Biology subjects

Gupta, R.

Publications and source records attributed to Gupta, R..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

MRCKα represses GEF-H1 mediated RhoA activation to promote ovarian cancer spheroid growth and invasion.

High-grade serous ovarian carcinoma (HGSOC) is characterized by high mortality rates and the frequent development of chemotherapy resistance. A hallmark of HGSOC progression is the formation of multicellular spheroids in malignant ascites that facilitate peritoneal dissemination and metastasis. While the CDC42-regulated kinases MRCK and MRCK{beta} (MRCK) were previously found to be highly expressed in ovarian tumors and to be essential for cell migration and spheroid growth, the underlying molecular mechanisms were poorly defined. Mass spectrometry identified the RhoA-selective guanine nucleotide exchange factor GEF-H1 as a primary interacting partner of MRCK. Functional assays revealed that MRCK inhibition or knockdown led to significantly increased levels of active GEF-H1 and subsequent RhoA activation. MRCK was found to phosphorylate GEF-H1 on Ser174, and pharmacological inhibition of MRCK reduced this phosphorylation and decreased the association of GEF-H1 with -Tubulin. Live-cell imaging and 3D assays demonstrated that MRCK inhibition disrupted cell-cell contacts and impaired the compaction of multicellular structures, ultimately reducing the viability of patient-derived organoids. These findings delineate a novel signaling crosstalk mechanism in which MRCK represses GEF-H1-mediated RhoA activation to facilitate the formation of cell-cell contacts that contribute to the survival and growth of HGSOC cells in 3D multicellular structures. This study highlights MRCK as a potential therapeutic target to inhibit the growth and spread of HGSOC.

cell biology↗

bioRxiv2026

Measurement intensification for antibody formulations: combined measurement of protein size, interactions, and viscosity by differential dynamic microscopy

High-throughput screening and optimization of high-value protein formulations requires intensified measurements to extract a wide range of properties using a small number of measurement techniques, small sample volumes, and short measurement times. We demonstrate how differential dynamic microscopy (DDM) can fill this need by measuring a broad range of key biophysical properties relevant to protein formulations from a single workflow on microliter-scale samples using label-free video optical microscopy. We show that the use of phase contrast imaging dramatically enhances measurement resolution for protein solutions at dilute and semidilute concentrations, enabling measurement of colloidal properties such as protein-protein interactions, protein size, aggregation, and solution viscosity from a single set of measurements. DDM measurements on a representative human immunoglobulin (IgG) system yield estimates for the hydrodynamic radius (Rh), second osmotic virial coefficient (B2), and hydrodynamic interaction (kd) that are consistent with independently measured values, validating the ability of DDM to extract these parameters from a single set of measurements. Observed trends in B2 with pH and ionic strength are consistent with the antibodys charge and screened electrostatics, demonstrating the ability of DDM to provide insight on protein-protein interactions. To show the utility of DDM as a "multitool" for quantifying multiple formulation properties from a single measurement, we use the results to test a predictive colloidal model for the solution viscosity, which is in fair agreement with measurements obtained using DDM-based microrheology. Combined with low sample requirements and short measurement times, DDM thus offers a high-throughput and efficient route to accelerate protein biophysics and formulation development. SIGNIFICANCE STATEMENTThe formulation of stable, high-concentration antibodies and other protein solutions requires extensive biophysical measurements that are often material- and time-intensive. We demonstrate that differential dynamic microscopy (DDM) provides a powerful alternative by providing rapid access to a broad range of industrially relevant colloidal properties from a single measurement on microliter-scale samples using conventional video optical microscopy. This capability makes DDM an attractive, low-resource approach for routine biomolecular formulation screening and optimization.

biophysics↗

bioRxiv2025

Insulin-Regulated Actin Dynamics is Disrupted in a Human Keratinocyte Model of Hailey Hailey Disease

