and oligomer size, but also observe efficient advection of both anterior and posterior PAR proteins. Consequently, differential cortex engagement cannot account for selective size-dependent PAR protein transport. Instead, combining experiment and theory we demonstrate that segregation efficiency of PAR proteins by cortical flow is determined by the stability of membrane association, which is enhanced by clustering and specifies persistence of transport. Indeed, stabilizing membrane association was sufficient to invert polarity of a normally posterior PAR protein. Our data therefore indicate that advection of membrane-associated proteins is more pervasive than anticipated and thus cells must tune membrane association dynamics to achieve differential transport by cortical flows.

cell biology↗

bioRxiv2022

Hypoxia shapes the immune landscape in lung injury promoting inflammation persistence

Acute Respiratory Distress Syndrome (ARDS), an often-fatal complication of pulmonary or systemic inflammation, has no cure. Hypoxemia is a defining feature, yet its impact on inflammation is often neglected. Patients with ARDS are monocytopenic early in the onset of the disease. Endotoxin or Streptococcus pneumoniae acute lung injury (ALI) in the context of hypoxia replicates this finding, through hypoxia-driven suppression of type I interferon signalling. This results in failed lung monocyte-derived interstitial macrophages (IM) niche expansion and unchecked neutrophilic inflammation. Administration of colony stimulating factor 1 (CSF1) rescues the monocytopenia, alters the circulating classical monocyte phenotype in hypoxic endotoxin-driven ALI and enables lung IM population expansion, thus limiting lung injury in endotoxin- and virally-induced hypoxic ALI. Hypoxia directly alters immune dynamics to the detriment of the host and manipulation of this aberrant response offers new therapeutic strategies for ARDS.

cell biology↗

bioRxiv2022

SAIBR: A simple, platform-independent method for spectral autofluorescence correction

Biological systems are increasingly viewed through the lens of mathematics, physics, and systems approaches that demand accurate quantification of gene expression and local protein concentrations. Such approaches have benefited greatly from the revolution in genetic engineering sparked by CRISPR/Cas9. By facilitating the tagging of genes at their genomic loci, CRISPR/Cas9 allows us to use fluorescence to monitor proteins that are expressed at or near endogenous levels under native regulatory control. However, due to their typically lower expression levels, quantitative experiments using endogenously-tagged genes can run into limits imposed by autofluorescence (AF). AF is often a particular challenge in the illumination bands occupied by the most efficient fluorescent proteins (GFP, mNeonGreen). Stimulated by our work in C. elegans, we describe and validate Spectral Autofluorescence Image correction By Regression (SAIBR), a simple, platform-independent protocol, and associated GUI-based FIJI plugin to correct for autofluorescence using standard filter sets and illumination conditions. Fully validated for use in C. elegans embryos and tested in diverse systems, including starfish oocytes and fission yeast, SAIBR achieves accurate quantitation of fluorophore signal and enables reliable detection and quantification of even weakly expressed proteins. Thus, SAIBR provides a highly accessible, low barrier way to incorporate AF correction as standard for researchers working on a broad variety of cell and developmental systems. Summary StatementImplemented as an easy-to-use Fiji Plugin, SAIBR provides effective autofluorescence correction for cells and tissues using standard imaging conditions.

cell biology↗

bioRxiv2021

The transcription factor EGR2 is indispensable for tissue-specific imprinting of alveolar macrophages in health and tissue repair

Alveolar macrophages are the most abundant macrophages in the healthy lung where they play key roles in homeostasis and immune surveillance against air-borne pathogens. Tissue-specific differentiation and survival of alveolar macrophages relies on niche-derived factors, such as colony stimulating factor 2 (CSF-2) and transforming growth factor beta (TGF-{beta}). However, the nature of the downstream molecular pathways that regulate the identity and function of alveolar macrophages and their response to injury remains poorly understood. Here, we identify that the transcriptional factor EGR2 is an evolutionarily conserved feature of lung alveolar macrophages and show that cell-intrinsic EGR2 is indispensable for the tissue-specific identity of alveolar macrophages. Mechanistically, we show that EGR2 is driven by TGF-{beta} and CSF-2 in a PPAR-{gamma}-dependent manner to control alveolar macrophage differentiation. Functionally, EGR2 was dispensable for lipid handling, but crucial for the effective elimination of the respiratory pathogen Streptococcus pneumoniae. Finally, we show that EGR2 is required for repopulation of the alveolar niche following sterile, bleomycin-induced lung injury and demonstrate that EGR2-dependent, monocyte-derived alveolar macrophages are vital for effective tissue repair following injury. Collectively, we demonstrate that EGR2 is an indispensable component of the transcriptional network controlling the identity and function of alveolar macrophages in health and disease. One Sentence SummaryEGR2 controls alveolar macrophage function in health and disease

immunology↗

bioRxiv2019

Genome-wide association study of susceptibility to idiopathic pulmonary fibrosis

RationaleIdiopathic pulmonary fibrosis (IPF) is a complex lung disease characterised by scarring of the lung that is believed to result from an atypical response to injury of the epithelium. The mechanisms by which this arises are poorly understood and it is likely that multiple pathways are involved. The strongest genetic association with IPF is a variant in the promoter of MUC5B where each copy of the risk allele confers a five-fold risk of disease. However, genome-wide association studies have reported additional signals of association implicating multiple pathways including host defence, telomere maintenance, signalling and cell-cell adhesion.\n\nObjectivesTo improve our understanding of mechanisms that increase IPF susceptibility by identifying previously unreported genetic associations.\n\nMethods and measurementsWe performed the largest genome-wide association study undertaken for IPF susceptibility with a discovery stage comprising up to 2,668 IPF cases and 8,591 controls with replication in an additional 1,467 IPF cases and 11,874 controls. Polygenic risk scores were used to assess the collective effect of variants not reported as associated with IPF.\n\nMain resultsWe identified and replicated three new genome-wide significant (P<5x10-8) signals of association with IPF susceptibility (near KIF15, MAD1L1 and DEPTOR) and confirm associations at 11 previously reported loci. Polygenic risk score analyses showed that the combined effect of many thousands of as-yet unreported IPF risk variants contribute to IPF susceptibility.\n\nConclusionsNovel association signals support the importance of mTOR signalling in lung fibrosis and suggest a possible role of mitotic spindle-assembly genes in IPF susceptibility.

genomics↗