Biology subjects

Banerjee, D.

Publications and source records attributed to Banerjee, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Variant-Specific Rewiring of Lysosomal Positioning by STARD9 Produces Opposite Cholesterol Trafficking Outcomes

Residual cardiovascular risk persists despite lipid-lowering therapy, independent of LDL and Lp(a), reflecting cholesterol dysregulation. We identify STARD9, a lysosomal cholesterol-sensing kinesin, as a causal gene for divergent familial dyslipidemias and premature atherosclerosis. Its START domain binds cholesterol to govern lysosomal positioning. Rare variants segregate with autosomal dominant hypercholesterolemia and premature coronary disease, while common variants associate with reduced HDL and elevated triglycerides. Both converge on lysosomal cholesterol sequestration, ER depletion, mTORC1 SREBP2 activation, impaired autophagy, and NF-kB inflammation, yet diverge through opposite lysosomal positioning: the rare variant disperses lysosomes peripherally, phenocopying START domain loss across cholesterol sequestration, lysosomal positioning, and TFEB activation, triggering LDLR degradation and CASM/TFEB-dependent efflux that preserves HDL, whereas the common variant causes perinuclear retention that suppresses TFEB dependent lipid-handling transcripts, yielding hypertriglyceridemia and low HDL. In Stard9-knockout mice, enterocyte cholesterol sequestration drives SREBP2 dependent NPC1L1 upregulation and apical localization, increasing intestinal cholesterol absorption. These findings position lysosomal cholesterol trafficking as a targetable node in statin-refractory cardiovascular disease.

genetics↗

bioRxiv2026

FTO-Dependent m6A RNA Dysregulation Underlies Memory Deficits Induced by Early-Life Stress

Cognitive functions in adults are mainly attributed to experience-dependent plasticity. Nonetheless, the developmental encoding of memory deficits is still inadequately addressed. Here, we demonstrate that early-life stress (ELS) reprograms the hippocampal epitranscriptome by enhancing N6-methyladenosine (m6A) deposits during early development leading to memory deficit in adulthood. We observed a shift toward hypermethylation of transcripts including coding and non-coding RNAs (lncRNAs) following maternal separation. We also observed that these transcripts encoding proteins necessary for translational regulation, ribosome biogenesis and mitochondrial function. This epitranscriptomic change is driven by ELS-induced downregulation of the m6A demethylase FTO (Fat mass and obesity-associated protein). We observe that the overexpression of FTO in young adult mice selectively rescues memory deficits without ameliorating elevated anxiety. Further, the knockdown of FTO in primary hippocampal neuron, mimicking ELS - induced reduction of its expression, leads to reduced translation as detected by puromycin labelling. Taken together, our study demonstrated previously uncharacterized mechanism of ELS-induced epitranscriptomic change linked with memory deficit via the regulation of protein synthesis.

neuroscience↗

bioRxiv2026

Evaluation of Significance of SERPINA3 and SPP1 in Driving Glioma Progression Through Dysregulation of Brain Inflammatory Pathway

Glioma is a highly aggressive malignancy with a poor prognosis, particularly in grade IV glioblastoma. The monitoring of disease progression remains challenging due to high heterogeneity in the tumour and a lack of progressive markers to keep track of the tumour progression. This scarcity of good progressive biomarkers has led us to search for better options. SERPINA3 and SPP1 were investigated as potential dual biomarkers reflecting tumour microenvironment and enabling assessment of progression. In silico analysis was conducted, where correlation analysis was performed to evaluate the cell-type specificity of SERPINA3 in astrocytes and SPP1 in microglial cells, with comparisons across other neural populations in both low-grade glioma and glioblastoma. Pan-cancer expression analysis was conducted to determine whether these biomarkers remain significantly elevated in glioma relative to other malignancies, including hepatocellular carcinoma, given their hepatic origin. Alzheimers disease datasets were analysed to verify the relevance in neurodegenerative diseases. The in-silico analysis revealed that SERPINA3 and SPP1 show astrocytic and microglial specificity, respectively, and exhibit their highest expression levels in glioma across cancers. Co-expression analysis further identified enrichment of immunoregulatory pathways alongside upregulated oxidative stress-associated markers, highlighting the functional relevance of these biomarkers within the glioma microenvironment.