Hailey Hailey Disease (HHD) is an autosomal dominant cutaneous disorder caused by mutations in ATP2C1, the gene encoding the Golgi/secretory pathway Ca2+-ATPase SPCA1. Characterized by suprabasal acantholysis and intertriginous blistering of the skin, HHD treatment focuses on managing symptoms as there is no cure. Challenges to targeted therapy are due to the lack of facile and reliable models, both human and rodent, for mechanistic studies. Here we validate and characterize CRISPR/Cas9 mediated single and bi-allelic ATP2C1 knockouts in immortalized human hTERT keratinocytes. Whereas SPCA1 expression, Golgi morphology and Golgi Ca2+ accumulation were proportionately affected in heterozygous and homozygous ATP2C1 null mutants as expected, both single and double allelic mutants showed near complete loss of cadherins associated with desmosomal and adherens junctions. HHD is characterized by poor wound healing and impaired keratinocyte migration. We show that SPCA1 is required for dynamic reorganization of actin cytoskeleton in keratinocyte spreading. We identified an insulin activated PI3K-AKT-Rac1 signaling pathway required for lamellipodia formation and keratinocyte spreading, defective in SPCA1 mutants. Transgenic expression of hSPCA1 or treatment with CDN1163, a small molecule Ca2+-ATPase agonist, restored defective phenotypes in the HHD model, paving the way for future therapeutic approaches to treat this disorder.

cell biology↗

bioRxiv2025

CRISPRi-mediated validation of candidate Myocobacterium abscessus drug targets during host infection

Mycobacterium abscessus (Mab) is a multidrug-resistant nontuberculous mycobacterium that causes debilitating TB-like pulmonary infections for which effective treatment options are lacking. Poor in vivo drug efficacy may stem from altered vulnerability of drug targets driven by host-specific environmental conditions. To enable validation and prioritization of candidate drug targets in vivo, we exploited CRISPRi (CRi) gene silencing in multiple mouse infection models. Inducible silencing of ftsZMab, a previously validated target, and three predicted targets (leuSMab, folPMab, fusAMab) confirmed their essentiality in vitro. We then assessed the in vivo vulnerability of these targets in both immunocompetent C57BL/6N and immunodeficient NSG mice by assessing the impact of CRi silencing on pulmonary mycobacterial burden. In NSG mice, silencing of all four genes led to comparable decreases in Mab burden. However, in C57BL/6N mice, the degree of Mab clearance varied among targets, suggesting that immune pressure may influence the outcome of CRi-mediated gene silencing. Notably, repression of fusAMab yielded a larger decline in mycobacterial burden in C57BL/6N mice despite a lower level of gene silencing in vitro, consistent with enhanced vulnerability of this target. Overall, this study demonstrated that ftsZMab, leuSMab, folPMab, and fusAMab are essential for Mab growth in vitro and, for the first time, validated their vulnerability to inhibition by CRi during infection. These data also identified potential context-dependent target vulnerabilities, which could inform the prioritization of bacterial drug targets and accelerate the development of effective therapeutics for Mab infections.

microbiology↗

bioRxiv2025

Dual Preconditioned Mesenchymal Stem Cells-Derived Culture Conditioned Media Augment Immunomodulation and Drive Metabolic Reprogramming in Acute Graft-versus-Host Disease

