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Biswas, K.

Publications and source records attributed to Biswas, K..

At least 19 recordsLinked to original sources

Using Bayesian inference to characterize cell-size regulation across organisms

How organisms regulate cell size and whether this varies with growth conditions remains a fundamental question. Inferring how cells regulate their size requires separating biological control from statistical effects. Yet regulatory strategies are commonly classified by estimating the size-control parameter, , from single-cell measurements using linear regression. We show that this conventional estimator is systematically biased by measurement noise, lineage-to-lineage extrinsic variability, and finite lineage length. Consequently, the same underlying regulatory mechanism can be misclassified as sizer-, adder-, or timer-like. We develop a Bayesian framework that jointly infers and the amplitudes of intrinsic, extrinsic, and measurement noise while accounting for lineage heterogeneity and finite sampling. Across simulations spanning experimentally relevant noise levels and lineage lengths, the framework recovers and outperforms conventional regression, particularly for short and heterogeneous lineages. Reanalysis of diverse bacterial and eukaryotic datasets collected under multiple growth conditions indicates that statistical bias accounts for much of the reported variation in across organisms and growth conditions. After accounting for these biases, the datasets are broadly consistent with adder-like regulation. Thus, our results provide a general framework for distinguishing genuine biological differences from noise-induced changes in inferred regulatory strategy and revise how cell-size regulation should be inferred from lineage data.

biophysics↗

Mirror-image mRNA display uncovers isoform-selective D-peptide macrocycles targeting a cryptic KRAS pocket

Activating KRAS mutations drive millions of cancers diagnosed worldwide,1 yet for decades this oncoprotein was deemed "undruggable", reflecting the challenge of discovering molecules capable of perturbing its complex biological functions, and of translating these discoveries into effective cancer therapeutics.2 Recent advances propelled by innovative screening have identified diverse modalities that bind at or near the switch-II pocket (SII-P) of RAS proteins, including molecular glues,3 macrocyclic peptides,4 fragment-derived small molecules,5 and approved therapies that covalently target KRASG12C.6,7 Unfortunately, resistance to approved therapies has emerged,8,9 highlighting the need for molecules that engage new or underexploited binding sites on RAS oncoproteins with mechanisms complementary to established SII-P inhibitors.10,11 Here we show that mirror-image mRNA display12 enabled the discovery of all-D macrocyclic peptide ligands targeting a cryptic RAS back pocket (CRB-P).13 These ligands engage KRAS(OFF) and KRAS(ON) with equal affinity, exploit a single-residue difference among isoforms to bind KRAS selectively, and successfully inhibit oncogenic signaling in KRAS-mutant cells through a mechanism distinct from SII-P binders. Mirror-image screening directly afforded nanomolar peptide ligands stable toward cellular proteolysis and delivered probes targeting distinct epitopes not accessible by homochiral peptide-display methods. Together, these findings establish the CRB-P as a specifically druggable and mechanistically differentiated site on KRAS with potential for combination with emerging RAS-targeting therapies and substantiate mirror-image mRNA display as a strategy for discovering stable all-D macrocyclic peptides targeting previously inaccessible epitopes on challenging targets.

cancer biology↗

Cell Growth and Division Shape mRNA-Protein Correlations

1Correlations between cellular variables, such as gene-expression levels, provide insights into regulatory mechanisms. We focus here on correlations between mRNA and protein levels and re-examine previously derived analytical predictions. We test this prediction on single-cell E. coli data and see substantial disagreement. We hypothesize that this discrepancy arises from the assumption of constant cell volume and develop a theoretical framework for mRNA-protein correlations in growing and dividing cells. Within this framework, we derive an analytical expression for mRNA- protein correlations and show that explicit incorporation of growth and division substantially alters these correlations. The resulting relation is invariant to upstream transcriptional dynamics, and we validate it using stochastic simulations across multiple gene-regulatory architectures. Finally, we show that the derived predictions are consistent with the E. coli data.

biophysics↗

A searchable database of publications using fluorescent probes and flow cytometry to study antigen-specific B cells

