Biology subjects

Yang, L. M.

Publications and source records attributed to Yang, L. M..

5 recordsLinked to original sources

bioRxiv2026

Human Genome-Scale Models of Metabolism and Gene Expression Reveal Resource Constraints of Cancer Cell Lines

Genome-scale metabolic models (M-models) provide mechanistic insight into intracellular metabolism by simulating fluxes subject to nutrient and energy resource constraints. However, they cannot account for a major component of resource allocation, since they do not explicitly account for the cost of producing and maintaining enzymes. Genome-scale models of metabolism and gene expression (ME-Models) address this by including gene expression reactions, but these have only been developed for prokaryotes due to the additional complexity and challenges of modeling eukaryotes. Here, we present the human ME-Model, which encodes transcription, translation, complex formation, and turnover reactions for all enzymes catalyzing metabolic reactions, and couples these processes to constrain metabolic fluxes. We introduce humanME, a Python package to build and analyze human ME-Models. With this, we constructed 16 cancer cell line ME-Models. We found that resource constraints improve growth-rate predictions, and that ME-Model flux predictions are more biologically plausible and efficient. Moreover, transcriptional fluxes recapitulate RNA-Seq expression levels, with discrepancies revealing potential trade-offs involving multiple cellular objectives. Finally, the ME-Model recapitulates the Warburg effect, with increasing growth rate inducing glycolytic shifts, in part due to machinery costs of the electron transport chain. Altogether, we show ME-modeling can mechanistically link gene expression, resource allocation, and metabolism in human cells, substantially expanding the predictive scope of constraint-based models.

systems biology↗

bioRxiv2026

Dynamic optimization of extrachromosomal DNA copy number drives tumour evolution

Extrachromosomal DNA (ecDNA) is common in human cancers and is associated with poor clinical outcomes, yet how ecDNA-driven genetic heterogeneity is translated into functional heterogeneity remains unclear. Using single-cell multiomics sequencing and multiplexed IF-FISH, we show that asymmetric inheritance of ecDNA generates copy number heterogeneity that propagates to gene expression programs, including oncogenic signaling and cellular stress responses. Transgenerational live-cell lineage tracking directly shows that ecDNA heterogeneity arises within only a few cell divisions and modulates daughter cell division timing in a copy number-dependent manner, a property not observed for evenly inherited chromosomal amplicons. We identify an optimal middle ecDNA copy number range that maximizes proliferative fitness at baseline, while drug selection pressure induced by low-dose CHK1 inhibition selects for cells with a new optimal range at low ecDNA copy numbers. These low ecDNA copy number cells pre-exist in the population and can be generated de novo, driving copy number shifts promoting drug resistance. In vivo experiments further demonstrate that shifts toward ecDNA copy numbers that are optimal under the tumour microenvironment enhance tumourigenicity. Together, these findings establish ecDNA copy number plasticity as a central driver of tumour evolution.

cancer biology↗

bioRxiv2025

Mitotic chromatin compaction tethers extrachromosomal DNA to chromosomes and prevents their mis-segregation into micronuclei

Extrachromosomal DNA (ecDNA) is linked to aggressive cancer growth, treatment resistance, and shorter survival across a wide variety of cancers. ecDNA promotes intratumoral genetic heterogeneity, enhanced oncogene expression, and accelerated tumor evolution, driving tumor pathogenesis. ecDNA lack centromeres and segregate to daughter cell nuclei during mitosis by tethering to chromosomes. However, the mechanisms involved in this tethering are incompletely understood. Here, I present evidence that ecDNA tethering to chromosomes is coupled to chromatin compaction during mitotic chromosome formation, which acts to generally increase chromatin-chromatin interaction. Using a cancer cell line model, I show that decompacting mitotic chromatin under hypotonic conditions and by increasing histone acetylation untethers ecDNA from chromosomes, leading to their mis-segregation into micronuclei after mitosis. Additionally, overexpression of the mitotic chromosome surfactant Ki67 untethers ecDNA from chromosomes, leading to their mis-segregation into micronuclei. These findings show that the mechanisms involved in chromatin compaction are important for tethering ecDNA to chromosomes and preventing their mis-segregation into micronuclei. I propose a model in which interactions between ecDNA chromatin fibers and chromosomal chromatin contribute to ecDNA segregation into daughter cells during cell division.

cancer biology↗

bioRxiv2020

Analysis of FGF20-regulated genes in organ of Corti progenitors by translating ribosome affinity purification

