bioRxiv Science⌕ Search

Biology subjects

Goswami, S.

Publications and source records attributed to Goswami, S..

At least 37 records · Page 2Linked to original sources

Dual effects of ARX poly-alanine mutations in human cortical and interneuron development

Infantile spasms, with an incidence of 1.6 to 4.5 per 10,000 live births, are a relentless and devastating childhood epilepsy marked by severe seizures but also leads to lifelong intellectual disability. Alarmingly, up to 5% of males with this condition carry a mutation in the Aristaless-related homeobox (ARX) gene. Our current lack of human-specific models for developmental epilepsy, coupled with discrepancies between animal studies and human data, underscores the gap in knowledge and urgent need for innovative human models, organoids being one of the best available. Here, we used human neural organoid models, cortical organoids (CO) and ganglionic eminences organoids (GEO) which mimic cortical and interneuron development respectively, to study the consequences of PAE mutations, one of the most prevalent mutation in ARX. ARXPAE produces a decrease expression of ARX in GEOs, and an enhancement in interneuron migration. That accelerated migration is cell autonomously driven, and it can be rescued by inhibiting CXCR4. We also found that PAE mutations result in an early increase in radial glia cells and intermediate progenitor cells, followed by a subsequent loss of cortical neurons at later timepoints. Moreover, ARX expression is upregulated in COs derived from patients at 30 DIV and is associated with alterations in the expression of CDKN1C. Furthermore, ARXPAE assembloids had hyperactivity which were evident at early stages of development. With effective treatments for infantile spasms and developmental epilepsies still elusive, delving into the role of ARXPAE mutations in human brain organoids represents a pivotal step toward uncovering groundbreaking therapeutic strategies.

neuroscience↗

Histone Lactylation Drives CD8 T Cell Metabolism and Function

The activation and functional differentiation of CD8 T cells are linked to metabolic pathways that result in the production of lactate. Lactylation is a lactate-derived histone post-translational modification (hPTM); however, the relevance of histone lactylation in the context of CD8 T cell activation and function is not known. Here, we show the enrichment of H3K18-lactylation (H3K18la) and H3K9-lactylation (H3K9la) in human and murine CD8 T cells which act as transcription initiators of key genes regulating CD8 T cell phenotype and function. Further, we note distinct impacts of H3K18la and H3K9la on CD8 T cell subsets linked to their specific metabolic profiles. Importantly, we demonstrate that modulation of H3K18la and H3K9la by targeting metabolic and epigenetic pathways regulates CD8 T cell effector function including anti-tumor immunity in preclinical models. Overall, our study uncovers the unique contributions of H3K18la and H3K9la in modulating CD8 T cell phenotype and function intricately associated with metabolic state.

immunology↗

Ribosome subunit attrition and activation of the p53-MDM4 axis dominate the response of MLL-rearranged cancer cells to WDR5 WIN site inhibition

The chromatin-associated protein WD Repeat Domain 5 (WDR5) is a promising target for cancer drug discovery, with most efforts blocking an arginine-binding cavity on the protein called the "WIN" site that tethers WDR5 to chromatin. WIN site inhibitors (WINi) are active against multiple cancer cell types in vitro, the most notable of which are those derived from MLL-rearranged (MLLr) leukemias. Peptidomimetic WINi were originally proposed to inhibit MLLr cells via dysregulation of genes connected to hematopoietic stem cell expansion. Our discovery and interrogation of small molecule WIN site inhibitors, however, revealed that they act in MLLr cell lines to suppress ribosome protein gene (RPG) transcription, induce nucleolar stress, and activate p53. Because there is no precedent for an anti-cancer strategy that specifically targets RPG expression, we took an integrated multi-omics approach to further interrogate the mechanism of action of WINi in MLLr cancer cells. We show that WINi induce depletion of the stock of ribosomes, accompanied by a broad yet modest translational choke and changes in alternative mRNA splicing that inactivate the p53 antagonist MDM4. We also show that WINi are synergistic with agents including venetoclax and BET-bromodomain inhibitors. Together, these studies reinforce the concept that WINi are a novel type of ribosome-directed anti-cancer therapy and provide a resource to support their clinical implementation in MLLr leukemias and other malignancies.

