Biology subjects

Dey, A.

Publications and source records attributed to Dey, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Interactions of Natural Compounds and Biomolecules with Hepatitis C Virus RNA Untranslated Regions: Exploring Structural Modifications to Advance Pathogenesis Understanding and Antiviral Strategy Design

Hepatitis C virus (HCV), a 10 kb positive-strand RNA virus, primarily infects liver cells and is a major cause of liver cirrhosis, which can progress to hepatocellular carcinoma. The HCV RNA untranslated regions (UTRs) adopt topologies that serve as binding sites for host proteins and miRNAs, crucial for viral replication and pathogenesis. However, the precise interactors and mechanisms of these interactions remain unclear. This study investigates the architectural landscape of HCV UTRs alone and in the presence of various interactors. Structural analysis reveals stable HCV UTR topologies, but significant alterations occur upon interaction with miRNAs and phytochemicals, potentially critical for viral pathogenicity. Additionally, proteins SRSF7 and AKAP8L are identified as novel interactors, which could have implication in host immune evasion and enhanced virulence. These findings highlight new miRNAs, proteins, and small molecules as interactors of HCV UTRs, offering insights into HCV infectivity and therapeutic targets for antiviral interventions.

molecular biology↗

bioRxiv2025

Longitudinal single cell RNA-sequencing reveals evolution of micro- and macro-states in chronic myeloid leukemia

Single cell RNA sequencing (scRNA-seq) has revolutionized our understanding of cancer, yet identifying meaningful disease states from single cell data remains challenging. Here, we systematically explore the chronic myeloid leukemia (CML) specific information content encoded in single cell versus bulk transcriptomics to resolve this paradox and clarify how discrete disease-defining states emerge from inherently noisy single cell data. We demonstrate that, while CML single cell transcriptomes exist along continuous transcriptional microstates, clinically relevant leukemia phenotypes clearly manifest only at the pseudobulk (macrostate) level. By leveraging state-transition theory, we reveal how robust disease phenotype state-transitions are governed by cell type specific contributions. Our results establish a theoretical framework explaining why discrete disease phenotypes remain hidden at the single cell scale but emerge clearly at the aggregated macrostate level, enabling previously inaccessible biological insights into leukemia evolution. By resolving how single-cell variation aggregates into macroscopic disease states, our framework provides new insight into CML progression and offers a broadly applicable strategy for exploring disease dynamics across cancers and other complex conditions.

systems biology↗

bioRxiv2025

Oxidative Base Damage to Telomeres Sensitizes Cancer Cells to ATR Inhibition

Targeted inhibition of DNA damage response proteins has received significant clinical attention owing to the success of PARP inhibitors. Due to the loss of the G1/S checkpoint, cancer cells are reliant on the G2/M checkpoint to cope with elevated DNA replication stress. We previously demonstrated a single induction of 8-oxo-guanine at telomeres in cancer cells was sufficient to induce replication stress, but was well tolerated at the cellular level. Here, we found inhibition of ATR, Chk1, or Wee1 after induction of telomere oxidative stress significantly induced genome instability and reduced cell viability. This occurred at doses markedly less than those required to increase instability in non-cancer cells. We determined the mechanism of this instability is due to cells progressing through S-phase with telomere damage and exiting G2-phase prematurely, prolonging their mitosis. This study demonstrates targeted oxidative base damage at telomeres can enhance the therapeutic efficacy of ATR inhibition in cancer.

cancer biology↗

bioRxiv2025

Th9-endothelial cell crosstalk promotes inflammatory atherosclerotic cardiovascular disease

