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Biology subjects

Saxena, V.

Publications and source records attributed to Saxena, V..

14 recordsLinked to original sources

Phase Separation of Intracellular Proteins Influences Synaptic Bistability

Synaptic bistability at the post synaptic density has been proposed to be the result of the nucleation and evaporation of receptor clusters. The exact biophysical mechanism underlying these inter-receptor attractions that can trigger nucleation remains to be elucidated. Emerging evidence demonstrates that numerous postsynaptic density submembrane proteins, that interact with various membrane receptors, can undergo phase separation, necessitating a revised conceptual model. By employing Langevin dynamics simulations of coarse-grained scaffold proteins and interacting membrane receptors, we study how phase transitions of scaffold proteins alter receptor clustering at the membrane. In our model, scaffold macromolecules can undergo phase separation and interact with receptor molecules at the model membranes. We observed that the presence of scaffold polymers across the membrane creates an attractive interaction between otherwise purely repulsive receptors. By systematically varying the number of receptors at the membrane, we dissected the coupling between receptor clustering and the phase behavior of scaffold macromolecules. We show that the propensity for receptor clustering is enhanced by the condensation of scaffold proteins. We then used two different scaffolds and systematically varied the interaction between them, to change the spatial organization of two condensed phases w.r.t. one another. Interestingly, we observed that receptor clustering can be reduced by co-phase separation of scaffold macromolecules, indicating the role of competing interactions in receptor clustering. Our work advances understanding of receptor-mediated signaling and phase separation, providing insights into cellular compartmentalization and biochemical regulation at the synapse.

biophysics↗

CLARA: Compound Library Active Learning with Reasoning Agents

Batch active learning for ligand discovery requires a recurring decision about whether to exploit high predicted affinity, reduce model uncertainty, or broaden chemical coverage. We test whether a language model can make this strategy-level decision while candidate ranking and label revelation remain controlled by a deterministic Gaussian-process environment. Across four protein targets, ten paired seeds, and a 360-compound assay budget, a GPT-5.6 Sol agent outperformed random sampling in all 40 matched campaigns. Its final top-2\% recall was 0.412 on D2R, 0.374 on Mpro, 0.448 on TYK2, and 0.683 on USP7. It was statistically tied with the strongest fixed policy on Mpro and USP7 but underperformed target-specific leaders on D2R and TYK2. The agent shifted from exploration-oriented early batches toward exploitation and produced 686 testable threshold claims with an 86.3\% atomic success rate, although 19.8\% of forecasts were not numerically scorable. In 200 prespecified information-ablation campaigns, removing uncertainty, diversity, or memory caused only small endpoint changes, while shuffling explanatory evidence reproduced the full allocation path in 39 of 40 paired campaigns. A deterministic 80\% availability constraint reduced recall on every target but preserved the target-dependent pattern of wins and losses. These results support language-model strategy control as a feasible and auditable layer.

bioinformatics↗

Bioengineered recombinant kisspeptins with extended half-life exhibit novel peripheral function in a large-animal model

Kisspeptins are the small peptide products encoded by the KISS1 gene and physiologically exist in various isoforms of variable length. They are the central regulators of reproduction, being a prominent driver of GnRH hormone secretion. Additionally, they have emerged as an important peripheral therapeutic target for many metabolic diseases like diabetes, obesity, and polycystic ovary syndrome (PCOS). Despite their therapeutic potential, their utility is severely limited by their short half-life. We have rationally bioengineered two versions of native kisspeptins, which we named HSK-1 and HSK-2. HSK-1 (8kDa) and HSK-2 (13kDa) are derived from the fusion of the albumin-binding ZAG domain from Streptococcus zooepidemicus with KP-10 and KP-52 versions of kisspeptins (KPs), respectively. In vitro assays confirmed that the proteins were functionally active and triggered downstream signalling. Molecular dynamics simulations of the proteins revealed their structural features relative to the native kisspeptin isoforms. Both molecules demonstrated stable receptor engagement, and ligand-induced conformational changes were observed, suggesting receptor activation. HSK proteins demonstrated an extended half-life and mostly acted peripherally in young animals. They reduced peripheral luteinizing hormone levels in young animals, likely representing a previously unrecognized mode of peripheral kisspeptin action. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/703727v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@7b02fdorg.highwire.dtl.DTLVardef@13da0org.highwire.dtl.DTLVardef@174d467org.highwire.dtl.DTLVardef@124c653_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

