Biology subjects

Sachdev, S.

Publications and source records attributed to Sachdev, S..

11 recordsLinked to original sources

bioRxiv2026

Cytoplasmic localization of 5hmC reveals RNA hydroxymethylation in breast cancer

DNA methylation (5-methylcytosine, 5mC) is a major repressive epigenetic mark that can be iteratively oxidized by ten-eleven-translocation (TET) enzymes to 5-hydroxymethylcytosine (5hmC); beyond DNA, modifications of RNA can also affect transcript stability and processing, yet RNA hydroxymethylation remains unexplored in breast cancer (BC). Here, we identify a quantifiable cytoplasmic 5hmC signal in BC cell lines and, more prominently, in human BC tissue, using immunoassays and digital pathology, and confirm with an adapted, RNase-sensitive, RNA-specific ELISA that this signal reflects hydroxymethylation of total RNA and mRNA. Cytoplasmic 5hmC was significantly enriched in triple-negative (ER-/PR-/HER2-) and grade 3 tumors, and correlated with increased cytoplasmic TET2/TET3 in tissue and TET3 upregulation in TCGA. As a leading candidate mechanism, TET3 expression was associated with RNA-processing/spliceosomal transcripts, and TET3 knockdown in three TNBC cell lines reduced a subset of these targets, independently supported across 70 DepMap breast cancer lines.

cancer biology↗

bioRxiv2025

Spurring and Siloing: Identity Navigation in Scientific Writing Among Asian Early-Career Researchers

Scientific writing and publication are critical sites where students must navigate between personal identities and presumed scientific objectivity. For non-white student researchers, particularly those stereotyped as "model minorities," this process involves complex negotiations. This qualitative study examines how Asian and Asian American students navigate ethnic and cultural identities within scientific writing processes. Using an integrated theoretical framework combining cultural community wealth, narrative identity, and border crossing, we analyzed how participants deployed cultural resources while navigating institutional expectations. Drawing on interviews with 23 student participants who engaged with the [Blinded Journal], we identified two primary approaches: "spurring," wherein ethnic and cultural backgrounds catalyze research questions, and "siloing," wherein these identities are deliberately compartmentalized during writing. Findings reveal that while participants drew upon familial capital to inform research interests, most practiced disciplinary compartmentalization and adhered to perceived scientific norms. This tension demonstrates how students negotiate cultural scripts while developing professional identities. Our findings suggest that science educators could help students recognize their cultural backgrounds as valuable epistemic resources rather than sources of bias, explicitly address the myth of value-neutral science, and provide models of how scientists integrate personal and cultural perspectives into rigorous scientific work.

scientific communication and education↗

bioRxiv2025

Evaluation of Alphafold modeling for elucidation of nanobody-peptide epitope interactions

Models of Ab-antigen complexes can be used to understand interaction mechanisms and for improving affinity. This study evaluates the use of the protein structure prediction algorithm AlphaFold (AF) for exploration of interactions between peptide epitope tags and the smallest functional antibody fragments, nanobodies (Nbs). Although past studies of AF for modeling antibody-target (antigen) interactions suggested modest algorithm performance, those were primarily focused on Ab-protein interactions, while the performance and utility of AF for Nb-peptide interactions, which are generally less complex due to smaller antigens, smaller binding domains, and fewer chains, is less clear. In this study we evaluated the performance of AF for predicting the structures of Nbs bound to experimentally validated, linear, short peptide epitopes (Nb-tag pairs). We expanded the pool of experimental data available for comparison through crystallization and structural determination of a previously reported Nb-tag complex (Nb127). Models of Nb-tag pair structures generated from AF were variable with respect to consistency with experimental data, with good performance in just over half (4 out of 6) of cases. Even among Nb-tag pairs successfully modeled in isolation, efforts to translate modeling to more complex contexts failed, suggesting an underappreciated role of the size and complexity of inputs in AF modeling success. Finally, the model of a Nb-tag pair with minimal previous characterization was used to guide the design of a peptide-electrophile conjugate that undergoes covalent crosslinking with Nb upon binding. These findings highlight the utility of minimized antibody and antigen structures to maximize insights from AF modeling.

biochemistry↗

bioRxiv2025

Nanobody-based conjugates targeting small molecule-binding GPCRs and exhibiting logic-gated signaling