cancer biology↗

Differential expression of miRNAs between Young-Onset and Late-Onset Indian colorectal carcinoma patients

Early-Onset Colorectal Carcinoma (EOCRC) is a growing concern as reports indicate a worldwide increase in the incidence of CRC among young adults (<50 years old). In an effort to understand the different mode of pathogenesis in young-onset CRC, we performed a pilot study wherein we looked at colorectal tumors from both young (< 50 years old) and old patients (>55 years old) and screened them to eliminate tumors positive for Microsatellite Instability (MSI) and showing activation of the Wnt pathway, known canonical factors in CRC pathogenesis. RNA isolated from EOCRC and Late-Onset (LOCRC) tumors and paired normal tissues without MSI, nuclear {beta}-catenin and APC mutations were sent for small RNA seq to identify miRNA alterations between the two subsets. Comparative analysis revealed differential expression of 23 miRNAs specific to EOCRC and 11 miRNAs specific to LOCRC. We validated the top 10 EOCRC DEMs in TCGA-COAD cohorts followed by validation in additional EOCRC and LOCRC cohorts. Our integrated analysis revealed upregulation of hsa-miR-1247-3p, hsa-miR-148a-3p and hsa-miR-27a-5p and downregulation of hsa-miR-326 between the two subsets. Experimentally validated targets of the above miRNAs were compared with differentially expressed genes in the TCGA dataset to identify targets with physiological significance in EOCRC development. Our analysis revealed downregulation of epithelial gene expression and intercellular junction proteins potentially leading to dissolution of epithelial intercellular junctions in EOCRC development and EMT progression. Upregulated targets included genes whose expression have been reported to correlate with CRC tumor invasion, liver metastasis, disease recurrence and poor prognosis.

cancer biology↗

Myeloid-specific KDM6B inhibition sensitizes Glioblastoma to PD1 blockade

Glioblastoma (GBM) tumors are enriched in immune-suppressive myeloid cells and are refractory to immune checkpoint therapy (ICT). Targeting epigenetic pathways to reprogram the functional phenotype of immune-suppressive myeloid cells to overcome resistance to ICT remains unexplored. Single-cell and spatial transcriptomic analyses of human GBM tumors demonstrated high expression of an epigenetic enzyme - histone 3 lysine 27 demethylase (KDM6B) in intra- tumoral immune-suppressive myeloid cell subsets. Importantly, myeloid-cell specific Kdm6b deletion enhanced pro-inflammatory pathways and improved survival in GBM tumor-bearing mice. Mechanistic studies elucidated that the absence of Kdm6b enhances antigen-presentation, interferon response and phagocytosis in myeloid cells by inhibiting mediators of immune suppression including Mafb, Socs3 and Sirpa. Further, pharmacological inhibition of KDM6B mirrored the functional phenotype of Kdm6b deleted myeloid cells and enhanced anti-PD1 efficacy. Thus, this study identified KDM6B as an epigenetic regulator of the functional phenotype of myeloid cell subsets and a potential therapeutic target to improve response to ICT.

immunology↗

Rapid generation of precision preclinical cancer models using regulatable in vivo base editing

Single nucleotide variants (SNVs) comprise the majority of cancer-associated genetic changes and can have diverse effects on protein function. Despite a comprehensive catalogue of SNVs across human cancers, little is known about their impact on tumor initiation and progression. To enable the functional interrogation of cancer-associated SNVs, we developed a murine system for temporal and regulatable in vivo cytosine base editing (iBE). The iBE mice show robust, doxycycline-dependent expression across a broad range of tissues with no evidence of DNA or RNA off-target effects. Transient iBE induction drives efficient creation of individual or multiple SNVs in intestinal, lung, and pancreatic organoids, while temporal iBE regulation allows controlled sequential genome editing. Moreover, in situ delivery of plasmid-based or synthetic sgRNAs to target tissues facilitates the simple and rapid generation of pre-clinical cancer models. Overall, iBE is a powerful in vivo platform to define and interrogate the genetic drivers of cancer.

