Biology subjects

Sarkar, S.

Publications and source records attributed to Sarkar, S..

At least 73 records · Page 4Linked to original sources

bioRxiv2025

Sewing the future of cotton: a multi-omics study combining nanomechanics, transcriptomics, and phenotypic traits

Cellulose microfibrils that are essential for mechanical strength and overall quality of cotton fibers. This study quantifies and compares the nanoscale structural and mechanical properties of cellulose microfibrils such as microfibril dimensions, crossover count and angles, roughness, and Youngs modulus for two popular cotton species: Gossypium hirsutum (Gh) and Gossypium barbadense (Gb) fibers across four growth stages (8, 12, 18, and 22 days post-anthesis) using atomic force microscopy (AFM). Our results revealed for the first time that Gb fibers exhibit a better alignment, finer dimensions, and higher stiffness compared to Gh fibers at nanoscale, resulting in smoother fiber surfaces, and improved quality at macroscale. We are also the first to develop machine-learning models to predict macroscale phenotypic traits specifically boll length and cellulose content using nanoscale features alone and in combination with multi-omics modalities, substantially enhancing the predictive accuracy and highlighting opportunities for robust cross-species modeling of cotton fiber traits.

biophysics↗

bioRxiv2025

Of condensates and coats - reciprocal regulation of clathrin assembly and the growth of protein networks

Clathrin-mediated endocytosis is essential for membrane traffic, impacting a diverse range of cellular processes including cell signaling homeostasis, cell adhesion, and receptor recycling. During endocytosis, invagination of the plasma membrane is coordinated by a network of proteins that recruit and assemble the clathrin coat. Recent work demonstrated that clathrin accessory proteins which arrive early at endocytic sites, such as Eps15 and Fcho2, form phase-separated condensates that recruit downstream machinery, promoting assembly and maturation of clathrin-coated vesicles. However, the mechanisms by which protein condensates regulate - and are regulated by - clathrin assembly remain unclear. Using in vitro reconstitution and nuclear magnetic resonance spectroscopy, we demonstrate that protein condensates provide a platform for recruitment and assembly of clathrin triskelia. This condensate driven assembly is enhanced in the presence of the accessory protein, AP2, which is readily incorporated within condensates. In turn, clathrin assembly restricted the growth of condensates, exhibiting surfactant-like behavior that stabilized protein-protein interactions while imposing the preferred curvature of the clathrin lattice. This mutual regulation promotes efficient assembly of clathrin-coated vesicles while preventing uncontrolled expansion of protein condensates. More broadly, reciprocal regulation of protein condensates and clathrin coats may provide a framework for understanding how intrinsically disordered and structured protein assemblies can work together to build complex cellular architectures.

biophysics↗

bioRxiv2025

Correlations among hydrogen bond fluctuations in the apo state are enough to reveal allosteric networks in proteins

Allostery is essential for regulating biochemical pathways, where ligand binding at one site influences enzymatic activity at a distant functional site. Identifying allosteric sites and mapping signal transduction pathways in biomolecules remain a significant challenge. Existing experimental or computational methods, in general, can identify a subset of total allosteric network. Here, we consider that in addition to providing structural stability and flexibility of proteins, hydrogen bonds inside the protein may act as conduits for long-range communication. To this end, we develop a computational framework that predicts allosteric sites and total allosteric network by analyzing correlations among hydrogen bond fluctuation from equilibrium molecular dynamics trajectory of apo state of proteins. We demonstrated that this method can accurately captures experimentally verified allosteric sites and suggest allosteric signal transduction pathways across three different proteins. Furthermore, since our predictions are derived solely from the simulation trajectory of the apo state, these findings reinforce the idea that the signature of allostery is inherently encoded in the apo state of the protein. This approach offers a useful strategy to decode allosteric network and pockets, with broad implications for drug discovery and the targeted modulation of allostery in proteins. SignificanceAllostery, distal ligand-induced functional modulation of biomolecules, is central to biological regulation, yet its intricate mechanisms remain elusive. Precise identification of allosteric sites and pathways is essential for targeted drug development, minimizing off-target effect. Here, we introduce a novel computational approach, Hydrogen Bond Allosteric Map (HBAlloMap), which leverages the dynamic fluctuations of hydrogen bond networks derived from microsecond molecular dynamics simulations to comprehensively map allosteric modules within proteins. By analyzing the fluctuation of correlated hydrogen bonds, our method effectively reveals key allosteric hotspots and signal transduction pathways in PDZ3, PDZ2, and Pin1. By providing a robust and efficient tool for deciphering allosteric mechanisms, this method has the potential to accelerate drug discovery and deepen our understanding of allostery.

