Biology subjects

Pal, A.

Publications and source records attributed to Pal, A..

At least 55 records · Page 3Linked to original sources

bioRxiv2024

Resolving the three-dimensional interactome of Human Accelerated Regions during human and chimpanzee neurodevelopment

Human Accelerated Regions (HARs) are highly conserved across species but exhibit a significant excess of human-specific sequence changes, suggesting they may have gained novel functions in human evolution. HARs include transcriptional enhancers with human-specific activity and have been implicated in the evolution of the human brain. However, our understanding of how HARs contributed to uniquely human features of the brain is hindered by a lack of insight into the genes and pathways that HARs regulate. It is unclear whether HARs acted by altering the expression of gene targets conserved between HARs and their chimpanzee orthologs or by gaining new gene targets in human, a mechanism termed enhancer hijacking. We generated a high-resolution map of chromatin interactions for 1,590 HARs and their orthologs in human and chimpanzee neural stem cells (NSCs) to comprehensively identify gene targets in both species. HARs and their chimpanzee orthologs targeted a conserved set of 2,963 genes enriched for neurodevelopmental processes including neurogenesis and synaptic transmission. Changes in HAR enhancer activity were correlated with changes in conserved gene target expression. Conserved targets were enriched among genes differentially expressed between human and chimpanzee NSCs or between human and non-human primate developing and adult brain. Species-specific HAR gene targets did not converge on known biological functions and were not significantly enriched among differentially expressed genes, suggesting that HARs did not alter gene expression via enhancer hijacking. HAR gene targets, including differentially expressed targets, also showed cell type-specific expression patterns in the developing human brain, including outer radial glia, which are hypothesized to contribute to human cortical expansion. Our findings support that HARs influenced human brain evolution by altering the expression of conserved gene targets and provide the means to functionally link HARs with novel human brain features.

genomics↗

bioRxiv2024

AP2/ERF transcription factors enriched in the drought-response transcriptome of the Thar desert tree Prosopis cineraria show higher copy number and greater DNA-binding affinity than orthologs in drought-sensitive species

We sequenced the drought-response transcriptome of the keystone tree species Prosopis cineraria from the Indian Thar desert to understand the key factors in its drought tolerance mechanism. We identified a network of genes activated in P. cineraria involved in osmotic stress response, phytohormone, calcium, and phosphorelay signal transduction. Of these, up-regulation of 54 APETALA2/Ethylene-Responsive Factor (AP2/ERF) transcription factor genes, validated by real-time PCR, suggests their key role in the drought tolerance of P. cineraria. We conducted a genome-wide study of the AP2/ERF superfamily in P. cineraria, classifying its 232 proteins into 15 clades and analyzing their protein structures, gene structure, and promoter organization. The P. cineraria genome contains more copies of AP2/ERF genes than drought-sensitive plants. Further, we identified sequence polymorphisms in AP2/ERF genes between Arabian and Indian cultivars of P. cineraria. We modeled the DNA-protein complex structures of AP2/ERFs from drought-tolerant and sensitive species using AlphaFold to compare their DNA binding ability. Though the DNA binding domain (DBD) is relatively conserved across species, the unstructured region of these proteins possesses different charge distributions, which might contribute differently to their DNA search and binding. Using all-atom molecular dynamics simulations, we teased out a higher number of specific DBD-DNA hydrogen bonds in P. cineraria, leading to a stronger DNA-binding affinity compared to drought-sensitive Arabidopsis thaliana. These results directly support copy number expansion of AP2/ERF transcription factors and the evolution of their structures for more efficient DNA search and binding as drought adaptation mechanisms in P. cineraria.

plant biology↗

bioRxiv2024

Post-transcriptional regulation of insulin mRNA storage by G3BP1/2+ condensates in beta cells

