Biology subjects

Saxena, M.

Publications and source records attributed to Saxena, M..

12 recordsLinked to original sources

bioRxiv2026

Biomarker-driven and gene-enhanced viral therapy for malignant peripheral nerve sheath tumor

Background: High-grade malignant peripheral nerve sheath tumors (MPNST) frequently lose Polycomb Repressive Complex 2 (PRC2), reducing the repressive histone mark, H3K27me3. We hypothesized that H3K27me3 loss sensitizes MPNST to oncolytic HSV due to impaired transcriptional resistance. HSV replication is also restricted by the integrated stress response, normally countered by HSV ICP34.5, representing an additional resistance pathway to ICP34.5-attenuated HSV. Methods: PRC2 loss-of-function was evaluated as a biomarker of HSV G47{Delta} ({Delta}ICP34.5) susceptibility in MPNST using isogenic, pharmacologic inhibition, and genetic rescue models. CUT&RUN and RNA-sequencing defined PRC2-dependent viral and host responses. We engineered a G47{Delta}-derived vector (G47{Delta}2) with tumor-regulated ICP34.5 expression [G47{Delta}2,ins(BIRC5>ICP34.5)] and evaluated efficacy in MPNST xenografts. Results: H3K27me3 deficiency increased G47{Delta} sensitivity and viral spread in vitro. CUT&RUN demonstrated PRC2-dependent H3K27me3 accumulation on the viral genome, explaining G47{Delta} activity in H3K27me3-deficient MPNST. RNA sequencing of G47{Delta} infected MPNST cells revealed heightened integrated stress response activity and blunted induction of translation-associated programs in the PRC2-deficient state (both p<0.001), consistent with compensatory resistance at the level of viral protein translation. Accordingly, tumor-regulated ICP34.5 HSV limited daily tumor-volume growth to 0.6% (95% CI, -2.9-4.2%), improving upon both G47{Delta}2 (8.3%; 4.5-12.2%) and controls (22.5%; 17.4-27.8%). A murine gastrointestinal toxicity phenotype reduced all-cause event-free survival, indicating vector and dosing optimizations are needed to widen the therapeutic window. Conclusions: H3K27me3 loss creates a paradoxical antiviral state that tumor-selective ICP34.5 overcomes to rescue HSV anti-tumor activity, supporting biomarker-driven viral engineering to exploit the permissive transcriptional state of H3K27me3-deficient MPNSTs.

cancer biology↗

bioRxiv2025

Uncertainty Modeling Outperforms Machine Learning for Microbiome Data Analysis

Microbiome sequencing measures relative rather than absolute abundances, providing no direct information about total microbial load. Normalization methods attempt to compensate, but rely on strong, often untestable assumptions that can bias inference. Experimental measurements of load (e.g., qPCR, flow cytometry) offer a solution, but remain costly and uncommon. A recent high-profile study proposed that machine learning could bypass this limitation by predicting microbial load from sequencing data alone. To evaluate this claim, we assembled mutt, the largest public database of paired sequencing and load measurements, spanning 35 studies and over 15,000 samples. Using mutt, we show that published machine learning models fail to generalize: on average they perform worse than a naive baseline that always predicted the training set mean. These failures stem from covariate shift-limited shared taxa between studies, differences in community composition, and differences in preprocessing pipelines-that silently derail model inputs. In contrast, Bayesian partially identified models do not attempt to impute microbial load, but instead propagate scale uncertainty through downstream analyses. Across 30 benchmark datasets, Bayesian partially identified models consistently outperformed normalization and machine learning approaches, providing a principled and reproducible foundation for microbiome inference.

bioinformatics↗

bioRxiv2024

Gene-Dose-Dependent Reduction Fshr Expression Improves Spatial Memory Deficits in Alzheimer's Mice

Alzheimers disease (AD) is a major progressive neurodegenerative disorder of the aging population. High post-menopausal levels of the pituitary gonadotropin follicle-stimulating hormone (FSH) are strongly associated with the onset of AD, and we have shown recently that FSH directly activates the hippocampal Fshr to drive AD-like pathology and memory loss in mice. To establish a role for FSH in memory loss, we used female 3xTg;Fshr+/+, 3xTg;Fshr+/- and 3xTg;Fshr-/- mice that were either left unoperated or underwent sham surgery or ovariectomy at 8 weeks of age. Unoperated and sham-operated 3xTg;Fshr-/-mice were implanted with 17{beta}-estradiol pellets to normalize estradiol levels. Morris Water Maze and Novel Object Recognition behavioral tests were performed to study deficits in spatial and recognition memory, respectively, and to examine the effects of Fshr depletion. 3xTg;Fshr+/+mice displayed impaired spatial memory at 5 months of age; both the acquisition and retrieval of the memory were ameliorated in 3xTg;Fshr-/- mice and, to a lesser extent, in 3xTg;Fshr+/- mice-- thus documenting a clear gene-dose-dependent prevention of hippocampal-dependent spatial memory impairment. At 5 and 10 months, sham-operated 3xTg;Fshr-/- mice showed better memory performance during the acquisition and/or retrieval phases, suggesting that Fshr deletion prevented the progression of spatial memory deficits with age. However, this prevention was not seen when mice were ovariectomized, except in the 10-month-old 3xTg;Fshr-/-mice. In the Novel Object Recognition test performed at 10 months, all groups of mice, except ovariectomized 3xTg;Fshr-/- mice showed a loss of recognition memory. Consistent with the neurobehavioral data, there was a gene-dose-dependent reduction mainly in the amyloid {beta}40 isoform in whole brain extracts. Finally, serum FSH levels <8 ng/mL in 16-month-old APP/PS1 mice were associated with better retrieval of spatial memory. Collectively, the data provide compelling genetic evidence for a protective effect of inhibiting FSH signaling on the progression of spatial and recognition memory deficits in mice, and lay a firm foundation for the use of an FSH-blocking agent for the early prevention of cognitive decline in postmenopausal women.

