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Reese, J.

Publications and source records attributed to Reese, J..

3 recordsLinked to original sources
bioRxiv2021

SvAnna: efficient and accurate pathogenicity prediction for coding and regulatory structural variants in long-read genome sequencing

Structural variants (SVs) are implicated in the etiology of Mendelian diseases but have been systematically underascertained owing to limitations of existing technology. Recent technological advances such as long-read sequencing (LRS) enable more comprehensive detection of SVs, but approaches for clinical prioritization of candidate SVs are needed. Existing computational approaches do not specifically target LRS data, thereby missing a substantial proportion of candidate SVs, and do not provide a unified computational model for assessing all types of SVs. Structural Variant Annotation and Analysis (SvAnna) assesses all classes of SV and their intersection with transcripts and regulatory sequences in the context of topologically associating domains, relating predicted effects on gene function with clinical phenotype data. We show with a collection of 182 published case reports with pathogenic SVs that SvAnna places over 90% of pathogenic SVs in the top ten ranks. The interpretable prioritizations provided by SvAnna will facilitate the widespread adoption of LRS in diagnostic genomics.

bioinformatics↗
bioRxiv2021

Supervised learning with word embeddings derived from PubMed captures latent knowledge about protein kinases and cancer

Inhibiting protein kinases (PKs) that cause cancers has been an important topic in cancer therapy for years. So far, almost 8% of more than 530 PKs have been targeted by FDA-approved medications and around 150 protein kinase inhibitors (PKIs) have been tested in clinical trials. We present an approach based on natural language processing and machine learning to the relations between PKs and cancers, predicting PKs whose inhibition would be efficacious to treat a certain cancer. Our approach represents PKs and cancers as semantically meaningful 100-dimensional vectors based on co-occurrence patterns in PubMed abstracts. We use information about phase I-IV trials in ClinicalTrials.gov to construct a training set for random forest classification. In historical data, associations between PKs and specific cancers could be predicted years in advance with good accuracy. Our model may be a tool to predict the relevance of inhibiting PKs with specific cancers.

bioinformatics↗
bioRxiv2021

Identification of mundulone and mundulone acetate as natural products with tocolytic efficacy in mono- and combination-therapy with current tocolytics

Currently, there are a lack of FDA-approved tocolytics for the management of preterm labor. We previously observed that the isoflavones mundulone and mundulone acetate (MA) inhibit intracellular Ca2+-regulated myometrial contractility. Here, we further probed the potential of these natural products to be small molecule leads for discovery of novel tocolytics by: (1) examining uterine-selectivity by comparing concentration-response between human primary myometrial cells and a major off-target site, aortic vascular smooth muscle cells (VSMCs), (2) identifying synergistic combinations with current clinical tocolytics to increase efficacy or and reduce off-target side effects, (3) determining cytotoxic effects and (4) investigating the efficacy, potency and tissue-selectivity between myometrial contractility and constriction of fetal ductus arteriosus (DA), a major off-target of current tocolytics. Mundulone displayed significantly greater efficacy (Emax = 80.5% vs. 44.5%, p=0.0005) and potency (IC50 = 27 M and 14 M, p=0.007) compared to MA in the inhibition of intracellular-Ca2+ from myometrial cells. MA showed greater uterine-selectivity, compared to mundulone, based on greater differences in the IC50 (4.3 vs. 2.3 fold) and Emax (70% vs. 0%) between myometrial cells compared to aorta VSMCs. Moreover, MA demonstrated a favorable in vitro therapeutic index of 8.8, compared to TI = 0.8 of mundulone, due to its significantly (p<0.0005) smaller effect on the viability of myometrial (hTERT-HM), liver (HepG2) and kidney (RPTEC) cells. However, mundulone exhibited synergism with two current tocolytics (atosiban and nifedipine), while MA only displayed synergistic efficacy with only nifedipine. Of these synergistic combinations, only mundulone + atosiban demonstrated a favorable TI = 10 compared to TI=0.8 for mundulone alone. While only mundulone showed concentration-dependent inhibition of ex vivo mouse myometrial contractions, neither mundulone or MA affected mouse fetal DA vasoreactivity. The combination of mundulone and atosiban yielded greater tocolytic efficacy and potency on term pregnant mouse and human myometrial tissue compared to single-drugs. Collectively, these data highlight the difference in uterine-selectivity of Ca2+-mobilization, effects on cell viability and tocolytic efficacy between mundulone and MA. These natural products could benefit from medicinal chemistry efforts to study the structural activity relationship for further development into a promising single- and/or combination-tocolytic therapy for management of preterm labor. Chemical compounds studied in this articleatosiban (Pubchem CID: 5311010); indomethacin (Pubchem CID: 3715); mundulone (Pubchem CID: 4587968); mundulone acetate (Pubchem CID: 6857790); nifedipine (Pubchem CID: 4485); oxytocin acetate (Pubchem CID: 5771); U46619 (Pubchem CID: 5311493)

pharmacology and toxicology↗