BackgroundThe toxicity associated with conventional conditioning regimens limits treatment outcomes in autoimmune disorders such as acute graft-versus-host disease (aGVHD). Developing effective adjunctive interventions to restore immune balance is therefore essential. This study investigated the immunomodulatory potential of mesenchymal stem cells (MSCs)-derived culture-conditioned media (CCM) from naive and preconditioned MSCs-hypoxic (MSCsHYP), apoptotic (MSCsAPO), and dual preconditioned (MSCsHYP+APO) in aGVHD. MethodsHuman MSCs isolated from bone marrow and Whartons Jelly were preconditioned under hypoxia (1% O2), apoptosis (1 {micro}M staurosporine, 24 h), or both. The immunoregulatory and antioxidant properties of their CCM were evaluated through T-cell proliferation assays, Treg induction, macrophage polarization, mitochondrial function, and T-cell bioenergetics. Comparative proteomic profiling of CCM from WJ-MSCs and WJ-MSCsHYP+APO co-cultured with aGVHD patient-derived activated PBMNCs was performed using LC-MS/MS, alongside in vivo validation in a chemotherapy-induced aGVHD murine model. ResultsWJ-MSCsHYP+APO-CCM exhibited superior immunomodulatory efficacy, suppressing T-cell proliferation, promoting Treg and Th2/Th9 differentiation, and driving M2 macrophage polarization. It reduced mitochondrial ROS, enhanced mitochondrial polarization, and shifted T-cell metabolism from glycolysis toward oxidative phosphorylation. Proteomic analysis revealed modulation of IL-12, IL-17, and JAK-STAT pathways, along with regulation of complement, coagulation, and metabolic cascades. Interaction with immune cells further enhanced its antioxidant and tissue-reparative properties via extracellular matrix remodeling. ConclusionDual preconditioning under hypoxia and apoptosis amplifies the immunomodulatory, antioxidant, and reparative efficacy of WJ-MSC-CCM, offering a potent non-cellular therapeutic strategy for aGVHD management. GRAPHICAL ABSTRACTImmunomodulatory and immune metabolic reprogramming potential of naive and preconditioned MSCs (MSCs, MSCsHYP, MSCsAPO, MSCsHYP+APO) derived CCM in Acute GVHD (created using Biorender.com) O_FIG O_LINKSMALLFIG WIDTH=95 HEIGHT=200 SRC="FIGDIR/small/686182v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@f7ed73org.highwire.dtl.DTLVardef@1063015org.highwire.dtl.DTLVardef@13ed827org.highwire.dtl.DTLVardef@e103c0_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

TOM: Transformer Optimization of mRNA initiation

Recombinant Protein Production enables scientists to insert custom DNA into host cells to produce specific proteins. Current industry standard tools to optimize recombinant DNA use the Codon Adaptation Index (CAI), yet doing this changes local mRNA secondary structure and Minimum Free Energy (MFE) at the translation initiation region, creating hairpins that block ribosome loading and initiation, thus limiting protein production. mRNA secondary structure around the start codon (disrupting ribosome docking/initiation) is the true rate limiting barrier to protein synthesis, and its 22x more correlated to protein production than CAI. This project introduces TOM, a novel Transformer deep learning model that optimizes mRNA secondary structure at the critical translation initiation region. Over 40 million natural E. Coli initiation sequences were downloaded, where through a rigorous data filtration effort, only 10,000 ideal, non redundant, and naturally occurring sequences were used to train the model. TOM is benchmarked on MFE, adenine count, codon usage, and a negative element analysis against industry standard optimizers and significantly outperforms. TOMs improvement of the MFE at the initiation region offers a significant increase in protein production by addressing the rate-limiting step of translation initiation.

bioinformatics↗

bioRxiv2025

Neuronal glycolytic reprogramming drives lethality via accelerated aging in a Drosophila model of tauopathy

Neurometabolic dysfunction is a hallmark of Alzheimers disease (AD) and tauopathies. Whether these changes drive pathology or represent compensatory, protective responses remains unresolved. Here, we demonstrate that human tau induces Warburg-like metabolism in Drosophila neurons, characterized by coordinated upregulation of glycolytic enzymes and lactate dehydrogenase that mirrors metabolic signatures in human AD. Despite intact mitochondrial oxidative phosphorylation, tau-expressing fly neurons preferentially utilize glycolysis for ATP production and operate with diminished metabolic reserve. Crucially, this metabolic reprogramming drives rather than protects against pathology as genetic suppression of glycolysis or lactate dehydrogenase completely rescued tau-induced lethality. Further, Gompertz mortality analysis revealed that hyperactive glycolysis in tau neurons drives premature lethality by accelerating biological aging rate without affecting baseline mortality. Collectively, these findings establish aberrant neuronal glycolysis as a cause rather than a consequence of tau pathology, and demonstrate that sustained glycolytic metabolism in mature neurons exacts a specific cost in the form of accelerated aging.

