Biology subjects

Mallick, A.

Publications and source records attributed to Mallick, A..

18 recordsLinked to original sources

bioRxiv2026

Spike antibodies targeting GRP78 predispose to cardiovascular complications compared to Dengue

One major aftermath of COVID-19 pandemic is cardiovascular consequences. SARS-CoV-2 binds to ACE2 and downregulates vasodilation. Dengue favors hypotension by weakening endothelial glycocalyx leading to plasma leakage. C1q levels, immune complexes (ICs), and proteomic profiles in serum samples from 52 COVID-19 and 19 pre-pandemic Dengue cases were studied. Unlike Dengue, COVID-19 serums showed elevated coagulation proteins promoting vaso-occlusion and peripheral artery diseases. The stress-induced chaperone and atherosclerosis marker, GRP78 (gene/ protein) was found upregulated upon SARS-CoV-2 spike expression in cardiac/ lung cell lines. Elevated GRP78 levels were also observed in serum samples from COVID-19-diagnosed individuals and subjects with myocardial infarction (MI) in post COVID-era. Surprisingly, spike antibodies (Abs) showed cross-binding to GRP78 and possibly contributed to the observed higher-level ICs in COVID-19 serums (cardiovascular embolism?). Co-localization studies showed that spike Abs (analogous to pro-atherosclerotic GRP78 auto-Abs) could directly bind to upregulated cellular GRP78 (type II hypersensitivity?). Both pathways could worsen vascular injury and atherosclerosis, leading to cardiac complications in COVID-19 cases with narrowed vessels.

microbiology↗

bioRxiv2026

Impaired Endosomal Recycling of Signaling Receptors Activates an Extracellular UPR

Mitochondrial dysfunction and extracellular protein aggregation occur in neurodegenerative diseases such as Alzheimers disease (AD). However, it remains unclear if these processes are functionally linked. Here, we identify a signaling pathway that is activated upon accumulation of aggregation-prone proteins in the extracellular space. We find that the transcription factor ATFS-1, which regulates the mitochondrial unfolded protein response, also regulates transcripts required for endosomal recycling, multiple plasma membrane-localized signaling receptors, and secreted proteins that bind aggregation-prone proteins in the extracellular space, including transthyretin and A{beta}, and promote their degradation. Interestingly, A{beta}(1-42) aggregation induces atfs-1-dependent transcription by promoting degradation of the bZIP protein ZIP-3, which antagonizes ATFS-1. ZIP-3 accumulates in the cytosol when it is phosphorylated by kinases that function downstream of plasma membrane-localized signaling receptors, including the WNT and glutamate receptors. Upon ligand binding, the signaling receptors stimulate the cognate kinase, many of which we found phosphorylate ZIP-3, impeding ZIP-3 degradation, allowing it to antagonize atfs-1-dependent transcription. However, accumulation of aggregation-prone proteins such as A{beta}(1-42) causes endosomal swelling, which impairs endosomal recycling, instead diverting signaling receptors to lysosomes for degradation. In turn, the depletion of signaling receptors reduces the level of ZIP-3 phosphorylation, resulting in ZIP-3 degradation and activation of atfs-1-dependent transcription, which promotes extracellular proteostasis. Our findings uncover an unexpected coupling between endocytic quality control and mitochondrial signaling, revealing a circuit that preserves extracellular proteostasis and promotes organismal resilience.

cell biology↗

bioRxiv2026

Actomyosin active torques determine body plan handedness in C. elegans

Left-right (LR) asymmetries are a defining feature of bilaterian body plans, but the mechanisms that convert molecular chirality into a conserved body-axis handedness remain unclear. In C. elegans, LR axis specification proceeds via a chiral spindle skew that establishes a handed cell-cell contact pattern (CCP) at the 6-cell stage; an arrangement that, when reversed, leads to situs inversus nematodes [1]. Chiral acto-myosin flows that arise from active chiral torques have been previously identified as the driver of this LR asymmetric spindle skew [2]. Here, we show that high amounts of Lifeact::mKate2, widely used to visualize F-actin, reverse the handedness of active torques in the cortex. We find that this results in reversed chiral acto-myosin flows during LR symmetry breaking, leading to mirrored 6-cell embryos and situs inversus nematodes. Our findings demonstrate that reversing the handedness of active torques changes the LR handedness at the organismal level and establish active chiral torques as instructive for LR axis specification in worms.

