Biology subjects

Ghosh, U.

Publications and source records attributed to Ghosh, U..

10 recordsLinked to original sources

bioRxiv2026

Pervasive Somatic Mutations in NF1 Drive Cell Type and Spatially Specific Clonal Selection in Neurofibromatosis

Tumorigenesis is a multi-step process shaped by the accumulation of somatic driver mutations, but identifying the earliest steps and cell of origin of tumorigenesis remains challenging. Single cell genomics in >1.7 million single cells across donors with the cancer predisposition syndrome neurofibromatosis type 1 (NF-1), shows that somatic 'second-hit' mutations in NF1 are pervasive and show positive clonal selection in oligodendrocytes (OLs) and OL precursor cells (OPCs), but are exceedingly rare in neurons and other lineages. Combined spatial genotyping and transcriptomic analysis enabled dissection of cell autonomous and non-autonomous effects of second-hit mutations including clonal expansion of mutant OPCs with strong bias for cerebral gray matter versus white matter, suggesting that gray matter influences OPC proliferation and differentiation via non-cell autonomous interactions between OPCs and neurons. NF1-null OL lineage cells upregulate CDKN2A--a tumor suppressor frequently lost in NF1-mutant tumors--whereas brain cancers from these same individuals show CDKN2A loss across multiple cancer cell states, suggesting CDKN2A loss in OPCs is a critical step in tumor progression. Our findings reveal developmentally early, exquisitely lineage-specific NF1 somatic mutations in premalignant NF-1 brain, suggest cell autonomous and non-autonomous roles in clonal selection in brain, and suggest that clones harboring cancer driver mutations can persist over a lifetime in phenotypically normal tissues.

genetics↗

bioRxiv2026

Surface-stabilized sub-micron condensates for compartmentalizing synthetic cells and enhanced enzyme kinetics

Living cells harbor numerous membraneless organelles (MOs), which are dynamic protein/nucleic acid assemblies responding to specific physicochemical triggers. Liquid-liquid phase separation (LLPS) plays a crucial role in their formation and activity. Inspired by the natural MOs that maintain their individual identities, this work presents a bioengineering strategy to generate LLPS-driven, isochemical MO populations using surfactant-like peptides that stabilize the MO interface. The result is highly stable, monodispersed, sub-{micro}m-sized MO populations, which are not only capable of compartmentalizing synthetic cells but also provide superior environments for enzymatic reactions. This is achieved using pH-responsive elastin-like polypeptides (PREs) as MOs and formulating an amphiphilic PRE-based peptide to stabilize the MO interface. Relative abundance of the surface-active peptide, as well as the rate of pH change, allows direct control over the MO size. Encapsulating these components within synthetic vesicles using a microfluidic platform leads to on-demand multi-compartmentalization via an external pH trigger. Lastly, a functional consequence of the acute size control is shown through a phosphatase reaction, where the highest reaction rate is observed in size-controlled MOs when compared to dilute environments and surfactant-free MOs. The presented strategy provides a new avenue for designing programmable MOs and thus achieve functional compartmentalization within synthetic cells.

bioengineering↗

bioRxiv2026

Cell-Permeable Morpholino Inhibits Programmed Death-Ligand 1 at mRNA Level and Potentiates Antitumor Immunity in Breast Cancer

Morpholino-based ASOs with nuclease-resistant backbone and high sequence specificity could modulate the PD-L1/PD-1 axis to overcome T regulatory cell mediated inhibition but poor cell-permeability limits their clinical applications. Here, we develop a guanidinium-modified cell-permeable morpholino specifically targeting PD-L1 in breast cancer. It suppresses PD-L1 expression through effectively mitigating cytokine induced PD-L1 upregulation and enhancing autophagic flux. Notably, the ASO synergistically with durvalumab (anti-PD-L1 antibody) disrupt, hyperglycosylated PD-L1 by mRNA-level interference and also reduced PD-1 T-cell populations. Importantly, systemic and intra-tumoral administration of ASO demonstrated no abnormalities in cardiac tissues which show no off-target toxicity but it reprogrammed the tumor microenvironment by upregulating inducible nitric-oxide synthase and suppressed regulatory cells, collectively enhancing antitumor immune responses. Together, these findings establish morpholino ASO as a promising targeting therapeutic strategy to overcome tumor-induced immunosuppression, opening new avenues for precision treatment in breast-cancer.

