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Biology subjects

Chakraborty, P.

Publications and source records attributed to Chakraborty, P..

At least 37 records · Page 2Linked to original sources

Apoptotic caspases silence spontaneous innate immune signals by specifically cleaving activated mitochondrial antiviral signalling protein (MAVS)

Caspases-9, -3 and -7 are activated in the mitochondrial apoptosis pathway and lead to the apoptotic phenotype. Caspases also function to limit inflammation upon apoptotic mitochondrial permeabilization through degradation of the signalling proteins cGAS, MAVS and IRF3. Cells and mice lacking caspases have higher interferon levels and are resistant to viral infection. We report that in unstimulated, non-apoptotic cells caspase-3 functions to cleave specifically activated MAVS and very likely cGAS. In unstimulated HeLa cells, constitutive caspase-9- and -3-but not 7-dependent proteolytic events were observed. Inhibition of the mitochondrial apoptosis pathway in various healthy cells induced type I interferon (IFN I) through increased cGAS activity in the absence of changes to cGAS levels. We observed enhanced MAVS-dependent signals upon RIG-I-like helicase stimulation in the absence of BAX, caspase-9 or caspase-3 or upon caspase-inhibition. During activation, MAVS forms complexes, and blockade of mitochondrial apoptosis signalling increased complex abundance in unstimulated and stimulated cells. MAVS complexes were more sensitive to caspase-degradation than the monomer, and mutation of caspase-3-cleavage sites in MAVS spontaneously increased complex formation. Inhibition of voltage-dependent anion channel 1 (VDAC1) oligomerization blocked BAX/BAK- and caspase-regulated IFN induction, suggesting a stimulating role of leakage of mitochondrial DNA. We propose that low level, spontaneous activity of the mitochondrial apoptosis pathway, through specific caspase-3-mediated cleavage of only active signaling proteins, counteracts mitochondrial release of nucleic acids to reduce inflammation in the absence of infection. Caspase-3 therefore has a novel function in conformation- and activation-specific cleavage of substrates.

cell biology↗

Estrogens increase cancer cell efferocytosis to establish an immunosuppressive tumor microenvironment

Phagocytic clearance of apoptotic cancer cells (efferocytosis) by tumor-associated macrophages (TAMs) contributes in a substantial manner to the establishment of an immunosuppressive tumor microenvironment. This puts in context our observation that the female steroid hormone 17{beta}- estradiol (E2) facilitates tumor immune resistance through cancer cell extrinsic Estrogen Receptor (ER) signaling in TAMs. Notable was the finding that E2 induces the expression of CX3CR1 in TAMs to enable efferocytosis of apoptotic cancer cells which results in the suppression of type I interferon (IFN) signaling. Mechanistically, E2 facilitates calcium-dependent activation of the transcription factor NFATC1, which in turn induces CX3CR1 expression. This drives macrophage polarization towards an immune-suppressive state, increasing the ability of TAMs to engulf pro- inflammatory apoptotic cancer cells. Genetic or pharmacological inhibition of the E2/ER/CX3CR1 axis reversed the efferocytic activity of TAMs, rescued E2-dependent suppression of type I IFN signaling, and potentiated intratumoral adaptive immune cell function. Efferocytosis following radiation-induced cancer cell apoptosis limits the efficacy of radiation therapy. Importantly, we determined that preconditioning with either ER-directed endocrine therapies or CX3CR1 inhibition enhanced the antitumor efficacy of radiation therapy by reversing macrophage suppression and reviving intratumoral T cell activation. Our work defines the mechanisms by which E2 increases the efferocytotic activity of TAMs to establish an immunosuppressive tumor microenvironment and demonstrates how this process can be reversed with endocrine therapies which target ER.

cancer biology↗

SARS-CoV-2 Nsp14 binds Tollip and activates pro-inflammatory pathways while downregulating interferon alpha and interferon gamma receptors