biophysics↗

bioRxiv2026

LONP-1 deficiency causes dysregulated protein synthesis within mitochondria that is restored by mitoribosomal mutations

Mitochondrial homeostasis is maintained by multiple molecular chaperones and proteases located within the organelle. The mitochondrial matrix-localized protease LONP-1 degrades oxidatively damaged or misfolded proteins. Importantly, LONP-1 also regulates mitochondrial DNA replication. Here, we show that mutations in C. elegans that impair LONP-1 function cause dysregulation of mitochondrial DNA replication, mitochondrial RNA transcription and protein synthesis within the mitochondrial matrix. LONP-1 deficient worms had reduced levels of oxidative phosphorylation proteins despite increased mtDNA-encoded protein synthesis. Via a forward genetic screen, we identified three mutations that restored mitochondrial function and the rate of development in lonp-1 mutants to levels comparable to those in wildtype worms. Interestingly, all three suppressor mutations were found in genes encoding mitochondrial ribosome proteins. A point mutation in the mitochondrial ribosome protein MRPS-38 restored oxidative phosphorylation in lonp-1 mutant worms. Combined, our results suggest that LONP-1 regulates mitochondrial protein synthesis and that the suppressor mutations within MRPS-38 or MRPS-15 enhance oxidative phosphorylation complex assembly by slowing translation.

cell biology↗

bioRxiv2025

Role of Dengue in SARS-CoV-2 Evolution in Dengue Endemic Regions

Evidence suggests that dengue virus (DV) antibodies (Abs) and SARS-CoV-2 Abs were cross-reactive, resulting in reciprocal serological cross-interaction and providing cross-protection in populations in co-endemic regions. It became apparent from the present study that SARS-CoV-2 variants were preferentially selecting mutation(s)/deletions in the spike to evade interaction with DV Abs. We looked at mutations in the SARS-CoV-2 spike protein and how they affected the antigenicity, focusing on successively emergent major variants such as B.1.1.7 (Kent), B.1.617 (Delta), B.1.617.2.1 (Delta-Plus), B.1.1.529 (Omicron-BA.1) and B.1.1.529 (Omicron-BA.2). To further understand the effect of cross-reactive DV Abs on SARS-CoV-2 spike mutation(s), structural studies and docking simulations were performed using DV-2 envelope (E) Abs. Signature mutation (s) in spike variants implied that majority of the above changes in the spike were driven by DV Abs rather than immune pressure of SARS-CoV-2 (preceding variants). This was supported by the fact that the lately emergent SARS-CoV-2 variants like Omicrons (2022-23) were at least 50% less cross-reactive to DV compared to preceding predominant strains. This was further supported by the observed cross-binding of pre-pandemic DV Ab-positive serums to spike synthetic peptides in ELISA, designed from certain regions of the spike RBD which showed maximum cross-interactions with DV E Abs.

microbiology↗

bioRxiv2025

Inhibition of cytosolic translation mitigates mitochondrial dysfunction in C. elegans

The mitochondrial unfolded protein response (UPRmt), which promotes mitochondrial proteostasis and biogenesis is regulated by the transcription factor ATFS-1. In C. elegans, impaired atfs-1 expression perturbs mitochondrial function and slows development. Here, via an RNAi suppressor screen, we found that inhibition of the nuclear hormone receptor NHR-180 increases mitochondrial function and the rate of development in atfs-1(null) worms. NHR-180 is activated during mitochondrial dysfunction and induces transcription of genes required for protein synthesis on cytosolic and mitochondrial ribosomes. Importantly, the NHR-180 ligand binding domain interacts with AMP, which results in increased protein synthesis potentially to promote mitochondrial biogenesis and recovery from transient mitochondrial perturbations. However, NHR-180 exacerbates the mitochondrial dysfunction caused by mutations in genes required for oxidative phosphorylation. Consistent with these findings, we found that inhibition of the S6 kinase homolog RSKS-1 also increased mitochondrial function in atfs-1(null) worms. Importantly, treatment with an S6 kinase inhibitor also increased respiration and mtDNA content in mammalian ATF5-knockout cells and OXPHOS-deficient models, suggesting that translation regulation is a conserved, targetable approach for restoring mitochondrial function in disease.