neuroscience↗

bioRxiv2025

A Novel Therapeutic Approach: Notch Inhibition Enhances Radiotherapy and Checkpoint Blockade Therapy via Reprogramming of the Tumor Microenvironment

BackgroundHigh-dose radiotherapy (RT) in cancer is immunogenic but also induces an immunosuppressive tumor microenvironment (TME) that limits the efficacy of immune checkpoint inhibitors (ICIs). Overcoming this immunosuppressive barrier is therefore critical to unlocking the full potential of RT-ICI combinations. As Notch signaling regulates tumor microenvironment, we hypothesized that the {gamma}-secretase inhibitor (GSI), AL101, would suppress radiation-induced immunosuppression and enhance antitumor efficacy when combined with RT and anti-PD-1 (aPD-1) therapy. MethodsSyngeneic neuroblastoma (9464D) and triple-negative breast cancer (EO771) tumors were established in C57BL/6, macrophage-depleted C57BL/6 mice, or athymic mice. Mice received 12 Gy RT (day 3), AL101 (6.5 mg/kg daily, day 0-9), and aPD-1 (days 0, 3, 6). Tumors were analyzed by spectral flow cytometry and single-cell RNA sequencing (scRNA-seq), and lung metastases were evaluated histologically. ResultsThe triple combination of RT, aPD-1, and GSI produced durable tumor growth inhibition and significantly prolonged survival in both models, with median survival more than doubled compared to all other treatment groups. Triple therapy also markedly reduced lung metastases in EO771 mice. These effects were abrogated in athymic nude mice and macrophage-depleted immunocompetent mice, consistent with an immune-dependent mechanism. Based on scRNA-seq and spectral flow cytometry analysis, RT alone increased exhausted T cells and immunosuppressive macrophages, while triple therapy reversed these effects, including expansion of activated CD8 T cells, reduction of Tregs and exhausted T cells, restoration of cross-presenting CD103 dendritic cells, and reprogramming of myeloid cells toward a proinflammatory state. ConclusionsGSI remodels the RT-induced immunosuppressive TME and potentiates the efficacy of RT + ICI. GSI combined with RT+aPD-1 reprograms the TME toward an immunostimulatory state and supports GSI as a promising immuno-radiotherapeutic strategy with strong translational potential.

cancer biology↗

bioRxiv2025

Quantifying the impact of genetic mutations on enhancer dynamics

Transcriptional regulation is mediated by enhancers, yet how genetic perturbations alter enhancer activity and gene expression remains poorly understood. We developed UDI-UMI-STARR-seq, which integrates dual indexes and unique molecular identifiers, and combined it with RNA-seq to profile the effects of perturbations on enhancer activity and target gene expression. We applied this approach to a library of 253,632 fragments representing 46,142 cell type-specific candidate enhancers and assessed the impact of CRISPR/Cas9-mediated deletion of six transcription factors (or TFs; ATF2, CTCF, FOXA1, LEF1, TCF7L2, and SCRT1) with diverse regulatory roles. Across knockout lines, we identified responsive enhancers that were either repressed or induced, often through motifs such as the p53 family of TFs. Enhancer-gene mapping revealed TF-specific programs, including repression of Wnt/p53 targets with ATF2 or LEF1 loss, downregulation of the FIRRE locus with CTCF loss, and compensatory upregulation of RNA polymerase II regulators following FOXA1 depletion. A deep learning model trained on enhancer sequences recapitulated core principles of enhancer grammar, including cooperative motif syntax and the influence of flanking sequence context. Applying this framework to the neurodevelopmental disorder-associated 16p12.1 deletion identified responsive enhancers linked to genes involved in axon guidance, synaptic plasticity, and translational control, providing a scalable readout of enhancer dynamics generalizable to genetic mutations.

genomics↗

bioRxiv2025

RNA 2'-OH modification with stable reagents enabled bynucleophilic catalysis

RNA modification at 2-OH has typically required highly reactive acylating species that exhibit short half-lives in water, challenging purification, and limited shelf lives. Here, we investigate the use of more stable species as electrophilic reagents, employing nucleophilic catalysis to promote reactions. Results show that multiple previously unreported electrophiles can react in high stoichiometric yields with RNA under appropriate catalysis. Most notably, aryl esters can transfer acyl groups to RNA in one hour, but are stable for months even in pure water. The results expand the functional chemotypes of RNA-reactive species, and identify reagent classes with improved stability and selectivity.