Spontaneous Phase Separation Enables Rapid, Polymerization-Free Fabrication of Dissolvable Hydrogels

Hydrogels are cross-linked polymeric networks with wide applications in drug delivery, tissue engineering, biosensing, and environmental remediation. These hydrogels additionally host living cells, small molecules and biological propagules, which further expand the applications of these materials. However, most if not all fabrication methods require covalent modifications. In this work, for the first time, we demonstrate that polymer mixtures can access an additional material state beyond the conventionally described homogeneous and two-phase regimes. By deliberately selecting polymers with a known propensity to phase separate and formulating compositions far from the binodal boundary, the system transitions directly into a mechanically stable hydrogel. We demonstrate this technique using a model system of poly (ethylene glycol) (PEG) and dextran (DEX). We have systematically characterized the hydrogels through FTIR, MALDI-TOF to discern the molecular compositions of the hydrogels. We also modulate the optical transparency of these hydrogels by varying the molecular weight of the polymers. These experimental findings are supplemented with coarse grained (CG) simulation insights to investigate the mechanistic origins of phase separation propensity with varying molecular weights of dextran. We utilized coexisting densities in the two phases using CG simulations to predict the role of dextran molecular weight on the partitioning of PEG and DEX in the two phases. Finally, we exploit the fabricated hydrogels ability to encapsulate live cells, antibiotics and plant seeds. We anticipate that this ATPS-based fabrication technique will provides a scalable, crosslinker-free route to multifunctional hydrogels enabling advanced applications in drug delivery and responsive materials.

bioengineering↗

Dual Targeting for Enhanced Tumor Immunity: Conditionally Active CD28xVISTA Bispecific Antibodies Promote Myeloid-Driven T-Cell Activation

Reinvigoration of tumor-reactive T-cells using co-stimulatory bispecific antibodies (bsAbs) targeting CD28 or CD137 is emerging as a promising therapeutic strategy. Conditional, tumor-specific recruitment can offer a necessary layer of control and specificity. We developed pH-selective CD28xVISTA bsAbs to act specifically within the acidic tumor microenvironment (TME), aiming for enhanced T-cell-mediated cancer cell killing while minimizing systemic T-cell activation and Cytokine Release Syndrome (CRS) risk. CD28 agonism by CD28xVISTA bsAbs relies on pH-selective engagement of VISTA, a protein robustly expressed on myeloid cells highly prevalent in most solid tumors. This modality avoids engagement of tumor-associated antigens (TAAs) with the potential to provide highly tumor specific activity with minimal on-target/off-tumor side effects. We report the identification of a lead candidate with pH-dependent simultaneous engagement of both targets, and VISTA-dependent CD28 signaling in a reporter cell line. CD28xVISTA avidly bound VISTA-positive cells, and co-stimulation was shown in vitro by its ability to activate and expand T-cells and enhance T-cell mediated cancer cell killing in co-cultures of human PBMCs and cancer cells in the presence of a TAA-targeted anti-CD3 T-cell engager. Interestingly, our findings support both signaling in cis (between T-cell and cell displaying peptide-MHC complex) and in trans with stimulation occurring through CD28 clustering outside of the immune synapse. Our lead candidate displayed efficient tumor growth inhibition of human VISTA-expressing MC38 cells in a humanized CD28 syngeneic mouse model in combination with PD-1 blockade. Importantly, our CD28xVISTA bsAb showed no signs of superagonistic properties in several in vitro assays geared towards revealing induction of CRS. Our data supports clinical development in combination with anti-PD-1 or any TAA-targeted anti-CD3 T-cell engagers developed for solid tumors.