G protein-coupled receptors (GPCRs) are the largest family of plasma membrane embedded signaling proteins. These receptors are involved in a wide array of physiological processes, marking them as attractive targets for drug development. Bitopic ligands, which are comprised of a pharmacophore that targets the receptor orthosteric site and a linked moiety that binds to a separate site, have considerable potential for addressing GPCR function. Here, we report the synthesis and evaluation of novel bitopic conjugates consisting of a small molecule pharmacophore that activates the adenosine A2A receptor (A2AR) linked to antibody fragments (nanobodies, Nbs). This approach leverages the high affinity and specificity binding of Nbs to non-orthosteric sites on engineered A2AR variants to provide bitopic Nb-ligand conjugates that stimulate strong and enduring signaling responses. We further demonstrate that such bitopic conjugates can induce activation by spanning two distinct receptor protomers. This property enables the selective targeting of receptor pairs over either individual receptor, as a form of "logic-gated" activity. We showcase the broad applicability of bitopic conjugates in this context by demonstrating their activity in targeting several pairs of co-expressed receptors, including GPCR monomers from different classes. Furthermore, we demonstrate that this dual-targeting strategy initiates signaling responses that diverge from those induced by monovalent ligands. The ability to target receptor pairs using nanobody-ligand conjugates offers a powerful strategy with potential for cell type-selective signaling and implications for GPCR drug discovery efforts more broadly.

pharmacology and toxicology↗

bioRxiv2023

Highly biased agonism for GPCR ligands via nanobody tethering

Ligand-induced activation of G protein-coupled receptors (GPCRs) can initiate signaling through multiple distinct pathways with differing biological and physiological outcomes. There is intense interest in understanding how variation in GPCR ligand structure can be used to promote pathway selective signaling ("biased agonism") with the goal of promoting desirable responses and avoiding deleterious side effects. Here we present a new approach in which a conventional peptide ligand for the type 1 parathyroid hormone receptor (PTHR1) is converted from an agonist which induces signaling through all relevant pathways to a compound that is highly selective for a single pathway. This is achieved not through variation in the core structure of the agonist, but rather by linking it to a nanobody tethering agent that binds with high affinity to a separate site on the receptor not involved in signal transduction. The resulting conjugate represents the most biased agonist of PTHR1 reported to date. This approach holds promise for facile generation of pathway selective ligands for other GPCRs.

pharmacology and toxicology↗

bioRxiv2022

The Arabidopsis ARID-HMG protein AtHMGB15 modulates JA signalling by regulating MYC2 during pollen development

In flowering plants, jasmonic acid (JA) signalling regulates the complex process of male gametophyte development. JA signalling initiates with the activation of MYC2 transcription factor, for the expression of several JA responsive genes throughout stamen development and pollen maturation. However, the regulation of JA signalling during different developmental stages of male gametophytes is still less understood. In this study we have characterized T-DNA insertion line of AtHMGB15. Phenotypic characterization of athmgb15-4 mutant plants showed delayed bolting, shorter siliques and reduced seed set compared to wildtype. Moreover, deletion of AtHMGB15 resulted in defective pollen morphology, delayed pollen germination, abberant pollen tube growth and a higher percentage of non-viable pollen population in athmgb15-4 compared to wildtype. Molecular analysis indicated down-regulation of JA-biosynthesis and JA-signalling genes viz MYC2, MYB21 and MYB24 in athmgb15-4 mutant. Furthermore, jasmonic acid and its derivatives were found almost ten-fold lower in athmgb15-4 flowers. However, exogenous application of jasmonate could restore pollen morphology and pollen germination, suggesting that impaired JA signalling is responsible for the pollen phenotype in athmgb15 mutant. AtHMGB15 physically interacts with MYC2 protein to form the transcription activation complex for promoting transcription of genes responsible for JA signalling during stamen and pollen development. Collectively, our findings indicate that AtHMGB15, a plant specific DNA binding protein of the ARID-HMG group, acts as a positive regulator of JA signalling to control the spatiotemporal expression of key regulators responsible for stamen and pollen development.

developmental biology↗

bioRxiv2022

Characterization of a nanobody-epitope tag interaction and its application for receptor engineering

Peptide epitope tags offer a valuable means for detection and manipulation of protein targets for which high quality detection reagents are not available. Most commonly used epitope tags are bound by conventional, full-size antibodies (Abs). The complex architecture of Abs complicates their application in protein engineering and intracellular applications. To address these shortcomings, single domain antibodies (nanobodies, Nbs) that recognize short peptide epitopes have become increasingly prized. Here we characterize the interaction between a Nb (Nb6E) and a 14-mer peptide epitope. We identify residues in the peptide epitope essential for high affinity binding. Using this information in combination with computational modeling we propose a mode of interaction between Nb6E and this epitope. We apply this nanobody-epitope pair to augment the potency of a ligand at an engineered adenosine A2A receptor. This characterization of the nanobody-epitope pair opens the door to diverse applications including mechanistic studies of G protein-coupled receptor function.

