Biology subjects

Lee, C. A.

Publications and source records attributed to Lee, C. A..

7 recordsLinked to original sources

bioRxiv2026

Beta-Adrenergic Stimulation and MYH7 G256E Mutant Gene Dosage Drive Hypertrophic Cardiomyopathy Phenotype Penetrance

AimsHypertrophic cardiomyopathy (HCM) is the most prevalent genetic heart disorder, characterized by significant phenotypic variability even among individuals with identical MYH7 mutations. This study aims to elucidate factors contributing to this variability and identify drivers of phenotype penetrance. We compared the baseline phenotypes of a highly penetrant MYH7 H251N mutation and the variably penetrant MYH7 G256E mutation and investigated the impact of adding beta-adrenergic stimulation and homozygosity on disease phenotype penetrance using cardiomyocytes from an isogenic line of human induced pluripotent stem cells (hiPSC-CMs). Methods and ResultsIsogenic hiPSCs with MYH7 H251N and MYH7 G256E mutations were generated using CRISPR/Cas9 technology and differentiated into cardiomyocytes (CMs). Single-cell RNA sequencing (scRNAseq) and functional analysis of contractile function revealed consistent HCM phenotype presentation in H251N CMs, whereas G256E CMs exhibited a subtle and more variable phenotype. Beta-adrenergic stimulation induced a distinct metabolic stress response in G256E CMs, characterized by impaired mitochondrial ATP upregulation. Increasing mutant gene dosage from hetero- to homozygosity led to consistent increase in hypertrophic and structural gene expression changes in G256E CMs at RNA and protein levels. These changes were distinct from the changes observed with stress response. Importantly, homozygous G256E CMs exhibited a hypercontractile functional and disorganized structural phenotype. Across multiple experimental conditions, we identified consistent increase in cardiomyocyte specific transcriptomic markers such as NPPB, APOE, PDLIM3 and ANKRD1. ConclusionsOur study highlights the use of a variably penetrant MYH7 mutation to investigate factors that influence HCM phenotype penetrance. Specifically, we found that mutant gene dosage and beta-adrenergic stimulation induce distinct HCM disease phenotypes, providing novel insights into mechanisms that may contribute to variable disease expression in HCM. Translational PerspectiveHCM is characterized by significant phenotypic variability, complicating both diagnosis and clinical management. This study explores the factors driving HCM phenotype penetrance using isogenic hiPSC-CMs with MYH7 mutations. We demonstrate that beta-adrenergic stimulation and increased mutant gene dosage significantly impact HCM disease penetrance. Beta-adrenergic stimulation triggers metabolic stress responses, while increased gene dosage leads to a hypercontractile and structurally disorganized phenotype. These findings provide insight into how specific modifiers can shape disease-associated phenotypes in HCM model systems. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/729411v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@16a72d7org.highwire.dtl.DTLVardef@1999ca6org.highwire.dtl.DTLVardef@1fb8752org.highwire.dtl.DTLVardef@7148b2_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

Spatial and temporal coordination of signaling pathways in tissue differentiation: developmental atlas of protein expression during zebra finch beak maturation

BackgroundMorphogenesis depends on spatial and temporal coordination of signaling pathways, yet the colocalization of proteins across pathways remains poorly understood. Here we examine cellular and histological localization of regulatory proteins forming core craniofacial developmental pathways during beak morphogenesis of the zebra finch (Taeniopygia guttata). ResultsWe present an atlas of spatiotemporal coexpression of {beta}-catenin, Bmp4, CaM, Dkk3, Fgf8, Ihh, Tgf{beta}2, and Wnt4 across embryonic stages HH29-42 revealing both established and novel patterns of expression. Overall, in the earliest stages (HH29-32), most proteins show broad and overlapping expression across epithelial and mesenchymal tissues. By stage HH36, expression becomes increasingly compartmentalized, with pronounced differentiation among tissue types. Notably, at later stages, proteins showed tissue-specific distributions in boundary versus core regions of chondrogenic and osteogenic domains indicating coordinated cross-pathway patterning during cartilage and bone formation. ConclusionsOsteogenesis in the zebra finch beak is organized by coordinated signaling between boundary-associated cells and differentiating cores, with cross-pathway feedback establishing bone and cartilage differentiation while maintaining boundaries. Our results corroborated core elements of craniofacial signaling dynamics, while revealing unexpected subcellular localization for several proteins that showed regulatory complexity not captured by prior transcript-level maps. This atlas provides a protein-level baseline for comparative and mechanistic studies of beak morphogenesis.

developmental biology↗

bioRxiv2025

Ultimate paths of least resistance: Intrinsically disordered links as developmental resets in regulatory protein networks

Development and evolution require both stability and adaptability, yet how these opposite properties are reconciled is unclear. Here, we show that intrinsically disordered proteins (IDPs) act as reset mechanisms in conserved regulatory networks facilitating developmental transitions by integrating physical processes with genetic regulation. By tracing the ontogeny of mesenchymal cells in avian beak primordia, we demonstrate that mechanosensitive IDPs mediate shifts between physical cell states via dosage-dependent binding plasticity, converting stochastic protein variation into discreet regulatory networks. The disorder-enabled connectivity in these proteins resets their regulatory specialization and promotes population divergence. Comparative analyses across avian proteomes confirm that binding plasticity in transcriptional IDPs drives their diverse regulatory associations and accelerates their evolution. By resetting specialized states in conserved regulatory networks, IDPs flexibly regulate developmental pathways and reconcile precision with evolvability.