cancer biology↗

Predicting Metabolic Dysfunction Associated Steatotic Liver Disease Risk Using Patient-Derived Induced Pluripotent Stem Cells

Background and AimsMetabolic Dysfunction Associated Steatotic Liver Disease (MASLD) is reversible at early stages, making early identification of high-risk individuals clinically valuable. Previously, we demonstrated that patient-derived induced pluripotent stem cells (iPSCs) harboring MASLD DNA risk variants exhibit greater oleate-induced intracellular lipid accumulation than those without these variants. This study aimed to develop an iPSC-based MASLD risk predictor using functional lipid accumulation assessments. MethodsWe quantified oleate-induced intracellular lipid accumulation in iPSCs derived from three cohorts of diverse ancestry: 1) CIRM cohort (20 biopsy-confirmed MASH cases, 2 biopsy-confirmed MASLD cases, 17 controls), 2) POST cohort (18 MASLD cases, 17 controls), and 3) UCSF cohort (4 biopsy-confirmed MASH cases, 8 controls). Lipid accumulation levels in the CIRM cohort were used to define an iPSC-based MASLD risk score, which was used to predict case/control status in the POST and UCSF cohorts. ResultsIn all three cohorts, lipid accumulation was higher in MASLD/MASH cases vs. controls (CIRM cases vs. controls 3.32 {+/-} 0.25 vs. 2.70 {+/-} 0.19 -fold change, p=0.06; POST cases vs. controls 3.63 {+/-} 0.33 vs. 2.70 {+/-} 0.31, p=0.05; and UCSF cases vs. controls 4.39{+/-}0.46 vs. 2.03{+/-}0.20, p=0.0002). The iPSC-based MASLD risk score achieved a sensitivity of 44% and specificity of 75% in the POST cohort and 75% and 100%, respectively, in the UCSF cohort. Differences in cohort disease severity and cardiometabolic profiles may explain performance variability. ConclusionWhile validation in larger cohorts is needed, these findings suggest that oleate-induced intracellular lipid accumulation in subject-derived iPSCs is predictive of MASH development. Additional cellular phenotypes and donor information should be explored to improve predictive accuracy to inform MASLD surveillance and prevention strategies.

cell biology↗

Transplant immunosuppressant therapies induce unique functional changes in lymph node and re-shape gut immune homeostasis

BackgroundLifelong immunosuppressive therapy is required to prevent allograft rejection in organ transplantation. Current immunosuppressants effectively suppress adaptive and innate immune responses, but their broad, antigen-non-specific effects often result in severe off-target complications. It remains a significant unmet medical need in transplant medicine. ResultsIn this study we investigated immunosuppressant effects of four major immunosuppressant classes, including tacrolimus, prednisone, mycophenolate mofetil (MMF), and fingolimod (FTY), on the gut microbiome, metabolic pathways, lymphoid architecture and lymphocyte trafficking after up to 30-day chronic exposure. Despite their distinct mechanisms of action and not designed to target the gut, all immunosuppressive drugs induced profound and time-dependent alterations in both intestine gene expression and gut microbiome composition. Progressive alterations from moderate early, drug-specific changes to a strikingly convergent microbial dysbiosis, marked by significant expansion of pathobionts of Muribaculaceae, occurred across all drug classes. Concurrently, all drugs uniformly induced significant suppression of mucosal immunity including B cell, immunoglobulin, and antigen recognition. Time-dependent changes in lymph node (LN) reorganization and cellular composition were also observed, marked by a progressive shift toward pro-inflammatory phenotypes in gut-draining mesenteric LNs and a gradual loss of tolerogenic architecture in peripheral LNs. Drug-specific metabolic alterations and distinct phases of intestinal transcriptional responses were also characterized. Notably, MMF and FTY demonstrated the most robust immunomodulatory properties, and were able to suppress alloantigen-induced inflammation through mediating regulatory T cell distribution and LN remodeling. ConclusionsTogether, these findings highlight the underappreciated complexity and temporal dynamics immunosuppressants effects, particularly their impact on the gut and compartmentalized regulation of alloimmune in lymphoid tissues. Understanding these relationships offers new opportunities for refining immunosuppressive strategies to reduce treatment-related off-target complications and improve long-term organ transplant outcomes.

