Biology subjects

Schwartz, B.

Publications and source records attributed to Schwartz, B..

6 recordsLinked to original sources

bioRxiv2026

Antisense Oligonucleotides Targeting an LDLR Regulatory RNA Increase LDLR Expression and Reduce LDL-cholesterol in Vivo

Regulatory RNAs (regRNAs) are non-coding RNAs expressed from promoters and enhancers that modulate gene transcription. Targeting regRNAs with antisense oligonucleotides (ASOs) can increase transcription and presents a potential therapeutic strategy to restore expression in haploinsufficient diseases. This approach requires high-quality regRNA maps, identification of ASOs targeting actionable sequences, and translation of efficacy to relevant animal models. Here, we describe this approach for human low-density lipoprotein receptor (LDLR). We characterized LDLR regRNAs in HepG2 cells and human liver using epigenomic mapping and regRNA Capture-seq, and designed ASOs targeting these regRNAs. Several ASOs increased LDLR expression in cells and a lead was evaluated for efficacy in a humanized liver mouse model. ASO administration increased human LDLR mRNA and protein, while lowering LDL-cholesterol in plasma. These data provide a framework for the discovery and translation of ASOs that increase gene expression as a potential therapeutic approach for the treatment of haploinsufficient diseases.

molecular biology↗

bioRxiv2025

High-throughput screening and structure-guided design of small molecules enable modulation of SAL-PAP stress signaling

Chloroplasts sense environmental stress and activate chloroplast-to-nucleus retrograde signalling, reprogramming nuclear gene expression to drive plant acclimation. One such pathway is regulated by the chloroplastic phosphatase, SAL, which hydrolyses the nucleotide signal 3-phosphoadenosine 5-phosphate (PAP). In Arabidopsis thaliana, genetic loss of AtSAL1 elevates PAP and enhances stress tolerance but causes pleiotropic growth defects, complicating the interpretation of the role of PAP in cellular signalling. To uncouple stress signalling from genetic pleiotropy, we conducted a high-throughput in vitro screen of 13,000 small molecules and identified V20, a competitive inhibitor of AtSAL1 with three-fold greater potency than the known Li inhibitor. Structural analoguing of V20 and biochemical assays defined key pharmacophore features required for inhibition, including an ortho-halogenated aromatic ring, hydrogen-bond donor capacity at the triazole carboxamide, and electron-withdrawing substitutions that enhance {pi}-{pi} stacking with aromatic residues. Accelerated molecular dynamics simulations using a new high-resolution crystal structure revealed two previously uncharacterised V20 binding pockets adjacent to the catalytic site. V20 binding induces conformational changes which restrict substrate access to the catalytic site. Exogenous application of V20 to Arabidopsis led to increased PAP accumulation, activated PAP-responsive gene expression and enhanced oxidative tolerance, demonstrating cellular uptake and in vivo efficacy in the energy organelles, chloroplasts and mitochondria, where AtSAL1 is localised. Collectively, our findings reveal new insights into the regulatory domains of SAL enzymatic activity for control of PAP-mediated signalling and establish a proof-of-concept for targeted chemical modulation of SAL activity, which offers novel strategies to selectively manipulate chloroplast-to-nucleus retrograde signalling in plants. Significance StatementWe applied drug discovery strategies to test 13,000 small molecules for inhibition of AtSAL1, a key regulator of plant stress signalling from chloroplasts. Using biochemical assays, chemical analogues and molecular dynamic simulations, we defined the structural-activity relationship of a lead compound, V20, and elucidated its inhibitory mechanism. Application of V20 to plant leaves elevated the levels of AtSAL1s natural substrate, PAP (a chloroplast stress signalling molecule), activated stress-responsive genes and improved oxidative stress tolerance in Arabidopsis. This on-demand activation of SAL-PAP chloroplast signalling avoids pleotropic effects observed in loss-of-function mutants. Our approach provides a new strategy to study chloroplast-mediated cellular signaling pathways that are crucial for plant acclimation to stressful environmental conditions such as excessive sunlight.