biochemistry↗

bioRxiv2019

Differential activation of G protein-mediated signalling by synthetic cannabinoid receptor agonists

Synthetic cannabinoid receptor agonists (SCRAs) are new psychoactive substances associated with acute intoxication and even death. However, the molecular mechanisms through which SCRAs may exert their toxic effects remain unclear - including the potential differential activation of G protein subtypes by CB1, a major target of SCRA. We measured CB1-mediated activation of Gs and Gi/o proteins by SCRAs by examining stimulation (PTX-treated) as well as inhibition (non-PTX treated) of forskolin-induced cAMP accumulation in HEK cells stably expressing CB1. Real-time measurements of stimulation and inhibition of cAMP levels were made using a BRET biosensor. We found that the maximum concentration of SCRAs tested (10 M), increased cAMP levels 12 to 45% above that produced by forskolin alone, while the phytocannabinoid THC did not significantly alter cAMP levels in PTX-treated HEK-CB1 cells. All SCRAs had greater potency to inhibit of forskolin-induced cAMP levels than to stimulate cAMP levels. The rank order of potencies for SCRA stimulation of cAMP (Gs) was PB-22 > 5F-MDMB-PICA > JWH-018 > AB-FUBINACA > XLR-11. By contrast, the potency of SCRAs for inhibition of cAMP (Gi/o) was 5F-MDMB-PICA > AB-FUBINACA > PB-22 > JWH-018 > XLR-11. The different rank order of potency of the SCRAs to stimulate Gs-like signalling compared to Gi/o signalling suggests differences in G protein preference between SCRAs. Understanding the apparent differences among these drugs may contribute to unravelling their complex effects in humans.

pharmacology and toxicology↗

bioRxiv2019

Brodifacoum does not modulate human cannabinoid receptor-mediated hyperpolarization of AtT20 cells or inhibition of adenylyl cyclase in HEK 293 cells

BackgroundSynthetic cannabinoids are a commonly used class of recreational drugs that can have significant adverse effects. There have been sporadic reports of co-consumption of illicit drugs with rodenticides such as warfarin and brodifacoum (BFC) over the past 20 years but recently, hundreds of people have been reported to have been poisoned with a mixture of synthetic cannabinoids and BFC. We have sought to establish whether BFC directly affects cannabinoid receptors, or their activation by the synthetic cannabinoid CP55940 or the phytocannabinoid {Delta}9-tetrahydrocannabinol ({Delta}9-THC).\n\nMethodsThe effects of BFC on the hyperpolarization of wild type AtT20 cells, or AtT20 cells stably expressing human CB1- and CB2-mediated receptors, were studied using a fluorescent assay of membrane potential. The effects of BFC on CB1 and CB2 mediated inhibition of forskolin-stimulated adenylyl cyclase (AC) activation was measured using a BRET assay of cAMP levels in HEK 293 cells stably expressing human CB1 and CB2.\n\nResultsBFC did not activate CB1 or CB2 receptors, or affect the hyperpolarization of wild type AtT20 cells produced by somatostatin. BFC (10 {micro}M) did not affect the hyperpolarization of AtT20-CB1 or AtT20-CB2 cells produced by CP55940 or {Delta}9-THC. BFC (1 {micro}M) did not affect the inhibition of forskolin-stimulated AC activity by CP55940 in HEK 293 cells expressing CB1 or CB2. BFC (1 {micro}M) also failed to affect the desensitization of CB1 and CB2 signalling produced by prolonged (30 min) application of CP55940 or {Delta}9-THC to AtT20 cells.\n\nDiscussionBFC is not a cannabinoid receptor agonist, and appeared not to affect cannabinoid receptor activation. Our data suggests there is no pharmacodynamic rationale for mixing BFC with synthetic cannabinoids, however, it does not speak to whether BFC may affect synthetic cannabinoid metabolism or biodistribution. The reasons underlying the mixing of BFC with synthetic cannabinoids are unknown, and it remains to be established whether the \"contamination\" was deliberate or accidental. However, the consequences for people who ingested the mixture were often serious, and sometimes fatal, but this seems unlikely to be due to BFC action at cannabinoid receptors.