immunology↗

TSSK homologue regulates the expression of protamine and mosquito testes specific genes in Anopheles stephensi

The testis-specific serine/threonine-protein kinase (tssk) gene is known to play an important role in spermiogenesis in mammals. This study identifies tssk homologues, As_tssk3 and Aea_tssk1 in Anopheles stephensi and Aedes aegypti, respectively. Both As_tssk3 and Aea_tssk1 were found to express in a male-specific manner throughout the development. Efficient knockdown in the expression of As_tssk3 gene was observed upon feeding An. stephensi larvae with target dsRNA. As_tssk3 knockdown led to a reduced sperm reservoir in male adults. Additionally, the knockdown of As_tssk3 resulted in the reduced expression of two male specifically expressed genes, protamine & mosquito testes specific (mts- a sperm-specific marker) homologues of An. stephensi. In-silico interaction analysis suggests that As_TSSK3 protein interacts with the Nucleosome Assembly Protein1 like-4 (NAP1like-4), a putative transcription factor. We hypothesize that As_TSSK3 regulates the transcription of protamine and mts genes via NAP, as both NAP and protamine have previously been shown to function in the establishment and maintenance of chromatin dynamics, in independent studies. The study presented here is the first report of characterisation of tssk homologues in any mosquito species. The knockout studies and phosphorylation assays would provide more insights to explore the mechanism by which As_tssk3 regulates protamine and mts genes in Anopheles stephensi. HighlightsO_LIThis study identifies the tssk homologues in Ae. aegypti and An. stephensi and showed their male-specific expression in both the mosquito species. C_LIO_LIdsRNA mediated knockdown of As_TSSK3 resulted into the males with a reduced size of sperm reservoir. C_LIO_LIdsRNA mediated knockdown of As_TSSK3 led to the reduction in the expression of As_prot and As_mts, homologues of protamine and mosquito testis specific, genes in An. stephensi. C_LIO_LIIn-silico studies suggest that As_TSSK3 regulates the expression of As_prot and As_mts genes via NAP. C_LI

genetics↗

Regulatory T cells crosstalk with tumor and endothelium through lymphotoxin signaling

Regulatory T cells (Tregs) are suppressors of anti-tumor immunity that exert multifaceted functions by signaling surrounding cells. We revealed Tregs use their high-level surface lymphotoxin (LT)1{beta}2 to preferentially stimulate LT{beta} receptor (LT{beta}R) nonclassical NF{kappa}B signaling on both tumor and lymphatic endothelial cells (LECs) to accelerate tumor growth and metastasis. Selectively targeting LT{beta}R nonclassical NF{kappa}B pathways on both tumors and LECs cocultured with Tregs, inhibited tumor growth and migration in vitro. Further, we identified protumorigenic chemokines and interferon-stimulated response genes selectively driven by LT{beta}R nonclassical NF{kappa}B in melanoma cells. Endothelial specific genes related to oncogenic process such as SOX18 and FLRT2 were identified to be driven under LT{beta}R nonclassical NF{kappa}B in LECs. Leveraging in vivo Treg LT1{beta}2 interactions with LT{beta}R on tumor and LECs, transfer of WT but not LT-deficient Tregs promoted transplanted WT B16F10 growth and tumor cell-derived CXCL1 and CXCL10 secretion in LT{beta}R-deficient host mice, and increased endothelial specific genes related to tumor angiogenesis and lymphangiogenesis, in WT mice bearing LT{beta}R-depleted melanoma. Selectively blocking LT{beta}R nonclassical NF{kappa}B pathways remarkably suppressed tumor growth and lymphatic metastasis by reducing tumor cell and LEC-derived CXCL1 and CXCL10 production, restricting Treg and myeloid-derived suppressor cell (MDSC) recruitment to tumor. It also retained intratumoral effector T cells, especially IFN{gamma}+ CD8 T cells by restraining Treg facilitated lymphatic vessel permeability. Our data revealed that Treg LT1{beta}2 promotes LT{beta}R nonclassical NF{kappa}B signaling in tumor cells and LECs providing a rational strategy to modulate Treg-mediated protumorigenic molecules to prevent tumor growth and metastasis.