Atherosclerotic cardiovascular disease (ASCVD) is a leading cause of death, and understanding its pathogenic drivers is critical for effective prevention and treatment. Inflammation has a critical role in ASCVD, and patients with inflammatory diseases are at increased risk. However, the key inflammatory mediator promoting ASCVD are incompletely understood, a major barrier when targeting inflammation to prevent ASCVD. Here, we found that interleukin-9 (IL-9) producing T helper cells (Th9) were significantly associated with ASCVD in patients with the autoimmune disease psoriasis. Th9 cells were poised to migrate to coronary vessels and were identified in atherosclerotic plaque. In vivo, murine inflammatory atherogenesis was prevented by IL-9 blockade and by IL-9 receptor (IL-9R) deletion in endothelial cells. In human arterial endothelial cells, IL-9R/STAT3 signaling promoted endothelial dysfunction, angiogenesis, and release of leukocyte chemoattractants. These findings suggest that in autoimmune diseases like psoriasis, Th9/IL-9 promote atherosclerosis by directly targeting endothelial cells, and that IL-9R/STAT3 signaling could be a promising therapeutic target for ASCVD. eTOC SummaryBaral et. al. investigate individuals who are at high risk for atherosclerosis due to underlying inflammatory disease and use mouse models of cardiovascular disease to uncover a role for interleukin-9-producing T helper 9 cells in the pathogenesis of inflammatory atherosclerosis.

immunology↗

bioRxiv2025

Promoter-centric gene regulation in drug-resistant cancer

In eukaryotic cells, gene-distal regulatory elements (REs) facilitate long-range gene regulation, ensuring cell type-specific transcriptional programs. This mechanism is frequently disrupted in cancer, often driven by transcription factors (TFs) that serve as targets for cancer therapy. However, targeting these TFs can lead to acquired resistance mechanisms that are not fully understood. We demonstrate that mesothelioma cancer cells, dependent on the oncogenic driver TF family TEAD, develop resistance to a pan-TEAD inhibitor and revert to an evolutionarily ancient, promoter-centric gene regulatory mechanism to recover gene expression following TEAD inhibition. Base-pair-resolution 3D chromatin conformation mapping reveals that RE-promoter interactions are disrupted in resistant cells, despite epigenetic and transcriptomic recovery. Mechanistically, in resistant cells, TF complexes, including resistance-specific FOSL1 and KLF4, preferentially bind and enhance promoter activity to recover gene expression, rendering distal REs dispensable. Our findings highlight promoter elements and promoter-specific TFs as potential therapeutic targets using a model of drug-resistant cancer.

cancer biology↗

bioRxiv2025

Supramolecular assembly of collagen mimetic peptide D-periodic fibrils and nanoassemblies

The collagen triple helix assembles hierarchically into bundled oligomers, solvated networks and fibers. Synthetic peptide assemblies, driven by supramolecular interactions, can form single triple helices through intrahelical amino acid pairs, but the principles guiding interhelical associations into higher-order structures remain unclear. Here, we incorporate cation-{pi} and electrostatic charge pairs to probe interhelical interactions and elucidate the mechanisms driving triple helix assembly into fibrils, nanotubes, and nanosheets. Introducing cation-{pi} pairs into a fibrillating collagen mimetic resulted in D-periodic fibrils with pH-sensitive gelation. Modifying the presentation of interhelical interactions also enabled the characterization of another D-periodic fibril resembling cartilage collagens, featuring inner and outer triple helix layers. Enhancing electrostatic charge pairs promoted antiparallel assembly, leading to the formation of nanotubes and nanosheets. The packing behavior of triple helices correlates with the interhelical interactions, where parallel associations favor fibril formation, and antiparallel interactions drive nanotube and nanosheet assembly.

biochemistry↗

bioRxiv2024

Histone H3.3 ensures cell proliferation and genomic stability during myeloid cell development