biophysics↗

bioRxiv2025

Knock-out of Tpm4.2/actin filaments alters neuronal signaling, neurite outgrowth and behavioral phenotypes in mice.

Tropomyosins (Tpm) are master regulators of actin dynamics through forming co-polymers with filamentous actin. Despite the well-understood function of muscle Tpms in the contractile apparatus of muscle cells, much less is known about the diverse physiological function of cytoplasmic Tpms in eukaryotic cells. Here, we investigated the role of the Tpm4.2 isoform in neuronal processes including signaling, neurite outgrowth and receptor recycling using primary neurons from Tpm4.2 knock-out mice. Live imaging of calcium and electro-physiology data demonstrated increased frequency, yet reduced strength of single neuron spikes. Calcium imaging further showed increase in neuronal networks. In vitro assays of Tpm4.2 knock-out neurons displayed impaired recycling of the AMPA neurotransmitter receptor subunit GluA1. Morphometric analysis of neurite growth showed increased dendritic complexity and altered dendritic spine morphology in Tpm4.2 knock-out primary neurons. Behavioral analysis of Tpm4.2 knock-out mice displayed heightened anxiety in Open field test whilst Elevated Plus maze displayed heightened anxiety only in females. A sex-dependent phenotype was also seen in the Social Preference test with impaired social memory and socialization in female Tpm4.2 knock-out mice, whilst male and female knock-out mice had impaired recognition memory in a Novel Object Recognition test. Our study depicts the multi-faceted role of the Tpm4.2 isoform and its co-polymer F-actin population in neurons, with potential implications for better understanding diseases of the nervous system which involve actin cytoskeleton dys-function.

neuroscience↗

bioRxiv2025

Extracellular Vesicles Derived from Mesenchymal Stromal Cells Reduce Pseudomonas aeruginosa Lung Infection and Inflammation in Mice

The World Health Organization and the U.S. Centers for Disease Control and Prevention have reported that antibiotic resistant infections with Pseudomonas aeruginosa present a significant health risk world-wide. In the genetic disease Cystic Fibrosis (CF), chronic antibiotic resistant Pseudomonas lung infections and persistent inflammation remain the leading causes of mortality. While highly effective modulator therapy (HEMT) dramatically improves lung function in CF, they fail to eradicate chronic infections or eliminate the associated hyperinflammatory state. Thus, there is an urgent need for innovative therapies that can simultaneously eliminate antibiotic resistant P. aeruginosa lung infection and the attendant hyperinflammatory lung environment. Mesenchymal stromal cell-derived extracellular particles (MSC EPs) represent a promising solution, offering potent anti-inflammatory and antimicrobial properties while being safe and non-toxic. This study demonstrates using a CF mouse model of infection that MSC EPs reduce acute P. aeruginosa lung infection and inflammation. As the first investigation of MSC EPs in CF mice, this research underscores the dual effects of MSC EPs; reducing inflammation and bacterial burden. These findings mark an important advancement in antimicrobial therapy, addressing the unmet need for reducing antibiotic resistant infections and hyperinflammation in CF as well as other diseases with chronic, antibiotic resistant P. aeruginosa infections.

microbiology↗

bioRxiv2025

KCa3.1 Contributes to Neuroinflammation and Nigral Dopaminergic Neurodegeneration in Experimental models of Parkinson's Disease