neuroscience↗

bioRxiv2025

EGFL7 promotes immune evasion in glioma through its interaction with integrin β2

Glioblastoma is the most aggressive form of malignant brain cancer, characterized by an immunosuppressive microenvironment and immune evasion. Despite the success of immune checkpoint inhibitors in other cancers, immunotherapies such as anti-PD1 have shown limited efficacy in glioblastoma, underscoring the need to identify tumor-intrinsic mechanisms that sustain this immunosuppressive microenvironment and to develop more effective therapeutic strategies targeting them. Previously, the secreted factor epidermal growth factor-like protein 7 (EGFL7) has been shown to promote brain tumor growth by affecting the glioblastoma microenvironment (GME). However, its impact on the immune system remained enigmatic. Here, we studied the role of EGFL7 in shaping the immune landscape in glioblastoma and identified the underlying molecular mechanisms it engages to drive glioma immune evasion. Single-cell transcriptomic profiling of immune cells derived of glioblastoma revealed that EGFL7 promotes an immunosuppressive GME, characterized by enhanced T cell exhaustion and polarization of macrophages towards a protumorigenic state. Proteomic profiling of EGFL7s interactome in glioma revealed its interaction with integrin {beta}2 (ITGB2), an immune cell surface receptor involved in cell adhesion and migration. Mechanistic studies uncovered the central role of this interaction for immune evasion, which promoted T cell exhaustion and the polarization of macrophages towards a pro-tumorigenic state. Genetic perturbation of the EGFL7-ITGB2 axis attenuated immunosuppression and prolonged the survival of glioblastoma-bearing mice. Remarkably, a combinatorial regimen of anti-EGFL7 and the checkpoint inhibitor anti-PD1 improved the efficacy of this drug, which by itself did not improve glioma patient survival so far. In conclusion, our study provides unequivocal evidence that EGFL7 mediates immune evasion in glioma and has great potential to serve as an add-on drug target to improve immunotherapies not functional in glioblastoma patients so far.

cancer biology↗

bioRxiv2025

GPR68, a proton-sensing GPCR, mediates acid-induced visceral nociception

Background & AimsLocalised acidification from immune cell infiltration and heightened glycolysis contributes to colitis pathology by activating acid-sensing receptors such as GPR68, a proton-sensing GPCR expressed on immune and stromal cells. Single-cell RNAseq analysis revealed GPR68 is also expressed in colonic sensory neurons, prompting us to investigate its role in acid-induced colonic nociception. MethodsExpression of GPR68 in colonic nociceptors and tissue from people with colitis was confirmed by in silico analysis of our RNAseq databases. Its contribution to disease activity was assessed using the acute dextran sulphate sodium (DSS) model of colitis. Acid-evoked sensory signalling was evaluated via colonic afferent recordings and Ca{superscript 2} imaging in DRG neurons from wild-type and GPR68-/- mice, supported by pharmacological studies using Ogerin (a GPR68 positive allosteric modulator) and Ogremorphin (a GPR68 antagonist). ResultsRNAseq analysis showed GPR68 is robustly expressed in Trpv1 colonic nociceptors and upregulated in tissue from people with inflammatory bowel disease, consistent with reduced disease activity in DSS-treated GPR68-/- mice. Genetic deletion of GPR68 abolished colonic afferent responses to acid, which were also attenuated by Ogremorphin and enhanced by Ogerin. In Ca{superscript 2}-free buffer, DRG neurons from GPR68-/- mice or those pre-treated with Ogremorphin showed significantly reduced acid-evoked intracellular Ca{superscript 2} responses. By contrast the colonic afferent and DRG Ca2+ response (in Ca2+-containing buffer) to capsaicin was comparable between tissue from wild-type and GPR68-/- mice highlighting the involvement of divergent proton-dependent cellular signalling cascades. ConclusionsThese findings identify GPR68 as a key mediator of acid-induced colonic nociception and highlight its potential as a therapeutic target for the treatment of pain in colitis. SynopsisWe demonstrate that the proton-sensing receptor GPR68 mediates acid-induced signalling in colonic sensory neurons. Genetic and pharmacological modulation confirms GPR68s role in visceral nociception and supports its potential as a therapeutic target for pain management in colitis.