SARS coronavirus 2 (SARS-CoV-2) non-structural protein 14 (Nsp14) possesses an N-terminal exonuclease (ExoN) domain that provides a proofreading function for the viral RNA-dependent RNA polymerase and a C-terminal N7-methyltransferase (N7-MTase) domain that methylates viral mRNA caps. Nsp14 also modulates host functions. This includes the activation of NF-{kappa}B and downregulation of interferon alpha/beta receptor 1 (IFNAR1). Here we demonstrate that Nsp14 exerts broader effects, activating not only NF-{kappa}B responses but also ERK, p38 and JNK MAP kinase (MAPK) signaling, promoting cytokine production. Further, Nsp14 downregulates not only IFNAR1 but also IFN-{gamma} receptor 1 (IFNGR1), impairing cellular responses to both IFN and IFN{gamma}. IFNAR1 and IFNGR1 downregulation is via a lysosomal pathway and also occurs in SARS-CoV-2 infected cells. Analysis of a panel of Nsp14 mutants reveals a consistent pattern. Mutants that disable ExoN function remain active, whereas N7-MTase mutations impair both pro-inflammatory pathway activation and IFN receptor downregulation. Innate immune modulating functions also require the presence of both the ExoN and N7-MTase domains likely reflecting the need for the ExoN domain for N7-MTase activity. We further identify multi-functional host protein Tollip as an Nsp14 interactor. Interaction requires the phosphoinositide-binding C2 domain of Tollip and sequences C-terminal to the C2 domain. Full length Tollip or regions encompassing the Nsp14 interaction domain are sufficient to counteract both Nsp14-mediated and Nsp14-independent activation of NF-{kappa}B. Knockdown of Tollip partially reverses IFNAR1 and IFNGR1 downregulation in SARS-CoV-2 infected cells, suggesting relevance of Nsp14-Tollip interaction for Nsp14 innate immune evasion functions. SignificanceSARS-CoV-2 protein Nsp14 both activates NF-{kappa}B, which promotes virus replication and inflammation, and downregulates IFNAR1, which can render infected cells resistant to the antiviral effects of IFN-/{beta}. Our study demonstrates that Nsp14 also activates MAPK signaling and downregulates IFNGR1, causing broader impacts than previously recognized. Data from a panel of Nsp14 mutants suggests a common underlying effect of Nsp14 may be responsible for its multiple innate immune activities. We further describe a novel interaction between Nsp14 and Tollip, a selective autophagy receptor. We show that Tollip expression downregulates Nsp14 activation of NF-{kappa}B and that Tollip knockdown reverses IFNAR1 and IFNGR1 downregulation in SARS-CoV-2 infection, suggesting that Tollip functions as a regulator of Nsp14 innate immune modulation.

microbiology↗

Rapid adaptation and increased genetic parallelism in experimental metapopulations of Pseudomonas aeruginosa

Natural populations are often spatially structured, meaning they are best described as metapopulations composed of subpopulations connected by migration. We know little about how the topology of connections in metapopulations impacts adaptive evolution. Topologies that concentrate dispersing individuals through a central hub can accelerate adaptation above that of a well-mixed system in some models, however empirical support is lacking. We provide evidence to support this claim and show acceleration is accompanied by high rates of parallel evolution resulting from a reduced probability that rare beneficial mutations are stochastically lost. Our results suggest metapopulation topology can be a potent force driving evolutionary dynamics and patterns of genomic repeatability in structured landscapes such as those involving the spread of pathogens or invasive species.

evolutionary biology↗

Contributions of sub-community based on short and long-range white matter tracts in personalized age-associated neurocompensatory mechanism

Brain function is shaped by the local and global connections between its dynamical units and biological parameters. With aging, the anatomical connectivity undergoes significant deterioration (e.g., long-range white matter fiber loss), which affects the brains overall function. Despite the structural loss, previous research has shown that normative patterns of functions remain intact across the lifespan, defined as the compensatory mechanism of the aging brain. However, the crucial components in guiding the compensatory preservation of the dynamical complexity and the underlying mechanisms remain uncovered. Moreover, it remains largely unknown how the brain readjusts its biological parameters to maintain optimal brain dynamics with age; in this work, we provide a parsimonious mechanism using a whole-brain generative model to uncover the role of sub-communities comprised of short-range and long-range connectivity in driving the dynamic compensation process in the aging brain. We utilize two neuroimaging datasets to demonstrate how short--and long-range white matter tracts affect compensatory mechanisms. We unveil their modulation of intrinsic global scaling parameters, such as global coupling strength and conduction delay, via a personalized large-scale brain model. Our two key findings suggest that (1) the optimal coupling strength and delay play complementary roles in preserving the brains optimal working state. (2) Short-range tracts predominantly amplify global coupling strength with age, potentially representing an epiphenomenon of the compensatory mechanism. This mechanistically explains the significance of short-range connections in compensating for the major loss of long-range connections during aging. This insight could help identify alternative avenues to address aging-related diseases where long-range connections are significantly deteriorated.