Chronic neuroinflammation and misfolded -synuclein (Syn) have been identified as key pathological correlates driving Parkinsons disease (PD) pathogenesis; however, the contribution of ion channels to microglia activation in the context of -synucleinopathy remains elusive. Herein, we show that KCa3.1, a calcium-activated potassium channel, is robustly upregulated within microglia in multiple preclinical models of PD and, most importantly, in human PD and dementia with Lewy bodies (DLB) brains. Pharmacological inhibition of KCa3.1 via senicapoc or TRAM-34 inhibits KCa3.1 channel activity and the associated reactive microglial phenotype in response to aggregated Syn, as well as ameliorates of PD like pathology in diverse PD mouse models. Additionally, proteomic and transcriptomic profiling of microglia revealed that senicapoc ameliorates aggregated Syn-induced, inflammation-associated pathways and dysregulated metabolism in primary microglial cells. Mechanistically, FYN kinase in a STAT1 dependent manner regulates KCa3.1 mediated the microglial reactive activation phenotype after -synucleinopathy. Moreover, reduced neuroinflammation and subsequent PD-like neuropathology were observed in SYN AAV inoculated KCa3.1 knockout mice. Together, these findings suggest that KCa3.1 inhibition represents a novel therapeutic strategy for treating patients with PD and related -synucleinopathies.

neuroscience↗

bioRxiv2025

Differential interfacial tension between oncogenic and wild-type populations forms the mechanical basis of tissue-specific oncogenesis in epithelia

Why does the same oncogenic mutation drive tumor formation in some tissues but not in others? While cancer driver mutations are well-documented, their tissue-specific effects remain largely attributed to genetic factors, leaving the biophysical aspects underexplored. Here, we demonstrate that mechanical interactions, specifically interfacial tension between newly transformed and wildtype epithelial cells are critical in determining survival and growth of HRasV12 oncogenic mutants in human mammary and bronchial epithelia, leading to contrasting outcomes in the two tissues. In mammary epithelium, isolated oncogenic cells are extruded-a typical mechanism of defense against cancer in epithelia-while oncogenic groups become spatially confined in a kinetically arrested, jammed state, marked by an actomyosin belt at the interface. In contrast, bronchial epithelium permits persistent spreading of the same oncogenic cells, which form long protrusions regardless of colony size. Furthermore, oncogenic clusters in these two tissues exhibit distinct biophysical properties, including variations in cell shapes, intracellular pressure, cell-cell tension, and cellular motility. Using a cell shape-tension coupled bi-disperse vertex model, we reveal that differences in interfacial tension at mutant-wild-type boundaries dictate whether oncogenic cells are eliminated, restrained, or expanded and that modulating the heterotypic interfacial tension alters mutant cell fate within the epithelium. Together, our findings uncover a mechanical basis for tissue-specific oncogenesis by highlighting how differential cellular mechanics at the oncogenic-host cell interface regulate tumor initiation and progression.

biophysics↗

bioRxiv2025

A unique serum-free murine cortical astrocyte culture to study endoplasmic reticulum stress in response to amyloid-β

Astrocytes are integral to understand Alzheimers disease (AD) pathology but the existing serum-supplemented in vitro astrocyte culture models are not suitable to study certain stress response mechanisms. Here, we developed a serum-free murine primary cortical astrocyte culture model to study endoplasmic reticulum (ER) stress and inflammation to see the effect of amyloid-beta (A{beta}1-42). Astrocytes were cultured in a controlled serum-free environment to minimize interference from serum components. Serum-free astrocytes were exposed to oligomeric A{beta} to induce ER stress and inflammation. Initially no significant activation of eIF2, a key marker of ER stress, was observed under serum-free condition but with the removal of N-acetyl cysteine ER stress response was enhanced after 24 hours of A{beta} exposure. Subsequently, the inflammatory response, assessed through TNF- expression, was minimal in the presence of growth factors but became pronounced when these factors were withdrawn. Astrocytic reactivity, assessed by GFAP expression, was observed with prolonged A{beta} exposure, indicating a reactive astrogliosis response. Transcript analysis revealed a time-dependent shift in the expression of inflammatory modulators, with early time points showing increased anti-inflammatory markers and late exposure promoting pro-inflammatory responses. These findings highlight the potential of serum-free cultures for studying ER stress and inflammation together in astrocytes and offer insights into the complex role of these cells in AD pathophysiology.

