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Lau, K.

Publications and source records attributed to Lau, K..

At least 37 records · Page 2Linked to original sources

Transposable element co-option drives transcription factor neofunctionalization

Gene duplication and domain acquisition are key mechanisms driving protein diversification. However, the impact of these processes on the function and evolution of transcription factors (TFs) remains poorly characterized. Here, we show that the DUF3669 domain, found in a subset of KRAB zinc-finger proteins (KZFPs), originated from the co-option of a fragment of a LINE-1 transposable element ORF1p. Similar to its LINE-1-encoded ancestor, the DUF3669 domain promotes KZFPs trimerization and enables the formation of nuclear condensates with ribonucleoparticle properties, which critically influence the genomic recruitment and action of these TFs. Thus, our study uncovers a direct link between TE co-option and TF neofunctionalization, highlighting how mobile genetic elements shape the evolution of protein functionality.

genetics↗

Myelin transcription factors 1 and 3 have overlapping but distinct roles in insulin secretion and survival of human β cells

Aims/hypothesisGenetic and environmental factors work together to cause islet beta-cell failure, leading to type 2 diabetes (T2D). How these factors are integrated to regulate beta cells remains largely unclear. Based on our previous findings that the family of Myelin transcription factors (MYT1, MYT1L, and ST18) prevents mouse beta-cell failure by repressing the overactivation of stress response, their regulation by obesity-related nutrition signals in human beta cells, and their association with T2D, we postulate that these factors prevent human beta-cell failure under normal physiology and obesity-related stress. MethodsMYT1 or ST18 were knocked down in primary human beta cells using shRNA. Beta-cell survival, secretory function, and gene expression were examined after islet cells were cultured in vitro or xenotransplanted into mice under normal or obesity-related stress. ResultsIn culture, MYT1-knockdown (KD) caused beta-cell death, while ST18-KD compromised glucose-stimulated insulin secretion. Under obesity-induced stress as xenotransplants, ST18-KD also caused beta-cell death. Accordingly, MYT1-KD deregulated several genes and genesets in cell death and cellular stress response, while ST18-KD deregulated those regulating stress response, mitochondria, and ion channels. Corresponding to these gene expression changes, ST18-KD reduces glucose-stimulated Ca2+ influx in beta cells. In addition, the MYT1- and ST18-regulated genes are enriched for T2D-associated loci, with an enrichment of 2.05-fold relative to random distribution. Conclusions/interpretationThe MYT TFs complement each other to integrate genetic and environmental factors to prevent beta-cell failure and T2D, with their major effects exerted on beta-cell viability and/or Ca2+ influx. Graphical AbstractNutrient-responsive transcription factors MYT1 and ST18 regulate human beta-cell survival and secretory functions. Under low metabolic stress, MYT1 regulates cell survival while ST18 regulates insulin secretion. Under high metabolic stress, ST18 also regulates beta-cell survival. MYT1, at least partly, regulates cell survival through stress-related apoptotic processes, while ST18 regulates insulin secretion via Ca2+ influx. Research in context summaryO_ST_ABSBackgroundC_ST_ABSO_LIThe myelin transcription factors (MYT TFs, including MYT1, MYT1l, and ST18) prevent mouse beta-cell failure by depressing the overactivation of stress-response genes. C_LIO_LISNPs in all three MYT loci are associated with human type 2 diabetes. C_LIO_LIThe expression and nuclear localization of MYT1 and ST18 were increased in primary human beta cells under acute metabolic stress but downregulated in type 2 diabetes. C_LIO_LIThe co-knockdown of MYT1, MYT1L, and ST18 in a human beta-cell line resulted in apoptosis. C_LI Key questionO_LIHow does MYT1 or ST18 regulate human beta-cell function and survival? C_LI New findingsO_LIMYT1 prevents human beta-cell death under normal and metabolic stress conditions, corresponding to deregulation of a few genes involved in cell death under cellular stress. C_LIO_LIST18 promotes insulin secretion under normal physiological conditions by regulating Ca2+ influx and prevents beta-cell death under metabolic stress. C_LIO_LIThe MYT1- and ST18-regulated genes are enriched for type 2 diabetes-risk loci. C_LI Clinical impactO_LIRegulators of the MYT-TF activities could be explored to delay/prevent beta-cell failure and the development of type 2 diabetes. C_LI