biochemistry↗

bioRxiv2025

C-Nucleosides Stabilize RNA by Reducing Nucleophilicity at 2'-OH

Nucleotides with carbon substitution for heteroatoms are common in biological and therapeutic RNAs. Important examples include the C-nucleosides pseudouridine and N1-methyl-pseudouridine; these modifications were reported to slow degradation of large RNAs, but the mechanism is unknown. We measured kinetics of spontaneous and enzymatic cleavage at a single bond of synthetically modified RNAs, and find that carbon substitution markedly reduces strand cleavage rates in RNA by both mechanisms. Studies of nucleophilic acylation reactions of RNAs and of small alcohols of varied pKa suggest that reduced inductive effects resulting from carbon substitution for electronegative atoms results in both higher pKa and lower nucleophilicity. The results provide insight into native transcriptome modifications as well as RNA therapies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=157 SRC="FIGDIR/small/666442v2_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@73c194org.highwire.dtl.DTLVardef@1aa0af7org.highwire.dtl.DTLVardef@b5f8a0org.highwire.dtl.DTLVardef@d601fa_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOTOC GraphicC_FLOATNO C_FIG SynopsisThis study reveals mechanisms by which modifications found in native and therapeutic RNAs enhance RNA stability. Carbon substitution for nitrogen or oxygen results in reduced 2'-OH nucleophilicity.

biophysics↗

bioRxiv2024

Transcriptome signatures of the medial prefrontal cortex underlying GABAergic control of resilience to chronic stress exposure

Analyses of postmortem human brains and preclinical studies of rodents have identified somatostatin (SST)-positive interneurons as key elements that regulate the vulnerability to stress-related psychiatric disorders. Conversely, genetically induced disinhibition of SST neurons or brain region-specific chemogenetic activation of SST neurons in mice results in stress resilience. Here, we used RNA sequencing of mice with disinhibited SST neurons to characterize the transcriptome changes underlying GABAergic control of stress resilience. We found that stress resilience of male but not female mice with disinhibited SST neurons is characterized by resilience to chronic stress-induced transcriptome changes in the medial prefrontal cortex. Interestingly, the transcriptome of non-stressed stress-resilient male mice resembled the transcriptome of chronic stress-exposed stress-vulnerable mice. However, the behavior and the serum corticosterone levels of non-stressed stress-resilient mice showed no signs of physiological stress. Most strikingly, chronic stress exposure of stress-resilient mice was associated with an almost complete reversal of their chronic stress-like transcriptome signature, along with pathway changes indicating stress-induced enhancement of mRNA translation. Behaviorally, the mice with disinhibited SST neurons were not only resilient to chronic stress-induced anhedonia -- they also showed an inversed anxiolytic-like response to chronic stress exposure that mirrored the chronic stress-induced reversal of the chronic stress-like transcriptome signature. We conclude that GABAergic dendritic inhibition by SST neurons exerts bidirectional control over behavioral vulnerability and resilience to chronic stress exposure that is mirrored in bidirectional changes in expression of putative stress resilience genes, through a sex-specific brain substrate.

neuroscience↗

bioRxiv2024

Flynotyper 2.0: A tool for rapid quantitative assessment of Drosophila eye phenotypes

About two-thirds of the genes in the Drosophila melanogaster genome are also involved in its eye development, making the Drosophila eye an ideal system for genetic studies. We previously developed Flynotyper, a software that uses image processing operations to identify and quantify the degree of roughness by measuring disorderliness of ommatidial arrangement in the fly eye. This software has enabled researchers to quantify morphological defects of thousands of eye images caused by genetic perturbations. Here, we present Flynotyper 2.0, a software that has an updated computer vision library, improved performance, and a streamlined pipeline for high-throughput analysis of multiple eye images. We also tested several batches of Drosophila eye images to ensure robustness and reproducibility of the updated Flynotyper 2.0 software. Availability and implementationThe source code for Flynotyper 2.0 can be downloaded and installed from https://github.com/girirajanlab/flynotyper-desktop-application.