Hyperglycemia upregulates insulin translation in pancreatic beta cells. Several RNA- binding proteins involved in this process have been identified, including G3BP1, a stress granule marker downregulated in islets of subjects with type 2 diabetes. We show that in mouse insulinoma MIN6-K8 cells exposed to fasting glucose levels G3BP1 and its paralog G3BP2 colocalize to cytosolic condensates with eIF3b and Ins1/2 mRNA. Upon glucose stimulation, the condensates dissolve and G3BP1/2, eIF3b, and insulin mRNAs redistribute throughout the cytosol. Intriguingly, G3BP1+ condensates in MIN6-K8 cells differ from sodium arsenate-induced stress granules in regards to eIF2 and AMPK phosphorylation. Knockout of G3BP1 or G3BP2 prevented condensate assembly, but only G3BP1 deletion decreased the levels of Ins1/2 mRNA and proinsulin and impaired polysome formation. Like glucose, other insulin secretagogues such as Exendin-4 and palmitate, but not high KCl, prompted the dissolution of G3BP1+ condensates. G3BP1+/Ins mRNA+ condensates were also present in mouse and human beta cells from normoglycemic donors. Hence, G3BP1+ condensates represent a glucose-regulated compartment for the physiological storage and protection of insulin mRNA in resting beta cells.

molecular biology↗

bioRxiv2024

Influence of Incorporating Full-Fat Black Soldier Fly Larvae Meal (BSFLM) in Meat Type Chicken Diets on the Lower Gut Short Chain Fatty Acids profile, Gut Morphology and Intestinal Lesion Score

Though protein demand is increasing day by day but the animal protein industry on a global scale is facing the biggest challenge of replacing antibiotic growth promoters (AGP) to raise broiler chickens. Using AGP is a long-standing practice to include in poultry diets for improving the intestinal health and subsequent performance of the broiler chicken. Due to increased restrictions and bans on the usage of antibiotics, the poultry-producing community is in search of a suitable and sustainable alternative to AGPs. The present study was aimed at to evaluate and analyte the potential impacts and consequences associated with the inclusion of black soldier fly larvae meal (BSFLM) in a commercially available meat type chicken when compared to diets that either contained or lacked the presence of antibiotic growth promoters, specifically enramycin at a concentration of 8% and chlortetracycline at a concentration of 15%. Our study also assessed the influence of inclusion of BSFLM on cecal short chain fatty acids (SCFAs), and the gut health. 180 male day-old Vencobb430Y chicks (mean BW 42.52 g) (P > 0.05) were randomly allocated into isonitrogenous and isoenergetic dietary treatments in three equal groups. BSFLM group has exhibited significant higher concentration of short chain fatty acids in cecum like acetate, isobutyrate, butyrate, and total SCFAs compared to both the AGP and CONTROL groups (P<0.05). The villi height of duodenum and jejunum remained significantly higher in BSFLM supplemented birds as compared to the AGP group (P<0.05). From the analysis of frequency plots depicting the severity of intestinal lesions, it was observed that the presence of serosa and mucosa congestion in the anterior sections of the gastrointestinal tract was within the expected range for both the CONTROL and AGP groups, thus indicating that this particular physiological condition can be considered as normal in these experimental groups. In the duodenal part, incorporating BSFL meal showed significantly higher villi height and crypt depth compared with CONTROL and AGP (P<0.05). Inclusion of full-fat BSF has improved overall intestinal health and lower lesion scores compared to the CONTROL and AGP groups. The present investigation explored thepotential of incorporating full-fat black soldier fly larvae (BSFL) meal into the dietary regimens of broilers for sgnificantly bolstering the health and functionality of their gastrointestinal tract, particularly in instances where the inclusion of antimicrobial growth promoters (AGP) is deliberately omitted from said diets.

zoology↗

bioRxiv2024

Physics-informed machine learning for automatic model reduction in chemical reaction networks

Physics-informed machine learning emerges as a transformative approach, bridging the gap between the high fidelity of mechanistic models and the adaptive, data-driven insights afforded by artificial intelligence and machine learning. In the realm of chemical reaction network modeling, this synergy is particularly valuable. It offers a solution to the pro-hibitive computational costs associated with detailed mechanistic models, while also capitalizing on the predictive power and flexibility of machine learning algorithms. This study exemplifies this innovative fusion by applying it to the critical biomedical challenge of A{beta} fibril aggregation, shedding light on the mechanisms underlying Alzheimers disease. A corner-stone of this research is the introduction of an automatic reaction order model reduction framework, tailored to optimize the scale of reduced order kinetic models. This framework is not merely a technical enhancement; it represents a paradigm shift in how models are constructed and refined. By automatically determining the most appropriate level of detail for modeling reaction networks, our proposed approach significantly enhances the efficiency and accuracy of simulations. This is particularly crucial for systems like A{beta} aggregation, where the precise characterization of nucleation and growth kinetics can provide insights into potential therapeutic targets. The potential generalizability of this automatic model reduction technique to other network models is a key highlight of this study. The methodology developed here has far-reaching implications, offering a scalable and adaptable tool for a wide range of applications beyond biomedical research. The ability to dynamically adjust model complexity in response to the specific demands of the system under study is a powerful asset. This flexibility ensures that the models remain both computationally feasible and scientifically relevant, capable of accommodating new data and evolving understandings of complex phenomena.