developmental biology↗

bioRxiv2024

autoFISH - a modular toolbox for sequential smFISH experiments

Fluorescence in situ hybridization (FISH) allows for spatial and quantitative profiling of gene expression by visualizing individual RNA molecules. Here, we introduce automated FISH (autoFISH), a comprehensive toolbox to conduct automated single molecule FISH (smFISH) experiments that is both cost-effective and versatile. This includes detailed plans for constructing the necessary equipment, open-source software for control, reliable experimental protocols, and analysis workflows based on our FISH-quant analysis package. Validation experiments with both cell lines and tissue samples confirmed the systems robustness. We demonstrate standard and amplified smFISH, along with a modified protocol for tissue clearing that enhances nuclear retention while preserving background reduction efficiency.

molecular biology↗

bioRxiv2024

Radiotherapy triggers pro-angiogenic signaling in human lung

Radiotherapy is one of the main therapeutic options for the treatment of lung cancer. Although highly efficient, radiation cause severe damages to normal tissue and radio-induced toxicities vary from mild pneumonitis to pulmonary fibrosis. The mechanism leading to these toxicities remain unclear. To investigate the molecular responses of human lung to radiotherapy, we analyzed, by single cell RNAseq, lung tissue resected in the vicinity of the tumor (i.e. treated with radiation) and compared the transcriptional profiles of the distinct lung populations from the same patient removed at distance from the tumor (i.e. non-treated with radiation). Analysis of six lung samples from patients suffering from Pancoast tumor, a rare lung malignancy that requires neo-adjuvant radiotherapy before surgery, revealed a strong induction of VEGF signaling after radiotherapy. Expression of VEGFA, one of the canonical pro-angiogenic ligands, was found upregulated in multiple cell populations in lung exposed to high doses of radiation. Irradiated capillaries, particularly gCap cells, expressing KDR/VEGFR2, present transcriptional profile similar to tip cells, characterized by sprouting and motility capacities. In addition, we identified a sub-population of alveolar macrophages expressing FLT1/VEGFR1, a receptor for VEGFA, in lung tissues treated by radiotherapy. Cell-Cell communication analysis revealed that FLT1/VEGFR1 positive macrophages interact with tip cells after radiotherapy through IL1B-IL1R signaling. Lastly, analysis of mouse single cell dataset confirmed the increase in the proportion of gCap cells presenting a tip-like phenotype after radiation injury. Altogether, this study describes, at the single cell level, the pro-angiogenic responses of human lung after radiotherapy. These results will lead to a better understanding of the physiopathology of lung radiation injury and may pave the way to optimize treatments to improve patients quality of life.

cancer biology↗

bioRxiv2024

Serotonin acts through multiple cellular targets during an olfactory critical period.

Serotonin (5-HT) is known to modulate early development during critical periods when experience drives heightened levels of plasticity in neurons. Here, we take advantage of the genetically tractable olfactory system of Drosophila to investigate how 5-HT modulates critical period plasticity in the CO2 sensing circuit of fruit flies. Our study reveals that 5HT modulation of multiple neuronal targets is necessary for experience-dependent structural changes in an odor processing circuit. The olfactory CPP is known to involve local inhibitory networks and consistent with this we found that knocking down 5-HT7 receptors in a subset of GABAergic local interneurons was sufficient to block CPP, as was knocking down GABA receptors expressed by olfactory sensory neurons (OSNs). Additionally, direct modulation of OSNs via 5-HT2B expression in the cognate OSNs sensing CO2 is also essential for CPP. Furthermore, 5-HT1B expression by serotonergic neurons in the olfactory system is also required during the critical period. Our study reveals that 5-HT modulation of multiple neuronal targets is necessary for experience-dependent structural changes in an odor processing circuit.