cancer biology↗

Rapamycin Immunomodulation Utilizes Time-Dependent Alterations of Lymph Node Architecture, Leukocyte Trafficking, and Gut Microbiome

Transplant recipients require lifelong, multimodal immunosuppression to prevent rejection by reducing alloreactive immunity. Rapamycin, a mechanistic target of rapamycin (mTOR) inhibitor, is known to modulate adaptive and innate immunity, while the full spectrum of its immunosuppressive mechanisms remains incompletely understood. Given the broad expression of mTOR, we investigated the understudied effects of rapamycin on lymph node (LN) architecture, leukocyte trafficking, and the gut microbiome and metabolism after 3, 7, and 30 days of rapamycin treatment, to characterize the early, intermediate, and late changes. Rapamycin significantly reduced CD4+ T cells, CD8+ T cells, and regulatory T (Treg) cells in peripheral LNs, mesenteric LNs, and the spleen over time. Rapamycin induced early pro-inflammation transition to pro-tolerogenic status, by modulating the LN laminin 4:5 expression ratios through LN stromal cells laminin 5 expression and by adjusting Treg numbers and distribution. Additionally, rapamycin significantly altered gut microbiota composition and metabolic functions, shifting the Bacteroides to Firmicutes ratio and increasing amino acid bioavailability in the gut lumen. These effects were evident by 7 days and became most pronounced by 30 days in naive mice, with notable changes as early as 3 days in allogeneic splenocyte-stimulated mice. These findings reveal a novel mechanism of rapamycins action through time-dependent modulation of LN architecture and gut microbiome, which orchestrates changes in immune cell trafficking, providing a new framework for understanding and optimizing immunosuppressive therapies.

immunology↗

Local genetic adaptation to habitat in wild chimpanzees

How populations adapt to their environment is a fundamental question in biology. Yet we know surprisingly little about this process, especially for endangered species such as non-human great apes. Chimpanzees, our closest living relatives, are particularly interesting because they inhabit diverse habitats, from rainforest to woodland-savannah. Whether genetic adaptation facilitates such habitat diversity remains unknown, despite having wide implications for evolutionary biology and conservation. Using 828 newly generated exomes from wild chimpanzees, we find evidence of fine-scale genetic adaptation to habitat. Notably, adaptation to malaria in forest chimpanzees is mediated by the same genes underlying adaptation to malaria in humans. This work demonstrates the power of non-invasive samples to reveal genetic adaptations in endangered populations and highlights the importance of adaptive genetic diversity for chimpanzees. One-Sentence SummaryChimpanzees show evidence of local genetic adaptation to habitat, particularly to pathogens, such as malaria, in forests.

evolutionary biology↗

Early immunomodulatory program triggered by pro-tolerogenic Bifidobacterium pseudolongum drives cardiac transplant outcomes