BackgroundUnderstanding the mechanisms that regulate hair cell (HC) differentiation in the organ of Corti (OC) is essential to designing genetic therapies for hearing loss due to HC loss or damage. We have previously identified Fibroblast Growth Factor 20 (FGF20) as having a key role in HC and supporting cell differentiation in the mouse OC. To investigate the genetic landscape regulated by FGF20 signaling in OC progenitors, we employ Translating Ribosome Affinity Purification combined with Next Generation mRNA Sequencing (TRAPseq) in the Fgf20 lineage. ResultsWe show that TRAPseq targeting OC progenitors effectively enriched for mRNA within this rare cell population. TRAPseq identified differentially expressed genes downstream of FGF20, including Etv4, Etv5, Etv1, Dusp6, Hey1, Hey2, Heyl, Tectb, Fat3, Cpxm2, Sall1, Sall3, and cell cycle regulators such as Cdc20. Analysis of Cdc20 conditional-null mice identified decreased cochlea length, while analysis of Sall1-{Delta}Zn2-10 mice, which harbor a mutation that causes Townes-Brocks syndrome, identified a decrease in outer hair cell number. ConclusionsWe present two datasets: genes with enriched expression in OC progenitors, and genes regulated by FGF20 in the embryonic day 14.5 cochlea. We validate select differentially expressed genes via in situ hybridization and in vivo functional studies in mice. Key findingsO_LITranslating Ribosome Affinity Purification (TRAP) with Fgf20-Cre enriches for prosensory cell mRNA C_LIO_LITRAP combined with RNAseq identifies genes downstream of FGF20 during prosensory cell differentiation C_LIO_LIFGF20 regulates Sall1, gene implicated in human sensorineural hearing loss C_LI Grant Sponsor and NumberNational Institute on Deafness and Other Communication Disorders - DC017042 (DMO) Washington University Institute of Clinical and Translational Sciences and National Center for Advancing Translational Sciences - CTSA grant UL1TR002345 (JIT471 to DMO) March of Dimes - 6-FY13-127 (MR)

developmental biology↗

bioRxiv2018

Sox2 and FGF20 define a temporal separation between specification and differentiation required for organ of Corti development

The mouse organ of Corti develops in two steps: progenitor specification and differentiation. Fibroblast Growth Factor (FGF) signaling is important in this developmental pathway, as deletion of FGF receptor 1 (Fgfr1) or its ligand, Fgf20, leads to the loss of hair cells and supporting cells from the organ of Corti. However, whether FGF20-FGFR1 signaling is required during specification or differentiation, and how it interacts with the transcription factor Sox2, also important for hair cell and supporting cell development, has been a topic of debate. Here, we show that while FGF20-FGFR1 signaling functions during progenitor differentiation, FGFR1 has an FGF20-independent, Sox2-dependent role in specification. We also show that a combination of reduction in Sox2 expression and Fgf20 deletion recapitulates the Fgfr1-deletion phenotype. Furthermore, we uncovered a strong genetic interaction between Sox2 and Fgf20, especially in regulating the development of hair cells and supporting cells towards the basal end and the outer compartment of the organ of Corti. To explain this genetic interaction and its effects on the basal end of the organ of Corti, we provide evidence that decreased Sox2 expression delays specification, which begins at the organ of Corti apex, while Fgf20-deletion results in premature onset of differentiation, which begins near the organ of Corti base. Thereby, Sox2 and Fgf20 interact to ensure that specification occurs before differentiation towards the cochlear base. These findings reveal an intricate developmental program regulating organ of Corti development along the basal-apical axis of the cochlea. Author summaryThe mammalian cochlea contains the organ of Corti, a specialized sensory epithelium populated by hair cells and supporting cells that detect sound. Hair cells are susceptible to injury by noise, toxins, and other insults. In mammals, hair cells cannot be regenerated after injury, resulting in permanent hearing loss. Understanding genetic pathways that regulate hair cell development in the mammalian organ of Corti will help in developing methods to regenerate hair cells to treat hearing loss. Many genes are essential for hair cell and supporting cell development in the mouse organ of Corti. Among these are Sox2, Fgfr1, and Fgf20. Here, we investigate the relationship between these three genes to further define their roles in development. Interestingly, we found that Sox2 and Fgf20 interact to affect hair cell and supporting cell development in a spatially-graded manner. We found that cells toward the outer compartment and the base of the organ of Corti are more strongly affected by the loss of Sox2 and Fgf20. We provide evidence that this spatially-graded effect can be partially explained by the roles of the two genes in the precise timing of two sequential stages of organ of Corti development, specification and differentation.

developmental biology↗