Biology subjects

Rusyn, I.

Publications and source records attributed to Rusyn, I..

7 recordsLinked to original sources

bioRxiv2026

A Deep Learning-Based Scoring Framework for Large-Scale Multi-Donor Cardiotoxicity Screening

Cardiotoxicity remains a major cause of drug attrition and post-market withdrawal, yet the vast majority of environmental chemicals to which humans may be exposed remain uncharacterized for cardiotoxicity risk. Human induced pluripotent stem cell (hiPSC)-based testing has been proposed to address this gap. Here we present an unsupervised deep learning framework for multi-donor cardiotoxicity screening using high-throughput calcium transient recordings from hiPSC-derived cardiomyocytes (hiPSC-CMs). We used data from a library of 1,029 compounds that were tested in hiPSC-CM from five donors in concentration-response. An autoencoder trained exclusively on baseline signals quantified chemical-induced functional perturbations through reconstruction error, bypassing the need for labeled training data while capturing the full spectrum of calcium handling disruptions. Using this framework, we generated effect levels. Aggregation of donor-specific scores revealed substantial inter-individual variability in potential cardiotoxicity, underscoring the value of this approach for population-level risk prediction. We found that microbiocides, dyes, and pesticides to have potential concern, characterized by high toxicity scores and low inter-donor variability. This framework establishes a scalable, human-relevant, and genetically diverse platform for cardiotoxicity surveillance across both pharmacological and environmental chemical spaces, with direct implications for drug and chemical safety evaluation and prioritization for additional studies.

bioengineering↗

bioRxiv2025

Reference Library for Suspect Non-targeted Screening of Environmental Toxicants Using Ion Mobility Spectrometry-Mass Spectrometry

As our health is affected by the xenobiotic chemicals we are exposed to, it is important to rapidly assess these molecules both in the environment and our bodies. Targeted analytical methods coupling either gas or liquid chromatography with mass spectrometry (GC-MS or LC-MS) are commonly utilized in current exposure assessments. While these methods are accepted as the gold standard for exposure analyses, they often require multiple sample preparation steps and more than 30 minutes per sample. This throughput limitation is a critical gap for exposure assessments and has resulted in an evolving interest in using ion mobility spectrometry and MS (IMS-MS) for non-targeted studies. IMS-MS is a unique technique due to its rapid analytical capabilities (millisecond scanning) and detection of a wide range of chemicals based on unique collision cross section (CCS) and mass-to-charge (m/z) values. To increase the availability of IMS-MS information for exposure studies, here we utilized drift tube IMS-MS to evaluate 4,685 xenobiotic chemical standards from the Environmental Protection Agency Toxicity Forecaster (ToxCast) program including pesticides, industrial chemicals, pharmaceuticals, consumer products, and per- and polyfluoroalkyl substances (PFAS). In the analyses, 3,993 [M+H]+, [M+Na]+, [M-H]- and [M+]+ ion types were observed with high confidence and reproducibility ([≤]1% error intra-laboratory and [≤]2% inter-laboratory) from 2,140 unique chemicals. These values were then assembled into an openly available multidimensional database and uploaded to PubChem to enable rapid IMS-MS suspect screening for a wide range of environmental contaminants, faster response time in environmental exposure assessments, and assessments of xenobiotic-disease connections.

ecology↗

bioRxiv2025

Derivation of cardiac reference ranges for Mus musculus using the Collaborative Cross and identification of new cardiac models

Contemporary approaches for developing interventions and assessing pre-clinical cardiovascular risk frequently utilize animal and in vitro models. However, these models currently lack normal species-specific reference ranges similar to what exists for humans. The genetically diverse Collaborative Cross (CC) population that models human genetic heterogenetiety was characterized to develop mouse-specific cardiac reference ranges for Mus muscuslus, the most commonly used pre-clincial model. Heart function was analyzed in males and females from 58 CC strains and C57BL/6J using high-frequency ultrasound under both conscious and anesthetized conditions, as well as conscious electrocardiography to develop two standard deviation-based reference ranges. The sources and magnitude of measurement variability were identified, and inter-laboratory comparisons determined to quantify phenotypic robustness and heritability. Strain was the largest source of variability, while laboratory where data were collected was also significant but sex was not. Additionally, strains were identified that have characteristics of disease-associated phenotypes in cardiac function and electrophysiology similar to human cases including dilated cardiomyopathy, systolic cardiomyopathy, cancer therapy-related cardiac dysfunction, and long QT. These new models allow a more natural, and therefore more translatable progession to a cardiac disease state, supporting development of strain-specific models for cardiac pathologies, ultimately allowing more accurate diagnoses and informative safety assessments in humans. Article SummaryThe Collaborative Cross (CC) mouse reference population, modeling human genetic diversity, was utilized to derive cardiac reference values for Mus musculus. Strain was the primary source of variability, with the laboratory also playing a significant role, while sex had no impact. Despite inter-laboratory reproducibility challenges, the study identified strains resembling disease-associated phenotypes that offer a more natural progression to cardiac disease and provide crucial data for early disease identification and accurate safety assessments in humans.

