Biology subjects

Yeung, K.

Publications and source records attributed to Yeung, K..

13 recordsLinked to original sources

bioRxiv2026

Germline BRCA1 Mutation Deregulates Irradiation-Induced Cell Cycle Checkpoints in Human Mammary Luminal Progenitors

Mammary ductal tree comprises two epithelial lineages, basal and luminal, which harbour stem and progenitor cell subsets essential to breast physiology and are cancer-initiating precursors. Dysregulated cellular stress response is an early event in tumorigenesis, yet lineage-rooted study of primary breast epithelium pertinent to familial mutation carriers is limited. Here, we establish a lineage-resolved monolayer culture system that enables propagation of primary human mammary epithelial populations while preserving lineage identity across passages. We identify intrinsically distinct cell cycle response of luminal progenitors and basal cells to irradiation stress where the former engages both G1/S and G2/M checkpoints to achieve cell cycle arrest and the latter relies on the G2/M checkpoint. These lineage distinctions are diminished in germline BRCA1 mutation carriers with an attenuated G1/S checkpoint in luminal progenitors. Paired transcriptomic-proteomic profiling of acute irradiation response uncovers BRCA1+/- luminal progenitor population with sustained AKT-mTOR signaling and compromised cell cycle arrest marking an early deviation in the stress response of these purported cells-of-origin of aggressive breast cancers known to arise in BRCA1 germline mutation carriers. Our study provides a functional framework for determining critical events in the expansion of genomically altered mammary epithelial cells in the high-risk breast to enable future preventive interventions.

cell biology↗

bioRxiv2026

CORe Designer: a CRISPR design tool for proteome engineering

Precision proteome engineering requires tools that leverage CRISPR technologies, yet most current design platforms remain gene-centric. To bridge this gap, we introduce CORe Designer. Featuring an intuitive graphical user interface, CORe Designer enables researchers to design guide RNAs and homology-directed repair templates in a protein-centric manner. By automating these workflows, CORe Designer enables the design of targeted mutagenesis experiments for precision proteome engineering to be completed in minutes.

bioengineering↗

bioRxiv2026

Coordinated IL-2 and TGF-β Signaling via a Novel Fusion Protein Selectively Expands and Activates Regulatory T Cells

Establishing immune tolerance requires the integration of cytokine signals that favor regulatory T cell (Treg) function over effector differentiation, yet how such coordination can be achieved selectively in vivo remains incompletely defined. Regulatory T cells are essential for maintaining immune homeostasis and peripheral tolerance, and both interleukin-2 (IL-2) and transforming growth factor-{beta} (TGF-{beta}) contribute to Treg activation, differentiation, and stability in a highly context-dependent manner. Here, we examine the consequences of coordinated IL-2 and TGF-{beta}3 signaling using an engineered cytokine construct combining attenuated IL-2 with receptor-masked TGF-{beta}3. In vitro, attenuated IL-2/TGF-{beta}3 signaling promoted conversion of naive CD4 T cells into Foxp3 induced Tregs, expanded endogenous Tregs, and suppressed inflammatory cytokine production by memory and effector CD4 T cells. In vivo, a single administration selectively increased the frequency of CD4Foxp3 regulatory T cells exhibiting an activated and stable phenotype, while minimally activating Foxp3- conventional CD4 T cells relative to IL-2 alone. In a Treg-deficiency-driven adoptive transfer model of autoimmunity, early exposure to coordinated IL-2/TGF-{beta}3 signaling enhanced Treg activation, reduced tissue infiltration by autoreactive T cells, and conferred sustained protection from autoimmune gastritis in the absence of continued treatment. Together, these findings identify a mode of coordinated IL-2 and TGF-{beta}3 signaling sufficient to stabilize regulatory T cell responses and promote immune tolerance while limiting activation of conventional CD4 T cells, highlighting signal integration as a determinant of tolerogenic immune regulation in vivo. One Sentence SummaryCUE-401 coordinates IL-2 and TGF-{beta} signaling to expand and activate regulatory T cells and restrain autoimmune responses.