neuroscience↗

bioRxiv2023

A point cloud segmentation framework for image-based spatial transcriptomics

Recent progress in image-based spatial RNA profiling enables to spatially resolve tens to hundreds of distinct RNA species with high spatial resolution. It hence presents new avenues for comprehending tissue organization. In this context, the ability to assign detected RNA transcripts to individual cells is crucial for downstream analyses, such as in-situ cell type calling. Yet, accurate cell segmentation can be challenging in tissue data, in particular in the absence of a high-quality membrane marker. To address this issue, we introduce ComSeg, a segmentation algorithm that operates directly on single RNA positions and that does not come with implicit or explicit priors on cell shape. ComSeg is thus applicable in complex tissues with arbitrary cell shapes. Through comprehensive evaluations on simulated datasets, we show that ComSeg outperforms existing state-of-the-art methods for in-situ single-cell RNA profiling and cell type calling. On experimental data, our method also demonstrates proficiency in estimating RNA profiles that align with established scRNA-seq datasets. Importantly, ComSeg exhibits a particular efficiency in handling complex tissue, positioning it as a valuable tool for the community.

bioinformatics↗

bioRxiv2021

A force-balance model for centrosome positioning and spindle elongation during Interphase and Anaphase B

A computational model in one dimension is proposed to position a single centrosome using astral microtubules (MTs) interacting with the cell cortex. The mechanism exploits mutually antagonistic pulling and pushing forces arising from the astral MTs binding to cortical dynein motors in the actin-rich cell cortex and their buckling while growing against the cell cortex, respectively. The underlying mechanism is extended to account for the elongation and positioning of the bipolar spindle during mitotic anaphase B. Besides astral MTs, the model for bipolar spindle involves interpolar microtubules (IPMTs). The composite model can predict spindle elongation and position under various circumstances. The outcome reveals that the bipolar spindle elongation, weakened by decreasing overlap between the antiparallel IPMTs in the spindle mid-zone, is recovered by the astral MTs. The one-dimensional models are extended in two dimensions to include the effect of cortical sliding of the astral MTs for studying the dynamics of the interphase centrosome and the anaphase B spindles in elongated cells. The results reveal that the dynamics in two dimensions stay qualitatively similar to the one dimension.

biophysics↗

bioRxiv2021

picd-1, a gene that encodes CABIN1 domain-containing protein, interacts with pry-1/Axin to regulate multiple processes in Caenorhabditis elegans

AXIN family members control diverse biological processes in eukaryotes. As a scaffolding protein, AXIN facilitates interactions between cellular components and provides specificity to signaling pathways. Despite its crucial roles in metazoans and discovery of a large number of family members, the mechanism of AXIN function is not very well understood. The C. elegans AXIN homolog PRY-1 provides a powerful tool to identify interacting genes and downstream effectors that function in a conserved manner to regulate AXIN-mediated signaling. Previous work demonstrated pry-1s essential role in developmental processes such as reproductive system, seam cells, and a P lineage cell P11.p. More recently, our lab carried out a transcriptome profiling of pry-1 mutant and uncovered the essential role of the gene in lipid metabolism, stress response, and aging. In this study, we have extended the work on pry-1 by reporting a novel interacting gene picd-1 (pry-1-interacting CABIN1 domain containing). Our findings have revealed that picd-1 plays an essential role in C. elegans and is involved in several pry-1-mediated processes including regulation of stress response and lifespan maintenance. In support of this, picd-1 expression overlaps with pry-1 in multiple tissues throughout the lifespan of animals. Further experiments showed that picd-1 inhibits CREB-regulated transcriptional coactivator homolog CRTC-1 function, which promotes longevity in a calcineurin-dependent manner. These data provide evidence for an essential role of the CABIN1 domain protein PICD-1 in mediating PRY-1 signaling in C. elegans.

genetics↗

bioRxiv2021

Genetic analysis of Caenorhabditis elegans pry-1/Axin suppressors identifies genes involved in reproductive structure development, stress response, and aging