plant biology↗

bioRxiv2025

Nutrition-dependent development of the Oral Microbiome in Early Pregnancy

BackgroundMost studies of the oral microbiome during pregnancy have focused on the second and third trimesters (T2, T3, respectively). Findings remain inconsistent-some report shifts in specific taxa, whereas others observe little change in diversity. To date, no large-scale longitudinal study has examined oral microbiome development across all three trimesters, leaving early gestational dynamics (during the first trimester; T1) largely unexplored. MethodsWe conducted a longitudinal analysis of the oral microbiome in 346 pregnant women from Israel and validated key findings in an independent cohort of 154 pregnant women from Russia. In Israel, saliva samples were collected during T1 (11-14 weeks), T2 (24-28 weeks), and T3 (32-38 weeks) trimesters; in Russia, samples were collected during T2 and T3 with similar ranges of gestational weeks. Alongside sample collection, participants completed dietary and health questionnaires to assess maternal factors that could influence microbial composition. Microbial profiles were analyzed to test for (i) differential abundance across trimesters and (ii) the influence of maternal nutrition and lifestyle factors on these dynamics. ResultsSignificant shifts in oral microbial composition were observed as early as the transition from T1 to T2. Alpha diversity decreased progressively across pregnancy (Shannon index: T1 = 3.261, T2 = 3.173, T3 = 3.109; Kruskal-Wallis p = 0.0023). Notable taxonomic changes included a significant reduction in Verrucomicrobiota (particularly Akkermansia muciniphila) and an increase in Synergistota from T1 to T2 (adjusted p < 0.01), alongside an increase in Gammaproteobacteria and a decrease in Erysipelotrichia, suggesting an ecological shift towards potentially pro-inflammatory communities. Despite these systematic population-level changes, within-subject microbial distances across trimesters were smaller than between-subject distances, indicating that individual women maintained relatively stable microbial profiles over time. Among 54 maternal variables examined, gluten-free diet showed the strongest and most consistent associations with oral microbiome composition across all trimesters, followed by smoking history and conception method. Key findings were validated in an independent cohort of 154 Russian women. ConclusionsThis study provides the first large-scale evidence of significant oral microbiome changes beginning in early pregnancy, characterized by reduced diversity and a directional shift toward potentially pro-inflammatory communities. The strong associations with gluten consumption and smoking suggest a large-scale effect of lifestyle on the pregnancy oral microbiome. The alteration in the microbial composition highlights the oral microbiome as a sensitive marker of gestational physiology.

microbiology↗

bioRxiv2025

Two mutations in the same MYC-bHLH transcription factor cause segregation of purple coloration of stolons and seed heads in Zoysia japonica x Zoysia matrella F2 and F1 populations

Anthocyanins play diverse roles in plants, including attracting pollinators and protecting cells from oxidative damage. In zoysiagrass, a warm season turfgrass, their accumulation in seed heads and stolons can decrease the aesthetic appeal. In this study, a high-density genetic map with [~]8000 single nucleotide polymorphism (SNP) markers organized into 20 linkage groups was generated in a Zoysia japonica acc. Meyer x Zoysia matrella acc. PI 231146 F2 population. Using this genetic map, a large-effect quantitative trait locus (QTL) for anthocyanin variation in stolons and seed heads was mapped to chromosome 12 (PP locus). Variant analysis of a candidate gene for PP, Zjn_sc00004.1.g07010.1.sm.mk, which encodes a MYC-bHLH transcription factor that regulates anthocyanin biosynthesis, revealed a SNP at an exon-intron boundary in Meyer that led to intron retention. Interestingly, an F1 population derived from the same parents segregated for seed head color but uniformly displayed purple stolons. Seed head color in the F1 population co-mapped with the PP locus which, combined with genotypic and yeast two-hybrid analyses, revealed that a SNP in PI 231146 leading to an Ala163Ser substitution in the MYB-interacting N-terminal domain of the same MYC-bHLH transcription factor was likely causal. The Ala163Ser substitution affected interaction of MYC-bHLH with MYB in a MYB-dependent manner. The identified mutations can be exploited to develop cultivars with green seed heads and stolons. The high-marker-density interspecific Z. japonica x Z. matrella F2 genetic map also provides a robust tool for identifying genomic regions and genes of agronomic interest that differentiate the two species.