neuroscience↗

bioRxiv2025

Mechanism of age-related accumulation of mitochondrial DNA mutations in human blood

One of the strongest signatures of aging is an accumulation of mutant mitochondrial DNA (mtDNA) heteroplasmy. Here we investigate the mechanism underlying this phenomenon by calling mtDNA sequence, abundance, and heteroplasmic variation in human blood using whole genome sequences from [~]750,000 individuals. Our analyses reveal a simple, two-step mechanism: first, individual cells randomly accumulate low levels of "cryptic" mtDNA mutations; then, when a cell clone proliferates, the cryptic mtDNA variants are carried as passenger mutations and become detectable in whole blood. Four lines of evidence support this model: (1) the mutational spectrum of age-accumulating mtDNA variants is consistent with a well-established model of mtDNA replication errors, (2) these mutations are found primarily at low levels of heteroplasmy and do not show evidence of positive selection, (3) high mtDNA mutation burden tends to co-occur in samples harboring somatic driver mutations for clonal hematopoiesis (CH), and (4) nuclear GWAS reveals that germline variants predisposing to CH (such as those near TERT, TCL1A, and SMC4) also increase mtDNA mutation burden. We propose that the high copy number and high mutation rate of mtDNA make it a particularly sensitive blood-based marker of CH. Importantly, our work helps to mechanistically unify three prominent signatures of aging: common germline variants in TERT, clonal hematopoiesis, and observed mtDNA mutation accrual.

genetics↗

bioRxiv2025

Histone H3 tail charge patterns govern nucleosome condensate formation and dynamics

Emerging models of nuclear organization suggest that chromatin forms functionally distinct microenvironments through phase separation. As chromatin architecture is organized at the level of the nucleosome and regulated by histone post-translational modifications, we investigated how these known regulatory mechanisms influence nucleosome phase behavior. By systematically altering charge distribution within the H3 tail, we found that the terminal and central regions modulate the phase boundary and tune nucleosome condensate viscosity differentially, as revealed by microscopy-based assays, microrheology, and simulations. Nuclear magnetic resonance relaxation experiments revealed that H3 tails remain dynamically mobile within condensates, and their mobility correlates with condensate viscosity. These results demonstrate that the number, identity, and spatial arrangement of basic residues in the H3 tail critically regulate nucleosome phase separation. Our findings support a model in which nucleosomes, through their intrinsic properties and modifications, actively shape the local chromatin microenvironment--providing new insight into the histone language in chromatin condensates.

biophysics↗

bioRxiv2025

Cucumber extracellular vesicles-localized tetraspanin and phloem protein 2 mediates the cross-kingdom trafficking of a pathogenic non-coding RNA

The plant apoplast and extracellular vesicles (EVs) contain diverse RNA species, including small RNAs, long non-coding RNAs, and circular RNAs, many of which cross kingdom boundaries through EV-mediated transport. Viroid RNAs--pathogenic circular non-coding RNAs--are known to move from plants to fungi and insects, though the mechanism remains unclear. Using apple scar skin viroid (ASSVd) and cucumber as a host, we demonstrate that viroid RNAs in circular, linear, and small RNA forms are present in cucumber EVs. ASSVd RNA exhibits features of extracellular RNAs, such as m6A methylation and five EXOmotifs. Through mass spectrometry and immunoblotting, we identify tetraspanin 8 (CsTET8) as a conserved EV marker and report CsPP2, a phloem lectin with an RNA-binding domain, as a novel EV-associated protein. RNA co-immunoprecipitation and immuno-enrichment assays reveal that CsPP2 and ASSVd co-localize in CsTET8-positive EVs, with direct interactions between CsPP2-CsTET8 and CsPP2-ASSVd. We propose CsPP2 functions as an RNA-sorting protein that mediates RNA loading into EVs. Further, we show that whiteflies can acquire ASSVd via EVs and transmit it to healthy plants, indicating a cross-kingdom transmission route. These findings establish viroid RNAs as a model system to study the molecular basis of RNA trafficking across biological kingdoms.