neuroscience↗

bioRxiv2025

Measurement Quality Metrics to Improve Absolute Microbial Cell Counting

Total and viable microbial cell counts are increasingly important for applications including live biotherapeutic products, food safety, and probiotics. In microbiology, cells are quantified using methods such as colony forming unit (CFU), flow cytometry, and polymerase chain reaction (PCR), but different methods measure different aspects of the cells (measurands), and results may not be directly comparable across methods. In the absence of a ground-truth reference material for cell count, one cannot quantify the accuracy of any cell counting method, which limits method performance assessments and comparisons. Herein, a modified analysis of cell counting methods based on the ISO 20391-2:2019 standard was developed and demonstrated for microbial cell samples diluted over a log-scale range of concentrations. Escherichia coli samples ranging in concentration from approximately 5 x 105 cells/mL to 2 x 107 cells/mL were quantified using CFU, Coulter principle, fluorescence flow cytometry, and impedance flow cytometry. Quality metrics modified from the ISO standard were calculated for each method and shown to be repeatable across replicate experiments. The quality metrics illustrate large differences in proportionality and variability across methods, with total cell counts in good agreement and viable cell count having more variability. As the ISO standard is meant to guide fit-for-purpose method selection, interpretation of the results and quality metrics can drive method choice and optimization. The framework introduced here will help researchers select fit-for-purpose counting methods for quantification of microbial total and viable cells across a range of applications.

microbiology↗

bioRxiv2025

Epsin1 enforces a condensation-dependent checkpoint for ubiquitylated cargo during clathrin-mediated endocytosis

Clathrin-mediated endocytosis internalizes proteins and lipids from the cell surface, supporting nutrient uptake, signaling, and membrane trafficking. Recent work has demonstrated that a flexible, liquid-like network of initiator proteins is responsible for catalyzing assembly of clathrin-coated vesicles in diverse organisms including yeast, mammals, and plants. How do cells regulate the assembly of this dynamic network to produce cargo-loaded vesicles? Here we reveal the ability of an endocytic adaptor protein, Epsin1, to conditionally stabilize the initiator protein network, creating a cargo-dependent checkpoint during clathrin-mediated endocytosis. Epsin1 is known to recruit ubiquitylated transmembrane proteins to endocytic sites. Using in vitro assays, we demonstrate that Epsin1 uses competitive binding and steric repulsion to destabilize condensation of initiator proteins in the absence of ubiquitin. However, when polyubiquitin is present, Epsin1 binds to both ubiquitin and initiator proteins, creating attractive interactions that stabilize condensation. Similarly, in mammalian cells, endocytic dynamics and ligand uptake are disrupted by removal of either ubiquitin or Epsin1. Surprisingly, when Epsin1 and ubiquitin are removed simultaneously, endocytic defects are rescued to near wildtype levels, although endocytic sites lose the ability to distinguish between ubiquitylated and non-ubiquitylated cargos. Taken together, these results suggest that Epsin1 tunes protein condensation to ensure the presence of ubiquitylated cargo during assembly of clathrin-coated vesicles. More broadly, these findings illustrate how a balance of attractive and repulsive molecular interactions controls the stability of liquid-like protein networks, providing dynamic control over key cellular events.

cell biology↗

bioRxiv2025

Delineating JunB's Crucial Function in Mature Th17 Cells through Inducible Targeted Protein Degradation