The study of antigen-specific B cells has resulted in important advances in all fields of immunology, the development of experimentally and/or clinically useful antibodies, and as a starting point for rationally designed vaccine antigens. A key innovation allowing for widespread study of antigen-specific B cells was the development of fluorescent antigen probes for use with flow cytometry. Initially these studies were mostly focused upon B cells specific for a variety of model antigens, but over the past decade focus has shifted towards the study of B cells specific for antigens from pathogens such as SARS-CoV-2, HIV, and Influenza virus. Importantly however, these types of approaches have been used for hundreds of different antigens and could be used for thousands more. Unfortunately, studies of B cells specific for an antigen of interest are not easily searchable on current publication databases since these assays are often a small portion of a larger publication. To overcome this, we built a searchable database of studies analyzing antigen-specific B cells by flow cytometry using fluorescent antigen probes that is located at www.immunology.virginia.edu/Taylor/Bcell/Database.php. Using this database, we assessed the number of publications per year revealing rapid growth in the use of this approach in recent years. While much of this rapid growth was focused upon the assessment of B cells specific for SARS-CoV-2, HIV-1, or Influenza virus, studies assessing B cells specific for hundreds of different antigens derived from numerous microbes, animals, plants, or other sources can be found in the database. Combined, the antigen-specific B cell database was built to facilitate identification of studies assessing these cells and for analysis of the field as a whole. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=18 SRC="FIGDIR/small/680531v1_ufig1.gif" ALT="Figure 1"> View larger version (6K): org.highwire.dtl.DTLVardef@f07f5forg.highwire.dtl.DTLVardef@13a3b95org.highwire.dtl.DTLVardef@1dcd79org.highwire.dtl.DTLVardef@9cddaa_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

dCas9 targeted proteome profiling reveals p300-mediated reciprocal regulation of SMAD and SP1 as a driver of GM2 synthase transcription in renal cell carcinoma

Glycolipids constitute an important component of the plasma membrane based on both abundance as well as function. Gangliosides, being a class of structurally diverse and functionally varied glycolipids, can act both as a receptor as well as a ligand and therefore is established as a crucial player in several normal cellular processes. In certain diseases, and in particular cancer, select gangliosides are over-expressed often leading to disease manifestation. GM2-synthase, the enzyme responsible for the formation of a pro-tumorigenic ganglioside, GM2 is well reported to be over-expressed across various cancer tissues and cell lines. This over-expression of GM2-synthase has been linked with increased migration, invasion and epithelial to mesenchymal transition (1) as well as induction of a local and systemic host immune suppression in cancer. Despite only a handful of studies demonstrating an epigenetic regulation underlying the transcriptional regulation of GM2-synthase (B4GalNT1) gene, the detailed mechanism still remains unclear. Here we identified the total proteome associated with the GM2-synthase promoter through a two-step CRISPR-dCas9 based proteome profiling approach by categorizing all the identified proteins leading to a detailed elucidation of the molecular drivers behind GM2-synthase transcription. While the previous study identified an acetylation-dependent de-repression of the transcription factor SP1 causing GM2-synthase activation, the underlying molecular mechanism driving its activation wasnt clear. This study demonstrated that the histone acetyl transferase (2), p300 acts as a pivotal factor which on one hand cause acetylation-mediated degradation of SP1, and on the other hand activates SMAD2/4 to have a direct positive impact on GM2-synthase gene transcription. We identified p300 to have an activator role in GM2-synthase gene transcription through knock out, knock down and over-expression experiments. Furthermore, SP1 degradation, SMAD activation and their DNA binding patterns show the reciprocal role of p300 on SP1 and SMAD complexes. Altogether we have identified SMAD 2/4 as an activator complex, p300 as a positive regulator and uncovered a critical p300-SMAD-SP1 regulatory axis in GM2-synthase transcriptional regulation.

molecular biology↗

Genome-wide analysis reveals pathways important for the development and maturation of excitatory synaptic connections to GABAergic neurons

