Biology subjects

Ghosh, A. K.

Publications and source records attributed to Ghosh, A. K..

11 recordsLinked to original sources

bioRxiv2026

Hidden introns and repeated gains shape the heavily interrupted tRNA genes of Asgard archaea

Transfer RNA (tRNA) genes are usually compact, yet in some Asgard archaea-the closest known prokaryotic relatives of eukaryotes-most are interrupted by introns. Studying this has been hampered by circularity: archaeal introns are catalogued by software that finds them partly through the splicing motif later used to explain where they persist. We built a motif-free census that detects intervening sequences by comparing each tRNA gene with compact relatives, and applied it to 90 Asgard genomes and 18 reference archaea. The standard annotator, tRNAscan-SE, had missed 30% of intervening sequences in the three focal families, mostly in the D-arm, but almost none in reference archaea; six independent checks supported the census. After correction, focal tRNA genes carry 2.2 intervening sequences on average, and in 30 genomes chosen before analysis the two focal families ranked first and second of 21 (exact P = 1/210). A reconstruction based on the census rather than on annotated introns placed 129 high-confidence gains at 65 loci on 37 branches of the species tree, 71 of them terminal; the two intron-rich classes are not sister lineages and carry mostly different intron positions, consistent with independent accumulation. Intervening sequences sat at canonical bulge-helix-bulge splicing motifs six to ten times more often than the average of three matched null models, including those the annotator missed and the reconstructed gains. Tests of copying between tRNA genes, mobile elements and reverse transcription found no general route of intron arrival. Asgard tRNA introns were thus gained repeatedly and sit preferentially at sites predicted to allow splicing; how they arrive remains open.

bioinformatics↗

bioRxiv2026

A neuropsychiatric disease-associated mutation in LRRC8B disrupts cellular calcium signaling, mitochondrial function, and bioenergetics

Leucine-rich repeat-containing 8 (LRRC8) proteins form the volume-regulated anion channel (VRAC) and participate in diverse physiological processes, including cell volume regulation, gliotransmitter release, and insulin secretion. In mammals, five paralogs (LRRC8A-E) exist; LRRC8A is the obligatory subunit that assembles into functional hexameric channels with LRRC8C, D, or E. LRRC8B is distinct: we previously demonstrated its role in regulating endoplasmic reticulum (ER) Ca{superscript 2} homeostasis and ER Ca{superscript 2} leak. A LRRC8B variant (Y380S) identified in an Indian family with severe mental illness has been associated with disease pathology, but its molecular and cellular consequences remain unknown. Here, we show that this disease-associated mutant perturbs Ca{superscript 2} signalling, mitochondrial bioenergetics, and redox homeostasis. Both wild-type and mutant LRRC8B localize to the ER and mitochondria. LRRC8B knockdown significantly reduced mitochondrial Ca{superscript 2} uptake and maximal respiratory the Y380S mutant phenocopied LRRC8B knockdown, altering ER Ca{superscript 2} release, elevating basal cytosolic Ca{superscript 2}, and impairing mitochondrial Ca{superscript 2} uptake, consistent with a dominant-negative mechanism. The mutant further induced mitochondrial dysfunction, including loss of membrane potential, oxidative stress, and defective antioxidant responses, ultimately compromising cellular bioenergetics and viability. Mechanistically, the Y380S mutation disrupted LRRC8B interaction with the mitochondrial outer membrane channel VDAC. These findings identify LRRC8B-VDAC coupling as a key determinant of mitochondrial Ca{superscript 2} handling and provide a mechanistic link between LRRC8B dysfunction and neuropsychiatric disease. HighlightsO_LIA psychiatric disease-associated LRRC8B variant (Y380S) acts as a dominant-negative regulator of ER Ca{superscript 2} homeostasis. It enlarges the releasable ER Ca{superscript 2} pool and reduces cell viability. C_LIO_LILRRC8B promotes mitochondrial Ca{superscript 2} uptake through interaction with VDAC. The Y380S mutation disrupts this interaction, reducing mitochondrial Ca{superscript 2} uptake. C_LIO_LIThe Y380S mutant increases mitochondrial superoxide production without activating compensatory antioxidant responses. C_LIO_LIThe mutant also causes mitochondrial membrane depolarization and bioenergetic failure, as evidenced by reduced oxygen consumption rate and ATP production. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/718892v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@1f314d3org.highwire.dtl.DTLVardef@1dc3908org.highwire.dtl.DTLVardef@124445aorg.highwire.dtl.DTLVardef@39326_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