bioinformatics↗

bioRxiv2024

Plasma Proteomics of Genetic Brain Arteriosclerosis and Dementia Syndrome Identifies Signatures of Fibrosis, Angiogenesis, and Metabolic Alterations

Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is the most common monogenic form of vascular cognitive impairment and dementia. A genetic arteriolosclerotic disease, the molecular mechanisms driving vascular brain degeneration and decline remain unclear. With the goal of driving discovery of disease-relevant biological perturbations in CADASIL, we used machine learning approaches to extract proteomic disease signatures from large-scale proteomics generated from plasma collected from three distinct cohorts in US and Colombia: CADASIL-Early (N = 53), CADASIL-Late (N = 45), and CADASIL-Colombia (N = 71). We extracted molecular signatures with high predictive value for early and late-stage CADASIL and performed robust cross- and external-validation. We examined the biological and clinical relevance of our findings through pathway enrichment analysis and testing of associations with clinical outcomes. Our study represents a model for unbiased discovery of molecular signatures and disease biomarkers, combining non-invasive plasma proteomics with clinical data. We report on novel disease-associated molecular signatures for CADASIL, derived from the accessible plasma proteome, with relevance to vascular cognitive impairment and dementia.

neuroscience↗

bioRxiv2024

Bottlenecks in the Implementation of Genome Scale Metabolic Model Based Designs for Bioproduction from Aromatic Carbon Sources

Genome scale metabolic models (GSMM) are commonly used to identify gene deletion sets that result in growth coupling, pairing product formation with substrate utilization. While such approaches can improve strain performance beyond levels typically accessible using targeted strain engineering approaches, sustainable feedstocks often pose a challenge for GSMM-based methods due to incomplete underlying metabolic data. Specifically, we address a four-gene deletion design for the lignin-derived non-sugar carbon source, para-coumarate, that proved challenging to implement. We examine the performance of the fully implemented design for p-coumarate to glutamine, a useful biomanufacturing intermediate. In this study glutamine is then converted to indigoidine, an alternative sustainable pigment and a model heterologous product. Through omics, promoter-variation and growth characterization of a fully implemented gene deletion design, we provide evidence that aromatic catabolism in the completed design is rate-limited by fumarate hydratase activity in the citrate cycle and required careful optimization of the final fumarate hydratase protein (PP_0897) expression to achieve growth and production. A metabolic cross-feeding experiment with the completed design strain also revealed an unanticipated nutrient requirement suggesting additional functions for the fumarate hydratase protein. A double sensitivity analysis confirmed a strict requirement for fumarate hydratase activity in the strain where all genes in the growth coupling design have been implemented. While a complete implementation of the design was achieved, this study highlights the challenge of precisely inactivating metabolic reactions encoded by under-characterized proteins especially in the context of multi-gene edits.

microbiology↗

bioRxiv2024

Wastelands or Preferred-lands? Indicators for redefining Desert conservation

Desert ecosystems though crucial in shaping global climate, are often perceived to have limited function and are frequently designated as wastelands due to low biotic diversity and abundance. We explore the functional properties of desert through assessment of spatio-temporal variations of avian species richness and insect abundance of the relatively understudied Thar in Rajasthan. The study was conducted across four contrasting ecoregions (Western Thar (WT), Eastern Thar (ET), Transitional Zone (TZ), and Cultivated Zone (CZ) spanning 33 counties of Rajasthan. Monthly avian diversity were obtained from crowdsourced eBird data. Insect diversity and abundance accross the ecoregions were curated from the annual surveys of ZSI, India. The leads were corroborated with five years feeding behaviour observational data recorded from a representative site spanning 852 acres. There was a significant seasonal differences in bird species richness between the ecoregions with the most pronounced variations between summer and winter and CZ exhibiting the highest spatial variability followed by WT. WT also recorded the highest insect diversity and abundance, especially the orders Orthoptera, Hymenoptera, Coleoptera, Lepidotera and Diptera. The correlation matrix between bird and insect abundance and Kernel Density Estimation (KDE) plot indicated the relation between diverse dietary preferences and migratory patterns. These observations challenge the conventional notion that resource-limited environments harbour lesser biodiversity especially in arid environments. The dominance of insectivory among winter migrants aligns with the higher density of resident arthropods and emphasizes the pivotal role of insects as a food source during the migratory period. The adaptability of resident species to varied food sources, particularly arthropods, provides a means to strategically navigate during resource constraints. This study thus provides a unique framework to (a) redefine the functional importance of desert using migratory birds as prominent ecological indicators. (b) include an ecological criteria during policy formulation for biodiversity conservation. It also emphasizes reevaluation of deserts during designation of wastelands especially in the unique WT eco-regions when evolving developmental as well as ecological restoration strategies.