neuroscience↗

Acquiring social safety engages oxytocin neurons in the supraoptic nucleus - role of Magel2 deficiency

IntroductionExposure to social trauma may alter engagement with both fear-related and unrelated social stimuli long after. Intriguingly, how simultaneous discrimination of social fear and safety is affected in neurodevelopmental conditions like autism remains underexplored. The role of the neuropeptide oxytocin is established in social behaviors, and yet unexplored during such a challenge post-social trauma. MethodsUsing Magel2 knockout mice, an animal model of Prader Willi Syndrome (PWS) and autism spectrum disorders, we tested memory of social fear and safety after a modified social fear conditioning task. Additionally, we tracked the activity of oxytocin neurons in the supraoptic (SON) and paraventricular (PVN) nuclei of the hypothalamus by fibre photometry, as animals were simultaneously presented with a choice between a fear and safe social cue during recall. ResultsMale Magel2 KO mice trained to fear females with electrical footshocks avoided both unfamiliar females and males during recalls, lasting even a week post-conditioning. On the contrary, trained Magel2 WT avoided only females during recalls, lasting days rather than a week post-conditioning. Inability to overcome social fear and avoidance of social safety in Magel2 KO mice were associated with reduced engagement of oxytocin neurons in the SON, but not the PVN. ConclusionIn a preclinical model of PWS, we demonstrated region-specific deficit in oxytocin activity associated with behavioral generalization of social fear to social safety. Insights from this study add to our understanding of oxytocin action in the brain at the intersection of social trauma, PWS and related autism spectrum disorders.

neuroscience↗

p23-FKBP51 chaperone complex regulates tau aggregation

The pathological deposition of tau into insoluble amyloid fibrils is a pathological hallmark of tauopathies. Molecular chaperones are important cellular factors contributing to the regulation of tau misfolding and aggregation. Here we reveal an Hsp90-independent modulation of tau aggregation by a molecular complex of the two Hsp90 co-chaperones p23 and FKBP51. Integrating NMR spectroscopy, SAXS, molecular docking, and site-directed mutagenesis we reveal the structural basis of the p23-FKBP51 complex. We show that p23 specifically recognizes the TPR domain of FKBP51 and interacts with tau through its C-terminal disordered tail. We further show that the p23-FKBP51 complex binds tau to form a dynamic p23-FKBP51-tau trimeric complex that inhibits tau aggregation and thus may counteract Hsp90-FKBP51 mediated toxicity. Taken together, our findings reveal a co-chaperone mediated Hsp90-independent chaperoning of tau protein.

biophysics↗

GSK3β phosphorylation catalyzes the aggregation of Tau into Alzheimer's disease-like amyloid strain

The pathological deposition of proteins is a hallmark of several devastating neurodegenerative diseases. These pathological deposits comprise aggregates of proteins that adopt distinct structures named strains. However, the molecular factors responsible for the formation of distinct aggregate strains are unknown. Here we show that the serine/threonine kinase GSK3{beta} catalyzes the aggregation of the protein tau into an Alzheimers disease-like amyloid strain. We demonstrate that phosphorylation by GSK3{beta}, but not by several other kinases, promotes the aggregation of full-length tau through enhanced phase separation into gel-like condensate structures. Cryo-electron microscopy further reveals that the amyloid fibrils formed by GSK3{beta}-phosphorylated tau adopt a fold comparable to that of paired helical filaments isolated from the brains of AD patients. Our results elucidate the intricate relationship between post-translational modification and the formation of tau strains in neurodegenerative diseases.

biophysics↗

CRISPR/Cas9 gene editing to generate Drosophila LexA lines in secondary school classes