biochemistry↗

bioRxiv2024

A molecularly engineered lectin destroys EGFR and inhibits the growth of non-small cell lung cancer

Survival rates for non-small cell lung cancer (NSCLC) remain low despite the advent of novel therapeutics. Tyrosine kinase inhibitors (TKIs) targeting mutant epidermal growth factor receptor (EGFR) in NSCLC have significantly improved mortality but are plagued with challenges--they can only be used in the small fraction of patients who have susceptible driver mutations, and resistance inevitably develops. Aberrant glycosylation on the surface of cancer cells is an attractive therapeutic target as these abnormal glycosylation patterns are typically specific to cancer cells and are not present on healthy cells. H84T BanLec (H84T), a lectin previously engineered by our group to separate its antiviral activity from its mitogenicity, exhibits precision binding of high mannose, an abnormal glycan present on the surface of many cancer cells, including NSCLC. Here, we show that H84T binds to and inhibits the growth of diverse NSCLC cell lines by inducing lysosomal degradation of EGFR and leading to cancer cell death through autophagy. This is a mechanism distinct from EGFR TKIs and is independent of EGFR mutation status; H84T inhibited proliferation of both cell lines expressing wild type EGFR and those expressing mutant EGFR that is resistant to all TKIs. Further, H84T binds strongly to multiple and diverse clinical samples of both pulmonary adenocarcinoma and squamous cell carcinoma. H84T is thus a promising potential therapeutic in NSCLC, with the ability to circumvent the challenges currently faced by EGFR TKIs.

cancer biology↗

bioRxiv2024

3-epicaryoptin induces G2/M phase cell cycle arrest and apoptosis in human breast cancer cells by disrupting the microtubule network, an in vitro and in silico investigation

Breast cancer (BC) is a prevalent form of cancer observed in women across the globe, constituting over a quarter of all female BC cases. The treatment of BC continues to require significant efficacy, aiming to achieve high success rates while minimizing adverse effects on the body as a whole. In the current study, 3-epicaryoptin was tested for the molecular mechanism of its anti-cancer activity in the human breast cancer cell line, MCF-7. We investigated cell viability by MTT assay, cell cycle kinetics and apoptosis, immunofluorescence straining, molecular modelling, and ADMET profiling. MTT assay results showed that 3-epicaryoptin was found cytotoxic against MCF-7 cells with an IC50 value of 344.64 {micro}g mL-1 for 48 h. Flow cytometric analysis exhibited that 3-epicaryoptin halted the MCF-7 cells in the G2/M phase and subsequently induced apoptosis in a time-dependent manner. Our immunofluorescence studies indicated that 3-epicaryoptin inhibited microtubule polymerization in MCF-7 cells. Furthermore, molecular docking followed by molecular dynamics (MD) simulation studies demonstrated the ability of 3-epicaryoptin to interact with the tubulin protein at the colchicine binding pockets. Overall, our results suggest that 3-epicaryoptin can inhibit the proliferation of human breast cancer cells by depolymerizing of cellular microtubule networks, which causes cell cycle arrest and promotes apoptotic cell death. Therefore, it has been indicated that the natural product 3-epicaryoptin exhibited considerable promise as a potent therapeutic agent capable of inducing apoptosis in breast cancer cells.

cancer biology↗

bioRxiv2023

Ovine MyD88 have active role in host resistance against Haemonchus contortus infection