p53 preserves genome stability in dividing cells under hypo-osmotic stress

Cells respond to frequent osmotic stress to maintain structural integrity and function. Whereas acute volume regulation is well-known, the cellular response to prolonged osmotic stress and its long-term consequences remain poorly understood. In this study, we investigate how lasting hypo-osmotic stress influences cell growth and division and the associated cellular response. We observe that cells undergoing their first division under hypo-osmotic stress experience delayed mitotic entry, lengthened mitotic duration, elevated mitotic errors and aneuploidy formation. However, continued cell division is halted through a p53/p21-dependent G1 arrest. p53 activation occurs post-mitotically and is associated with hyper-condensed chromatin and impaired nuclear expansion in daughter cells after mitotic exit. We show that the altered nuclear size dynamics lead to nuclear accumulation of p53 and activation of downstream gene expression. These findings uncover a mechanosensitive, p53-mediated mechanism that safeguards genome integrity by suppressing erroneous mitosis under hypo-osmotic stress.

cell biology↗

bioRxiv2025

Metatranscriptomic Insights into Host-Microbiome Interactions Underlying Asymptomatic COVID-19 Cases

In recent years, the research on Coronavirus disease 2019 (COVID-19) has surged rapidly due to its infectious nature and epidemiological importance as a pandemic. Association of other pathogenic microbes or different human microbiomes with COVID-19 severity is well established. While much is known about COVID-19, studies exploring how host-pathogen interactions at the transcriptomic level influence disease severity are still limited. This research focuses on metatranscriptomic perspective of COVID-19 patients from different Bangladeshi cohorts. Metatranscriptomic sequencing was performed using the extracted RNA of forty different nasopharyngeal samples. After preprocessing and assembly of the genome sequence data, taxonomic identification and diversity along with antibiotic resistance pattern was analyzed using different bioinformatic pipelines. COVID-19 positive and asymptomatic positive patients had a higher abundance of pathogenic and multidrug resistant bacteria whereas the Healthy or recovered patients had higher fungal population. Differential gene expression analysis was also performed to identify the upregulated and downregulated genes responsible for different biological and immunological pathways of humans. Here, immunological response related genes were mostly upregulated in positive cases which was also evident in the proinflammatory cytokines upregulation. Moreover, asymptomatic positive cases showed low TLR-4 expression, which is key to recognizing pathogen-associated molecular patterns (PAMPs) and triggering pro-inflammatory immune responses. This study can clarify the gene expression and signaling pattern of COVID-19 patients with different severity. This may also suggest that some populations exhibit reduced basal expression of TLR-4, which may suppress innate immune activation following infection and contribute to asymptomatic clinical outcomes; however, this hypothesis requires further investigation. Future studies should aim to validate these associations using larger, ethnically diverse cohorts with comprehensive clinical and demographic data.

microbiology↗

bioRxiv2023

The Neuroprotective Effect of Short-chain Fatty Acids Against Hypoxia-reperfusion Injury