The Axin family of scaffolding proteins regulates a wide array of developmental and post-developmental processes in eukaryotes. Studies in the nematode, Caenorhabditis elegans, have shown that the Axin homolog, PRY-1, plays essential roles in multiple tissues. To understand the genetic network of pry-1, we focused on a set of genes that are differentially expressed in the pry-1-mutant transcriptome and are linked to reproductive structure development. Eight of the genes (ard-1, rpn-7, cpz-1, his-7, cdk-1, rnr-1, clsp-1, and spp-1), when knocked down by RNA interference, efficiently suppressed the plate-level multivulva phenotype of pry-1 mutants. In every case, other than clsp-1 and spp-1, the ectopic vulval precursor cell (VPC) induction was also inhibited. The suppressor genes are members of known gene families in eukaryotes and perform essential functions. Our genetic interaction experiments revealed that except for clsp-1, the genes participate in one or more pry-1-mediated biological events. While four of them (cpz-1, his-7, cdk-1, and rnr-1) function in VPC induction, stress response, and aging, the other three (spp-1, ard-1, and rpn-7) are specific to one or more of these processes. Further analysis of the genes involved in aging showed that his-7, cdk-1, and rnr-1 also interacted with daf-16/FOXO. The results of genetic epistasis experiments suggested that his-7 functions upstream of daf-16, whereas cdk-1 and rnr-1 act downstream of the pry-1-daf-16 pathway. Altogether, these findings demonstrate the important role of pry-1 suppressors in C. elegans. Given that all of the genes described in this study are conserved, future investigations of their interactions with Axin and their functional specificity promises to uncover the genetic network of Axin under normal and disease states.

genetics↗

bioRxiv2020

SARS-CoV-2 has observably higher propensity to accept uracil as nucleotide substitution: Prevalence of amino acid substitutions and their predicted functional implications in circulating SARS-CoV-2 in India up to July, 2020

SARS-CoV-2 has emerged as pandemic all over the world since late 2019. In this study, we investigated the diversity of the virus in the context of SARS-CoV-2 spread in India. Full-length SARS-CoV-2 genome sequences of the circulating viruses from all over India were collected from GISAID, an open data repository, until 25thJuly, 2020. We have focused on the non-synonymous changes across the genome that resulted in amino acid substitutions. Analysis of the genomic signatures of the non-synonymous mutations demonstrated a strong association between the time of sample collection and the accumulation of genetic diversity. Most of these isolates from India belonged to the A2a clade (63.4%) which has overcome the selective pressure and is spreading rapidly across several continents. Interestingly a new clade I/A3i has emerged as the second-highest prevalent type among the Indian isolates, comprising 25.5% of the Indian sequences. Emergence of new mutations in the S protein was observed. Major SARS-CoV-2 clades in India have defining mutations in the RdRp. Maximum accumulation of mutations was observed in ORF1a. Other than the clade-defining mutations, few representative non-synonymous mutations were checked against the available crystal structures of the SARS-CoV-2 proteins in the DynaMut server to assess their thermodynamic stability. We have observed that SARS-CoV-2 genomes contain more uracil than any other nucleotide. Furthermore, substitution of nucleotides to uracil was highest among the non-synonymous mutations observed. The A+U content in SARS-CoV-2 genome is much higher compared to other RNA viruses, suggesting that the virus RdRp has a propensity towards uracil incorporation in the genome. This implies that thymidine analogues may have a better chance to competitively inhibit SARS-CoV-2 RNA replication than other nucleotide analogues.

microbiology↗

bioRxiv2020

Axin-mediated regulation of lifespan and muscle health in C. elegans involves AMPK-FOXO signaling

Aging is a significant risk factor for several diseases. Studies have uncovered multiple signaling pathways that modulate the process of aging including the Insulin/IGF-1 signaling (IIS). In C. elegans the key regulator of IIS is DAF-16/FOXO whose activity is regulated by phosphorylation. A major kinase involved in DAF-16-mediated lifespan extension is the AMPK catalytic subunit homolog, AAK-2. In this study, we demonstrate a novel role of PRY-1/Axin in AAK-2 activation to regulate DAF-16 function. The pry-1 transcriptome contains many genes associated with aging and muscle function. Consistent with this, pry-1 is strongly expressed in muscles and muscle-specific overexpression of pry-1 extends the lifespan, delays muscle aging, and improves mitochondrial morphology in DAF-16-dependent manner. Furthermore, PRY-1 is necessary for AAK-2 phosphorylation. Together, our data demonstrate a crucial role of PRY-1 in maintaining the lifespan and muscle health. Since muscle health declines with age, our study offers new possibilities to manipulate Axin function to delay muscle aging and improve lifespan.