A high degree of cell and circuit-specific regulation has presented challenges for efforts to precisely define molecular mechanisms controlling synapse formation and maturation. Here, we pursue an unbiased forward genetic approach to identify C. elegans genes involved in the formation and maturation of cholinergic synaptic connections with GABAergic motor neurons as indicated by the distribution of GFP-tagged postsynaptic acetylcholine receptors (AChR) on GABAergic dendrites. We identified mutations in 3 genes that identify key processes in synapse/circuit maturation. Mutation of the RUN domain (RPIP8, UNC-14, and NESCA) cargo adaptor gene unc-14 dramatically impacts overall GABAergic neuron morphology and dendritic spines. Mutation of the nicotinic acetylcholine alpha subunit gene unc-63 causes a failure in AChR assembly in GABAergic neurons but does not significantly alter dendritic spine structure or abundance. Finally, a mutation in the Liprin- synaptic scaffold gene syd-2 severely disrupts both dendritic spines and AChR localization. The identification of these three genes from our screen highlights how mechanisms for cargo trafficking, receptor assembly, and synapse structural organization each make distinct contributions to synapse assembly and circuit connectivity.

neuroscience↗

Stochasticity in mammalian cell growth rates drives cell-to-cell variability independently of cell size and divisions

Cell growth rates exhibit cell-intrinsic cell-to-cell variability, which influences cell fitness and size home-ostasis from bacteria to cancer. Whether this variability arises from noise in cell growth or cell division processes, or originates from cell-size-dependent growth rates, remains unclear. To separate these potential sources of growth variability, single-cell growth rates need to be examined across different timescales. Here, we study cell-intrinsic size and growth regulation by tracking lymphocytic leukemia cell mass accumulation with high precision and minute-scale temporal resolution along long ancestral lineages. We first show that cell-size-dependent growth regulation and asymmetric division of cell size do not explain cell-to-cell growth variability. We then isolate growth fluctuations from overlapping cell-cycle-dependent growth using a Gaussian process regression analysis. We find that these growth fluctuations drive cell-to-cell growth variability within ancestral lineages despite being independent of cell divisions, cell cycle, and cell size. Overall, our results indicate that cell-intrinsic long-term patterns in cell growth are a byproduct of short-term growth fluctuations.

systems biology↗

Membrane Interfacial Potential Governs Surface Condensation andFibrillation of α-Synuclein in Neurons

Biomolecular condensates formed via liquid-liquid phase separation (LLPS) are essential for cellular organization. -Synuclein, an amyloidogenic protein linked to Parkinsons Disease (PD), undergoes phase separation at high concentrations, but the influence of lipid membranes on this process remains unclear. Here, combining in vitro reconstitution, cell biology, and simulations, we show that membranous interfaces promote -Synuclein condensation at physiologically relevant sub-critical concentrations ([~]10 nM) without crowding agents. Notably, condensation occurs only on membranes with a specific stoichiometry of lipids, underscoring the role of interfacial potential. These condensates serve as nucleation sites for fibril formation, leading to membrane deformation and rupture. A lattice gas model reveals this behavior as a prewetting-like transition, where an attractive membrane induces local phase separation below the bulk saturation concentration. Indeed altering interfacial potential by lipid composition and membrane depolarization not only drastically changes -Synuclein puncta size and number but also triggers their release from neurons. These findings reveal the crucial role of lipid membrane interfaces in regulating -Synuclein condensation, aggregation and release, shedding light on a potential mechanism of their cell-to-cell propagation during neurodegeneration.

biophysics↗

Emergent Homeostasis and Degeneracy from multi-Dimensional Attractors

Biological systems maintain homeostasis, ensuring stability in the face of internal and external perturbations and counteracting stochastic noise. Traditionally, this is understood through the lens of control mechanisms designed to offset deviations and maintain certain quantities near functionally desired set-points. Here, we propose an alternative perspective to understand homeostasis: the dynamic perspective, in which homeostasis emerges from high-dimensional interactions creating stable attractors in the phase space. These multi-dimensional attractor manifolds can constrain all components collectively, eliminating the need for explicit control of individual variables. The presence of null directions on an attractor allows for degenerate states that can add flexibility while preserving functionality. Using single cell growth and division homeostasis as a test case, we develop and support our perspective by models and meta-analysis of numerous single-cell datasets across organisms and conditions. Importantly, we do not reject the control-theory perspective but rather suggest that control circuit models can be seen as low-dimensional projections of a more complex, multi-dimensional system.