Gut microbe-derived short-chain fatty acids (SCFAs) are known to have a profound impact on various brain functions, including cognition, mood, and overall neurological health. However, their role, if any, in protecting against hypoxic injury and ischemic stroke has not been extensively studied. In this study, we investigated the effects of two major SCFAs abundant in the gut, propionate (P) and butyrate (B), on hypoxia-reperfusion injury using a neuronal cell line and a zebrafish model. Neuro 2a (N2a) cells treated with P and B exhibited reduced levels of mitochondrial and cytosolic reactive oxygen species (ROS), diminished loss of mitochondrial membrane potential, suppressed caspase activation, and lower rates of cell death when exposed to CoCl2-induced hypoxia, compared to the control group. Furthermore, adult zebrafish fed with SCFAs-supplemented feeds showed less susceptibility to hypoxic conditions compared to the control group, as indicated by multiple behavioral measures. Histological analysis of TTC-stained brain sections revealed lesser damage in the SCFAs-fed group. We also found that FABP7 (also known as BLBP), a neuroprotective fatty acid binding protein, was upregulated in the brains of the SCFAs-fed group. Additionally, when FABP7 was overexpressed in N2a cells, it protected the cells from hypoxia-reperfusion injury. Overall, our data clearly demonstrates a neuroprotective role of P and B against hypoxic brain injury and suggests the potential of dietary supplementation with SCFAs to mitigate stroke-induced brain damage. HighlightsO_LIShort-chain fatty acid (SCFA) Propionate (P) and Butyrate (B) protect N2a cells from hypoxia-reperfusion. C_LIO_LIZebrafish, when fed an SCFA-supplemented diet, are more resilient to hypoxia-reperfusion. C_LIO_LISCFAs in the diet boost brain expression of FABP7 (fatty acid binding protein). C_LIO_LIFABP7 overexpression in N2a cells provides protection against hypoxia-reperfusion. C_LIO_LISCFAs reduce reactive oxygen species (ROS) levels and increase FABP7, contributing to neuroprotection. C_LI

neuroscience↗

bioRxiv2021

H3K4me1-marked Enhancer Activation in Resistant Prostate Cancers Implicates SOX4 and MENIN Inhibition as Therapeutic Strategies

Chromatin elements and regulators play important roles during progression of prostate cancer, however, their involvement in response to therapy is less well understood. Using comprehensive chromatin profiling of patient-derived tumors, we find that enhancer elements marked by H3K4me1 are highly enriched in aggressive therapy-resistant prostate cancers on important resistance-driving genes, such as those involved in FOXA1, NOTCH and TGF-{beta} signaling. Importantly, by targeting H3K4me1-elements through inhibition of the MLL complex, a H3K4 methyltransferase, we reduced the proliferative capacity and H3K4me1-associated loci in enzalutamide-resistant prostate cancer lines. We identify AR, FOXA1, HOXB13 and SOX4 as a subset of core TFs that are critical for establishing transcriptional networks via active enhancer reprogramming during acquisition of resistance to therapy. Knock-down of SOX4 reduced cell proliferation and disrupted the H3K4me1 enhancer landscape, further suggesting a role for this TF in therapy-resistance. Overall, our data implicate H3K4me1-marked enhancers as a key epigenetic feature of therapy-resistance, implicate SOX4 in enhancer reprogramming and suggest use of MLL/MENIN inhibitors as a potential therapeutic strategy in high-grade and locally advanced prostate cancers that do not respond to traditional therapies.

cancer biology↗

bioRxiv2021

U2 snRNA structure is influenced by SF3A and SF3B proteins but not by SF3B inhibitors