Variant histone H3.3 is thought to be critical for survival of many cells, since it is deposited in expressed genes, a feature different from core histones. For example, H3.3 deletion leads to embryonic lethality in mice. However, requirement of H3.3 in later stage of development has remained unclear. The aim of this work was to elucidate the role of H3.3 for development of myeloid lineage, important for innate immunity. We conditionally knocked out (cKO) the H3.3 genes in myeloid progenitor cells differentiating into bone marrow derived macrophages (BMDMs). Progenitor cells lacking H3.3 were defective in replication, suffered from extensive DNA damage, and underwent apoptosis. Surviving H3.3cKO cells expressed many interferon stimulated genes (ISGs) throughout differentiation. Further, H3.3cKO BMDMs possessed chromatin accessible sites, and histone posttranslational modifications consistent with the gene expression profiles, Accordingly, H3.3cKO BMDMs retained general nucleosomal structure genome wide. In summary, H3.3 is required for proliferation of myeloid progenitor cells, but is in large part dispensable for differentiation of BMDMs.

cell biology↗

bioRxiv2024

Transition paths across the EMT landscape are dictated by network logic

During development and cancer metastasis, cells transition reversibly from epithelial to mesenchymal via intermediate cell states during epithelial-mesenchymal transition (EMT). EMT is controlled by gene regulatory networks (GRNs) and can be described by a three-node GRN that permits tristable EMT landscapes. In this GRN, multiple inputs regulate the transcription factor ZEB that induces EMT. It is unknown how to choose the network logic for such regulation. Here we explore the effects of network logic on a tristable EMT network. We discover that the choice of additive vs multiplicative logic affects EMT phenotypes, leading to opposing predictions regarding the factors controlling EMT transition paths. We show that strong inhibition of miR-200 destabilizes the epithelial state and initiates EMT for multiplicative (AND) but not additive (OR) logic, suggesting that AND logic is in better agreement with experimental measurements of the effects of miR-200 regulation on EMT. Using experimental single-cell data, stochastic simulations, and perturbation analysis, we demonstrate how our results can be used to design experiments to infer the network logic of an EMT GRN in live cells. Our results explain how the manipulation of molecular interactions can stabilize or destabilize EMT hybrid states, of relevance during cancer progression and metastasis. More generally, we highlight the importance of the choice of network logic in GRN models in the presence of biological noise and multistability.

systems biology↗

bioRxiv2024

TEAD-targeting small molecules induce a cofactor switch to regulate the Hippo pathway

TEAD proteins are the main transcriptional effectors of the Hippo signaling pathway and a pharmacological target in oncology. Most TEAD-targeting small molecules act by disrupting interaction with the oncogenic transcriptional activators YAP and TAZ. Here, we describe an alternative mechanism for TEAD lipid pocket binding molecules. We report that select sulfonamide-containing compounds promote TEAD interaction with the transcriptional repressor VGLL4 to induce a small molecule-mediated cofactor switch from YAP to VGLL4. Chemically induced VGLL4-TEAD complexes counteract YAP activity at chromatin to repress pro-growth gene networks, including genes involved in cellular proliferation and mechanosignaling. VGLL4 is required for an anti-proliferative response to these select compounds, and genetic deletion of VGLL4 causes resistance to these molecules in vitro and in vivo. Our data reveal a category of molecules that facilitate the repressive VGLL4-TEAD interaction and open up new understandings for curbing the oncogenic activity of Hippo pathway deregulation.

cancer biology↗

bioRxiv2024

BRDKRM: An Explainable Framework for Disease Modifying Drug Identification

Drug classification into disease-modifying (DM) and symptomatic (SYM) categories is crucial for clinical decision-making and therapeutic strategy development. To address the limitations of current methods, which often lack transparency and interpretability, we propose the Boundary Restricted Dynamic Key Route Mapping (BRDKRM) framework. This novel approach leverages the contextual overlap between disease and drug nodes in a heterogeneous graph, aggregating genes from the top K shortest paths to delineate disease neighborhood boundaries. Inspired by the classic Hansel and Gretel folklore, BRDKRM metaphorically marks boundary nodes along metapaths from disease to drug, akin to Hansel s breadcrumbs, which are then used to classify the therapeutic effect of candidate drugs. Our method achieved 86.78% accuracy in categorizing drug-disease treatments and identified 530 genes involved in both disease modification and symptomatic relief. The efficacy of BRDKRM is demonstrated through case studies on multiple sclerosis, offering an explainable approach to drug classification that bypasses extensive clinical trials. By providing biologically sound interpretations of drug classifications, our framework enhances understanding of therapeutic interventions, paving the way for more precise and efficient healthcare solutions while offering a novel approach to mapping disease-drug interactions.