genetics↗

bioRxiv2024

A Systematic Analysis of Read-Across Adaptations in Testing Proposal Evaluations by the European Chemicals Agency

An important element of the European Unions "Registration, Evaluation, Authorisation and Restriction of Chemicals" (REACH) regulation is the evaluation by the European Chemicals Agency (ECHA) of testing proposals submitted by the registrants to address data gaps in standard REACH information requirements. The registrants may propose adaptations, and ECHA evaluates the reasoning and issues a written decision. Read-across is a common adaptation type, yet it is widely assumed that ECHA often does not agree that the justifications are adequate to waive standard testing requirements. From 2008 to August 2023, a total of 2,630 Testing Proposals were submitted to ECHA; of these, 1,538 had published decisions that were systematically evaluated in this study. Each document was manually reviewed, and information extracted for further analyses. Read-across hypotheses were standardized into 17 assessment elements (AEs); each submission was classified as to the AEs relied upon by the registrants and by ECHA. Data was analyzed for patterns and associations. Testing Proposal Evaluations (TPEs) with adaptations comprised 23% (353) of the total; analogue (168) or group (136) read-across adaptations were most common. Of 304 read-across-containing TPEs, 49% were accepted; the odds of acceptance were significantly greater for group read-across submissions. The data was analyzed by Annex (i.e., tonnage), test guideline study, read-across hypothesis AEs, as well as target and source substance types and their structural similarity. While most ECHA decisions with both positive and negative decisions on whether the proposed read-across was adequate were context-specific, a number of significant associations were identified that influence the odds of acceptance. Overall, this analysis provides an unbiased overview of 15 years of experience with testing proposal-specific read-across adaptations by both registrants and ECHA. These data will inform future submissions as they identify most critical AEs to increase the odds of read-across acceptance.

pharmacology and toxicology↗

bioRxiv2023

Ten Years of Using Key Characteristics of Human Carcinogens to Organize and Evaluate Mechanistic Evidence in IARC Monographs on the Identification of Carcinogenic Hazards to Humans: Patterns and Associations

Systematic review and evaluation of the mechanistic evidence only recently been instituted in cancer hazard identification step of decision-making. One example of organizing and evaluating mechanistic evidence is the Key Characteristics approach of the International Agency for Research on Cancer (IARC) Monographs on the Identification of Carcinogenic Hazards to Humans. The Key Characteristics of Human Carcinogens were proposed almost 10 years ago and have been used in every IARC Monograph since 2015. We investigated the patterns and associations in the use of Key Characteristics by the independent expert Working Groups. We examined 19 Monographs (2015-2022) that evaluated 73 agents. We extracted information on the conclusions by each Working Group on the strength of evidence for agent-Key Characteristic combinations, data types that were available for decisions, and the role mechanistic data played in the final cancer hazard classification. We conducted both descriptive and association analyses within and across data types. We found that IARC Working Groups were cautious when evaluating mechanistic evidence: for only [~]13% of the agents was strong evidence assigned for any Key Characteristic. Genotoxicity and cell proliferation were most data-rich, while little evidence was available for DNA repair and immortalization Key Characteristics. Analysis of the associations among Key Characteristics revealed that only chemicals metabolic activation was significantly co-occurring with genotoxicity and cell proliferation/death. Evidence from exposed humans was limited, while mechanistic evidence from rodent studies in vivo was often available. Only genotoxicity and cell proliferation/death were strongly associated with decisions on whether mechanistic data was impactful on the final cancer hazard classification. The practice of using the Key Characteristics approach is now well-established at IARC Monographs and other government agencies and the analyses presented herein will inform the future use of mechanistic evidence in regulatory decision-making.