plant biology↗

bioRxiv2025

Predictive Modeling of acute Graft-versus-Host-Disease using Machine Learning on Immune Cell and Cytokine Profiles at Engraftment

BackgroundAcute Graft-versus-Host-Disease (aGvHD) is a major immune complication following allogenic hematopoietic stem cell transplantation (Allo-HSCT), initiated by conditioning regimen-associated tissue damage. It involves the complex interplay of immune cells and cytokines. Our study aims to leverage machine learning (ML) algorithms on the immune and cytokine profile of Allo-HSCT recipients to develop biomarker-based classification models to predict the onset of aGvHD at the time of engraftment. Materials and MethodsSeventy patients diagnosed with hematological disorders who had undergone Ist Allo-HSCT were recruited from All India Institute of Medical Sciences, New Delhi, India. Peripheral blood (PB) was collected from the patients at the time of engraftment, and the immune cell subtypes and cytokine profiles were analyzed using flow cytometry and ELISA respectively. The individual cell counts were then processed using basic ML models, including support vector classifier with RBF kernel, Decision Tree, and Random Forest, chosen for their mathematical simplicity and feature importance advantage of Decision Trees and Random Forests. Various data settings were utilized in the study: combined immune and cytokine counts, immune cell counts only, cytokine counts only, T-cell counts only, NK cell counts only, dendritic cell counts only, and B-cell counts only. These configurations were selected to investigate how different data sets impact the prediction of aGvHD before its onset. ResultsAt the engraftment flow cytometric analysis of reconstituted lymphocytes in patients who developed aGvHD revealed that there was a remarkable decrease in the ratio of CD4+/CD8+ T-cell and Tregs, with an increase in the cytotoxic regulatory NK-cell, dendritic cells, and B-cell. The levels of pro-inflammatory cytokines (IFN-{gamma}, IL-1{beta}, IP-10, TNF-, IL-17, IL-12p70, MIP-1, MIP-1{beta}, RANTES), and Th17-and Th1-cells were elevated with consequent decline of the levels of anti-inflammatory cytokine IL-10, IL-2, IL-4 and Th2-, Th9-cells. Machine learning based on 48 parameters [all immune cell subsets n=34 and all cytokines (n=14)]. The correlation heat map shows a higher correlation of aGvHD with the cytokine profile with or without immune cells (accuracy: 1), T-cell alone (accuracy: 0.96); NK-cell alone (accuracy: 0.93); dendritic cells alone (accuracy: 0.90), B-cell alone (accuracy: 0.86). ConclusionThe current models classify perfectly, indicating the potential for a ML algorithm in predicting the onset of aGvHD. However, a study with a larger sample size is required to validate these classification models and mitigate the risk of overfitting observed due to the consistently high performance. The study also highlights the potential of cytokine profiles as a viable alternative to T-cell counts, as evidenced by the correlation heat map and classifier models. These findings provide valuable insights into dataset requirements and future directions for integrating ML models into aGvHD prediction.

immunology↗

bioRxiv2025

Dose-Response Immunomodulatory Effects of Mesenchymal Stem Cells-Derived Culture-Conditioned Media in Acute Graft-versus-Host-Disease