The AP-1 transcription factor JunB is essential for the differentiation of pathogenic T helper 17 (Th17) cells, which are key mediators of autoimmune diseases such as multiple sclerosis and colitis. While the importance of JunB during Th17 polarization is known, its role in mature Th17 cells--critical therapeutic targets in these diseases--remains unclear. In this study, we employed the dTAG system, a targeted protein degradation approach, to deplete JunB in Th17 cells generated both in vitro and in vivo. During pathogenic Th17 cell differentiation, JunB degradation replicated known effects of JunB deficiency, including reduced expression of interleukin (IL)-17A and the genes encoding ROR{gamma}t (Rorc) and the IL-23 receptor (Il23r). In contrast, in mature pathogenic Th17 cells, JunB degradation downregulated Il23r without affecting IL-17A or Rorc expression. Furthermore, JunB degradation compromised the viability of mature pathogenic Th17 cells. Transcriptomic analyses revealed that JunB regulates distinct gene sets during Th17 polarization compared to mature Th17 cells. The gene Inhba, which encodes activin A, was identified as a JunB target in both stages. Supplementation with activin A restored IL-17A and Rorc expression during pathogenic Th17 cell differentiation. These findings demonstrate that JunB maintains mature pathogenic Th17 cell phenotypes, including IL-23 receptor expression, and supports pathogenic Th17 cell survival. As IL-23 signaling is crucial for sustaining pathogenic Th17 cells, targeting JunB may offer a therapeutic strategy to limit Th17-driven autoimmune inflammation.

immunology↗

bioRxiv2024

Phosphatidylinositol-3,5-bisphosphate mediated vacuolar morphology modulation is integral to ethanol stress response

Vacuoles enlarge in response to ethanol. We used quantitative imaging to show that even brief exposure to ethanol causes a rapid transition from multilobed vacuoles to a single compartment. Vacuole unlobing is essential as mutants restricted for vacuole fusion exhibit greater ethanol sensitivity. This response involves the inhibition of vacuole fission via downregulation of the activity of Fab1, a lipid kinase generating the signaling lipid phosphatidylinositol-3,5-bisphosphate. Ethanol exposure results in the redistribution of a phosphatidylinositol-3,5-bisphosphate sensor from the perivauolar dots to the cytoplasm and the dissociation of the effector of this lipid, Atg18, from the vacuolar membrane to the cytoplasm. Impaired Atg18 membrane recruitment also entails a loss of interaction between a scaffold of the Fab1 complex, Vac14, and Atg18. A hyperactive Fab1 mutant, with elevated pools of phosphatidylinositol-3,5-bisphosphate, shows delayed vacuole enlargement; the partial relocation of the phosphatidylinositol-3,5-bisphosphate probe to the perivacuolar dots and of Atg18 to the vacuole membrane. Since Atg18 is responsible for vacuole fragmentation, our results show that, under ethanol stress, cells actively regulate vacuole morphology by modulating phosphatidylinositol-3,5-bisphosphate levels.

cell biology↗

bioRxiv2024

Poly-ubiquitylated transmembrane proteins outcompete other cargo for limited space inside clathrin-coated vesicles

Endocytic recycling of transmembrane proteins is essential to cell signaling, ligand uptake, protein traffic and degradation. The intracellular domains of many transmembrane proteins are ubiquitylated, which promotes their internalization by clathrin-mediated endocytosis. How might this enhanced internalization impact endocytic uptake of transmembrane proteins that lack ubiquitylation? Recent work demonstrates that diverse transmembrane proteins compete for space within highly crowded endocytic structures, suggesting that enhanced internalization of one group of transmembrane proteins may come at the expense of other groups. Here we show that preferential internalization of poly-ubiquitylated transmembrane proteins results in reduced endocytosis of mono-ubiquitylated and non-ubiquitylated proteins. Using a combination of live-cell imaging and ligand uptake assays, we confirmed that increased ubiquitylation correlates with increased internalization by clathrin-coated vesicles. Further, poly-ubiquitylated receptors significantly outcompeted their mono-ubiquitylated and non-ubiquitylated counterparts for localization to endocytic sites and uptake of extracellular ligands. These findings demonstrate the inherent interdependence of transmembrane protein recycling, suggesting that clathrin-coated vesicles act as selective filters, prioritizing highly ubiquitylated transmembrane proteins for uptake while leaving proteins with little or no ubiquitylation behind. Given that poly-ubiquitylation is thought to signal protein aging and damage, our findings suggest a mechanism for selective internalization of high priority cargo proteins, with simultaneously exclusion and protection of functional proteins that lack poly-ubiquitylation.