biophysics↗

Transcriptional responses to prolonged oxidative stress require cholinergic activation of G-protein-coupled receptor signaling

Organisms have evolved protective strategies that are geared toward limiting cellular damage and enhancing organismal survival in the face of environmental stresses, but how these protective mechanisms are coordinated remains unclear. Here, we define a requirement for neural activity in mobilizing the antioxidant defenses of the nematode Caenorhabditis elegans both during chronic oxidative stress and prior to its onset. We show that acetylcholine-deficient mutants are particularly vulnerable to chronic oxidative stress. We find that extended oxidative stress mobilizes a broad transcriptional response which is strongly dependent on both cholinergic signaling and activation of the muscarinic G-protein acetylcholine coupled receptor (mAChR) GAR-3. Gene enrichment analysis revealed a lack of upregulation of proteasomal proteolysis machinery in both cholinergic-deficient and gar-3 mAChR mutants, suggesting that muscarinic activation is critical for stress-responsive upregulation of protein degradation pathways. Further, we find that GAR-3 overexpression in cholinergic motor neurons prolongs survival during chronic oxidative stress. Our studies demonstrate neuronal modulation of antioxidant defenses through cholinergic activation of G protein-coupled receptor signaling pathways, defining new potential links between cholinergic signaling, oxidative damage, and neurodegenerative disease.

neuroscience↗

Single-cell Growth Rate Variability in Balanced Exponential Growth

Exponential accumulation of cell size and highly expressed proteins is observed at the single-cell level in many bacterial species. While the exponential rates fluctuate from cycle to cycle, they remain stable on average over time and strongly correlated across different proteins and cell size. In this study, we investigate growth-rate variability at this state of balanced biosyn-thesis, and present a theoretical framework to explain its properties through the emergence of a high-dimensional collective dynamic attractor. This stable attractor arises from recurrent interactions among multiple cellular components, driving them to converge to the same expo-nential growth rate, thereby sustaining the balanced state. The convergence of growth rates induces a decay in instantaneous growth rate noise throughout the cell cycle, with a faster decay for higher average growth rates. Notably, our analysis identifies random deviations from symmetric division as the primary source of growth rate variability. The theory offers a coherent set of predictions for many observations, validated by extensive experimental single-cell data. The spontaneous emergence of homeostasis through dynamic interactions suggests that specific control mechanisms to compensate deviations from a target may not be necessary to maintain homeostasis in a balanced state.

biophysics↗

Molecular Sequestration Enhances Precision in Timing of Intracellular Events

Expressed gene products often interact ubiquitously with binding sites at nucleic acids and macromolecular complexes, known as decoys. Binding of transcription factors (TFs) to decoys is shown to be an indirect but crucial way to control the dynamics and stochasticity in gene regulation. Here, we explore how such decoys impact the timing of intracellular events, as captured by the time taken for the levels of a given TF to reach a critical threshold level, known as first passage time (FPT). As binding introduces nonlinearity, an exact mathematical analysis is challenging. However, assuming quasi-static equilibrium (QSE) for binding/unbinding reactions, we can analytically discern the impact of decoys on FPT statistics by using small noise approximation (SNA) and reformulating the FPT question in terms of a suitable variable whose dynamics is linear. The stability of the decoy-bound TFs influences the impact of decoys on FPT statistics. The presence of decoys makes the mean FPT long and even longer for unstable bound TFs. Decoys reduce noise in FPT, and stable decoy-bound TFs offer greater timing precision with less expression cost than their unstable counterparts. Interestingly, when both bound and free TFs decay at the same rate, the noise in FPT is not directly influenced by the number of decoys or their binding affinities. We verify these results by performing exact stochastic simulations. These results have important implications for the precise temporal scheduling of events involved in the functioning of biomolecular clocks, development processes, cell-cycle control, and cell-size homeostasis.