immunology↗

bioRxiv2025

Proteomics and Ex Vivo Plaque Culture Identify the Insulin-Like Growth Factor Axis as a Regulator of Carotid Plaque Stability

ObjectiveRupture of carotid atherosclerotic plaques leading to cerebral embolization, is a significant cause of stroke. We previously analyzed 21 plaques by mass spectrometry and reported that the proteomes of morphologically unstable (rupture-prone) and stable plaques are different. This dataset extends and includes non-atherosclerotic (thyroid) arteries to allow comparison with control tissue, and to investigate plaque stability using ex vivo plaques cultured. MethodsPlaques (n=76) and non-atherosclerotic superior thyroid artery segments (n=8) were retrieved from carotid endarterectomies. Additionally, 22 plaques were cultured ex vivo for 22 days to examine the role of insulin-like growth factor-1 (IGF-1) signalling. Proteins were analyzed by liquid chromatography-mass spectrometry. ResultsMass spectrometric proteome analysis identified three protein clusters associated with mor-phologically unstable (type A) and stable (type B) plaques, as well as non-atherosclerotic arteries. 2,876 proteins were differentially abundant in plaques compared to non-atherosclerotic arteries. 1,415 proteins were differentially abundant between plaque types A and B. Proteins linked to IGF transport and binding, particularly IGF-binding proteins, were more abundant in plaques compared to non-atherosclerotic arteries, and in type B compared to type A plaques. IGF-1, IGF-2 and the IGF-1 receptor were more abundant in type B plaques, whereas the IGF-2 receptor was more abundant in type A. IGF-1 treatment of ex vivo plaques decreased matrix metalloprotein 9 and increased collagen type XXI, consistent with a increased plaque stability. ConclusionsProteomic analyses of atherosclerotic plaques, and ex vivo plaques cultured with IGF-1, re-veals the IGF axis as a potential regulator of human atherosclerotic plaque stability. CLINICAL RELEVANCEThe protein composition of unstable carotid artery plaques differs from that of stable ones, which may explain their varying tendency to rupture. Components of the insulin-like growth factor (IGF) axis are more abundant in atherosclerotic plaques than in healthy tissue, and are more abundant in stable compared to unstable plaque morphology, suggesting a protective role of these proteins against plaque rupture. To investigate this, we treated plaques ex vivo with IGF-1. This data indicates that manipulating the IGF axis may promote plaque stability, with potential clinical relevance in prevention of plaque rupture. ARTICLE HIGHLIGHTSO_ST_ABSType of ResearchC_ST_ABSHuman study Key FindingsProteomic analysis of 76 carotid ath-erosclerotic plaques and 8 superior thyroid artery controls identified the insulin-growth factor (IGF) axis as potential regulators of plaque stability. Ex vivo cul-ture and IGF-1 treatment of 11 symptomatic carotid plaques induced proteome changes, compared to 11 controls, consistent with features of plaque stabiliza-tion. Take home MessageThe insulin-like growth factor axis is a potential regulator of carotid atherosclerotic plaque stability, as revealed by proteomic analysis and ex vivo plaque culture.

molecular biology↗

bioRxiv2025

Spatial proteomics of the human atherosclerotic microenvironment reveals heterogeneity in intra-plaque proteomes and extracellular matrix remodeling

The heterogeneity of atherosclerotic plaques is critical for their vulnerability to rupture and the associate risk of cardiovascular events. Most proteomic studies have only examined bulk changes, potentially obscuring key spatial differences in protein content and abundance. Here we report a high-resolution spatial proteomics workflow that allows exploration of the molecular landscape of human plaques and murine myocardial tissue. This combines laser capture microdissection of tissue areas (50,000 {micro}m{superscript 2} from 10 {micro}m-thick sections, corresponding to < 30 cells), with high-sensitivity ion-mobility mass spectrometry, allowing spatial profiling of cellular and extracellular matrix (ECM) proteomes. Over 2700 proteins were detected, revealing substantial intra-plaque proteome heterogeneity across distinct regions (lipid-rich, media layers, shoulder regions, necrotic core, intima) and distance from the lumen into the artery wall. Strong inverse correlations were detected between proteases (e.g. cathepsin-B) and core structural ECM components (e.g. perlecan, HSPG2) consistent with active ECM remodeling. Analysis of media layers indicated distinct protein signatures associated with smooth muscle contraction and cell-cell communication. Blood coagulation signatures, including platelet degranulation and fibrin clot formation were enriched at the intimal surface. Inflammatory markers (clusters of differentiation 4 and 68, CD4/CD68; vascular cell adhesion molecular 1, VCAM1) and vascular damage markers (tenascin-C, TNC) were enriched in shoulder regions. The necrotic core was dominated by blood proteins, consistent with intra-plaque hemorrhage. The capacity of this workflow to resolve changes over modest distances (225 {micro}m) provides unprecedented insights into the spatial organisation of the atherosclerotic microenvironment, offering a powerful tool for elucidating plaque biology and identifying potential therapeutic targets.