cancer biology↗

bioRxiv2024

Perinatal Reduction of Genetically Aberrant Neurons from Human Cerebral Cortex

Human neurons are postmitotic and long-lived, requiring precise genomic regulation to maintain function over a lifetime. Normal neuronal function is highly dependent on gene dosage, with copy number variants (CNVs) and heterozygous point mutations associated with a host of neurodevelopmental and neuropsychiatric conditions [1-5]. Here, we investigated the landscape of somatic CNVs arising in fetal human brains, and how they change over development, to understand the processes that generate normal neuronal genomes. We sequenced 2,158 single neurons from human postmortem brain using two distinct single cell whole genome sequencing (scWGS) approaches. Tn5-transposase based (TbA) scWGS of 1,327 neurons from 16 individuals ranging in age from gestational week 14 to 90 years old resulted in 8,765 CNVs. Primary template amplification (PTA) was used to assess for CNV from 831 neurons from 12 individuals. Up to 46% of neurons in prenatal cortex showed aberrant genomes, characterized by widespread CNVs of multiple chromosomes, but this proportion reduces by 4-5 fold after birth across the two scWGS approaches (p=7.5x10-6, Fisher meta-analysis). We identified micronuclei in the developing cortex in situ, reflecting chromosomal material missegregated during neurodevelopment [6-8]. Neurons with widespread CNVs were eliminated in the perinatal period, while neurons with smaller CNV burden slowly declined during postnatal aging. CNVs in surviving neurons were depleted for genes that are dosage-sensitive or involved in neurodevelopmental disorders (p<0.05), suggesting selective elimination of neurons with CNVs involving these critical genes. We surveyed 44,861 nuclei with 10X Genomics scATAC/RNAseq and determined that neurons with high CNV burdens also showed abnormal expression of synaptic gene sets, suggesting that abnormal synaptic gene regulation contributes to neuronal elimination. Elimination of defective neuronal genomes during synaptogenesis may represent a critical process of genome quality control and a vulnerable target of factors that contribute to neurodevelopmental disease.

neuroscience↗

bioRxiv2024

Spatial Single-cell Analysis Decodes Cortical Layer and Area Specification

The human cerebral cortex, pivotal for advanced cognitive functions, is composed of six distinct layers and dozens of functionally specialized areas1,2. The layers and areas are distinguished both molecularly, by diverse neuronal and glial cell subtypes, and structurally, through intricate spatial organization3,4. While single-cell transcriptomics studies have advanced molecular characterization of human cortical development, a critical gap exists due to the loss of spatial context during cell dissociation5,6,7,8. Here, we utilized multiplexed error-robust fluorescence in situ hybridization (MERFISH)9, augmented with deep-learning-based cell segmentation, to examine the molecular, cellular, and cytoarchitectural development of human fetal cortex with spatially resolved single-cell resolution. Our extensive spatial atlas, encompassing 16 million single cells, spans eight cortical areas across four time points in the second and third trimesters. We uncovered an early establishment of the six-layer structure, identifiable in the laminar distribution of excitatory neuronal subtypes by mid-gestation, long before the emergence of cytoarchitectural layers. Notably, while anterior-posterior gradients of neuronal subtypes were generally observed in most cortical areas, a striking exception was the sharp molecular border between primary (V1) and secondary visual cortices (V2) at gestational week 20. Here we discovered an abrupt binary shift in neuronal subtype specification at the earliest stages, challenging the notion that continuous morphogen gradients dictate mid-gestation cortical arealization6,10. Moreover, integrating single-nuclei RNA-sequencing and in situ whole transcriptomics revealed an early upregulation of synaptogenesis in V1-specific Layer 4 neurons, suggesting a role of synaptogenesis in this discrete border formation. Collectively, our findings underscore the crucial role of spatial relationships in determining the molecular specification of cortical layers and areas. This work not only provides a valuable resource for the field, but also establishes a spatially resolved single-cell analysis paradigm that paves the way for a comprehensive developmental atlas of the human brain.