cell biology↗

bioRxiv2024

Potent antitumor activity of a designed interleukin-21 mimic

Long-standing goals of cancer immunotherapy are to activate cytotoxic antitumor T cells across a broad range of affinities while dampening suppressive regulatory T (Treg) cell responses, but current approaches achieve these goals with limited success. Here, we report a de novo IL-21 mimic, 21h10, designed to have augmented stability and high signaling potency in both humans and mice. In multiple animal models and in ex vivo human melanoma patient derived organotypic tumor spheroids (PDOTS), 21h10 showed robust antitumor activity. 21h10 generates significantly prolonged STAT signaling in vivo compared with native IL-21, and has considerably stronger anti-tumor activity. Toxicities associated with systemic administration of 21h10 could be mitigated by TNF blockade without compromising antitumor efficacy. In the tumor microenvironment, 21h10 induced highly cytotoxic antitumor T cells from clonotypes with a range of affinities for endogenous tumor antigens, robustly expanding low-affinity cytotoxic T cells and driving high expression of interferon- (IFN-) and granzyme B compared to native IL-21, while increasing the frequency of IFN-+ Th1 cells and reducing that of Foxp3+ Tregs. As 21h10 has full human/mouse cross-reactivity, high stability and potency, and potentiates low-affinity antitumor responses, it has considerable translational potential.

biochemistry↗

bioRxiv2024

Interaction of plant-derived metabolites and rhizobiome functions enhances drought stress tolerance

BackgroundPlants evolved alongside microbes, enabling plants to better cope with abiotic and biotic stresses. The interactions between plant roots and local soil microbes are critical for environmental adaptation and plant health. Plants actively regulate the microbial community composition in their rhizospheres to recruit specific microorganisms that enhance their fitness in the ecosystem they inhabit. This study builds on prior research suggesting that plants have a "home field advantage" in recruiting microbes unique in their home environment, reflecting mutual recognition and the targeted recruitment of microbes. ResultsUsing gene- and genome-centric approaches, we assessed the functional potential of root-associated microbes and profiled the host metabolites to uncover the metabolic outputs potentially regulating host-microbe interactions. Our results showed that plants adapted to drier environments experience less stress, producing fewer stress-related metabolites and impacting the recruitment of microbes with genes linked to stress relief pathways. In particular, plant-derived trimethyllysine was highly associated with microbial populations capable of improving nutrient uptake, producing plant growth-promoting compounds, and modulating stress responses. ConclusionThis study highlights the critical interplay between host exudates and microbial substrate uptake as the primary mechanism of rhizosphere assembly. We demonstrate that plants actively produce metabolites to recruit microbial populations with the functional potential to enhance hosts ability to thrive in a stressful environment. This research provides insights into the mechanisms of plant-microbe communication, rhizosphere recruitment, and the complex interplay of plant-microbe interactions. Furthermore, it highlights promising avenues for manipulating rhizosphere microbiomes to support conservation agriculture in the face of climate change.