pharmacology and toxicology↗

bioRxiv2019

Absence of entourage: Terpenoids commonly found in Cannabis sativa do not modulate the functional activity of Δ9-THC at human CB1 and CB2 receptors

IntroductionCompounds present in Cannabis sativa such as phytocannabinoids and terpenoids, may act in concert to elicit therapeutic effects. Cannabinoids such as {Delta}9-tetrahydrocannabinol ({Delta}9-THC) directly activate cannabinoid receptor 1 (CB1) and cannabinoid receptor 2 (CB2), however, it is not known if terpenoids present in Cannabis also affect cannabinoid receptor signalling. Therefore, we examined 6 common terpenoids alone, and in combination with cannabinoid receptor agonists, on CB1 and CB2 signalling in vitro.\n\nMaterials and MethodsPotassium channel activity in AtT20 FlpIn cells transfected with human CB1 or CB2 receptors was measured in real-time using FLIPR(R) membrane potential dye in a FlexStation 3 plate reader. Terpenoids were tested individually and in combination for periods up to 30 minutes. Endogenous somatostatin receptors served as a control for direct effects of drugs on potassium channels.\n\nResults-Pinene, {beta}-pinene, {beta}-caryophyllene, linalool, limonene and {beta}-myrcene (up to 30-100 {micro}M) did not change membrane potential in AtT20 cells expressing CB1 or CB2, or affect the response to a maximally effective concentration of the synthetic cannabinoid CP55,940. The presence of individual or a combination of terpenoids did not affect the hyperpolarization produced by {Delta}9-THC (10{micro}M): (CB1: control, 59{+/-}7%; with terpenoids (10 {micro}M each) 55{+/-}4%; CB2: {Delta}9-THC 16{+/-}5%, with terpenoids (10 {micro}M each) 17{+/-}4%). To investigate possible effect on desensitization of CB1 responses, all six terpenoids were added together with {Delta}9-THC and signalling measured continuously over 30 min. Terpenoids did not affect desensitization, after 30 minutes the control hyperpolarization recovered by 63{+/-}6%, in the presence of the terpenoids recovery was 61{+/-}5%.\n\nDiscussionNone of the six of the most common terpenoids in Cannabis directly activated CB1 or CB2, or modulated the signalling of the phytocannabinoid agonist {Delta}9-THC. These results suggest that if a phytocannabinoid-terpenoid entourage effect exists, it is not at the CB1 or CB2 receptor level. It remains possible that terpenoids activate CB1 and CB2 signalling pathways that do not involve potassium channels, however, it seems more likely that they may act at different molecular target(s) in the neuronal circuits important for the behavioural effect of Cannabis.

pharmacology and toxicology↗

bioRxiv2018

In vitro determination of the CB1 efficacy of illicit synthetic cannabinoids

BACKGROUND AND PURPOSEThe morbidity and mortality associated with recreational use of synthetic cannabinoid receptor agonists (SCRAs) is a major health concern, and may involve over-activation of CB1 receptors. Thus, we sought to determine the efficacy of 13 SCRAs at CB1 using receptor depletion with the irreversible CB1 antagonist AM6544 followed by fitting the curve with the Black and Leff operational model to calculate efficacy.\n\nEXPERIMENTAL APPROACHReceptor depletion in mouse AtT-20 neuroblastoma cells stably expressing human CB1 was achieved by pre-treatment of cells with AM6544 (10 {micro}M, 60 mins). The CB1-mediated hyperpolarisation of AtT20 cells was measured using membrane potential dye. From data fit to the operational model, the efficacy (tau) and affinity (KA) parameters were obtained for each drug.\n\nKEY RESULTSAM6544 did not affect the potency or maximal effect of native somatostatin receptor-induced hyperpolarisation (Control, pEC50 9.13 {+/-} 0.05, Emax 38 {+/-} 1%; AM6544 treated pEC50 9.18 {+/-} 0.04, Emax 39 {+/-} 0.7%). The tau value of {triangleup}9-THC was 70-fold less than the reference CB-agonist CP55940, and 240-fold less than the highest efficacy SCRA, 5F-MDMB-PICA. Most of the SCRAs had about 50% of the efficacy of CP55940. There was no correlation between the tau and KA values for any SCRA.\n\nCONCLUSION AND IMPLICATIONSAll the SCRA tested showed substantially higher agonist activity at CB1 than {triangleup}9-THC, which may contribute to the adverse effects seen with these drugs but not {triangleup}9-THC, although the mechanisms underlying SCRA toxicity are still poorly defined.

pharmacology and toxicology↗