neuroscience↗

bioRxiv2022

A Single Multipurpose FSH-Blocking Therapeutic for Osteoporosis and Obesity

Pharmacological and genetic studies over the past decade have established FSH as an actionable target for diseases affecting millions, notably osteoporosis, obesity and Alzheimers disease (AD). Blocking FSH action prevents bone loss, fat gain and AD-like features in mice. We recently developed a first-in-class, humanized, epitope-specific FSH blocking antibody, MS-Hu6, with a KD of 7.52 nM. Using a GLP-compliant platform, we now report the efficacy of MS-Hu6 in preventing obesity and osteoporosis in mice, and parameters of acute safety in monkeys. Biodistribution studies using 89Zr-labelled, biotinylated or unconjugated MS-Hu6 in mice and monkeys showed localization to bone, bone marrow and fat depots. MS-Hu6 displayed a {beta} phase t[1/2] of 13 days (316 hours) in humanized Tg32 mice, and bound endogenous FSH. We tested 215 variations of excipients using the protein thermal shift assay to generate a final formulation that rendered MS-Hu6 stable in solution upon freeze-thaw and at different temperatures, with minimal aggregation, and without self-, cross-, or hydrophobic interactions or appreciable binding to relevant human antigens. MS-Hu6 showed the same level of "humanness" as human IgG1 in silico, and was non-immunogenic in ELISPOT assays for IL-2 and IFN{gamma} in human peripheral blood mononuclear cell cultures. We conclude that MS-Hu6 is efficacious, durable and manufacturable, and is therefore poised for future human testing as a multipurpose therapeutic.

pharmacology and toxicology↗

bioRxiv2022

Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types

Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors.

neuroscience↗

bioRxiv2021

Cochlear organoids reveal epigenetic and transcriptional programs of postnatal hair cell differentiation from supporting cells

We explored the transcriptional and epigenetic programs underlying the differentiation of hair cells from postnatal progenitor cells in cochlear organoids. Heterogeneity in the cells including cells with the transcriptional signatures of mature hair cells allowed a full picture of possible cell fates. Construction of trajectories identified Lgr5+ cells as progenitors for hair cells and the genomic data revealed gene regulatory networks leading to hair cells. We validated these networks, demonstrating dynamic changes both in expression and predicted binding sites of these transcription factors during organoid differentiation. We identified known regulators of hair cell development, Atoh1, Pou4f3, and Gfi1, and predicted novel regulatory factors, Tcf4, an E-protein and heterodimerization partner of Atoh1, and Ddit3, a CCAAT/enhancer-binding protein (C/EBP) that represses Hes1 and activates transcription of Wnt signaling-related genes. Deciphering the signals for hair cell regeneration from mammalian cochlear supporting cells reveals candidates for HC regeneration which is limited in the adult.

developmental biology↗

bioRxiv2018

Lipid Lowering Oxopropanylindole Hydrazone Derivatives with Antioxidant and Antihyperglycemic Activity

A series of substituted oxopropanylindole hydrazone derivatives was synthesized and evaluated for anti-oxidant and anti-dyslipidemic activity. Among these 12 compounds the three compounds 6c, 7b and 7d showed good anti-oxidant activity and the compound 6c attenuataed LDL oxidation by 32%. The compounds 6c and 7d also showed good anti-dyslipidemic activity by reducing serum levels of total cholesterol (TC), phospholipids (PL) and triglycerides (TG). These two compounds were further evaluated for anti-adipogenic and anti-hyperglycemic activity, where 6c was found most active compound with 44% reduction in lipid accumulation and 20.5% and 24.3% reduction in blood glucose at 5h and 24h respectively, as compared to standard drug metformin.

biochemistry↗

bioRxiv2018

Synthesis, SAR and Docking Studies of Substituted Aryl phenylthiazolyl phenylcarboxamide as potential Protein Tyrosine Phosphatase 1B Inhibitors