Host resistance against parasitic infestation is quite important to study in current days, since till date no effective vaccines against parasites have been developed. Moreover, indiscrimate use of regular deworming as a practice may lead to the development of resistance to antihelmiths (as in case of antibiotic resistance against bacteria) or development of antihelminth resistant strains among dreadly parasites. In this present study, we attempt to explore immune response gene against Haemonchus contortus as dreadly parasite against sheep model. In our lab, we have already detected some of such promising genes, namely RIGI (earlier known antiviral in action), CD14, IL6 and IL10 (earlier known antibacterial in action). In this current publication, we have explored the role of MyD88 in mediating resistance against parasitic infestation. We have characterized ovine MyD88 molecule, identified important domain, analyzed molecular docking, identified the binding site with H. contortus through in silico studies, network and pathway analysis, followed by differential mRNA expression profiling, ultimate confirmation through immunohistochemistry. Identification of immune response genes against parasites may lead to immunomodulation, genomic selection, gene therapy or even development of disease resistant stock of sheep through gene editing approach.

genomics↗

bioRxiv2023

DJ-1 products glycolic acid and D-lactate restore deficient axonal trafficking and DNA damage response in FUS and SOD1-associated amyotrophic lateral sclerosis

Amyotrophic Lateral Sclerosis (ALS) is the most common motor neuron disease leading to death within 2-5 years. Currently available drugs can only slightly prolong survival. Despite the progress that has been achieved in unravelling the molecular mechanisms of the disease so far, the underlying pathophysiology is not fully understood. We present novel insights into the pathophysiology of Superoxide Dismutase 1 (SOD1)- and in particular Fused In Sarcoma (FUS)-ALS by revealing a putatively central role of the Parkinsons disease (PD) associated glyoxylase DJ-1 and its products glycolic acid (GA) and D-lactic acid (DL). Combined, but not single, treatment with GA and DL restored axonal trafficking deficits of mitochondria and lysosomes in FUS- and SOD1-ALS patient-derived motoneurons (MNs). This was accompanied by restoration of mitochondrial membrane potential as well as mitochondrial fragmentation (FUS-ALS) or elongation (SOD1-ALS). Furthermore, GA and DL restored cytoplasmic mislocalization of FUS and FUS recruitment to DNA damage sites. We further show that despite presenting an early axonal transport deficiency as well, TDP-43 patient-derived MNs did not share this mechanism. While this points towards the necessity of individualized (gene-) specific therapy stratification, it also suggests common therapeutic targets across different gene variants of ALS. Thus, we introduce a putative novel treatment for ALS based on a combination of the two substances GA and DL which might be not only an interesting novel drug candidate in subsets of ALS cases but also in other neurodegenerative diseases characterized by mitochondrial depolarization.

neuroscience↗

bioRxiv2023

Metallo-protease Peptidase M84 from Bacillus altitudinis induces ROS dependent apoptosis in ovarian cancer cells by targeting PAR-1

In pursuit of isolating novel anticancer proteases from environmental microbial isolates, we have purified and identified an extracellular metallo-protease from Bacillus altitudinis named Peptidase M84. This protease selectively triggered apoptosis in human ovarian adenocarcinoma cells (PA-1, SKOV3) and mouse ovarian carcinoma cells (ID8), in addition to exhibiting no significant effect on normal human epithelial ovarian cell (IOSE) and mouse peritoneal macrophage (PEM[FE]) cell viabilities. Protease activated receptor-1 (PAR-1); a GPCR which is reported to be overexpressed in ovarian cancer cells was identified as a novel target of Peptidase M84. We observed that Peptidase M84 induced PAR-1 overexpression along with activating its downstream signalling effectors NF{kappa}B and MAPK to promote excessive reactive oxygen species (ROS) generation in ovarian cancer cells. This disrupted mitochondrial membrane potential, allowed cytosolic release of mitochondrial cytochrome c, increased the Bax (pro-apoptotic) to Bcl-2 (anti-apoptotic) ratio and promoted DNA damage to evoke apoptotic death of the ovarian cancer cells. Peptidase M84 also reduced nuclear ki-67 expression in these malignant cells to render an anti-proliferative role. In in vivo set-up, weekly intraperitoneal administration of Peptidase M84 (12 {micro}g/kg body-weight) in the ID8 mice model significantly diminished ascitic fluid accumulation through induction of oxidative stress, increasing murine survival rates by 60%. Collectively, our in vitro and in vivo findings suggested that Peptidase M84 triggered PAR-1 mediated oxidative stress to act as an apoptosis inducer in ovarian cancer cells. This established Peptidase M84 as a promising drug candidate for receptor mediated targeted-therapy of ovarian cancer. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=158 HEIGHT=200 SRC="FIGDIR/small/556500v2_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@6b0a19org.highwire.dtl.DTLVardef@1640510org.highwire.dtl.DTLVardef@1888b49org.highwire.dtl.DTLVardef@1708114_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2023