cell biology↗

bioRxiv2019

Investigation of the effect of estradiol and subculturing on the receptor expression within hormone-dependent breast cancer cells

It is now known that a very crucial role in breast cancer development, prognosis and occurrence is played by the estrogen receptor (ER). The steroid hormone estradiol (E2) acts via two nuclear receptors, estrogen receptor- (ER) and estrogen receptor-{beta} (ER{beta}). E2 was shown previously to increase breast cancer cell proliferation in a dose-dependent manner and also induce apoptosis in long term estrogen deprived breast cancer cells. Studies have also shown that the degree of subculturing affects cell line property including gene expression. The aim of this study was to investigate the effect of E2 concentration on cell proliferation, morphology and ER expression and to investigate the effect of subculturing on the expression of ER. Our results have shown that an increase in E2 concentration was found to increase MCF-7 cell proliferation, but extreme concentrations caused significantly low cell proliferation and induced apoptosis. Moreover, ER expression was significantly upregulated with an increase in E2 concentration, whereas ER{beta}2 expression was found to be unchanged at low E2 concentration and significantly upregulated at higher E2 concentration. ER expression at passage 3 ([E2]=1nM) was significantly downregulated compared to the cells at passage 0, in addition to the significant downregulation of the same at E2 concentrations of 1nM and 10{micro}M compared to the untreated control sample. Overall, our data suggests that high concentration of E2 can reduce proliferation and induce apoptosis in the breast cancer cells. Increased E2 exposure and subculturing also appear to change the ER expression significantly in the breast cancer cell line.

cancer biology↗

bioRxiv2018

PRY-1/AXIN signaling regulates lipid metabolism in Caenorhabditis elegans

The nematode Caenorhabditis elegans is a leading animal model to study how signaling pathway components function in conserved biological processes. Here, we describe the role of an Axin family member, pry-1, in lipid metabolism. As a central component of the canonical Wnt signaling pathway, pry-1 acts as a scaffold to multiprotein destruction complex that negatively regulates the expression of Wnt target genes. A genome-wide transcriptome profiling of pry-1 mutant revealed genes associated with aging and lipid metabolism such as vitellogenins (yolk lipoproteins), fatty acid desaturases, lipases, and fatty acid transporters. Consistent with this we found that pry-1 is crucial for the normal adult lifespan and maintenance of lipid levels. Knock-downs of vit genes in pry-1 mutant background restored lipid levels, suggesting that Vitellogenins contribute to PRY-1 function in lipid metabolic processes. Additionally, lowered expression of desaturases and lipidomics analysis provided evidence that the fatty acid synthesis is reduced in pry-1 mutants. In agreement with this an exogenous supply of oleic acid restored depleted lipids in somatic tissues of worms. Overall, our findings demonstrate that PRY-1/Axin signaling is essential for lipid metabolism and involves regulation of yolk proteins.

physiology↗

bioRxiv2018

Extensive genomic diversity among Mycobacterium marinum strains revealed by whole genome sequencing

Mycobacterium marinum is the causative agent for the tuberculosis-like disease mycobacteriosis in fish and skin lesions in humans. Ubiquitous in its geographical distribution, M. marinum is known to occupy diverse fish as hosts. However, information about its genomic diversity is limited. Here, we provide the genome sequences for 15 M. marinum strains isolated from infected humans and fish. Comparative genomic analysis of these and four available genomes of the M. marinum strains M, E11, MB2 and Europe reveal high genomic diversity among the strains, leading to the conclusion that M. marinum should be divided into two different clusters, the \"M\"- and the \"Aronson\"-type. We suggest that these two clusters should be considered, if not two separate species, at least two M. marinum subspecies. Our data also show that the M. marinum pan-genome for both groups is open and expanding and we provide data showing high number of mutational hotspots in M. marinum relative to other mycobacteria such as Mycobacterium tuberculosis. This high genomic diversity might be related to that M. marinum occupy different ecological niches.

genomics↗