biochemistry↗

bioRxiv2024

N-Terminal proteomics reveals distinct protein degradation patterns in different types of human atherosclerotic plaques

BACKGROUNDDestabilization and rupture of atherosclerotic plaques is a major cause of acute atherosclerotic cardiovascular events, including heart attack, ischemic stroke and peripheral arterial disease. Plaque destabilization is associated with extracellular matrix (ECM) modification and remodelling involving protease activity. Enzymatic cleavage generates protein fragments with new ends (N-termini). We hypothesized that plaques susceptible to rupture would contain elevated levels of fragmented proteins with new N-termini. Identification of active proteases and their target proteins might allow categorization of plaque stability. METHODSPlaques from 21 patients who underwent carotid surgery due to symptomatic carotid artery stenosis were examined in an observational/cross-sectional study. The plaques were solubilized, digested, enriched for N-terminal fragments and analyzed by liquid chromatography-mass spectrometry. RESULTSThe above methodology detected 35349 peptides, with 19543 being N-terminal species; 6561 were subsequently identified and quantified. Multidimensional scaling analysis and hierarchical clustering indicate the presence of three distinct clusters, which correlate with gross macroscopic plaque morphology (soft, mixed, and hard), ultrasound classification (echolucent/echogenic) and presence of hemorrhage/ulceration. Major differences were identified in the complement of peptide fragments, consistent with alternative turnover and degradation pathways dependent on plaque type. Identified peptides include signal and pro-peptides from ECM synthesis/turnover, and many from protein fragmentation. Sequence analysis indicates the targeted proteins (including ECM species) and the proteases (including meprins, cathepsins, matrix metalloproteinases, elastase, kallikreins) involved in fragment generation. CONCLUSIONSThis study provides a large dataset of peptide fragments and proteases involved in plaque stability, mechanistic insights into remodelling, and possible biomarkers for improved atherosclerosis risk profiling. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=124 SRC="FIGDIR/small/594251v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@f5e62forg.highwire.dtl.DTLVardef@1db3b07org.highwire.dtl.DTLVardef@7fe3org.highwire.dtl.DTLVardef@cc1329_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

LHPP expression in triple-negative breast cancer promotes tumor growth and metastasis by modulating the tumor microenvironment

Triple-negative breast cancer (TNBC) is a highly aggressive and metastatic form of breast cancer that lacks an effective targeted therapy. To identify new therapeutic targets, we investigated the phosphohistidine phosphatase, LHPP, which has been implicated in the development of several types of cancer. However, the full significance of LHPP in cancer progression remains unclear due to our limited understanding of its molecular mechanism. We found that levels of the LHPP phosphohistidine phosphatase were significantly increased in human breast cancer patients compared to normal adjacent tissues, with the highest levels in the TNBC subtype. When LHPP was knocked out in the MDA-MB-231 human TNBC cell line, cell proliferation, wound healing capacity, and invasion were significantly reduced. However, LHPP knockout in TNBC cells did not affect the phosphohistidine protein levels. Interestingly, LHPP knockout in MDA-MB-231 cells delayed tumor growth and reduced metastasis when orthotopically transplanted into mouse mammary glands. To investigate LHPPs role in breast cancer progression, we used next-generation sequencing and proximity-labeling proteomics, and found that LHPP regulates gene expression in chemokine-mediated signaling and actin cytoskeleton organization. Depletion of LHPP reduced the presence of tumor-infiltrating macrophages in mouse xenografts. Our results uncover a new tumor promoter role for LHPP phosphohistidine phosphatase in TNBC and suggest that targeting LHPP phosphatase could be a potential therapeutic strategy for TNBC.