cancer biology↗

Role for DNA exonuclease V resection activity of RecBCD in control of aberrant chromosomal replication initiation in Escherichia coli

Replication of the circular bacterial chromosome is initiated from a locus oriC with the aid of an essential protein DnaA. One approach to identify factors acting to prevent aberrant oriC-independent replication initiation in Escherichia coli has been that to obtain mutants which survive loss of DnaA. Here we show that a {Delta}recD mutation, associated with attenuation of RecBCDs DNA double strand end-resection activity, provokes abnormal replication and rescues {Delta}dnaA lethality in two situations: (i) in absence of 5-3 single-strand DNA exonuclease RecJ, or (ii) when multiple two-ended DNA double strand breaks (DSBs) are generated either by I-SceI endonucleolytic cleavages or by radiomimetic agents phleomycin or bleomycin. One-ended DSBs in the {Delta}recD mutant did not rescue {Delta}dnaA lethality. With two-ended DSBs in the {Delta}recD strain, {Delta}dnaA viability was retained even after linearization of the chromosome. Data from genome-wide DNA copy number determinations in {Delta}dnaA-rescued cells lead us to propose a model that nuclease-mediated DNA resection activity of RecBCD is critical for prevention of a {sigma}-mode of rolling-circle over-replication when convergent replication forks merge and fuse, as may be expected to occur during normal replication at the chromosomal terminus region or during repair of two-ended DSBs following "ends-in" replication.

microbiology↗

Prophylactic treatment of Glycyrrhiza glabra mitigates COVID-19 pathology through inhibition of pro-inflammatory cytokines in the hamster model and NETosis.

Severe coronavirus disease (COVID-19) is accompanied with acute respiratory distress syndrome & pulmonary pathology, and is presented mostly with inflammatory cytokine release, dysregulated immune response, skewed neutrophil/ lymphocyte ratio, and hypercoagulable state. Though vaccinations have proved effective in reducing the COVID-19 related mortality, the limitation of use of vaccine against immunocompromised, comorbidity, and emerging variants remains a concern. In the current study we investigate for the first-time the efficacy of Glycyrrhiza glabra (GG) extract, a potent immunomodulator, against SARS-CoV-2 infection in hamsters. Prophylactic treatment with GG showed protection against loss in body weight and 35-40% decrease in lung viral load along with reduced lung pathology in the hamster model. Remarkably, GG reduced the mRNA expression of pro-inflammatory cytokines and Plasminogen activator inhibito-1 (PAI-1). In-vitro, GG acted as potent immunomodulator by reducing Th2 and Th17 differentiation and IL-4 and IL-17A cytokine production. In addition, GG also showed robust potential to suppress ROS, mtROS and NETs generation in a concentration dependent manner in both human polymorphonuclear neutrophils (PMNs) and murine bone marrow derived neutrophils (BMDNs). Taken together, we provide evidence for the protective efficacy of GG against COVID-19 and its putative mechanistic insight, which might be developed as a future immunomodulatory approach against various pathologies with high cytokine production, aberrant neutrophil activation including coronavirus infection.

immunology↗

S100A8 and S100A9, biomarkers of SARS-Cov-2-infected patients, suppress HIV replication in primary macrophages

S100A8 and S100A9 are members of the Alarmin family; these proteins are abundantly expressed in neutrophils and form a heterodimer complex. Recently, both proteins were identified as novel biomarkers of SARS-CoV-2 infection and were shown to play key roles in inducing an aggressive inflammatory response by mediating the release of large amounts of pro-inflammatory cytokines, called the "cytokine storm." Although co-infection with SARS-CoV-2 in people living with HIV-1 may result in an immunocompromised status, the role of the S100A8/A9 complex in HIV-1 replication in primary T cells and macrophages is still unclear. Here, we evaluated the roles of the proteins in HIV replication to elucidate their functions. We found that the complex had no impact on virus replication in both cell types; however, the subunits of S100A8 and S100A9 inhibits HIV in macrophages. These findings provide important insights into the regulation of HIV viral loads in SARS-CoV2 co-infection.