bioinformatics↗

bioRxiv2024

BRD4 expression in microglia supports recruitment of T cells into the CNS and exacerbates EAE

In EAE, a mouse model of multiple sclerosis, immunization with MOG autoantigen results in the generation of Th1/Th17 T cells in the periphery. MOG-specific T cells then invade into the central nervous system (CNS), resulting in neuronal demyelination. Microglia, innate immune cells in the CNS are known to regulate various neuronal diseases. However, the role of microglia in EAE has remained elusive. BRD4 is a BET protein expressed in microglia, whether BRD4 in microglia contributes to EAE has not been determined. We show that EAE pathology was markedly reduced with microglia-specific Brd4 conditional knockout (cKO). In these mice, microglia- T cell interactions were greatly reduced, leading to the lack of T cell reactivation. Microglia specific transcriptome data showed downregulation of genes required for interaction with and reactivation of T cells in Brd4 cKO samples. In summary, BRD4 plays a critical role in regulating microglia function in normal and EAE CNS. SummaryThis study demonstrates that in a EAE model, microglia-specific Brd4 conditional knockout mice were defective in expressing genes required for microglia- T cells interaction and those involved in neuroinflammation, and demyelination resulting in fewer CNS T cell invasion and display marked reduction in EAE pathology.

neuroscience↗

bioRxiv2024

Foliar application of nano urea results in higher biomass, chlorophyll, and nitrogen content than equimolar bulk urea through differential gene regulation in Arabidopsis thaliana

Indian Farmers Fertilizer Cooperative (IFFCO)s liquid nano urea formulation (NUF) was applied to one-month-old Arabidopsis thaliana plants grown in vermiculite as a 0.4% foliar spray twice at an interval of 10 days and compared with sprays of equimolar bulk urea. NUF resulted in a 51 {+/-} 14.9% increase in biomass, 29.5 {+/-} 9.1% in chlorophyll, 8.4 {+/-} 3.1% in nitrogen, and 4.5 {+/-} 0.3% in amino acid content of the leaves, compared to bulk urea. NUFs zeta potential of -54.7 mV and particle size of [~=]27.7 nm, measured by dynamic light scattering and transmission electron microscopy, make it suitable for stomatal uptake. We conducted a differential gene expression analysis by mRNA sequencing to understand the molecular basis of the phenotypic gains under NUF rather than urea. NUF resulted in significantly higher expression levels of 211 genes (log2fold-change > 0.5, FDR < 0.05) involved in the biosynthesis of carbohydrates, amino acids, nucleotides, lipids, phytohormones, and secondary metabolites, cell wall biosynthesis and modification, growth and developmental processes, cell cycle, and stress response than bulk urea. On the other hand, 1,286 genes (log2fold-change < -0.5) involved in cell death, abscission, senescence, nitrogen transport and metabolism, and biotic stress response showed lower expression levels upon NUF application than bulk urea. Our results suggest that although NUF foliar spray suppresses nitrogen uptake genes, possibly due to nitrogen excess, it enhances growth by up-regulating the synthesis of essential biomolecules and growth-promoting genes, compared to bulk urea.

plant biology↗

bioRxiv2024

Multi-modal, Label-free, Optical Mapping of Cellular Metabolic Function and Oxidative Stress in 3D Engineered Brain Tissue Models