cancer biology↗

bioRxiv2024

Rigid, bivalent CTLA-4 binding to CD80 is required to disrupt the cis CD80 / PD-L1 interaction

The CTLA-4 and PD-1 checkpoints control immune responses to self-antigens and are key targets in cancer immunotherapy. Both pathways are connected via a cis interaction between CD80 and PD-L1, the ligands for CTLA-4 and PD-1 respectively. This cis interaction prevents PD-1 binding to PD-L1 but is reversed by CTLA-4 trans-endocytosis of CD80. However, the mechanism by which CTLA-4 selectively removes CD80 but not PD-L1 is unclear. Here we show that CTLA-4 - CD80 interactions are unimpeded by PD-L1 and that CTLA-4 binding with CD80 does not displace PD-L1 per se. Rather, both the rigidity and bivalency of the WT CTLA-4 molecule is required to orientate CD80 such that PD-L1 interactions are no longer permissible. Moreover, soluble CTLA-4 released PD-L1 only at specific expression levels of CD80 and PD-L1, whereas CTLA-4 trans-endocytosis released PD-L1 in all conditions. These data show that PD-L1 release from CD80 is driven by biophysical factors associated with orientation and bivalent cross-linking of proteins in the cell membrane and that trans-endocytosis of CD80 efficiently promotes PD-L1 availability.

immunology↗

bioRxiv2024

A single cell RNA sequence atlas of the early Drosophila larval eye

The Drosophila eye has been an important model to understand principles of differentiation, proliferation, apoptosis and tissue morphogenesis. However, a single cell RNA sequence resource that captures gene expression dynamics from the initiation of differentiation to the specification of different cell types in the larval eye disc is lacking. Here, we report transcriptomic data from 13,000 cells that cover six developmental stages of the larval eye. Our data show cell clusters that correspond to all major cell types present in the eye disc ranging from the initiation of the morphogenetic furrow to the differentiation of each photoreceptor cell type as well as early cone cells. We identify dozens of cell type-specific genes whose function in different aspects of eye development have not been reported. These single cell data will greatly aid research groups studying different aspects of early eye development and will facilitate a deeper understanding of the larval eye as a model system.

genomics↗

bioRxiv2023

Integrative Genomic Analyses Reveal Putative Cell Type-specific Targets of the Drosophila Ets Transcription Factor Pointed

The Ets domain transcription factors direct diverse biological processes throughout all metazoans and are implicated in development as well as in tumor initiation, progression and metastasis. The Drosophila Ets transcription factor Pointed (Pnt) is required for several aspects of eye development and regulates cell cycle progression, specification, and differentiation. Despite its critical role in development, very few targets of Pnt have been reported previously. Here, we used chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) to determine the genome-wide occupancy of Pnt in late larval eye discs. We identified enriched regions that mapped to an average of 6,941 genes, the vast majority of which are novel putative Pnt targets. Integrating ChIP-seq data with two other larval eye single cell genomics datasets (scRNA-seq and snATAC-seq) reveals genes that may be putative cell type-specific genes regulated by Pnt. Finally, our ChIP-seq data predict cell type-specific functional enhancers that were not reported previously. Our study provides a greatly expanded list of putative Pnt targets in the eye and is a resource for future studies that will allow mechanistic insights into complex developmental processes regulated by Pnt.

genomics↗

bioRxiv2023

A Single Cell Genomics Atlas of the Drosophila Larval Eye Reveals Distinct Developmental Timelines and Novel Markers for All Photoreceptor Subtypes