U2 snRNP is an essential component of the spliceosome. It is responsible for branch point recognition in the spliceosome A-complex via base-pairing of U2 snRNA with an intron to form the branch helix. Small molecule inhibitors target the SF3B component of the U2 snRNP and interfere with A-complex formation during spliceosome assembly. We previously found that the first SF3B inhibited-complex is less stable than A-complex and hypothesized that SF3B inhibitors interfere with U2 snRNA secondary structure changes required to form the branch helix. Using RNA chemical modifiers, we probed U2 snRNA structure in A-complex and SF3B inhibited splicing complexes. The reactivity pattern for U2 snRNA in the SF3B inhibited-complex is indistinguishable from that of A-complex, suggesting that they have the same secondary structure conformation, including the branch helix. This observation suggests SF3B inhibited-complex instability does not stem from an alternate RNA conformation and instead points to the inhibitors interfering with protein component interactions that normally stabilize U2 snRNPs association with an intron. In addition, we probed U2 snRNA in the free U2 snRNP in the presence of SF3B inhibitor and again saw no differences. However, increased protection of nucleotides upstream of Stem I in the absence of SF3A and SF3B proteins suggests a change of secondary structure at the very 5' end of U2 snRNA. Chemical probing of synthetic U2 snRNA in the absence of proteins results in similar protections and predicts a previously uncharacterized extension of Stem I. Because this stem must be disrupted for SF3A and SF3B proteins to stably join the snRNP, the structure has the potential to influence snRNP assembly and recycling after spliceosome disassembly.

molecular biology↗

bioRxiv2021

Pharmacological inhibition of PAI-1 alleviates cardiopulmonary pathologies induced by exposure to air pollutants PM2.5

OBJECTIVEExposure to air pollutants leads to the development of pulmonary and cardiovascular diseases, and thus air pollution is one of the major global threats to human health. Air pollutant particulate matter 2.5 (PM2.5)-induced cellular dysfunction impairs tissue homeostasis and causes vascular and cardiopulmonary damage. To test a hypothesis that elevated plasminogen activator inhibitor-1 (PAI-1) levels play a pivotal role in air pollutant-induced cardiopulmonary pathologies, we examined the efficacy of a drug-like novel inhibitor of PAI-1, TM5614, in treating PM2.5-induced vascular and cardiopulmonary pathologies. APPROACH AND RESULTSResults from biochemical, histological, and immunohistochemical studies revealed that PM2.5 increases the circulating levels of PAI-1 and thrombin and that TM5614 treatment completely abrogates these effects in plasma. PM2.5 significantly augments levels of pro-inflammatory cytokine IL-6 in bronchoalveolar lavage fluid, and this also can be reversed by TM5614, indicating its efficacy in amelioration of PM2.5-induced increases in inflammatory and pro-thrombotic factors. TM5614 reduces PM2.5-induced increased levels of inflammatory markers Mac3 and pSTAT3, adhesion molecule VCAM1, and apoptotic marker cleaved caspase 3. Longer exposure to PM2.5 induces pulmonary and cardiac thrombosis, but TM5614 significantly ameliorates PM2.5-induced vascular thrombosis. TM5614 also reduces PM2.5-induced increased blood pressure and heart weight. In vitro cell culture studies revealed that PM2.5 induces the levels of PAI-1, type I collagen, fibronectin, and SREBP-1/2, a transcription factor that mediates profibrogenic signaling, in cardiac fibroblasts. TM5614 abrogated that stimulation, indicating that it may block PM2.5-induced PAI-1 and profibrogenic signaling through suppression of SREBP-1. Furthermore, TM5614 blocked PM2.5-mediated suppression of Nrf2, a major antioxidant regulator in cardiac fibroblasts. CONCLUSIONSPharmacological inhibition of PAI-1 with TM5614 is a promising therapeutic approach to control air pollutant PM2.5-induced cardiopulmonary and vascular pathologies. O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