evolutionary biology↗

bioRxiv2025

Cell jamming transitions shape regulatory protein gradients and prime evolutionary divergence

A long-standing goal of evolutionary developmental biology is to identify the mechanisms underlying criticality of developmental transitions that allow processes governing individual cells scale up to the organism-level patterning. The viscoelastic properties of embryonic tissues imply collective cell behaviors, leading to the expectation that signaling networks should capitalize on the material properties of tissues, structuring morphogenesis around the spatial and temporal transitions that they induce. Here, we show that this interaction is evident even prior to tissue differentiation and is traceable to behavior of individual cells. In avian beak primordia, we find that fields of mesenchymal cells undergo cycles of local jamming dynamically modulating coordination of cell shape and movement. These cycles progressively alter the spatial reach of regulatory proteins, strongly expanding or restricting their gradients based on tissue mechanical state. Tissue-level gradients of proteins most sensitive to local cell jamming transitions also diverge the most across populations, priming tissue compartmentalization. These findings suggest that the material state transition is an effective interface for integration of stochastic physical processes and genetic regulation and is well placed to underlie criticality of developmental systems allowing local rules governing cell-state transitions scale up to tissue-level patterning. More broadly, our findings reveal how transient material transitions reset developmental trajectories and promote diversification while preserving robustness.

evolutionary biology↗

bioRxiv2024

Topoisomerase IIb binding underlies frequently mutated elements in cancer genomes

Type-II topoisomerases resolve topological stress in DNA through controlled double-strand breaks. While TOP2A is a chemotherapy target in proliferating cells, the ubiquitously expressed TOP2B is a potential off-target. Here we explore roles of TOP2B in mutagenesis by generating DNA-binding maps of TOP2B, CTCF, and RAD21 in human cancer samples and analysing these maps for driver mutations and mutational processes in 6500 whole cancer genomes. TOP2B-CTCF-RAD21 and TOP2B-RAD21 sites are enriched in somatic mutations and structural variants (SVs), especially at evolutionary conserved sites displaying high transcription and long-range chromatin interactions. TOP2B binding underlies SVs and hotspot mutations in cancer-driving genes such as TP53, MYC, FOXA1, and VHL, and many cis-regulatory elements. We show that the TOP2B-bound mutational hotspot at RMRP drives tumor initiation and growth in vivo. These data highlight TOP2B as a protector of the genome from topological challenges whose aberrant activity promotes driver and passenger mutations in cancer genomes.

cancer biology↗

bioRxiv2020

Functional and genetic determinants of mutation rate variability in regulatory elements of cancer genomes

BackgroundCancer genomes are shaped by mutational processes with complex spatial variation at multiple scales. Entire classes of regulatory elements are affected by local variations in mutation frequency. However, the underlying mutational mechanisms with functional and genetic determinants remain poorly understood. ResultsWe characterised the mutational landscape of 1.3 million gene regulatory and chromatin architectural elements in 2,419 whole cancer genomes with transcriptional and pathway activity, functional conservation and recurrent driver events. We developed RM2, a statistical model that quantifies mutational enrichment or depletion in classes of genomic elements through genetic, trinucleotide and megabase-scale effects. We report a map of localised mutational processes affecting CTCF binding sites, transcription start sites (TSS) and tissue-specific open-chromatin regions. We show that increased mutational frequency in TSSs correlates with mRNA abundance in most cancer types, while open-chromatin regions are generally enriched in mutations. We identified [~]10,000 CTCF binding sites with core DNA motifs and constitutive binding in 66 cell types that represent focal points of local mutagenesis. We detected site-specific mutational signatures, such as SBS40 in open-chromatin regions in prostate cancer and SBS17b in CTCF binding sites in gastrointestinal cancers. We also proposed candidate drivers of localised mutagenesis: BRAF mutations associate with mutational enrichments at CTCF binding sites in melanoma, and ARID1A mutations with TSS-specific mutations in pancreatic cancer. ConclusionsOur method and catalogue of localised mutational processes provide novel perspectives to cancer genome evolution, mutagenesis, DNA repair and driver discovery. Functional and genetic correlates of localised mutagenesis provide mechanistic hypotheses for future studies.

genomics↗

bioRxiv2019

Comprehensive analysis of lncRNAs reveals candidate prognostic biomarkers in multiple cancer types

Long non-coding RNAs (lncRNAs) are increasingly recognized as functional units in cancer pathways and powerful molecular biomarkers, however most lncRNAs remain uncharacterized. Here we performed a systematic discovery of prognostic lncRNAs in 9,326 patient tumors of 29 types using a proportional-hazards elastic net machine-learning framework. lncRNAs showed highly tissue-specific transcript abundance patterns. We identified 179 prognostic lncRNAs whose abundance correlated with patient risk and improved the performance of common clinical variables and molecular tumor subtypes. Pathway analysis revealed a large diversity of the high-risk tumors stratified by lncRNAs and suggested their functional associations. In lower-grade gliomas, discrete activation of HOXA10-AS indicated poor patient prognosis, neurodevelopmental pathway activation and a transcriptomic similarity to glioblastomas. HOXA10-AS knockdown in patient-derived glioblastoma cells caused decreased cell proliferation and deregulation of glioma driver genes and proliferation pathways. Our study underlines the pan-cancer potential of the non-coding transcriptome for developing molecular biomarkers and innovative therapeutic strategies.

cancer biology↗