The Drosophila eye is a powerful model system to study principles of cell differentiation, proliferation, survival and morphogenesis. However, a high-resolution single cell genomics resource that accurately captures all major cell types of the larval eye disc and their spatiotemporal relationships is lacking. Here, we report transcriptomic and chromatin accessibility data for all known cell types in the developing eye. Photoreceptors appear as streams of cells that represent dynamic developmental timelines. Photoreceptor subtypes are transcriptionally distinct when they begin to differentiate, but then converge upon a common transcriptome just 24 hours later. We identify novel cell type-specific marker genes, enhancers and potential regulators, as well as genes with distinct R3 or R4 photoreceptor specific expression. Finally, we observe that photoreceptor chromatin accessibility is more permissive than non-neuronal lens-secreting cone cells, which show a more restrictive chromatin profile. This single cell genomics atlas will greatly empower the Drosophila eye as a model system.

genomics↗

bioRxiv2022

Growth Signaling Autonomy in Circulating Tumor Cells Aids Metastatic Seeding

Self-sufficiency (autonomy) in growth signaling, the earliest recognized hallmark of cancer, is fueled by the tumor cells ability to secrete-and-sense growth factors; this translates into cell survival and proliferation that is self-sustained by auto-/paracrine secretion. A Golgi-localized circuitry comprised of two GTPase switches has recently been implicated in the orchestration of growth signaling autonomy. Using breast cancer cells that are either endowed or impaired (by gene editing) in their ability to assemble the circuitry for growth signaling autonomy, here we define the transcriptome, proteome, and phenome of such autonomous state, and unravel its role during cancer progression. We show that autonomy is associated with enhanced molecular programs for stemness, proliferation, and epithelial-mesenchymal plasticity (EMP). Autonomy is both necessary and sufficient for anchorage-independent growth factor-restricted proliferation and resistance to anti-cancer drugs and is required for metastatic progression. Transcriptomic and proteomic studies show that autonomy is associated, with a surprising degree of specificity, to self-sustained EGFR/ErbB signaling. Derivation of a gene expression signature for autonomy revealed that growth signaling autonomy is uniquely induced in circulating tumor cells (CTCs), the harshest phase in the life of tumor cells when it is deprived of biologically available EGF. We also show that autonomy in CTCs tracks therapeutic response and prognosticates outcome. These data support a role for growth signaling autonomy in multiple processes essential for the blood-borne dissemination of human breast cancer. GRAPHIC ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/518910v2_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@167b370org.highwire.dtl.DTLVardef@135b62dorg.highwire.dtl.DTLVardef@14b5e9forg.highwire.dtl.DTLVardef@1311e84_HPS_FORMAT_FIGEXP M_FIG C_FIG Significance StatementA Golgi-localized molecular circuitry has been recently implicated in the orchestration of secrete-and-sense auto-/paracrine loops that impart self-sufficiency in growth signaling, a.k.a., growth signaling autonomy. Using a transdisciplinary approach, this work shows that growth signaling autonomy is uniquely induced in tumor cells that are in circulation. Circulating tumor cells (CTCs) represent a brutish and risky phase in the lifetime of tumor cells when they are exposed to the immune system and hemodynamic sheer forces, all in the setting of growth factor starvation. Cancer cells appear to rely on the autonomy circuit to survive and enhance their fitness to seed metastases. Autonomy generates the kind of eat-what-you-kill entrepreneurial spirit which minimizes the risk of CTCs dying on an otherwise risky journey.

cancer biology↗

bioRxiv2022

Single Cell RNA Sequencing of the Adult Drosophila Eye Reveals Distinct Clusters and Novel Marker Genes for All Major Cell Types

The adult Drosophila eye is a powerful model system for phototransduction and neurodegeneration research. However, single cell resolution transcriptomic data are lacking for this tissue. We present single cell RNA-seq data on 1-day male and female, 3-day and 7-day old male adult eyes, covering early to mature adult eyes. All major cell types, including photoreceptors, cone and pigment cells in the adult eye were captured and identified. Our data sets identified novel cell type specific marker genes, some of which were validated in vivo. R7 and R8 photoreceptors form clusters that reflect their specific Rhodopsin expression and the specific Rhodopsin expression by each R7 and R8 cluster is the major determinant to their clustering. The transcriptomic data presented in this report will facilitate a deeper mechanistic understanding of the adult fly eye as a model system.

genomics↗