Genome editing in vivo with CRISPR/Cas9 generates powerful tools to study gene regulation and function. We developed CRISPR-based methods that permitted secondary school student scientists to convert Drosophila GAL4 lines to LexA lines. Our novel curricula implement a new donor strain optimizing Homology-assisted CRISPR knock-in (HACK) that simplifies screening using light microscopy. Successful curricula adoption by a consortium of schools led to the generation and characterization of 16 novel LexA lines. This includes extensive comparative tissue expression analysis between the parental Gal4 and derived LexA lines. From this collaboration, we established a workflow to systematically generate LexA lines from frequently-used GAL4 lines. Modular courses developed from this effort can be tailored to specific secondary school scheduling needs, and serve as a template for science educators to innovate courses and instructional goals. Our unique collaborations highlight that resources and expertise harnessed by university-based research laboratories can transform experiential science instruction in secondary schools while addressing research needs for the community of science.

genetics↗

Cell-autonomous BMP signalling plays a key role in the maintenance of tumour cell EMT and migration programs in human ovarian carcinoma

Epithelial-mesenchymal transition (EMT) plays a key role in tumour initiation, metastasis and resistance to therapy. Cells undergoing EMT, assume multiple semi-stable transitional states along the epithelial-mesenchymal axis that necessitates tight regulatory cascades. Although more is known about pathways involved in the initial induction of EMT, cascades that mediate/maintain the transitional states and/or the final mesenchymal phenotype are yet to be elucidated. In this study, we have assessed the role of bone morphogenic protein (BMP) signalling pathway in the regulation of cancer cell EMT and migration. Mining existing data from ovarian carcinomas, we defined the BMP pathway among the key pathways enriched in tumours with elevated EMT signatures, with a significant correlation in the expression of EMT markers with BMP ligands and downstream targets of the BMP pathway. Functional inhibition of the BMP pathway in ovarian cancer cells by a small molecule inhibitor, DMH1, resulted in impaired migration and depressed EMT signatures in both in vitro and in vivo models. Finally, ectopic induction of EMT in ovarian cancer cells through activation of an independent pathway, TNF, resulted in the selective induction of Smad-mediated BMP pathway suggesting a role in maintenance of EMT, secondary to EMT induction.

cancer biology↗

Neuromolecular interactions guiding homeostatic mechanisms underlying healthy ageing: A view from computational microscope

Ageing brain is associated with a slow drift in structural network properties over the lifespan accompanied by reorganization in neuromolecular interactions giving rise to changes in global functional markers. What are the guiding principles of the homeostatic mechanisms that maintain the desired performance of functional neural circuits and preserve brain health during healthy ageing? We hypothesize that an ageing brain alters two primary neurotransmitters, glutamate and{gamma} -aminobutyric acid (GABA), responsible for excitation-inhibition regulation, concomitant with anatomical demyelination to preserve critical neural dynamics that are necessary to uphold optimal network performance. Thus, often observed re-organized functional connectivity with age by several investigations is a byproduct of this adaptive process. We demonstrate that the adaptive mechanism is driven by the tuning of glutamate and GABA concentration over a very slow time scale (lifespan) that can be estimated by tracking criticality from co-ordinated neural dynamics at a resting state via a biophysically driven computational framework, introduced as a computational microscope. We validate several empirical observations and model predictions across three independent aging cohorts using this computational microscope. One of the key mechanisms we discover is the reduction in local glutamate levels employed by brain regions to maintain a homeostatic balance with aging. This is further supported by the invariance of measures of global functional integration during the healthy ageing process.

neuroscience↗

Similar structural area modulates local inhibitioninitiating post-lesion adaptive mechanism

The focal lesion, a form of biological perturbation damaging anatomical architecture, reasonably alters the normative healthy functional pattern but may recover over time. Nevertheless, how the brain counters deterioration in structure by global reshaping of functional connectivity (FC) after a lesion is largely unknown. We propose a novel equivalence principle based on structural and dynamic similarity analysis to predict specific compensatory areas initiating lost excitatory-inhibitory (E-I) regulation after lesion. We hypothesize that similar structural areas (SSAs) and dynamically similar areas (DSAs) corresponding to a lesioned site are the crucial dynamical units to restore lost homeostatic balance within the surviving cortical brain regions. SSAs and DSAs are independent measures, one based on structural similarity properties measured by Jaccard Index and the other based on post-lesion recovery time. Thereafter, a large-scale mean field model is deployed on top of a virtually lesioned structural connectome for characterizing the global brain dynamics and functional connectivity at the level of individual subjects. Despite inter-individual variability in SSAs, we found a general normative pattern in functional re-organization within the ipsi- and contra-lesional regions. The study demonstrates how SSAs and DSAs largely predict overlapping brain regions for different lesion centers/sites irrespective of the complexity of the lesion recovery process. The proposed computational framework captures the improvement of large-scale cortical cohesion by re-adjusting local inhibition. Our results further suggest that the predicted brain areas participating in recovery are not randomly distributed and widespread over the brain. Instead, the predicted brain areas are predominantly recruited from the ipsilesional hemisphere, barring a few regions from contra, suggesting that wiring proximity and similarity are the two major guiding principles of compensation-related utilization of hemisphere (CRUH) in the post-lesion FC re-organization process. Our finding further suggests that the re-organization of FC arises from the interplay between the underlying structural connectivity profile and the local inhibitory weights influencing compensatory coordinated brain dynamics during post-lesion recovery.