microbiology↗

Effect of prophylactic use of intra-nasal oil formulations in the hamster model of Covid-19

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) infection initiates with viral entry in upper respiratory tract leading to coronavirus disease 2019 (Covid-19). Severe Covid-19 is characterized by pulmonary pathologies associated with respiratory failure. Thus, therapeutics aimed at inhibiting entry of the virus or its internalization in the upper respiratory tract, are of interest. Herein, we report the prophylactic application of two intra-nasal formulations provided by the National Medicinal Plant Board (NMPB), Anu oil and Til tailya in SARS-CoV2 infection hamster model. Prophylactic nasal instillation of these oil formulations exhibited reduced viral load in lungs, and resulted in reduced body weight loss and pneumonitis. In line with reduced viral load, histopathlogical analysis revealed a reduction in lung pathology in Anu oil group as compared to the control infected group. However, Til tailya group did not show a significant reduction in lung pathology. Furthermore, molecular analysis using mRNA expression profiling indicated reduced expression of pro-inflammatory cytokines genes, including Th1 and Th17 cytokines for both the intra-nasal formulations as a result of decreased viral load. Together, the prophylactic intra-nasal application of Annu oil seems to be useful in limiting both the viral load and disease severity disease in SARS-CoV2 infection in hamster model.

microbiology↗

Comparative in vitro antioxidant and antibacterial activities of leaf extract fractions of Crimson bottlebrush, Callistemon citrinus (Curtis.) Skeels

ObjectivesThe present study aimed to analyze a comparative in vitro free radical scavenging and antibacterial potentials of leaf aqueous and the successive extract fractions of Callistemon citrinus. MethodsFor in vitro antioxidant activity assessments, 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging activity, Fe3+ ion reducing antioxidant power (FRAP) assay, and total antioxidant capacity of the extracts were tested. Antibacterial potentials were tested through Agar well diffusion method using both gram-positive and gram-negative bacterial strains. ResultsData indicate the polar successive aqueous fraction (AQF) possesses the highest free radicals scavenging capacity, with lowest EC50 (the required extract concentration to scavenge half of the free radicals) for DPPH and FRAP assays, and contains the highest total phenolics (308.2{+/-}5.9 {micro}g tannic acid equivalent/mg dry extract, DE), flavonoids (516.7{+/-}3.5 {micro}g quercetin equivalent/mg DE), total antioxidant capacity (441.48{+/-}12.8 {micro}g ascorbic acid equivalent/mg DE). Phenolics and flavonoids contents were positively correlated with the in vitro antioxidant activities. The antibacterial study indicates the petroleum ether and chloroform are suitable solvents for extracting antibacterial phytochemicals from C. citrinus leaves that are effective against both gram-positive and negative bacterial strains. ConclusionThe most polar fraction i.e. the successive aqueous extract fraction of C. citrinus leaves exhibited the highest antioxidant activities while the most non-polar petroleum ether extract fraction showed the highest antibacterial potentials thus these extract fractions might have therapeutic importance.

pharmacology and toxicology↗

Comparative assessment of allelopathic herbicidal actions and total phenolics content of seven Indian medicinal plants

Allelopathy is a vital ecological process that influences the dynamics of ecological succession, structure, and composition of plant communities. The present study aimed to evaluate a comparative account of allelopathic inhibitory actions in relation to total phenolic contents of aqueous extracts from seven traditionally used medicinal plants of India. Triticum aestivum and Cicer arietinum seedlings were used to test seed germination inhibition, seedling growth retardation and branch root sprouting inhibition. Allium cepa root tip cells were used for mitotic index inhibition and abnormal cell percentage analysis. The correlation between the total phenolics content and allelopathic activities was analyzed. The different extracts show the varied degree of allelopathic inhibitory activity. Out of these seven used extracts, Crinum asiaticum leaf extract (CaLAE) showed the highest allelopathic inhibitory action and it could reduce 94.3 and 79.59% root and shoot growth respectively at 96 h of treatment (1 mg/mL) and that was increased to 96.18 and 93.78% respectively with 2 mg/mL. The quantitative phytochemical analysis also revealed that CaLAE also possess relatively higher amounts of total phenolics. The growth retardation effects of the extract are in accordance with the mito-depression and increased chromosomal abnormality in A. cepa root tip cells. In conclusion, Crinum asiaticum may be considered as a prospective source of allelochemicals for plant growth regulation and a source of commercial herbicidal products.

plant biology↗

Comparative phytotoxicity and chironomid toxicity assessments of leaf successive extract fractions of Asiatic poison bulb, Crinum asiaticum L.