neuroscience↗

bioRxiv2024

Cryo-EM Structures Reveal Tau Filaments from Down Syndrome Adopt Alzheimer's Disease Fold

Down syndrome (DS) is a common genetic condition caused by trisomy of chromosome 21. Among their complex clinical features, including musculoskeletal, neurological, and cardiovascular disabilities, individuals with DS have an increased risk of developing progressive dementia and early-onset Alzheimers disease (AD). This dementia is attributed to the increased gene dosage of the amyloid-{beta} (A{beta}) precursor protein gene, the formation of self-propagating A{beta} and tau prion conformers, and the deposition of neurotoxic A{beta} plaques and tau neurofibrillary tangles. Tau amyloid fibrils have previously been established to adopt many distinct conformations across different neurodegenerative conditions. Here, we report the characterization of brain samples from four DS cases spanning 36 to 63 years of age by spectral confocal imaging with conformation-specific dyes and cryo-electron microscopy (cryo-EM) to determine structures of isolated tau fibrils. High-resolution structures revealed paired helical filament (PHF) and straight filament (SF) conformations of tau that were identical to those determined from AD cases. The PHFs and SFs are made of two C-shaped protofilaments, each containing a cross-{beta}/{beta}-helix motif. Similar to filaments from AD cases, most filaments from the DS cases adopted the PHF form, while a minority (approximately 20%) formed SFs. Samples from the youngest individual with no documented dementia had sparse tau deposits. To isolate tau for cryo-EM from this challenging sample we used a novel affinity-grid method involving a graphene oxide surface derivatized with anti-tau antibodies. This method improved isolation and revealed that primarily tau PHFs and a minor population of chronic traumatic encephalopathy type II-like filaments were present in this youngest case. These findings expand the similarities between AD and DS to the molecular level, providing insight into their related pathologies and the potential for targeting common tau filament folds by small-molecule therapeutics and diagnostics.

neuroscience↗

bioRxiv2023

Development of a Quorum-Sensing Based Bacterial GMO for Targeted Treatment of Bovine Mastitis.

Bovine mastitis, a prevalent and costly disease affecting dairy cows, severely impacts milk production, quality, and cow health and poses significant challenges to the dairy industry worldwide. Traditional treatment strategies relying on antibiotics face concerns of antibiotic resistance and residual antibiotic residues in dairy products. Therefore, there is an urgent need for innovative and sustainable approaches. Our study undertakes a preliminary investigation into the formulation and efficacy of a GMO-based antibiotic-free treatment in fighting Bovine mastitis. We propose to use the bioengineered defensin Nisin PV as the antimicrobial to specifically target the causative pathogen Staphylococcus aureus. To disrupt the biofilm formation, we have leveraged the potency of DNaseI. By hacking the quorum sensing technique of Staphylococcus aureus, our proposed genetically modified bacteria would sense the presence of pathogens and initiate their eradication by producing Nisin PV and DNaseI. Results show the efficacy of DNase I against bacterial biofilm formation, in addition to the efficacy of our proposed sensor, which is based on the agr quorum sensing system of Staphylococcus aureus, a major cause of bovine mastitis. Molecular dynamics and simulations show that our choice of the bacterial defensin, Nisin PV, is less susceptible to cleavage by bacterial strains resistant to the native bacteriocin Nisin A. Additionally, we theoretically propose a lysis-based kill switch to ensure the release of the therapeutic components. The solution proposed in this study has the potential to offer a sustainable and effective alternative to antibiotic-based treatments. Implementation of bioengineered defensins could reduce disease incidence, minimize economic losses, and promote responsible antimicrobial stewardship in the dairy industry.

synthetic biology↗

bioRxiv2022

Quantifying formations of Neutravidin clusters on biotinylated mixed silane Self-Assembled Monolayers.