systems biology↗

Design-Rules for Stapled Alpha-Helical Peptides with On-Target In Vivo Activity: Application toMdm2/X dual antagonists

Stapled -helical peptides can bind to and modulate historically intractable targets while addressing the traditional liabilities associated with peptide therapeutics. However, their pipeline advancement has been impeded by the challenges of identifying peptides with sufficient cellular uptake to engage the target protein while lacking off-target toxicities. Here, we advance the field to arrive at a workflow for identifying advanced stapled peptide lead molecules with on-target in vivo activity with no off-target cell proliferation effects. Specifically, we generated a >350-member library based on ATSP-7041, a stapled peptide Mdm2(X) antagonist with validated on-target cellular effects but with significant off-target activity. Key insights from library analysis include 1) a clear correlation between lipophilicity and permeability, 2) removal of positive charge to avoid off-target toxicities, 3) judicious placement of anionic residues to enhance peptide solubility/behavior, 4) optimization of C-terminal length and helicity to enhance cell activity, 5) optimization of staple type/number to avoid polypharmacology. Incorporation of one or more of these attributes led to molecules with improved in vitro and in vivo activities (up to a >292x improved cell proliferation EC50). A subset of peptides were devoid of off-target cell proliferation effects in cell lines lacking wild-type p53 protein (up to a >3800x on-target index). This latter improvement contrasted with clinical Mdm2 antagonistic molecules. Application of these design rules to a distinct Mdm2(X) peptide series resulted in rapid improvement in cellular activity (>150x) and removal of off-target toxicities. Overall, the detailed workflow outlined here should help researchers identify stapled -helical peptides for therapeutic impact.

biochemistry↗

Development of a high-throughput barrier function assay using primary human gut organoids

Disruptions in the gut epithelial barrier can lead to the development of chronic indications such as inflammatory bowel disease (IBD). Historically, barrier function has been assessed in cancer cell lines, which do not contain all human intestinal cell types, leading to poor translatability. To bridge this gap, we adapted human primary gut organoids grown as monolayers to assess barrier function. In this work we describe and characterize a novel 96-well human gut organoid-derived monolayer system that enables medium/high-throughput quantitative assessment of candidate therapeutics. Normal human intestine differentiation patterns and barrier function were characterized and confirmed to recapitulate key aspects of in vivo biology. Next, cellular response to TNF- (a central driver of IBD) was determined using a diverse cadre of readouts.These outputs included transcription factor phosphorylation, target gene expression, cytokine/chemokine production, and barrier function. Additionally, we showed that TNF- pathway antagonists rescued damage caused by TNF- in a dose-dependent manner, indicating that this system is suitable for quantitative assessment of barrier modulating factors. Taken together, we have established a robust primary cell-based 96-well system capable of interrogating questions around mucosal response. This system is well suited to provide pivotal functional data to support translational target and drug discovery efforts.

immunology↗

PKM2-mediated epigenetic reprogramming regulates hypoxic expression of PFKFB3 to promote breast cancer progression

The hypoxic milieu is a critical modulator of aerobic glycolysis, yet the regulatory mechanisms existing between the key glycolytic enzymes in hypoxic cancer cells are largely unexplored. In particular, M2 isoform of pyruvate kinase (PKM2) - the ratelimiting enzyme of glycolysis, is well-known to confer adaptive advantages under hypoxia. Herein, we report a non-canonical role of PKM2 in functioning as a co-activator of HIF-1 to govern the transcription of 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3). Nuclear PKM2 enhances HIF-1 and p300 occupancy at PFKFB3 hypoxia responsive elements (HREs) resulting in its upregulation. Consequently, absence of nuclear PKM2 fails to recruit HIF-1 which activates an opportunistic occupancy of HIF-2 at PFKFB3 HREs. Enhanced binding of HDAC3 also occurs in the absence of PKM2 which prevents HIF-2 from efficiently inducing PFKFB3 to hamper proliferation of hypoxic breast cancer cells. In addition, clinical relevance of the study has been investigated by demonstrating that Shikonin blocks nuclear translocation of PKM2 to suppress PFKFB3 expression. Furthermore, MCF7 cells-derived xenograft tumors in mice exhibited substantial tumor growth inhibition when treated with shikonin, highlighting the vitality of targeting PKM2. Taken in concert, this work provides novel insights into contributions of PKM2 in modulating hypoxic transcriptome and a previously unreported molecular axis exhibited by the hypoxic breast cancer cells for ensuring the maintenance of PFKFB3 expression essential for achieving high glycolytic flux. Statement of significanceNuclear PKM2 orchestrates the binding of histone modifiers to epigenetically alter PFKFB3 promoter and affects the binding of HIF-2. Notably, targeting this axis attenuates proliferation of hypoxic breast cancer cells.