pharmacology and toxicology↗

bioRxiv2022

Novel Adult Cortical Neuron Processing and Screening method illustrates Sex- and Age-dependent effects of pharmaceutical compounds

Neurodegenerative diseases and neurotraumatic injuries are typically age-associated disorders that can reduce neuron survival, neurite outgrowth, and synaptic plasticity leading to loss of cognitive capacity, executive function, and motor control. In pursuit of reducing the loss of said neurological functions, novel compounds are sought that promote neuron viability, neuritogenesis, and/or synaptic plasticity. Current high content in vitro screenings typically use cells that are iPSC-derived, embryonic, or originate from post-natal tissues; however, most patients suffering from neurodegenerative diseases and neurotrauma are of middle-age and older. The chasm in maturity between the neurons used in drug screens and those in a target population is a barrier for translational success of in vitro results. It has been historically challenging to culture adult neurons let alone conduct screenings; therefore, age-appropriate drug screenings have previously not been plausible. We have modified Miltenyis protocol to increase neuronal yield, neuron purity, and neural viability at a reduced cost to expand our capacity to screen compounds directly in primary adult neurons. Furthermore, we have developed the first morphology-based screening system using adult cortical neurons. By using primary adult cortical neurons from mice that were 4 to 48 weeks old for screening of a library of pharmaceuticals, we have demonstrated age- and sex-dependent effects on neuritogenesis and neuron survival in vitro. Utilizing age- and sex-appropriate in vitro models to find novel compounds increasing neuron survival and neurite outgrowth, made possible by our modified adult neuron processing method, will greatly increase the relevance of in vitro screening for finding neuroprotective compounds.

neuroscience↗

bioRxiv2019

Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation

Gene transcription profiles across tissues are largely defined by the activity of regulatory elements, most of which correspond to regions of accessible chromatin. Regulatory element activity is in turn modulated by genetic variation, resulting in variable transcription rates across individuals. The interplay of these factors, however, is poorly understood. Here we characterize expression and chromatin state dynamics across three tissues--liver, lung, and kidney--in 47 strains of the Collaborative Cross (CC) mouse population, examining the regulation of these dynamics by expression quantitative trait loci (eQTL) and chromatin QTL (cQTL). QTL whose allelic effects were consistent across tissues were detected for 1,101 genes and 133 chromatin regions. Also detected were eQTL and cQTL whose allelic effects differed across tissues, including local-eQTL for Pik3c2g detected in all three tissues but with distinct allelic effects. Leveraging overlapping measurements of gene expression and chromatin accessibility on the same mice from multiple tissues, we used mediation analysis to identify chromatin and gene expression intermediates of eQTL effects. Based on QTL and mediation analyses over multiple tissues, we propose a causal model for the distal genetic regulation of Akr1e1, a gene involved in glycogen metabolism, through the zinc finger transcription factor Zfp985 and chromatin intermediates. This analysis demonstrates the complexity of transcriptional and chromatin dynamics and their regulation over multiple tissues, as well as the value of the CC and related genetic resource populations for identifying specific regulatory mechanisms within cells and tissues.\n\nAuthor summaryGenetic variation can drive alterations in gene expression levels and chromatin accessibility, the latter of which defines gene regulatory elements genome-wide. The same genetic variants may associate with both molecular events, and these may be connected within the same causal path: a variant that reduces promoter region chromatin accessibility, potentially by affecting transcription factor binding, may lead to reduced expression of that gene. Moreover, these causal regulatory paths can differ between tissues depending on functions and cellular activity specific to each tissue. We identify cross-tissue and tissue-selective genetic regulators of gene expression and chromatin accessibility in liver, lung, and kidney tissues using a panel of genetically diverse inbred mouse strains. Further, we identify a number of candidate causal mediators of the genetic regulation of gene expression, including a zinc finger protein that helps silence the Akr1e1 gene. Our analyses are consistent with chromatin accessibility playing a role in the regulation of transcription. Our study demonstrates the power of genetically diverse, multi-parental mouse populations, such as the Collaborative Cross, for large-scale studies of genetic drivers of gene regulation that underlie complex phenotypes, as well as identifying causal intermediates that drive variable activity of specific genes and pathways.

genomics↗