cell biology↗

Hydrophobic tuning with non-canonical amino acids in a copper metalloenzyme

Hydrophobicity controls many aspects of protein and enzyme function. Although hydrophobic tuning can be achieved to a limited extent with canonical amino acids, the incorporation of non-canonical amino acids (ncAAs) further extends this ability to enable new and improved functionality. Herein, we engineer an aminoacyl-tRNA synthetase/tRNA pair for the site-specific genetic encoding of a set of bulky, hydrophobic amino acids, namely cyclopentylalanine, cyclohexylalanine, and cycloheptylalanine. With the resulting orthogonal translations systems, we demonstrate the utility of ncAA-based hydrophobic tuning to engineer a bacterial laccase, which is both a classical metalloenzyme and a high-value catalyst for industrial processes. The resulting mutations conveyed significant improvements in catalytic activity, particularly kcat and total turnover number. The redox potential and structure-function relationships were examined to elucidate the source of this improved functionality. We envision that these tools for hydrophobic tuning will be highly valuable for general enzyme engineering and also in other fields, including peptide chemistry.

synthetic biology↗

An integrated single-cell and spatial transcriptomic atlas of thyroid cancer progression identifies prognostic fibroblast subpopulations

Thyroid cancer progression from curable well-differentiated thyroid carcinoma to highly lethal anaplastic thyroid carcinoma is distinguished by tumor cell de-differentiation and recruitment of a robust stromal infiltrate. Combining an integrated thyroid cancer single-cell sequencing atlas with spatial transcriptomics and bulk RNA-sequencing, we define stromal cell subpopulations and tumor-stromal cross-talk occurring across the histologic and mutational spectrum of thyroid cancer. We identify distinct inflammatory and myofibroblastic cancer-associated fibroblast (iCAF and myCAF) populations and perivascular-like populations. The myCAF population is only found in malignant samples and is associated with tumor cell invasion, BRAFV600E mutation, lymph node metastasis, and disease progression. Tumor-adjacent myCAFs abut invasive tumor cells with a partial epithelial-to-mesenchymal phenotype. Tumor-distant iCAFs infiltrate inflammatory autoimmune thyroid lesions and anaplastic tumors. In summary, our study provides an integrated atlas of thyroid cancer fibroblast subtypes and spatial characterization at sites of tumor invasion and de-differentiation, defining the stromal reorganization central to disease progression.

cancer biology↗

Enzymatic epimerization of monoterpene indole alkaloids in Kratom

Monoterpene indole alkaloids (MIAs) are a large, structurally diverse class of bioactive natural products. These compounds are biosynthetically derived from a stereoselective Pictet-Spengler condensation that generates a tetrahydro-{beta}-carboline scaffold characterized by a 3S stereocenter. However, a subset of MIAs contain a non-canonical 3R stereocenter. Herein, we report the basis for 3R-MIA biosynthesis in Mitragyna speciosa (Kratom). We discover the presence of the iminium species, 20S-3-dehydrocorynantheidine, which led us to hypothesize that isomerization of 3S to 3R occurs by oxidation and stereoselective reduction downstream of the initial Pictet-Spengler condensation. Isotopologue feeding experiments implicated young leaves and stems as the sites for pathway biosynthesis, facilitating the identification of an oxidase/reductase pair that catalyzes this epimerization. This enzyme pair has broad substrate specificity, suggesting that the oxidase and reductase may be responsible for the formation of many 3R-MIAs and downstream spirooxindole alkaloids in Kratom. These enzymes allow biocatalytic access to a range of previously inaccessible pharmacologically active compounds.

biochemistry↗

Aberrant expression of histone H2B variants reshape chromatin and alter oncogenic gene expression programs