neuroscience↗

INO80 regulates chromatin accessibility to facilitate meiotic sex chromosome inactivation

The INO80 protein is the main catalytic subunit of the INO80-chromatin remodeling complex, which is critical for DNA repair and transcription regulation in murine spermatocytes. In this study, we explored the role of INO80 in silencing genes on meiotic sex chromosomes in male mice. INO80 immunolocalization at the XY body in pachytene spermatocytes suggested a role for INO80 in the meiotic sex body. Subsequent deletion of Ino80 resulted in high expression of sex-linked genes. Furthermore, the active form of RNA polymerase II at the sex chromosomes of Ino80-null pachytene spermatocytes indicates incomplete inactivation of sex-linked genes. A reduction in the recruitment of initiators of meiotic sex chromosome inhibition (MSCI) argues for INO80-facilitated recruitment of DNA repair factors required for silencing sex-linked genes. This role of INO80 is independent of a common INO80 target H2A.Z. Instead, in the absence of INO80, a reduction in chromatin accessibility at DNA repair sites occurs on the sex chromosomes. These data suggest a role for INO80 in DNA repair factor localization, thereby facilitating the silencing of sex-linked genes during the onset of pachynema. Summary StatementChromatin accessibility and DNA repair factor localization at the sex chromosomes are facilitated by INO80, which regulates sex-linked gene silencing during meiotic progression in spermatocytes.

developmental biology↗

Spatio-temporal Pattern Formation due to Host-Circuit Interplay in Gene Expression Dynamics

Biological systems are majorly dependent on their property of bistability in order to exhibit nongenetic heterogeneity in terms of cellular morphology and physiology. Spatial patterns of phenotypically heterogeneous cells, arising due to underlying bistability, may play significant role in phenomena like biofilm development, adaptation, cell motility etc. While nonlinear positive feedback regulation, like cooperative heterodimer formation are the usual reason behind bistability, similar dynamics can also occur as a consequence of host-circuit interaction. In this paper, we have investigated the pattern formation by a motif with non-cooperative positive feedback, that imposes a metabolic burden on its host due to its expression. In a cellular array set inside diffusible environment, we investigate spatio-temporal diffusion in one dimension as well as in two dimension in the context of various initial conditions respectively. Moreover, the number of cells exhibiting the same steady state, as well as their spatial distribution has been quantified in terms of connected component analysis. The effect of diffusion coefficient variation has been studied in terms of stability of related states and time evolution of patterns.

biophysics↗

Activation of ERK by altered RNA splicing in cancer

Many cancers carry change-of-function mutations affecting RNA splicing factors, however, less is known about the functional consequences of upregulated RNA splicing factors in cancer. Here, we demonstrate that SMNDC1, a poorly studied splicing factor, which we found to be upregulated in multiple carcinomas and associated with poor patient prognosis, promotes cell proliferation, clonal expansion, and tumor growth by promoting the retention of G-rich exons, which otherwise would be excluded or retained at a lower rate after RNA splicing in normal cells. Inclusion of exon 4 (E4) of MAPK3 (ERK1), which encodes both kinase phosphorylation sites (Thr202/Tyr204), was among the promoted exons by SMNDC1. Forced exclusion of MAPK3-E4 using anti-sense oligos inhibited the ERK1 phosphorylation, expression of target genes and decreased tumor cell growth. These data support that cancer cells exploit a "splicing switch" to promote ERK kinase activity and offer a druggable alternative to block oncogenic signaling and altered RNA splicing in cancer cells SIGNIFICANCEERK signaling promotes tumor growth and survival. Exon 4 of MAPK3 (ERK1) encodes the activation phosphorylation sites of ERK1 kinase. Aberrant RNA splicing induced by SMNDC1 in cancer cells increases the retention of exon 4 during mRNA splicing, unleashes the kinase activity. SMNDC1 potentializes as a cancer therapeutic target.