BackgroundMesenchymal stem cell-based therapy faces challenges that have driven interest in MSCs-derived culture-conditioned media (CCM) as a cell-free alternative. Our study aims to optimize the dose, and collection timing of CCM to enhance its therapeutic efficacy in aGVHD, while also standardizing co-culture conditions for CD3+ T-cell interaction with CCM. Material and MethodsHuman MSCs were isolated from BM and WJ and subsequently preconditioned under hypoxic conditions (1% O2) for 24 hours in a tri-gas incubator. Culture-conditioned media (CCM) was collected from both naive and hypoxia-preconditioned MSCs at 24, 48, and 72 hours and filtered using a 0.2 m membrane filter. CD3+ T-cell were isolated from PBMNCs derived from aGVHD patients. These T-cell were co-cultured at varying densities (2*106, 5*106, and 10*106 cells/ml) with different concentrations of CCM (25%, 50%, and 100%), and cell proliferation was assessed using the MTS assay. Furthermore, CD3+ T-cell proliferation and activation status were evaluated in a 2D co-culture model of CD3+ T-cell and CCM using flow cytometry. ResultsOur findings revealed that CCM collected at 48 hours, at a 50% concentration, exerted the most pronounced inhibitory effect on CD3+ T-cell proliferation, particularly at a density of 5*106 cells/ml, irrespective of the MSCs source. Hypoxia preconditioning significantly enhanced the immunomodulatory effects, with WJ-MSCsHYP-CCM demonstrating superior efficacy in suppressing T-cell proliferation, increasing the CD4+/CD8+ T-cell ratio, and reducing CD4+ T-cell activation compared to BM-MSCsHYP-CCM. ConclusionThese results emphasize the critical role of optimizing CCM collection timing and concentration to maximize therapeutic potential. Our study paves the way for the development of standardized, scalable, and effective cell-free therapies for aGVHD. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=198 HEIGHT=200 SRC="FIGDIR/small/640019v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@16ecc48org.highwire.dtl.DTLVardef@12591dborg.highwire.dtl.DTLVardef@18af4beorg.highwire.dtl.DTLVardef@1c9e8c9_HPS_FORMAT_FIGEXP M_FIG C_FIG Optimum conditions for CCM dose, collection time point, and CD3+ T-cell dose for effective immunomodulatory effect of MSCs-derived CCM in aGVHD. (created using Biorender.com)

immunology↗

bioRxiv2025

The Binary Cellular Biology of Human Growth I Quantifying the Creation and Growth of the Body and its Parts

Assessing and understanding the Growth and Development of animals generally, and of human fetuses specifically, provides essential information for the management of the health of the newborn and its mother. Here we show that a consideration of the formation of the body, in units of numbers of cells, N, and the change in these numbers by the binary either/or decisions of cells to divide or not, an approach we call Binary Cellular Analysis, provides new insights and new equations for quantifying the growth and development of the body and its parts. These equations include: 1) The Binary Cellular Universal Growth Equation, which captures growth from conception to adulthood, and provides a method for biologically-based, data-driven, Growth Curves; 2) The Binary Cellular Universal Mitotic Fraction Equation, which lies within the Binary Cellular Universal Growth Equation, and captures the mechanism of growth to adult size, control of cell division; 3) The Binary Cellular Allometric Growth Equation, which captures the creation and growth of the Tissues, Organs, and Anatomical Structures of the body, and how the embryo creates each Body Part from a Single Founder Cell; and, 4) Binary Cellular Estimated Fetal Weight Equations, derived from the Binary Cellular Allometric Growth Equation, which captures the relationship between Ultrasound Measurement and the Size of the body as a whole. These equations capture the developmental process of Cellular Selection, resulting from Differential Cellular Proliferation, which molds the formation of the body from a single fertilized ovum into a multicellular animal. The parameters of these equations both capture the differences in Size and Growth between animals across the taxonomic spectrum, and between human fetuses, as well as identify the individual mechanisms of mitosis that drive Growth and Development. From the Binary Cellular Universal Growth Equation, the Growth of human fetuses can be measured, thus providing a much-needed tool for understanding the biological forces that cause a fetus to grow to Small, Average, or Large Size at birth, for providing the basis of biologically-based, data-driven, Growth Curves, and for assisting the management of the obstetric care of the fetus and its mother.