cancer biology↗

Cell-division time statistics from stochastic exponential threshold-crossing

Some phenotypic properties in bacteria exhibit universal statistics, with distributions collapsing under scaling. The extent and origins of such universality are not well understood. Using phenomenological modeling of growth and division, we identify compound "shape-factors" that describe the distributions throughout a large set of single-cell data. We find that the emergence of universal distributions is associated with the robustness of shape-factors across conditions, explaining the universality of cell size and highly expressed protein content and the non-universality of times between consecutive divisions. A wide range of experimental data sets support our theory quantitatively.

biophysics↗

Recombinant Human ACE2-Fc : A promising therapy for SARS-CoV2 infection

SARS-CoV2 entry is mediated by binding of viral spike-protein(S) to the transmembrane Angiotensin-Converting Enzyme-2 (ACE2) of the host cell. Thus, to prevent transmission of disease, strategies to abrogate the interaction are important. However, ACE2 cannot be blocked since its normal function is to convert the Angiotensin II peptide to Angiotensin(1-7) to reduce hypertension. This work reports a recombinant cell line secreting soluble ACE2-ectopic domain (MFcS2), modified to increase binding and production efficacy and fused to human immunoglobulin-Fc. While maintaining its enzymatic activity, the molecule trapped and neutralized SARS CoV2 virus in vitro with an IC50 of 64 nM. In vivo, with no pathology in the vital organs, it inhibited the viral load in lungs in SARS-CoV2 infected Golden-Syrian-hamster. The Intravenous pharmacokinetic profiling of MFcS2 in hamster at a dose of 5 mg/Kg presented a maximum serum concentration of 23.45 {micro}g/mL with a half-life of 29.5 hrs. These results suggest that MFcS2 could be used as an effective decoy based therapeutic strategy to treat COVID19. This work also reports usage of a novel oral-cancer cell line as in vitro model of SARS-Cov2 infection, validated by over expressing viral-defence pathways upon RNA-seq analysis and over-expression of ACE2 and TMPRSS upon growth in hyperglycaemic condition.

molecular biology↗

Genome-wide association study of brain biochemical phenotypes reveals distinct genetic architecture of Alzheimer's Disease related proteins

Alzheimers disease (AD) is neuropathologically characterized by amyloid-beta (A{beta}) plaques and neurofibrillary tangles. Main protein components of these hallmarks include A{beta}40, A{beta}42, tau, phospho-tau and APOE. With the exception of the APOE-{varepsilon}4 variant, genetic risk factors associated with brain biochemical measures of these proteins have yet to be characterized. We performed a genome-wide association study in brains of 441 AD patients for quantitative levels of these proteins collected from three distinct fractions reflecting soluble, membrane-bound and insoluble biochemical states. We identified 123 genome-wide significant associations at seven novel loci and the APOE locus. Genes and variants at these loci also associate with multiple AD- related measures, regulate gene expression, have cell-type specific enrichment, and roles in brain health and other neuropsychiatric diseases. Pathway analysis identified significant enrichment of shared and distinct biological pathways. Although all biochemical measures tested reflect proteins core to AD pathology, our results strongly suggest that each have unique genetic architecture and biological pathways that influence their specific biochemical states in the brain. Our novel approach of deep brain biochemical endophenotype GWAS has implications for pathophysiology of proteostasis in AD that can guide therapeutic discovery efforts focused on these proteins.

genetics↗