Biology subjects

Sule, A.

Publications and source records attributed to Sule, A..

6 recordsLinked to original sources

bioRxiv2026

A single-nucleus multi-omic atlas of gene regulation across 21 adult human tissues

Diverse human cell types establish specialized functions through lineage- and context-specific regulatory programs. Interpreting non-coding genetic risk requires integrated multi-omic reference maps that directly connect regulatory DNA to cellular expression across human tissues. Here we present a single-nucleus multi-omic atlas comprising 459,856 transcriptomic and chromatin accessibility profiles from 21 adult human tissues and four donors, including paired measurements from 160,688 nuclei. The atlas resolves nine cell lineages, 61 broad cell types and 313 subclusters, and identifies 1,085,062 candidate cis-regulatory elements (cCREs), including 161,270 novel elements absent from ENCODE. Regulatory activity was dominated by cell identity but refined by tissue context. Joint profiling enabled 871,177 cCRE-gene associations and revealed lineage-specific regulatory architectures. Cross-tissue accessibility further identified lineage-restricted and constitutively inaccessible chromatin domains, the latter showing preferential hypomethylation across human cancers. Furthermore, we leverage this dataset to train sequence-to-function models to predict chromatin-accessibility effects for 548,656 fine-mapped variants, identifying 18,133 high-effect variants, including 1,120 broadly active variants. Models trained for eight endothelial subtypes further resolve predicted variant effects across vascular beds. Together, this atlas provides a comprehensive cellular and computational framework for interpreting regulatory sequence, context-dependent gene control, and complex trait genetics across the human body.

genomics↗

bioRxiv2023

Oblique Line Scan Illumination Enables Expansive, Accurate and Sensitive Single Protein Measurements in Solution and in Living Cells

Single-molecule localization microscopy (SMLM) techniques, such as single-molecule tracking (SMT), enable in situ measurements in cells from which data-rich metrics can be extracted. SMT has been successfully applied to a variety of biological questions and model systems, aiming to unravel the spatiotemporal regulation of molecular mechanisms that govern protein function, downstream pathway effects, and cellular function. While powerful, SMLM often suffers from low throughput and illumination inhomogeneity, along with microscope and user-induced technical biases. Due to technical limitations in scaling SMLM techniques, a tradeoff between spatiotemporal resolution and throughput has been made historically, restricting broad application of these technologies. Here we address these limitations using Oblique Line Scan (OLS), a robust single-objective light-sheet based illumination and detection modality that achieves nanoscale spatial resolution and sub-millisecond temporal resolution across a 250 x 190 m field of view. We demonstrate OLS-enabled SMT on Halo-Tagged proteins in living cells capturing protein motion up to 14 m2 /s. By exploiting the adaptability of the acquisition frame rate and the improved rejection of out of focus light, we extend the utility of OLS beyond cellular compartments with in-solution SMT (isSMT) for single-molecule measurement of ligand-protein interactions and disruption of protein-protein interactions (PPI). We illustrate the versatility of OLS by showcasing two-color SMT, STORM, and single molecule fluorescence recovery after photobleaching (FRAP). OLS expands the range of SMLM applications and paves the way for robust, high-throughput single-molecule investigations of protein dynamics required for drug screening and systems biology studies, both in cells and in solution.

biophysics↗

bioRxiv2023

High-throughput single molecule tracking identifies drug interactions and cellular mechanisms

The regulation of cell physiology depends largely upon interactions of functionally distinct proteins and cellular components. These interactions may be transient or long-lived, but often affect protein motion. Measurement of protein dynamics within a cellular environment, particularly while perturbing protein function with small molecules, may enable dissection of key interactions and facilitate drug discovery; however, current approaches are limited by throughput with respect to data acquisition and analysis. As a result, studies using super-resolution imaging are typically drawing conclusions from tens of cells and a few experimental conditions tested. We addressed these limitations by developing a high-throughput single-molecule tracking (htSMT) platform for pharmacologic dissection of protein dynamics in living cells at an unprecedented scale (capable of imaging > 106 cells/day and screening > 104 compounds). We applied htSMT to measure the cellular dynamics of fluorescently tagged estrogen receptor (ER) and screened a diverse library to identify small molecules that perturbed ER function in real time. With this one experimental modality, we determined the potency, pathway selectivity, target engagement, and mechanism of action for identified hits. Kinetic htSMT experiments were capable of distinguishing between on-target and on-pathway modulators of ER signaling. Integrated pathway analysis recapitulated the network of known ER interaction partners and suggested potentially novel, kinase-mediated regulatory mechanisms. The sensitivity of htSMT revealed a new correlation between ER dynamics and the ability of ER antagonists to suppress cancer cell growth. Therefore, measuring protein motion at scale is a powerful method to investigate dynamic interactions among proteins and may facilitate the identification and characterization of novel therapeutics.