microbiology↗

bioRxiv2024

Structural basis for gene silencing by siRNAs in humans

Small interfering RNAs (siRNAs) guide mRNA cleavage by human Argonaute2 (hAgo2), leading to targeted gene silencing. Despite their laboratory and clinical impact, structural insights into human siRNA catalytic activity remain elusive. Here, we show that disrupting siRNA 3-end binding by hAgo2 accelerates target cleavage and stabilizes its catalytic conformation, enabling detailed structural analysis. A 3.16 [A] global resolution cryo-EM reconstruction reveals that distortion of the siRNA-target duplex at position 6 allows target RNA entry into the catalytic cleft and shifts Lysine-709, a previously unrecognized catalytic residue, into the active site. A pyrimidine at target nucleotide t10 positions another unrecognized catalytic residue, Arginine-710, for optimal cleavage. Expansion of the guide-target duplex major groove docks the scissile phosphate for hydrolysis and subsequent groove compression after position 16 permits target RNAs to exit the catalytic cleft. These findings reveal how hAgo2 catalyzes siRNA target hydrolysis, providing a high-resolution model for therapeutic design.

molecular biology↗

bioRxiv2024

Centromere-proximal crossovers disrupt proper homologous chromosome disjunction during meiosis

Centromere-proximal crossovers (C-COs) are repressed during meiosis across all species. Moreover, aberrant C-COs are strongly correlated with meiotic aneuploidy such as in Down syndrome. Despite decades of work in understanding C-CO repression, the molecular basis of how they cause chromosomal mis-segregation is unclear. Here, we show that increased C-COs result in mis-segregation of homologs during meiosis I in Schizosaccharomyces pombe. C-COs cause either nondisjunction events where the entire bivalent moves into the same nucleus at meiosis I or result in biorientation of sister chromatids leading to their premature separation. Since meiosis I segregation appears normal in pericentric cohesion deficient mutants, we rule out centromeric cohesion disruption as the primary driver of segregation defects due to C-COs, as suggested in some other species. In contrast, reduced pericentric cohesion alleviates the meiosis I nondisjunction events, thereby supporting the previously suggested "entanglement model" that proposes physical entwining of the bivalent due to retention of sister-chromatid cohesion at centromeres, a hallmark of anaphase I. This alteration also uncovers biorientation of sister-chromatids in meiosis I suggesting mono-orientation disruption as a parallel way to promote mis-segregation in the presence of C-COs. These molecular insights will improve our understanding of infertility and aneuploidy-associated developmental disorders in humans.

genetics↗

bioRxiv2024

Identification and characterization of vasoactive intestinal peptide receptor antagonists with high-affinity and potent anti-leukemia activity

Vasoactive intestinal peptide (VIP) is a neuropeptide involved in tumor growth and immune modulating functions. Previous research indicated that a VIP antagonist (VIPhyb) enhances T-cell activation and induces T-cell-dependent anti-leukemic activity in mice. We created a combinatorial library of VIPhyb C-terminal sequence variations to develop a more potent VIP-receptor (VIP-R) antagonist, hypothesizing that specific amino acid substitutions would improve receptor binding and plasma stability. In silico screening analyses identified sequences with improved docking scores predicting increased binding affinity to human VIP receptors VPAC1 and VPAC2. Fifteen peptides were synthesized and tested for their ability to potentiate activation of purified mouse and human T cells and enhance T cell-dependent anti-leukemia responses in murine models of acute myeloid leukemia. Treating C57Bl/6 mice engrafted with a C1498 myeloid leukemia cell line with daily subcutaneous injections of VIP-R antagonist peptides induced T cell activation resulting in specific anti-leukemia responses. Strikingly, the predicted binding affinity of the VIP-R antagonists to VIP receptors correlated positively with their ability to augment mouse T-cell proliferation and anti-leukemia activity. ANT308 and ANT195 emerged as top candidates due to their high predicted VIP-R binding, low EC50 for in vitro T cell activation, and potent anti-leukemia activities. ANT308 decreased CREB phosphorylation, a downstream signaling pathway of the VIP receptor, and stimulated granzyme B and perforin expression in CD8+ T cells from AML patients. Combining in silico modeling, in vitro T cell activation properties, and in vivo anti-leukemia activity has identified promising VIP-R antagonist candidates for further development as novel immunotherapies for AML, especially for patients with relapsed disease.

immunology↗