Brain metabolism is essential for the function of organisms. While established imaging methods provide valuable insights into brain metabolic function, they lack the resolution to capture important metabolic interactions and heterogeneity at the cellular level. Label-free, two-photon excited fluorescence imaging addresses this issue by enabling dynamic metabolic assessments at the single-cell level without manipulations. In this study, we demonstrate the impact of spectral imaging on the development of rigorous intensity and lifetime label-free imaging protocols to assess dynamically metabolic functions over time in 3D engineered brain tissue models comprised of human induced neural stem cells, astrocytes, and microglia. Specifically, we rely on multi-wavelength spectral imaging to identify the excitation/emission profiles of key cellular fluorophores within human brain cells, including NAD(P)H, LipDH, FAD, and lipofuscin. These enable the development of methods to mitigate lipofuscins overlap with NAD(P)H and flavin autofluorescence to extract reliable optical metabolic function metrics from images acquired at two excitation wavelengths over two emission bands. We present fluorescence intensity and lifetime metrics reporting on redox state, mitochondrial fragmentation, and NAD(P)H binding status in neuronal monoculture and the triculture systems to highlight the functional impact of metabolic interactions between different cell types. Our findings reveal significant metabolic differences between neurons and glial cells, shedding light on metabolic pathway utilization, including the glutathione pathway, OXPHOS, glycolysis, and fatty acid oxidation. Collectively, our studies establish a label-free, non-destructive approach to assess the metabolic function and interactions among different brain cell types relying on endogenous fluorescence and illustrate the complementary nature of the information that is gained by combining intensity and lifetime-based images. Such methods can improve understanding of physiological brain function and dysfunction that occurs at the onset of cancers, traumatic injuries and neurodegenerative diseases.

bioengineering↗

bioRxiv2024

An intricate balancing act: Upstream and downstream frameshift co-regulatory elements

Targeting ribosomal frameshifting has emerged as a potential therapeutic intervention strategy against Covid-19. During ribosomal translation, a fraction of elongating ribosomes slips by one base in the 5' direction and enters a new reading frame for viral protein synthesis. Any interference with this process profoundly affects viral replication and propagation. For Covid-19, two RNA sites associated with ribosomal frameshifting for SARS-CoV-2 are positioned on the 5' and 3' of the frameshifting residues. Although much attention has been on the 3' frameshift element (FSE), the 5' stem-loop (attenuator hairpin, AH) can play a role. The formation of AH has been suggested to occur as refolding of the 3' RNA structure is triggered by ribosomal unwinding. However, the attenuation activity and the relationship between the two regions are unknown. To gain more insight into these two related viral RNAs and to further enrich our understanding of ribosomal frameshifting for SARS-CoV-2, we explore the RNA folding of both 5' and 3' regions associated with frameshifting. Using our graph-theory-based modeling tools to represent RNA secondary structures, "RAG" (RNA-As-Graphs), and conformational landscapes to analyze length-dependent conformational distributions, we show that AH coexists with the 3-stem pseudoknot of the 3' FSE (graph 3_6 in our dual graph notation) and alternative pseudoknot (graph 3_3) but less likely with other 3' FSE alternative folds (such as 3-way junction 3_5). This is because an alternative length-dependent Stem 1 (AS1) can disrupt the FSE pseudoknots and trigger other folds. In addition, we design four mutants for long lengths that stabilize or disrupt AH, AS1 or FSE pseudoknot to illustrate the deduced AH/AS1 roles and favor the 3_5, 3_6 or stem-loop. These mutants further show how a strengthened pseudoknot can result from a weakened AS1, while a dominant stem-loop occurs with a strengthened AS1. These structural and mutational insights into both ends of the FSE in SARS-CoV-2 advance our understanding of the SARS-CoV-2 frameshifting mechanism by suggesting a sequence of length-dependent folds, which in turn define potential therapeutic intervention techniques involving both elements. Our work also highlights the complexity of viral landscapes with length-dependent folds, and challenges in analyzing these multiple conformations.