Crinum asiaticum is an evergreen bulbous perennial shrub of Amaryllidaceae family with ethnomedicinal importance and our earlier study described a comparative account antimicrobial and antioxidant properties of the different solvent-mediated sequential extract fractions. The present study aimed to analyze their comparative account of induced phytotoxicity and chironomid toxicity. For phytotoxicity assessment, germination inhibition and seedlings root and shoot growth retardation effects on Triticum aestivum and Cicer arietinum were analyzed and for lethal concentration determination, the freshwater bottom-dwelling first instars chironomid larvae were used. The crude aqueous, petroleum ether and ethyl acetate extracts showed significant toxic effects on both meristematic tissue and aquatic midges. The phytotoxic assays indicate that the ethyl acetate fraction contains the most potent growth inhibitors, followed by the crude aqueous and petroleum ether fractions. The last aqueous fraction was found to be the least toxic, the highest LC50 and LT50 values and ethyl acetate extract fraction having highest toxicity. Thus the present study supplements to our earlier report, that indicated the last aqueous extract fraction of C. asiaticum has potent antioxidant and antibacterial potentials as well as its prospective use in livestock maintenance, as it is least toxic and the ethyl acetate extract, the most toxic fraction identified here, is needed to explore for pharmaceutical importance.

pharmacology and toxicology↗

Effects of faecal inorganic contents in accurate measures of stress and nutrition hormone in large felines: implications for physiological assessments in free-ranging animals

Non-invasive stress and nutritional hormones and their interactions are increasingly being used to monitor psychological and nutritional physiology in free-ranging animals at different ecological scales. However, a number of extrinsic and intrinsic factors including hormone-inert dietary materials, inorganic matters etc. are known to affect accurate hormone measures. Here we addressed the impacts of inorganic matter (IOM) on corticosterone and T3 measures in wild tiger (n=193 from Terai Arc landscape, India) and captive lion (n=120 from Sakkarbaug Zoological Garden, Gujarat, India) faeces and evaluated possible corrective measures. The wild tiger samples contained highly variable IOM content (9-98%, mostly with >40% IOM) compared to captive Asiatic lion (17-57%, majority with <40% IOM). We observed significant negative correlation between IOM content and tiger GC (r=-0.48, p=0.000) and T3 (r=-0.60, p=0.000) measures but not in captive lions (r=-0.05, p=0.579). Two corrective measures viz. removing samples with [&ge;]80% IOM and subsequently expressing concentrations as per gram of organic dry matter (instead of total dry matter) reduced IOM influence on tiger GC and T3 measures without affecting lion GC results. The corrective measures bring out alterations in the tiger T3 results but no changes in GC results. As faecal IOM content is associated with specific behaviours of many carnivore species, our results emphasize the need to reduce IOM-driven hormone data variation for ecologically relevant interpretations for species conservation.

physiology↗

Live imaging of breast tumors shows macrophage-dependent induction and TMEM-mediated enrichment of cancer stem cells during metastatic dissemination

Cancer stem cells (CSCs) play an important role during metastasis, but the dynamic behavior and induction mechanisms of CSCs are not well understood. We employed high-resolution intravital microscopy using a CSC biosensor to directly observe CSCs in live mice with mammary tumors. CSCs display the slow-migratory, invadopod-rich phenotype that is the hallmark of disseminating tumor cells. CSCs are enriched near macrophages, particularly near macrophage-containing intravasation sites called Tumor Microenvironment of Metastasis (TMEM) doorways. A dramatic enrichment of CSCs occurs on association with TMEM doorways, contributing to the finding that CSCs represent [~]>60% of circulating tumor cells. Mechanistically, stemness is induced in non-stem cancer cells upon their direct contact with macrophages via Notch signaling. In breast cancers from patients, the density of TMEM doorways correlates strongly with the proportion of cancer cells expressing stem cell markers, indicating that in human breast cancer TMEM doorways are not only cancer cell intravasation portals but also CSC programming sites. One Sentence SummaryIntravital imaging reveals macrophage-mediated induction of cancer stem cells in vivo and their dramatic enrichment on dissemination through TMEM doorways.