developmental biology↗

bioRxiv2025

The Binary Cellular Biology of Human Growth II Calculating the Size of the Human Fetus from the Size of its Parts

Assessing and understanding the Size of the human fetus provides essential information for the management of the health of the newborn and its mother, a quality that is commonly measured by Fetal Ultrasound. Many equations for making such calculations have been considered, none of which have been entirely satisfactory. As we have shown in the previous paper in this series, a consideration of the formation of the body, in units of numbers of cells, N, an approach we call Binary Cellular Analysis, provides new quantitative tools for estimating the Size and Age of the fetus. These tools include a new mathematical basis for creating useful expressions, Binary Cellular Estimated Fetal Weight Equations, for calculating human Fetal Weight from Ultrasound Measurements. As we show here, the most promising of these expressions, the Abdominal Circumference Binary Cellular Estimated Fetal Weight Equation, performs better than other currently used Fetal Weight Equations, while also yielding up new methods for improving ultrasound size assessment. Web-based calculators (https://kidzgrowth.com) make these mathematical manipulations available for obstetric care.

developmental biology↗

bioRxiv2025

Heterogeneity of anti-Caspr2 antibodies: specificity and pathogenicity

Maternal anti-Caspr2 (Contactin-associated protein-like 2) antibodies have been associated with increased risk for autism spectrum disorder (ASD). Previous studies have shown that in utero exposure to anti-Caspr2 antibodies results in a phenotype with ASD-like features in male mice. Here we ask whether four newly generated antibodies against Caspr2 are pathogenic to the developing fetal brain and whether they function through similar means. Our results show that the novel anti-Caspr2 antibodies recognize different epitopes of Caspr2. In utero exposure to these antibodies elicits differential ASD-like phenotypes in male offspring, tested in the social interaction, open field, and light-dark tasks. These results demonstrate variability in the antigenic specificity and pathogenicity of anti-Caspr2 antibodies which may have clinical implications.

immunology↗

bioRxiv2025

Hypoxia-Mediated Molecular Interactions of Tissue-Specific Mesenchymal Stem Cells Drive Metabolic Reprogramming and Immunomodulation in Acute Graft-versus-Host Disease

BackgroundMesenchymal stem cells (MSCs) mediate immunomodulation through various mechanisms, including apoptosis, efferocytosis, and mitochondrial transfer. Our study investigates the impact of hypoxia preconditioning on the immune metabolic reprogramming and immunomodulatory potential of MSCs in acute graft-versus-host disease (aGVHD). Additionally, we explored the differential immunomodulatory effects of tissue-specific MSCs, specifically bone marrow (BM) and Whartons Jelly (WJ), and elucidated the mechanisms underlying variability in their therapeutic efficacy. MethodsMSCs were isolated from BM and WJ and subjected to hypoxia preconditioning. Their immunometabolic programming potential was assessed by evaluating T-cell proliferation, regulatory T-cell (Treg) induction, effector T-cell differentiation toward Th2, Th9 phenotypes, and macrophage polarization, T-cell bioenergetics in the direct co-culture systems. ResultsWJ-MSCsHYP exhibited superior immunomodulatory properties compared to BM-MSCsHYP, by inhibiting T-cell proliferation, enhancing Treg induction, and promoting anti-inflammatory macrophage polarization. WJ-MSCsHYP demonstrated enhanced mitochondrial transfer to T-cell, improving mitochondrial health, reducing ROS, and promoting oxidative phosphorylation, leading to immune homeostasis. Unlike BM-MSCs, WJ-MSCs exhibited higher rates of apoptosis, which facilitated immune modulation through mechanisms independent of efferocytosis. ConclusionOur findings highlight that WJ-MSCsHYP is a superior candidate for aGVHD by utilizing apoptosis, mitochondrial transfer, and metabolic reprogramming to achieve immune regulation.

immunology↗