Inspired by the potent PTP1B inhibitory activity reported in a novel series of substituted aryl thiazolyl phenylsulphonamides (I), sulfonyl moiety in the most active compound (I, R= OCH3, R1= CF3, 73.6% PTP1B inhibition) was replaced by benzoyl group (region B) to afford compound II which showed lesser activity (50.5% PTP1B inhibition). To optimize the activity, further structural modifications were done on compound II at region A, B and C to design and synthesize a series of 24 aryl phenylthiazolyl phenylcarboxamides for evaluation against PTP1B enzyme. Among these compounds six compounds showed good PTP1B inhibitory activity in the order of compound 38 > 30 > 29 > 37 > 22 > 19. The lowest energy conformer of compound 38 at PTP1B active site shows favorable binding similar to known PTP1B binders and explains its selectivity towards PTP1B. Compound 38 also showed promising antihyperglycemic, antidyslipidemic and insulin resistant reversal activities in vivo in STZ model and db/db mice model. Altogether, the compound 38 present an excellent candidate for future PTP1B targeted drug discovery.

pharmacology and toxicology↗

bioRxiv2018

The Lineage-Specific Transcription Factor CDX2 Navigates Dynamic Chromatin to Control Distinct Stages of Intestine Development

Lineage-restricted transcription factors, such as the intestine-specifying factor CDX2, often have dual requirements across developmental time. Embryonic-loss of CDX2 triggers homeotic transformation of intestinal fate, while adult-onset Cdx2-loss compromises critical physiological functions but preserves intestinal identity. It is unclear how such diverse requirements are executed across the developmental continuum. Using primary and engineered human tissues, mouse genetics, and a multi-omics approach, we demonstrate that divergent CDX2 loss-of-function phenotypes in embryonic versus adult intestines correspond to divergent CDX2 chromatin-binding profiles in embryonic versus adult stages. CDX2 binds and activates distinct target genes in developing versus adult mouse and human intestinal cells. We find that temporal shifts in chromatin accessibility correspond to these context-specific CDX2 activities. Thus, CDX2 is not sufficient to activate a mature intestinal program, but rather, CDX2 responds to its environment, targeting stage-specific genes to contribute to either intestinal patterning or maturity. This study provides insights into the mechanisms through which lineage-specific regulatory factors achieve divergent functions over developmental time.

developmental biology↗

bioRxiv2018

Tumor suppressor DAPK1 catalyzes adhesion assembly on rigid but anoikis on soft matrices

Cancer cells will normally grow on soft surfaces, but if rigidity sensing modules are restored in cancer cells, they will undergo apoptosis on soft surfaces (anoikis) like most normal cells. DAPK1 is a major tumor suppressor that activates cell death, but it is unclear how DAPK1 could activate anoikis through rigidity sensing. Here we find that when rigidity sensing is decreased through inhibition of DAPK1 activity, cells are transformed for growth on soft matrices. Further, DAPK1 catalyzes matrix adhesion assembly and is part of adhesions on rigid surfaces. Additional factors include DAPK1 phosphorylation of tropomyosin2.1, talin1 head domain and tyrosine phosphorylation of DAPK1 by Src. On soft surfaces, DAPK1 rapidly dissociates from the adhesion complexes and activates apoptosis that requires PTPN12 activity and talin1 head. Thus, DAPK1 is important for adhesion assembly on rigid surfaces and the activation of anoikis on soft surfaces through its binding to rigidity-sensing modules.

cell biology↗

bioRxiv2018

Site-specific PEGylation crosslinking of L-asparaginase subunits to improve its therapeutic efficiency

L-Asparaginase is an enzyme successfully being used in the treatment of acute lymphoblastic leukemia, acute myeloid leukemia, and non-Hodgkins lymphoma. However, some disadvantages still limit its full application potential, e.g., allergic reactions, pancreatitis, and blood clotting impairment. Therefore, much effort has been directed at improving its performance. A popular strategy is to randomly conjugate L-asparaginase with mono-methoxy polyethylene glycol, which became a commercial FDA approved formulation widely used in recent years. To improve this formulation by PEGylation, herein we performed cysteine-directed site-specific conjugation of the four L-asparaginase subunits to prevent dissociation-induced loss of activity. The conjugation sites were selected at surface-exposed positions on the protein to avoid affecting the catalytic activity. Three conjugates were obtained using different linear PEGs of 1000, 2000, and 5000 g/mol, with physical properties ranging from a semi-solid gel to a fully soluble state. The soluble-conjugate exhibited higher catalytic activity than the non-conjugated mutant, and the same activity than the native enzyme. Site-specific crosslinking of the L-asparaginase subunits produced a higher molecular weight conjugate compared to the native tetrameric enzyme. This strategy might improve L-asparaginase efficiency for leukemia treatment by reducing glomerular filtration due to the increase in hydrodynamic size thus extending half-live, while at the same time retaining full catalytic activity.

bioengineering↗

bioRxiv2018

Myosin filaments reversibly generate large forces in cells

We present high resolution experiments performed on elementary contractile units in cells that challenge our current understanding of molecular motor force generation. The key features are the development of a force per motor considerably larger than forces measured in single molecule experiments, a force increase followed by relaxation controlled by a characteristic displacement rather than by a characteristic force, the observation of steps at half the actin filament period even though a large number of motors are at work in an elementary contractile unit. We propose a generic two-state model of molecular motor collections with hand-over-hand contractions and we find that these unexpected observations are spontaneously emerging features of a collective motor behavior.

biophysics↗