cell biology↗

bioRxiv2021

ATM phosphorylates PP2A subunit A resulting in nuclearexport and spatiotemporal regulation of the DNA damageresponse

Ataxia telangiectasia mutated (ATM) is a serine-threonine protein kinase and important regulator of the DNA damage response (DDR). One critical ATM target is the structural subunit A (PR65) of protein phosphatase 2A (PP2A), known to regulate diverse cellular processes such as mitosis and cell growth as well as dephosphorylating many proteins during the recovery from the DDR. We generated mouse embryonic fibroblasts expressing PR65-WT, -S401A (cannot be phosphorylated), and -S401D (phosphomimetic) transgenes. Significantly, S401 mutants exhibited extensive chromosomal aberrations, impaired DNA double-strand break (DSB) repair and underwent increased mitotic catastrophe after radiation. Our study demonstrates that the phosphorylation of a single, critical PR65 amino acid (S401) by ATM fundamentally controls the DDR, and balances DSB repair quality, cell survival and growth by spatiotemporal PR65 nuclear-cytoplasmic shuttling mediated by the nuclear export receptor CRM1.

cancer biology↗

bioRxiv2019

Salivary sex hormone levels following oxytocin administration in autistic and typical women

Oxytocin administration, which may be of therapeutic value for social disabilities, likely influences endogenous levels of other socially-relevant hormones. However, to date, the effects of oxytocin administration on endogenous hormones have only been examined in typical males. The need to consider multi-hormone interactions is particularly warranted in oxytocin trials for autism due to evidence of irregularities in both oxytocin and sex steroid systems. Here, as part of a larger trial with a double-blind cross-over design, we assessed salivary testosterone and oestradiol levels in 16 autistic and 29 typical women before and after intranasal administration of 24IU oxytocin or placebo. Distinct patterns of change in testosterone and oestradiol across time were observed between groups, with autistic women showing increases in both hormones 90 min post-administration and typical women showing small decreases (mean %change oestradiol: +12% Autism, -10% Typical, 95%CI of difference: 5.0-39.4%, p=0.01; mean %change testosterone: +8% Autism, -14% Typical, 95%CI of difference: 7.8-35.6%, p=0.002). Under the oxytocin condition, the group difference in %change testosterone was amplified (+14.4% Autism, -15.2% Typical, p=0.018). Although baseline hormone levels did not differ between groups, greater baseline oestradiol relative to testosterone was negatively correlated with autistic-like traits (r= -0.36, p=0.019) and positively correlated (r=0.35, p=0.02) with self-reported empathy in the overall sample. These results provide further evidence that oxytocin influences endogenous testosterone, with autistic women showing increases similar to previous reports in typical men. These findings may help to identify autistic people expected to benefit most from interventions involving oxytocin.

neuroscience↗

bioRxiv2018

Action-outcome knowledge dissociates from behavior in obsessive-compulsive disorder following contingency degradation

Goal-directed and habitual systems orchestrate action control. In disorders of compulsivity, their interplay seems disrupted and actions persist despite being inappropriate and without relationship to the overall goal. We manipulated action-outcome contingency to test whether actions are goal-directed or habitual in obsessive-compulsive disorder (OCD), the prototypical disorder of compulsivity, in which prominent theories have suggested that dysfunctional beliefs underlie the necessity for compulsive actions.\n\nOCD patients responded more than controls when an action was causally less related to obtaining an outcome, indicating excessive habitual responding. Patients showed intact explicit action-outcome knowledge but this was not translated normally into behavior; the relationship between causality judgment and responding was blunted. OCD patients actions were dissociated from explicit action-outcome knowledge, providing experimental support for the ego-dystonic nature of OCD and suggesting that habitual action is not sustained by dysfunctional belief.

neuroscience↗