Lam, C. K. | Search bioRxiv

bioRxiv2026

Down- to up-state transition is the default pathway in TREK K2P channel activation and does not involve a lipid occluded pore

Two crystallographic states of mechanosensitive TREK/TRAAK K2P channels - a low-activity down-state and a high-activity up-state - have been proposed to underlie gating, but the origin of the low activity remains debated. Competing models suggest either lipid-mediated pore block or selectivity filter (SF) inactivation. Using systematic mutagenesis of M2/M4 helices, we identified 16 highly active mutants and assessed their activation mechanisms via free-energy calculations, molecular dynamics simulations, and a state-dependent pharmacological probe. The computational approaches reliably predicted mutation-induced shifts in the down-up equilibrium. We further show that intracellular acidification and regulatory lipids primarily stabilize the up-state, consistent with stretch, temperature, and dephosphorylation. These findings support the down-up transition as the principal physiological activation pathway and suggest that mechanosensitivity arises from the larger membrane footprint of the up-state. Our data argue against a physiological role of a lipid-blocked pore and instead support gating via conformational control of the SF in TREK/TRAAK channels.

physiology↗

bioRxiv2022

Systems Analysis of de novo Mutations in Congenital Heart Diseases Identified a Molecular Network in Hypoplastic Left Heart Syndrome

Congenital heart diseases (CHD) are a class of birth defects affecting [~]1% of live births. These conditions are hallmarked by extreme genetic heterogeneity, and therefore, despite a strong genetic component, only a very handful of at-risk loci in CHD have been identified. We herein introduced systems analyses to uncover the hidden organization on biological networks of genomic mutations in CHD, and leveraged network analysis techniques to integrate the human interactome, large-scale patient exomes, the fetal heart spatial transcriptomes, and single-cell transcriptomes of clinical samples. We identified a highly connected network in CHD where most of the member proteins had previously uncharacterized functions in regulating fetal heart development. While genes on the network displayed strong enrichment for heart-specific functions, a sub-group, active specifically at early developmental stages, also regulates fetal brain development, thereby providing mechanistic insights into the clinical comorbidities between CHD and neurodevelopmental conditions. At a small scale, we experimentally verified previously uncharacterized cardiac functions of several novel proteins employing cellular assays and gene editing techniques. At a global scale, our study revealed developmental dynamics of the identified CHD network and observed the strongest enrichment for pathogenic mutations in the network specific to hypoplastic left heart syndrome (HLHS). Our single-cell transcriptome analysis further identified pervasive dysregulation of the network in cardiac endothelial cells and the conduction system in the HLHS left ventricle. Taken together, our systems analyses identified novel factors in CHD, revealed key molecular mechanisms in HLHS, and provides a generalizable framework readily applicable to studying many other complex diseases.

systems biology↗