cancer biology↗

Genetic dissection of crossover mutants defines discrete intermediates in mouse meiosis

Crossovers, the exchange of homolog arms, are required for accurate segregation during meiosis. Studies in yeast have established that the single end invasion intermediate is highly regulated to ensure crossover distribution. Single end invasions are thought to differentiate into double Holliday junctions that are resolved by MutLgamma (MLH1/3) into crossovers. Currently, we lack knowledge of early steps of mammalian crossover recombination or how intermediates are differentiated in any organism. Using comprehensive analysis of recombination and cytology, we infer that polymerized single-end invasion intermediates and nicked double Holliday junctions are crossover precursors in mouse spermatocytes. In marked contrast to yeast, MLH3 plays a structural role to differentiate single end invasions into double Holliday junctions with differentially polymerized 3 ends. Therefore, we show independent genetic requirements for precursor formation and asymmetry with regard to 3 end processing, providing mechanistic insight into crossover formation and patterning.

genetics↗

Immunodominant influenza epitope GILGFVFTL engage common and divergent TCRs when presented as a 9-mer or a 15-mer peptide

Antigen-specific T-cells are a powerful modality for treating cancer and other life-threatening viral and bacterial diseases. Technologies to identify and expand antigen-specific T-cells rapidly can shorten the time, and lower the cost of treatment. In this regard, screening short overlapping peptides to identify antigen-specific T-cells in ex vivo T-cell activation assay is becoming routine. Screening assays typically use 15-mer peptides to stimulate patient-derived, or healthy peripheral blood mononuclear cells to activate T-cells and identify expanded TCRs by next generation sequencing. Previous studies comparing the kinetics of T-cell activation using a 9 and a 15-mer peptide versions of a CMV immunodominant epitope demonstrated that 15-mer peptides induced CD8 T-cell activation at a slower kinetics reaching a lower magnitude compared to 9-mer peptides. The fact that 9-mer peptides are an optimal fit for the MHC class-I binding groove could explain this difference, with the 15-mer peptide requiring additional proteolytic processing before binding to the deeper binding groove of class-I MHC. Alternatively, the delay in kinetics and magnitude can result from the activation of a wider diversity of TCRs engaging novel epitopes generated from the 15-mer peptide whose activation profile may be different from the profile of TCRs that normally respond to the 9-mer immunodominant epitope. We sought to address these two possibilities by comparing T-cell engagement to the HLA-2-restricted GILGFVFTL epitope presented as a 9-mer, or a 15-mer peptide and analyzing CDR3 expansion as a measure of T-cell engagement diversity. This approach also addressed an important question as to whether optimal TCRs could be missed using a 15-mer peptide used routinely in screening assays.

immunology↗

Regulation of Store-Operated Ca2+ Entry by IP3 Receptors Independent of Their Ability to Release Ca2+

Loss of endoplasmic reticular (ER) Ca2+ activates store-operated Ca2+ entry (SOCE) by causing the ER localized Ca2+ sensor STIM to unfurl domains that activate Orai channels in the plasma membrane at membrane contact sites (MCS). Here we demonstrate a novel mechanism by which the inositol 1,4,5 trisphosphate receptor (IP3R), an ER-localized IP3-gated Ca2+ channel, regulates neuronal SOCE. In human neurons, SOCE evoked by pharmacological depletion of ER-Ca2+ is attenuated by loss of IP3Rs, and restored by expression of IP3Rs even when they cannot release Ca2+, but only if the IP3Rs can bind IP3. Imaging studies demonstrate that IP3Rs enhance association of STIM1 with Orai1 in neuronal cells with empty stores; this requires an IP3-binding site, but not a pore. Convergent regulation by IP3Rs, may tune neuronal SOCE to respond selectively to receptors that generate IP3.

cell biology↗