Mitochondrial genes affect the immune response against bacterial infection (Duck Pasteurellosis) through a cascade of mechanisms mediated by nuclear immune genes- a cross talk with nuclear and mitochondrial gene

Mitochondria possess 37 genes of its own, helpful for carrying out various functions including oxidative phosphorylation. But the mitochondria is neither independent in terms of its structure, nor its function, it depend upon nuclear gene for its functionality and replication. Our lab has earlier reported the role of mitochondrial genome in controlling health and reproduction in animal model. Reports also indicate that mitochondria have role in immune response against bacterial infection. In our current study, we depict the role of two polypeptide coding mitochondrial gene as cytochrome B and cytochrome C in providing host immunity against bacterial disease (Duck Pasteurellosis). We further observe that the mechanism was governed by cascade of mechanisms mediated through nuclear genes NRLP3, IL18 and Sting. In the first phase of the study, we have characterized Cytochrome B and Cytochrome C genes from Bengal duck and quantified through the assesment of the expression profiling with respect to healthy and Pasteurella infected ducks following a natural challenge with Pasteurella multocida. In the next phase of our study, we have characterized the above nuclear genes in Bengal duck and attempted to correlate the expression with mitochondrial genes. We attempted to explore the mechanism of pathway how mitochondrial DNA triggers the nuclear immune response leading to destruction of bacterial pathogen. Molecular docking revealed how IL18 directly binds with the pathogen. This is the first report in animal model.

genomics↗

bioRxiv2023

Role of NUMTs (Nuclear mitochondrial DNA) genes in affecting disease resistance in duck against Pasteurellosis

Ducks are mostly resistant to common avian diseases, but frequent occurrence of duck pasteurellosis, commonly kown as Duck Cholera, caused by Pasteurella multocida may cause a loss. In our earlier studies, we have identified certain immune response genes of nuclear origin as well as mitochondrial genes in duck, conferring resistance against duck cholera. In our current study, we have detected certain NUMT (Nuclear mitochondrial) genes in duck with certain role in disease resistance in case of duck cholera. NUMT genes are basically nuclear genes, but they act through mitochondria. Identified NUMT genes (Thymidine phosphorylase/ endothelial cell growth factor1 gene, TFAM Transcription factor A, mitochondrial, TK2 Thymidine kinase 2) were characterized and certain important domains were identified. Differential mRNA expression profiling revealed upregulation of the genes in healthy ducks compared to that of infected ducks. Exploitation of the identified genes may lead to development of ducks resistant to duck Cholera.

genomics↗

bioRxiv2023

Role of IL-6 and IL10 immune response genes against nematode Haemonchus contortus in ovis aries- a novel report

Haemonchus contortus is one of the most deadly parasites affecting sheep industry causing heavy economic loss. In our earlier study, we have reported RIGI, an earlier established antiviral molecule and CD14 (an earlier established antibacterial molecule) to have potential role in antiparasitic immunity for the first time. In this current study, we aim to clone and sequence the IL-6 and IL10 genes in sheep (Ovis aries) and utilized bioinformatics methods to analyze and compare the functional and structural domains of peptides produced from IL6 and IL10. Furthermore, the study explored these domains in three-dimensional structures. The findings of this study provide molecular characterization of IL-6 and IL10 in sheep, which is essential for advancing our understanding of functional immune responses in this animal. We report IL6 and IL10 to have potential antiparasitic role against H. contortus for first time. The production of these molecules opens up possibilities for its potential use as recombinant proteins to manipulate the immune response. Evaluating its value in vaccine research and gaining a broader understanding of its role in immune responses becomes feasible with the availability of IL-6 and IL10. Moreover, the differential mRNA expression levels of IL-6, IL10 between healthy and diseased sheep indicate its crucial role in maintaining homeostasis and mounting immune responses. IL10 acts as receptor for H. contortus. The identification of this immune-responsive gene also offers new avenues for investigating long-term resistance to H. contortus infection in sheep.