ecology↗

bioRxiv2023

Sustainable production of 2,3,5,6-Tetramethylpyrazine at high titer in engineered Corynebacterium glutamicum using statistical design of experiments

BackgroundThe industrial amino acid production workhorse, Corynebacterium glutamicum naturally produces low levels of 2,3,5,6-tetramethylpyrazine (TMP), a valuable flavor, fragrance and commodity chemical. We have previously reported serendipitous production of TMP in C. glutamicum strains. In the present study, we demonstrate TMP production in C. glutamicum type strain ATCC13032 via the expression of a heterologous TMP pathway in a defined medium followed by statistical design of experiments to understand the effect of the media composition on TMP production. ResultsThe C. glutamicum strain engineered to overexpress acetolactate synthase and alpha-acetolactate decarboxylase from Lactococcus lactis produced [~]0.8 g/L TMP in CGXII minimal medium supplemented with 40 g/L glucose in 24-deep well plates. This engineered strain also demonstrated growth and TMP production when the minimal medium was supplemented with up to 40% (v/v) hydrolysates derived from ionic liquid pretreated sorghum biomass. A screen for improvements in media composition on TMP titer was conducted using fractional factorial design that identified glucose and urea as significant components affecting TMP production. These two components were further optimized using response surface methodology. In the optimized CGXII medium, the engineered strain could produce up to 3.56 g/L TMP (4-fold enhancement in titers and 2-fold enhancement in yield, mol/mol) from 80 g/L glucose and 11.9 g/L urea in shake flask batch cultivation. ConclusionsWe engineered the industrially relevant host, C. glutamicum for targeted production of TMP by heterologous expression of pathway proteins. We demonstrated the capability of the engineered strain for growth and TMP production utilizing real world carbon streams such as hydrolysates. We further identified glucose and urea as the key minimal media components significantly affecting TMP production using statistical media optimization.

synthetic biology↗

bioRxiv2023

Gas5 regulates early life stress-induced anxiety and spatial memory

Early life stress (ES) induced by maternal separation (MS) remains a proven causality of anxiety and memory deficits at later stages of life. Emerging studies have shown that MS-induced gene expression in the hippocampus is operated at the level of transcription. However, the extent of involvement of non-coding RNAs in MS-induced behavioural deficits remains unexplored. Here, we have investigated the role of synapse-enriched long non-coding RNAs (lncRNAs) in anxiety and memory upon MS. We observed that MS led to an enhancement of expression of the lncRNA Gas5 (Growth Arrest Specific-5) in the hippocampus; accompanied by increased levels of anxiety and deficits in spatial memory. Gas5 knockdown in early life was able to reduce anxiety and partially rescue the spatial memory deficits of maternally separated adult mice. However, the reversal of MS-induced anxiety and memory deficits is not attributed to Gas5 activity during neuronal development as Gas5 RNAi did not influence spine development. Gene Ontology analysis revealed that Gas5 exerts its function by regulating RNA metabolism and translation. Our study highlights the importance of MS-regulated lncRNA in anxiety and spatial memory.

neuroscience↗

bioRxiv2023

A 3D Printed Ventilated Perfused Lung Model Platform to Dissect the Lung's Response to Viral Infection in the Presence of Respiration