biochemistry↗

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

Enhanced dynamic covalent chemistry for the controlled release of small molecules and biologics from a nanofibrous peptide hydrogel platform

Maintaining safe and potent pharmaceutical drug levels is often challenging. Multidomain peptides (MDPs) assemble into supramolecular hydrogels with a well-defined, highly porous nanostructure that makes them attractive for drug delivery, yet their ability to extend release is typically limited by rapid drug diffusion. To overcome this challenge, we developed self-assembling boronate ester release (SABER) MDPs capable of engaging in dynamic covalent bonding with payloads containing boronic acids (BAs). As examples, we demonstrate that SABER hydrogels can prolong the release of five BA-containing small-molecule drugs as well as BA-modified insulin and antibodies. Pharmacokinetic studies revealed that SABER hydrogels extended the therapeutic effect of ganfeborole from days to weeks, preventing Mycobacterium tuberculosis growth better than repeated oral administration in an infection model. Similarly, SABER hydrogels extended insulin activity, maintaining normoglycemia for six days in diabetic mice after a single injection. These results suggest that SABER hydrogels present broad potential for clinical translation.

bioengineering↗

bioRxiv2024

Abolished frameshifting for predicted structure-stabilizing SARS-CoV-2 mutants: Implications to alternative conformations and their statistical structural analyses

The SARS-CoV-2 frameshifting element (FSE) has been intensely studied and explored as a therapeutic target for coronavirus diseases including COVID-19. Besides the intriguing virology, this small RNA is known to adopt many length-dependent conformations, as verified by multiple experimental and computational approaches. However, the role these alternative conformations play in the frameshifting mechanism and how to quantify this structural abundance has been an ongoing challenge. Here, we show by DMS and dual-luciferase functional assays that previously predicted FSE mutants (using the RAG graph theory approach) suppress structural transitions and abolish frameshifting. Furthermore, correlated mutation analysis of DMS data by three programs (DREEM, DRACO, and DANCE-MaP) reveals important differences in their estimation of specific RNA conformations, suggesting caution in the interpretation of such complex conformational landscapes. Overall, the abolished frameshifting in three different mutants confirms that all alternative conformations play a role in the pathways of ribosomal transition.

molecular biology↗

bioRxiv2024

Fertilization by short-term stored sperm alters DNA methylation patterns in common carp (Cyprinus carpio) embryos at single-base resolution

Short-term storage of sperm in vitro is widely used for artificial fertilization in aquaculture. It has been shown that short-term storage affects sperm motility characteristics, resulting in diminished fertility. However, the detrimental effects of short-term sperm storage on embryos development have remained largely unexplored in single-base methylome resolution. The main aim of the present study was to investigate DNA methylation in the offspring of common carp (Cyprinus carpio) derived from short-term stored sperm. Sperm were stored in artificial seminal plasma on ice (0-2{degrees}C) for 0, 3 and 6 days in vitro, fertilization was performed using oocytes from a single female, and embryos were collected at the mid-blastula stage. Sperm and embryo DNA was extracted, analysed by liquid chromatography with tandem mass spectrometry (LC-MS/MS) and whole genome bisulfite sequencing (WGBS). DNA methylation was then assessed. Sperm storage showed negative effects on motility, viability and DNA integrity, but had no effect on global DNA methylation of spermatozoa and resulting embryos. Results from the WGBS showed that methylation of 3313 genes was affected in the embryos fertilized with the 6-day-stored sperm, and the differentially methylated regions (DMRs) identified were mainly involved in cell adhesion, calcium, mitogen-activated protein kinase and adrenergic signalling, melanogenesis, metabolism and RNA transport. Such results suggest that prolongation of storage time may have certain impacts on embryonic development. These initial results provide valuable information for future consideration of the DNA methylome in embryos generated from short-term stored sperm, which is widely used for genetic management of broodstock in aquaculture.

molecular biology↗