genomics↗

bioRxiv2023

Upstream regulator of genomic imprinting in rice endosperm is a small RNA-associated chromatin remodeler

Genomic imprinting is observed in endosperm, a placenta-like seed tissue, where transposable elements (TEs) and repeat-derived small(s)RNAs mediate epigenetic changes in plants. In imprinting, uniparental gene expression arises due to parent-specific epigenetic marks on one allele but not on the other. The importance of sRNAs and their regulation in endosperm development or in imprinting is poorly understood in crops. Here we show that a previously uncharacterized CLASSY (CLSY)-family chromatin remodeler named OsCLSY3 is essential for rice endosperm development and imprinting, acting as an upstream player in sRNA pathway. Comparative transcriptome and genetic analysis indicated its endosperm-preferred expression and its paternally imprinted nature. These important features were modulated by RNA-directed DNA methylation (RdDM) of tandemly arranged TEs in its promoter. Upon perturbation of OsCLSY3 in transgenic lines we observed defects in endosperm development and loss of around 70% of all sRNAs. Interestingly, well-conserved endosperm-specific sRNAs (siren) that are vital for reproductive fitness in angiosperms were dependent on OsCLSY3. We also observed many imprinted genes and seed development-associated genes under the control of CLSY3-dependent RdDM. These results support an essential role of OsCLSY3 in rice endosperm development and imprinting, and propose similar regulatory strategies involving CLSY3 homologs among other cereals. HighlightsO_LIUnlike among dicots, in rice and maize, CLSY3 is a maternally expressed imprinted gene majorly expressed in endosperm. C_LIO_LIEndosperm-preferred expression of OsCLSY3 is regulated by RNA-directed DNA methylation at two tandem transposon elements present in its promoter. C_LIO_LIOsCLSY3 is crucial for endosperm development and grain filling. It regulates expression of key seed development and endosperm-specific imprinted genes through RNA directed DNA methylation. C_LI

plant biology↗

bioRxiv2023

PP2A and GSK3 act as modifiers of FUS-ALS by modulating mitochondrial transport

ALS is a fatal neurodegenerative disease which currently lacks effective treatments. Mutations in the RNA-binding protein FUS are a common cause of familial ALS, accounting for around 4% of fALS cases. Studying the mechanisms by which mutant FUS is toxic to neurons may provide insight into the pathogenesis of both familial and sporadic forms of ALS. Here we identify Protein Phosphatase 2A (PP2A) and Glycogen Synthase Kinase 3 (GSK3) as novel modifiers of FUS-ALS in vivo, looking from fly to human. PP2A-C and GSK3{beta} inhibition rescued FUS-induced toxicity in Drosophila and disease-relevant phenotypes in human iPSC-derived spinal motor neurons (sMNs). In both Drosophila and human iPSC-sMNs, we observed reduced GSK3{beta} inhibitory phosphorylation, suggesting that FUS dysfunction results in GSK3{beta} hyperactivity. We found that PP2A acts upstream of GSK3, affecting its inhibitory phosphorylation, and in synergy they modulate mitochondrial transport through the motor protein kinesin. Our data provide in vivo evidence that PP2A and GSK3 are disease modifiers, and reveal an unexplored mechanistic link between PP2A, GSK3 and kinesin in FUS-associated ALS.

neuroscience↗

bioRxiv2023

Development of Gemcitabine-Modified miRNA Mimics as Cancer Therapeutics for Pancreatic Ductal Adenocarcinoma