In this study, we developed a three-dimensionally (3D) printed lung model that faithfully recapitulates the intricate lung environment. This 3D model incorporated alveolar and vascular components that allow for a comprehensive exploration of lung physiology and responses to infection in vitro. In particular, we investigated the intricate role of ventilation on formation of the alveolar epithelial layer and its response to viral infections. In this regard, we subjected our 3D printed, perfused lung model to a continuous respiratory cycle at the air-liquid interface (ALI) for up to 10 days followed by infection with two viruses: influenza virus (Pr8) and respiratory syncytial virus (RSV), at two different concentrations for 24 or 48 h. The results revealed that ventilation induced increased tight-junction formation with better epithelial barrier function over time, facilitated higher expression of alveolar epithelial specific genes, enabled higher level of infection with an increased progression of viral spread and replication over time, and modulated the production of pro-inflammatory cytokines and chemokines. Our findings represent a critical step forward in advancing our understanding of lung-specific viral responses and respiratory infections in response to ventilation, which sheds light on vital aspects of pulmonary physiology and pathobiology.

bioengineering↗

bioRxiv2023

Gestures Of Hunger: Uncovering Intentional Gestural Communication In Free-Ranging Hanuman Langurs

Contrary to previous beliefs, intentional gestural communication (IGC) is not exclusive to the hominoid lineage but is also present in other non-human primates. Here, we report the presence of IGC among free-ranging Hanuman langur troop in Dakshineswar, West Bengal, India. These langurs exhibit a food-requesting behaviour wherein they use several gestures to communicate with the humans nearby. Moreover, they can also assess the recipients mental state and persistently check if the signal (food request) has been received, waiting until they receive the desired food item. We have identified eight begging gestures used by langurs of all ages, except infants. The most common gesture is by holding cloth (BGc), but provocation-initiated begging (BGpi) and begging by embracing legs (BGe) efficiently direct these events to its success. The frequency of successful begging events is higher in the evening due to increased human interactions. Our findings suggest that ontogenetic ritualization might be at play here among these troop members as this gestural communication has been learned through imitation and reinforced by the reward of receiving food. Moreover, these successful begging events serve as an effective foraging strategy for urban-adapted langurs, allowing them to acquire high-calorie processed food items within a human-modified urban ecosystem.

animal behavior and cognition↗

bioRxiv2023

Transcriptomic analysis identifies synapse-enriched lncRNAs required for glutamatergic synapse development and fear memory consolidation.

Regulatory functions of lncRNAs in neurons have been majorly limited to the nucleus. The identity of synaptic lncRNAs and their functional roles associated with synapse development and plasticity are poorly understood. Transcriptomic analysis from synaptoneurosomes identified 94 synapse-enriched lncRNAs from the mouse hippocampus. We find Pvt1 to be a specific regulator of excitatory, not inhibitory, synapse development. Synapse-specific loss of Pvt1 regulates synaptic activity and the downregulation of mRNAs pertinent to synapse development. We also report a synapse-centric role for an uncharacterized lncRNA; 2410006H16Rik (SynLAMP); in translation and memory formation. SynLAMP demonstrates enhanced localization to the synapse following fear conditioning and regulates dendritic translation by sequestering the translation repressor FUS; acting as a molecular decoy. Synapse-specific knockdown of SynLAMP inhibits the localised, activity-dependent translation of CamK2a, a FUS target. SynLAMP RNAi occludes fear-memory formation. Comprehensively, our study highlights that de novo activity of lncRNAs are involved in diverse synaptic functions.

neuroscience↗

bioRxiv2023

Genome-scale and pathway engineering for the sustainable aviation fuel precursor isoprenol production in Pseudomonas putida

Sustainable aviation fuel (SAF) will significantly impact global warming in the aviation sector, and important SAF targets are emerging. Isoprenol is a precursor for a promising SAF compound DMCO (1,4-dimethylcyclooctane), and has been produced in several engineered microorganisms. Recently, Pseudomonas putida has gained interest as a future host for isoprenol bioproduction as it can utilize carbon sources from inexpensive plant biomass. Here, we engineer metabolically versatile host P. putida for isoprenol production. We employ two computational modeling approaches (Bilevel optimization and Constrained Minimal Cut Sets) to predict gene knockout targets and optimize the "IPP-bypass" pathway in P. putida to maximize isoprenol production. Altogether, the highest isoprenol production titer from P. putida was achieved at 3.5 g/L under fed-batch conditions. This combination of computational modeling and strain engineering on P. putida for an advanced biofuels production has vital significance in enabling a bioproduction process that can use renewable carbon streams.

synthetic biology↗