BackgroundDespite ongoing improvements in regimens to prevent allograft rejection, most cardiac and other organ grafts eventually succumb to chronic vasculopathy, interstitial fibrosis, or endothelial changes, and eventually graft failure. The events leading to chronic rejection are still poorly understood and the gut microbiota is a known driving force in immune dysfunction. We previously showed that gut microbiota dysbiosis profoundly influences the outcome of vascularized cardiac allografts and subsequently identified biomarker species associated with these differential graft outcomes. MethodsIn this study, we further detailed the multifaceted immunomodulatory properties of pro-tolerogenic and pro-inflammatory bacterial species over time, using our clinically relevant model of allogenic heart transplantation. ResultsIn addition to tracing longitudinal changes in the recipient gut microbiome over time, we observed that Bifidobacterium pseudolongum (Bifido) induced an early anti-inflammatory phenotype within 7 days, while Desulfovibrio desulfuricans (Desulfo) resulted in a pro-inflammatory phenotype, defined by alterations in leukocyte distribution and lymph node (LN) structure. Indeed, in vitro results showed that Bifido and Desulfo acted directly on primary innate immune cells. However, by 40 days after treatment, these two bacterial strains were associated with mixed effects in their impact on LN architecture and immune cell composition and loss of colonization within gut microbiota, despite protection of allografts from inflammation with Bifido treatment. ConclusionsThese dynamic effects suggest a critical role for early microbiota-triggered immunological events such as innate immune cell engagement, T cell differentiation, and LN architectural changes in the subsequent modulation of pro-tolerant versus pro-inflammatory immune responses in organ transplant recipients.

immunology↗

STING controls T cell memory fitness during infection through T cell intrinsic and IDO dependent mechanisms

Stimulator of interferon genes (STING) signaling has been extensively studied in inflammatory diseases and cancer while its role in T cell responses to infection is unclear. Using Listeria monocytogenes strains engineered to induce different levels of c-di-AMP, we found that strong STING signals impaired T cell memory upon infection via increased Bim levels and apoptosis. Unexpectedly, reduction of TCR signal strength or T cell-STING expression decreased Bim expression, T cell apoptosis and recovered T cell memory. We found that TCR signal intensity coupled STING signal strength to the Unfolded Protein Response (UPR) and T cell survival. Under strong STING signaling, IDO inhibition also reduced apoptosis and led to a recovery of T cell memory in STING sufficient CD8 T cells. Thus, STING signaling regulates CD8 T cell memory fitness through both cell-intrinsic and extrinsic mechanisms. These studies provide insight into how IDO and STING therapies could improve long-term T cell protective immunity. Significance StatementSTING signaling is an innate pathway that triggers host immunity against pathogens and cancer in response to cytosolic DNA. Additionally, STING signaling overactivation has been linked to autoimmunity. Yet, the interaction between antigenic and STING signaling and its impact in the development of protective immunity has remained unexplored. We found that strong levels of STING signaling impair CD8 T cell memory but only in response to high affinity TCR-pMHC interactions. Here, we provide evidence of how TCR signal strength controls STING signaling and IDO metabolism to regulate T cells survival as they mature to memory. These data have important implications for the design of STING and IDO combination immunotherapies

immunology↗

Strain-specific alterations in gut microbiome and host immune responses elicited by Bifidobacterium pseudolongum

The beneficial effects attributed to Bifidobacterium are thought to arise from their host immunomodulatory capabilities, which are likely to be species- and even strain-specific. However, their strain-specificity in direct and indirect immune modulation remain largely uncharacterized. We have shown that B. pseudolongum UMB-MBP-01, a murine isolate, is capable of suppressing inflammation and reducing fibrosis in vivo. To ascertain the mechanism driving this activity and to determine if it is specific to UMB-MBP-01, we compared it to B. pseudolongum type strain ATCC25526 of porcine origin using a combination of in vitro and in vivo experimentation and comparative genomics approaches. Despite many shared features, we demonstrate that these two strains possess distinct genetic repertoires in carbohydrate assimilation, differential activation signatures and cytokine responses in innate immune cells, and differential effects on lymph node morphology with unique local and systemic leukocyte distribution. Importantly, the administration of each B. pseudolongum strain resulted in major divergence in the structure, composition, and function of gut microbiota. This was accompanied by markedly different changes in intestinal transcriptional activities, suggesting strain-specific modulation of the endogenous gut microbiota as a key to host responses of immune modulation and changes in intestinal B. pseudolongum strains. These observations highlight the importance of strain-specificity characteristics of Bifidobacterium for prophylactic supplementation for immune modulation and advance our understanding of the mechanisms which drive the association between Bifidobacterium and health benefit.

microbiology↗