cancer biology↗

Effects of a combined enrichment intervention on the behavioural and physiological welfare of captive Asiatic lions (Panthera leo persica)

The endangered Asiatic lion (Panthera leo persica) is currently distributed as a single wild population of 670 individuals and [~]400 captive animals globally. Although the captive lions are major hope for the species long-term conservation through repatriation, their welfare status and management practises need research attention. To this end, we tested the efficacy of feeding, sensory and manipulable enrichment interventions on the welfare of Asiatic lions at the conservation breeding centre of Sakkarbaug Zoological Garden, Gujarat. We adopted a holistic approach by measuring physiological and behavioural responses of 35 captive Asiatic lions, divided into control (n=16) and test (n=19) groups. The test subjects approached feeding devices first and manipulable devices for a longer duration. Manipulable devices were used homogenously with two significant time peaks, but sensory devices were used sporadically throughout the day with no discernible peak usage. The control subjects remained unchanged in all welfare parameters compared to their pre-treatment levels. However, post-enrichment behavioural assessments showed higher behaviour diversity (95% increase from the baseline period), reduced enclosure zone bias (40.25% reduction) and aberrant repetitive behaviours (80.68%) in test samples. Similarly, faecal corticosterone measures showed lower stress levels in test samples (58% decrease), confirming significant improvement in all welfare indices than control groups. These results have universal applicability to assess welfare indices of other captive species in Indian zoos. We hope that the results will encourage zoo managers and regulatory agencies to improve animal welfare practices.

animal behavior and cognition↗

Cloning and In silico characterization of Heat shock factor (Hsf2) from Wheat (Triticum aestivum L.)

A gene that encodes for Heat Shock Factor (Hsf) was characterized and designated as TaHsf2 (Gen Bank ID: KP063542) from wheat. The genomic sequence was found to be 1551bp long with open reading frame of length1123bp. The amino acid sequence so concluded showed to have HSF domain having high degree of similarity (homology) with other HSF coding gene of related species. We have reported in-silico three-dimensional model of TaHsf2 and evaluation of the predicted model, analysed with various tools. The sudden climatic variations over the years especially elevation in temperature has adversely affected the growth and productivity of winter wheat (Triticum aestivum L.). A very less number of HSFs is being reported and characterized in wheat and the data so available for wheat calls for investigation and characterization of more HSPs coding HSFs. In our present study we have cloned one of the novel HSFs and have characterized it through in silico tools.

molecular biology↗

Lineage reversion drives WNT independence in intestinal cancer

The WNT pathway is a fundamental regulator of intestinal homeostasis and hyperactivation of WNT signaling is the major oncogenic driver in colorectal cancer (CRC). To date, there are no described mechanisms that bypass WNT dependence in intestinal tumors. Here, we show that while WNT suppression blocks tumor growth in most organoid and in vivo CRC models, the accumulation of CRC-associated genetic alterations enables drug resistance and WNT-independent growth. In intestinal epithelial cells harboring mutations in KRAS or BRAF, together with disruption of p53 and SMAD4, transient TGF{beta} exposure drives YAP/ TAZ-dependent transcriptional reprogramming and lineage reversion. Acquisition of embryonic intestinal identity is accompanied by a permanent loss of adult intestinal lineages, and long-term WNT-independent growth. This work delineates genetic and microenvironmental factors that drive WNT inhibitor resistance, identifies a new mechanism for WNT-independent CRC growth and reveals how integration of associated genetic alterations and extracellular signals can overcome lineage-dependent oncogenic programs.

cancer biology↗