Pancreatic cancer, including its most common subtype, pancreatic adenocarcinoma (PDAC), has the lowest five-year survival rate among patients with pancreatic cancer in the United States. Despite advancements in anticancer treatment, the overall median survival for patients with PDAC has not dramatically improved. Therefore, there is an urgent need to develop new strategies of treatment to address this issue. Non-coding RNAs, including microRNAs (miRNAs), have been found to have major roles in carcinogenesis and the subsequent treatment of various cancer types like PDAC. In this study, we developed a treatment strategy by modifying tumor suppressor miRNAs, hsa-miRNA-15a (miR-15a) and hsa-miRNA-194-1 (miR-194), with the nucleoside analog chemotherapeutic gemcitabine (Gem) to create Gem-modified mimics of miR-15a (Gem-miR-15a) and miR-194 (Gem-miR-194). In a panel of PDAC cell lines, we found that Gem-miR-15a and Gem-miR-194 induce cell cycle arrest and apoptosis, and these mimics are potent inhibitors with IC50 values up to several hundred fold less than their native counterparts or Gem alone. Furthermore, we found that Gem-miR-15a and Gem-miR-194 retained miRNA function by downregulating the expression of several key targets including WEE1, CHK1, BMI1, and YAP1 for Gem-miR-15a, and FOXA1 for Gem-miR-194. We also found that our Gem-modified miRNA mimics exhibit an enhanced efficacy compared to Gem alone in patient-derived PDAC organoids. Furthermore, we observed that Gem-miR-15a significantly inhibits PDAC tumor growth in vivo without observing any noticeable signs of toxicity. Overall, our results demonstrate the therapeutic potential of Gem-modified miRNAs as a treatment strategy for PDAC. One Sentence SummaryYuen and Hwang et. al. have developed a potent therapeutic strategy for patients with pancreatic cancer by modifying microRNAs with gemcitabine.

cancer biology↗

bioRxiv2023

microRNA-22 displaces ITAFs from the 5'UTR and inhibit the translation of Coxsackievirus B3 RNA

microRNAs play an essential role in gene regulation during virus infections and have major consequences on viral pathogenesis. During RNA virus infections, the host miRNAs can target both host mRNAs and the virus genomic RNA. Using the CVB3 virus as a model, we have investigated how a host miRNA can target viral genomic RNA and act as an antiviral factor limiting the growth of the virus. CVB3 is an RNA virus whose infection causes myocarditis and, eventually, dilated cardiomyopathy. We shortlisted miRNAs with a potential binding site in the CVB3 genomic RNA. Among these, miR-22 was picked for further studies as its binding site was putatively located in a region in the CVB3 5 UTR, important for recruiting ITAFs and ribosomes for IRES-mediated translation. Using mutational analysis and pull-down assays, we first confirmed the binding of miR-22 on the 5UTR. This binding negatively regulated the translation of CVB3 RNA. However, miR-22 binding-defective mutant of CVB3 RNA had no effect of miR-22 overexpression and could translate normally. Moreover, cells from which miR-22 was knocked out, showed a higher level of CVB3 infection as compared to the wild type. We have further demonstrated that the binding of miR-22 interferes with the recruitment of several ITAFs (La, PSF, and PTB) on viral mRNA. This abrogates the spatial structure necessary for ribosome recruitment on the CVB3 RNA, ultimately inhibiting its translation. Also, the level of miR-22 increases 4 hours post-infection, presumably after the synthesis of viral 2A protease, to regulate infection in the host cell more effectively. Along with the direct effect on viral RNA, the altered level of miR-22 affects the level of its cellular targets which might contribute to CVB3 infection. To identify the possible players, we obtained a list of miR-22 targets and performed pathway analysis. Several targets were shortlisted among the top hits and their levels upon CVB3 infection were checked. Protocadherin-1 (PCDH-1), a single-pass transmembrane protein, followed an expected trend, and its levels were significantly downregulated upon CVB3 infection in miR-22 dependent manner. miR-22 mediated suppression of PCDH1 levels during CVB3 infection points towards the possible role of miR-22 in either modulating antiviral signaling or in virus entry, in addition to regulating the viral translation.

molecular biology↗

bioRxiv2023

Avifaunal Species diversity from Southern West part of West Bengal, India

Birds are essential for stabilizing the balance between various ecosystems. To estimate their diversity, we studied species distribution and made an annotated checklist along with their feeding habitats in the Southwest part of West Bengal, India. We studied the bird diversity using the point count method on various habitats, including agroforest, grassland, sub-tropical forest, and plateau forest regions. A total of 343 species were identified during our study period (2015-2019). We found high species diversity and sightings in the study sites, with 55 new records for the region. The whole study was conducted using a citizen science approach and amateur bird watchers community. This study will emphasize the future biodiversity conservation practice for the avifauna.

ecology↗