pharmacology and toxicology↗

bioRxiv2021

AhNGE : A Database for Arachis hypogaea Nodule Developmental Gene Expression

Symbiotic nitrogen fixation (SNF) inside root-nodules is a primary and sustainable source of soil nitrogen. Understanding nodule development and metabolism in crop legumes may lead to more effective SNF in agriculture. Peanut (Arachis hypogaea) is an economically important allotetraploid legume with non-canonical nodule developmental features. Recent genome sequencing of peanut has opened the possibility of making peanut a model for studying atypical nodule development. To help the community of nodule biologists, we have developed a database called AhNGE (Arachis hypogaea Nodule Developmental Gene Expression: http://nipgr.ac.in/AhNGE/index.php). AhNGE contains RNAseq data from six data points of nodule development in A. hypogagea cv. Tifrunner. This data represents a dynamic view of gene expression during peanut nodule development. Research in model legumes has generated a huge knowledgebase in the last twenty years. To streamline comparative genomics among legumes, we performed ortholog analysis among four legumes (Cicer, Glycine, Lotus, and Medicago) and one non-legume (Arabidopsis). This will facilitate the integration of existing knowledge in nodule development with the Arachis transcriptome. The available data can be retrieved using a single or batch query or searching using gene ID, from above mentioned five species. The output displays the gene expression pattern in graphical as well as tabular form, along with further options to download the sequence data. The database is linked with PeanutBase, the main genomic resource of peanut. Additionally, the expression level of different splicing variants can be retrieved from the database. In summary, AhNGE serves as an important resource for the scientific community working on nodule development.

bioinformatics↗

bioRxiv2020

Identification of herboxidiene structural features that mediate conformation-dependent SF3B1 interactions to inhibit splicing.

Small molecules that target the spliceosome SF3B complex are potent inhibitors of cancer cell growth. The compounds affect an early stage of spliceosome assembly when U2 snRNP first engages the branch point sequence of an intron. Recent cryo-EM models of U2 snRNP before and after intron recognition suggest several large-scale rearrangements of RNA and protein interactions involving SF3B. Employing an inactive herboxidiene analog as a competitor with SF3B inhibitors, we present evidence for multiple conformations of SF3B in the U2 snRNP, only some of which are available for productive inhibitor interactions. We propose that both thermodynamics and an ATP-binding event promote the conformation conducive to SF3B inhibitor interactions. However, SF3B inhibitors do not impact an ATP-dependent rearrangement in U2 snRNP that exposes the branch binding sequence for base pairing. We also report extended structure activity relationship analysis of herboxidiene, which identified features of the tetrahydropyran ring that mediate its interactions with SF3B and its ability to interfere with splicing. In combination with structural models of SF3B interactions with inhibitors, our data leads us to extend the model for early spliceosome assembly and inhibitor mechanism. We postulate that interactions between a carboxylic acid substituent of herboxidiene and positively charged SF3B1 sidechains in the inhibitor binding channel are required to maintain inhibitor occupancy and counteract the SF3B transition to a closed state that is promoted by stable U2 snRNA interactions with the intron.

molecular biology↗

bioRxiv2020

Chromatin State Dynamics Confers Specific Therapeutic Strategies in Enhancer Subtypes of Colorectal Cancer

The extent and function of chromatin state aberrations during colorectal cancer (CRC) progression is not completely understood. Here, by comprehensive epigenomic characterization of 56 tumors, adenomas, and their matched normal tissues, we define the dynamics of chromatin states during the progression of colorectal cancer. H3K27ac-marked active enhancer state could distinguish between different stages of CRC progression. By epigenomic editing, we present evidence that gains of tumor-specific enhancers for crucial oncogenes, such as ASCL2 and FZD10, was crucial for excessive proliferation. Consistently, combination of MEK plus bromodomain (BET) inhibition was found to have synergistic effects in CRC patient-derived xenograft (PDX) models. Probing inter-tumor heterogeneity, we identified four distinct enhancer subtypes (EpiC), three of which correlate well with previously defined transcriptomic subtypes (CMSs). Importantly, CMS2 can be divided into two EpiC subgroups with significant survival differences. Leveraging such correlation, we devised a combinatorial therapeutic strategy of enhancer-blocking bromodomain inhibitors with pathway-specific inhibitors (PARPi, EGFRi, and TGF{beta}i) for three EPIC groups. Our data suggest that the dynamics of active enhancer underlies colorectal cancer progression and the patient-specific active enhancer patterns govern their unique gene expression patterns which can be leveraged for precision combination therapy.

cancer biology↗