genetics↗

bioRxiv2024

Peptide therapeutic leads for multi-target inhibition of inflammatory cytokines in Inflammatory Bowel Disease - computational design and in-vitro validation

Inflammatory Bowel Disease (IBD) are chronic and recurrent inflammatory disorders affecting the gastrointestinal tract, characterized by the involvement of numerous pro-inflammatory cytokines. These conditions profoundly impact both immune system dynamics and intestinal tissue integrity. Current therapeutic approaches predominantly rely on monoclonal antibodies, and frequently encounter limitations such as non-responsiveness, loss of efficacy over time, immunogenicity, adverse effects, and substantial cost. Consequently, there is a critical need for novel, targeted anti-inflammatory strategies. We present the computational structure guided design of peptidic inhibitors aimed at attenuating the activity of pivotal pro-inflammatory cytokines implicated in IBD pathogenesis, namely TNF, IL-1{beta}, and IL-6. These peptides were engineered to disrupt specific cytokine - receptor interactions, to block the release of pro-inflammatory cytokines. We structurally characterized key features in the studied interactions and used these to guide two computational design strategies, one based on the identification of dominant segments using our PeptiDerive approach, and one based on complementing fragments detected using our PatchMAN protocol. The designed peptides were synthesized and their efficacy was validated on Caco-2 intestinal epithelial cells and THP-1 macrophages, representative of the epithelial and immunological alterations typical of active IBD. The majority of the novel peptides effectively suppressed release of pro-inflammatory cytokines by both macrophages and intestinal epithelial cells, thereby reducing the risk of inflammation. This study underscores the efficacy of a rational design approach rooted in structural insights into inflammatory signaling complexes. Our findings demonstrate the potential of targeting key cytokines and receptor interaction with designed peptides as a promising therapeutic avenue for managing IBD and other inflammatory disorders.

bioinformatics↗

bioRxiv2021

Combined Inhibition of AKT and KIT Restores Expression of Programmed Cell Death 4 (PDCD4) in Gastrointestinal Stromal Tumor

The majority of gastrointestinal stromal tumor (GIST) patients develop resistance to the first-line KIT inhibitor, imatinib mesylate (IM), through acquisition of secondary mutations in KIT or bypass signaling pathway activation. AKT is a relevant target for inhibition, in addition to KIT, since the PI3K/AKT pathway is crucial for IM-resistant GIST survival. We evaluated the activity of a novel pan-AKT inhibitor, MK-4440 (formerly ARQ 751), as monotherapy and in combination with IM in GIST cell lines and preclinical models with varying IM sensitivities. Dual inhibition of KIT and AKT demonstrated significant synergistic effects in IM-sensitive and -resistant GIST cell lines. Proteomic analyses revealed upregulation of the tumor suppressor, PDCD4, in combination treated cells. Enhanced PDCD4 expression correlated to cell cycle arrest and cell death. In vivo studies revealed superior efficacy of MK-4440/IM combination in an IM-sensitive preclinical model of GIST compared with either single agent. The combination demonstrated limited efficacy in two IM-resistant models, including a GIST patient-derived xenograft model possessing an exon 9 KIT mutation. These studies provide strong rationale for further use of AKT inhibition in combination with IM in primary GIST; however, alternative agents will need to be tested in combination with AKT inhibition in the resistant setting.

cancer biology↗