Biology subjects

Chen, P.-T.

Publications and source records attributed to Chen, P.-T..

4 recordsLinked to original sources

bioRxiv2026

Rapid functional classification of cardiac genetic variants directly informs precision cardiology

Large-scale clinical genome sequencing yields vast numbers of variants of unknown significance (VUSs). The high frequency of VUSs and the paucity of platforms to characterize their functional impact pose significant challenges for clinical decision making. Here, we present an integrated end-to-end platform, REVi-SCOPE (Rapid evaluation of variants in single cells by optogenetics and prime editing), for characterization of the impact of VUSs on cardiac physiology. Our strategy consists of (1) introduction of variants directly into wild-type (WT) human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) via prime editing; (2) optogenetic assessment of calcium and membrane voltage dynamics in single hiPSC-CMs within the pool of edited and unedited cells; and (3) in situ single-cell genotyping of the phenotyped hiPSC-CMs with single-allele resolution. By optimizing and integrating each of these steps, we created a platform that enables VUS characterization in 10 days. We validated the REVi-SCOPEs capabilities by analyzing the properties of established arrhythmogenic variants. We then used REVi-SCOPE to reveal the functional impact of a VUS, TRPM4A320V, identified in a child with a conduction block. Together, our results show that REVi-SCOPE enables functional characterization of VUSs linked to cardiac arrhythmias with unprecedented throughput.

bioengineering↗

bioRxiv2026

Spatially correlated fluctuations govern relative chromatin motion

Essential nuclear processes require pairs of chromosomal loci to find each other in three-dimensional space. Polymer models of chromosome dynamics typically assume that the stochastic forces driving such locus motion are spatially uncorrelated, implying that relative diffusion follows directly from single-locus dynamics. Here we show that this assumption fails in living cells. Using live-cell imaging in fly embryos and mouse embryonic stem cells, we find that pairwise locus distances diffuse markedly slower than predicted for independent fluctuations. Combining stochastic trajectory analysis with polymer simulations, we demonstrate that this slowdown arises from non-equilibrium spatially correlated fluctuations (SCFs) in the nucleoplasm, which cause nearby loci to move coherently. We establish three experimentally testable signatures of SCFs: fluctuation amplitudes plateau at large distances, are independent of genomic separation, and show an anomalous temporal scaling. All three predictions are confirmed experimentally, including for loci on separate chromosomes. ATP depletion and disruption of cohesin-mediated loop extrusion reveal that both active processes and crosslinking contribute to correlation magnitudes. Because SCFs slow relative motion preferentially at short distances, they reduce encounter frequencies while prolonging encounter durations, generating a trade-off with direct implications for gene regulation. Our results identify spatially correlated fluctuations as a fundamental determinant of relative motion in confined active polymers.

biophysics↗

bioRxiv2025

Tissue-guided multi-omics profiling identifies extracellular vesicle biomarkers indicative of lung pathology in acute respiratory distress syndrome

BackgroundAcute respiratory distress syndrome (ARDS) remains a lethal inflammatory lung condition lacking reliable biomarkers that reflect lung-specific pathology. Extracellular vesicles (EVs) circulate systemically and may carry molecular signals from injured organs, but the correspondence between EV cargo and lung tissue alterations remains unclear. MethodsWe established aspiration-, lipopolysaccharide (LPS)-, and COVID-19-induced murine ARDS models and applied a tissue-guided multiomics framework integrating proteomic and metabolomic analyses of lung tissue and plasma-derived EVs to identify lung-originating circulating biomarkers. ResultsFour proteins--haptoglobin (HP), inter-alpha-trypsin inhibitor heavy chains 3 and 4 (ITIH3, ITIH4), and clusterin (CLU)--were consistently upregulated in both lung tissue and plasma EVs across all ARDS etiologies. Metabolomic integration revealed dysregulation of arachidonic acid metabolism as a unifying inflammatory axis. Multiomics network analysis further distinguished etiology-specific molecular programs, including glycolytic activation in aspiration-induced, platelet aggregation in LPS-induced, and vascular smooth muscle dysregulation in COVID-19-induced ARDS. ConclusionsThis study establishes a tissue-informed EV profiling framework that links local lung pathology to systemic molecular signatures, revealing HP, ITIH3, ITIH4, CLU, and arachidonic-acid-related metabolites as potential diagnostic markers for ARDS. These findings provide a foundation for developing clinically translatable, EV-based biomarker assays for early detection and molecular subtyping of lung injury.

biochemistry↗

bioRxiv2024

Elucidating the Mechanism Underlying UBA7-UBE2L6 Disulfide Complex Formation

We elucidate cryo-EM structure and formation of the ubiquitin-associated bovine UBA7*UBE2L6 disulfide complex, shedding light on a highly specific and evolutionarily conserved mechanism governing ISG15 conjugation, a pivotal process in the immune response. UBA7 displays a unique capacity to recognize UBE2L6, distinct from this latters homolog UBE2L3, highlighting the intricacies of cellular regulation. Inter-species interactions of the resulting complex further underscore its significance. We characterize three crucial factors that influence UBA7*UBE2L6 disulfide complex formation: (1) strong binding affinity and specificity; (2) conformational differences in the catalytic cysteine capping loop (CCL); and (3) increased thiolate/thiol ratios at catalytic cysteines. Modification of any of these factors profoundly impacts complex activation and the ISG15 transfer cascade. This redox-sensitive complex implies a link between oxidative stress and regulation of the immune response, highlighting a potential therapeutic target for modulating immune reactions arising from infections and inflammatory conditions.

biophysics↗