Towards the goal of developing bio-chip / lab-on-a-chip substrates capable of performing highly specific bio-chemical reactions, Neutravidin binding to mixed Biotinylated Silane Self-Assembled Monolayers were studied using Confocal Fluorescence Light Microscopy. Non-specific bindings, specifically the formations of Neutravidin clusters, were quantified. Several experiments were conducted to determine the concentrations of Neutravidin necessary to not saturate surface binding to Biotinylated Self-Assembled Monolayers, determine the effectiveness of using FBS blocking buffers to reduce non-specific binding, optimize the repeatability of Neutravidin binding to Biotinlyated mixed Self-Assembled Monolayers with Silane-PEG-Biotin compositions ranging from 0 to 15%, and quantify background Neutravidin bindings and the corresponding formations of Neutravidin clusters to Self-Assembled Monolayers as Silane-PEG-Biotin percent compositions increase from 0 to 15%. The Neutravidin, Silane-PEG-Biotin, and Silane mPEG concentrations and ratios needed to develop homogeneous Neutravidin films, without the formations of clusters, on the Self-Assembled Monolayers have been determined.

bioengineering↗

bioRxiv2021

High throughput screening of a new fluorescent G-quadruplex ligand having telomerase inhibitory activity in human A549 cells

Genome-wide analysis showed that putative G-quadruplex DNA structures are prevalent in the human genome. The presence of G-quadruplex structure in the telomere and promoter region of certain oncogenes inspired people to use G-quadruplex ligand as anti-cancer agents. G-quadruplex structures, stabilized by ligand at telomere are resolved by telomerase making the cancer cells resistant to G-quadruplex ligand. So, identification of a new G-quadruplex ligand having anti-telomerase activity would be a promising strategy for cancer therapy as about 85% of human cancers are telomerase positive. A set of the drug-like compounds were screened from the ZINC database randomly and 2284 ligands were chosen following Lipinskis rule of five that were docked with five different G-quadruplex DNA sequences in idock. We screened 43 potential G-quadruplex binders using Z-score as a normalization scoring function. The compound (ZINC ID-05220992) gave the best score (average idock = -10.17 kcal/mol, average normalized idock = -3.42). We performed G4 FID assay, CD analysis to understand its binding with three different G-quadruplex DNA sequences, and checked its anti-telomerase activity in A549 cells using TRAP assay. We observed that this compound had an intrinsic fluorescence, capability to stain live cells with a blue fluorescence, and a specific affinity to only 22AG out of three different G-quadruplex DNA sequences under study. It showed cytotoxicity, good permeability to live cells, and a significant reduction of telomerase activity in human A549 cells at a very low dose. So, this compound has strong potential to be an anti-cancer drug. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC="FIGDIR/small/470216v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@116cce1org.highwire.dtl.DTLVardef@1e500c1org.highwire.dtl.DTLVardef@194a0b3org.highwire.dtl.DTLVardef@c258fe_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIA set of compounds were screened randomly by a High throughput method and Lipinskis rule of five from ZINC database to identify potential G4-binders. C_LIO_LIThe compound (ZINC ID-05220992) was screened after docking with five G-quadruplex DNA C_LIO_LIIt binds G-quadruplex DNA 22AG as detected by TO displacement and CD spectroscopy. C_LIO_LIIt inhibits telomerase activity in A549 cells and also cytotoxic to this cell. C_LIO_LIIt penetrates live A549 cell in culture and stains it with blue fluorescence C_LI

molecular biology↗

bioRxiv2020

Molecular structure of a prevalent amyloid-β fibril polymorph from Alzheimer's disease brain tissue

Amyloid-{beta} (A{beta}) fibrils exhibit self-propagating, molecular-level polymorphisms that may underlie variations in clinical and pathological characteristics of Alzheimers disease. We report the molecular structure of a specific brain-derived polymorph that has been identified as the most prevalent polymorph of 40-residue A{beta} fibrils in cortical tissue of Alzheimers disease patients. This structure, developed from cryo-electron microscopy and supported by solid state NMR data, differs qualitatively from all previously described A{beta} fibril structures, both in its molecular conformation and its organization of cross-{beta} subunits. Knowledge of this brain-derived fibril structure may contribute to the development of structure-specific amyloid imaging agents and aggregation inhibitors with greater diagnostic and therapeutic utility.

biophysics↗