Chromatin architecture governs DNA accessibility and gene expression. Thus, any perturbations to chromatin can significantly alter gene expression programs and promote disease. Prior studies demonstrate that every amino acid in a histone is functionally significant, and that even a single amino acid substitution can drive specific cancers. We previously observed that naturally occurring H2B variants are dysregulated during the epithelial to mesenchymal transition (EMT) in bronchial epithelial cells. Naturally occurring H2B variants differ from canonical H2B by only a few amino acids, yet single amino acid changes in other histone variants (e.g., H3.3) can drive cancer. We therefore hypothesized that H2B variants might function like oncohistones, and investigated how they modify chromatin architecture, dynamics, and function. We find that H2B variants are frequently dysregulated in many cancers, and correlate with patient prognosis. Despite high sequence similarity, mutations in each H2B variant tend to occur at specific "hotspots" in cancer. Some H2B variants cause tighter DNA wrapping around nucleosomes, leading to more compact chromatin structures and reduced transcription factor accessibility to nucleosomal DNA. They also altered genome-wide accessibility to oncogenic regulatory elements and genes, with concomitant changes in oncogenic gene expression programs. Although we did not observe changes in cell proliferation or migration in vitro, our Gene Ontology (GO) analyses of ATAC-seq peaks and RNA-seq data indicated significant changes in oncogenic pathways. These findings suggest that H2B variants may influence early-stage, cancer-associated regulatory mechanisms, potentially setting the stage for oncogenesis later on. Thus, H2B variant expression could serve as an early cancer biomarker, and H2B variants might be novel therapeutic targets.

cancer biology↗

SATB2 and circ3915 RNA chromatin dysregulation drive KRAS-like oncogenic transformation

Even though epigenetic factors contribute to oncogenesis, most human cancer models still assume that disease originates from driver DNA mutations. Thus, it is still unclear if non-genetic mechanisms are sufficient to trigger malignant transformation. Special AT-rich binding protein 2 (SATB2) is a chromatin organizer that brings distal DNA elements into close proximity, thus remodeling chromatin structures to reprogram cell-specific and/or developmentally-sensitive gene networks. Here, we discover that SATB2 generates a co-expressed circ3915 RNA that is translated into a peptide and co-locates with SATB2 in the cell nucleus. Ectopic SATB2 or circ3915 over- expression rearranges global chromatin accessibility, generates KRAS- and NFE2L2-like oncogenic gene expression patterns, and transforms lung epithelial cells independent of driver mutations. Thus, oncogenic pathways can be activated in mammalian cells without pre-disposing mutations in oncogenes or epigenetic regulators. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=153 SRC="FIGDIR/small/616681v1_ufig1.gif" ALT="Figure 1000"> View larger version (32K): org.highwire.dtl.DTLVardef@1314b69org.highwire.dtl.DTLVardef@14df9e1org.highwire.dtl.DTLVardef@505bddorg.highwire.dtl.DTLVardef@1bf3fab_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

PoweREST: Statistical Power Estimation for Spatial Transcriptomics Experiments to Detect Differentially Expressed Genes Between Two Conditions

Recent advancements in Spatial Transcriptomics (ST) have significantly enhanced biological research in various domains. However, the high cost of current ST data generation techniques restricts its application in large-scale population studies. Consequently, there is a pressing need to maximize the use of available resources to achieve robust statistical power. One fundamental question in ST analysis is to detect differentially expressed genes (DEGs) among different conditions using ST data. Such DEG analysis is often performed but the associated power calculation is rarely discussed in the literature. To address this gap, we introduce, PoweREST (https://github.com/lanshui98/PoweREST), a power estimation tool designed to support power calculation of DEG detection with 10X Genomics Visium data. PoweREST enables power estimation both before any ST experiments or after preliminary data are collected, making it suitable for a wide variety of power analyses in ST studies. We also provide a user-friendly, program-free web application (https://lanshui.shinyapps.io/PoweREST/), allowing users to interactively calculate and visualize the study power along with relevant the parameters.

bioinformatics↗

Temporally discordant chromatin accessibility and DNA demethylation define short and long-term enhancer regulation during cell fate specification

Epigenetic mechanisms govern the transcriptional activity of lineage-specifying enhancers; but recent work challenges the dogma that joint chromatin accessibility and DNA demethylation are prerequisites for transcription. To understand this paradox, we established a highly-resolved timeline of DNA demethylation, chromatin accessibility, and transcription factor occupancy during neural progenitor cell differentiation. We show thousands of enhancers undergo rapid, transient accessibility changes associated with distinct periods of transcription factor expression. However, most DNA methylation changes are unidirectional and delayed relative to chromatin dynamics, creating transiently discordant epigenetic states. Genome-wide detection of 5-hydroxymethylcytosine further revealed active demethylation begins ahead of chromatin and transcription factor activity, while enhancer hypomethylation persists long after these activities have dissipated. We demonstrate that these timepoint specific methylation states predict past, present and future chromatin accessibility using machine learning models. Thus, chromatin and DNA methylation collaborate on different timescales to mediate short and long-term enhancer regulation during cell fate specification.

genomics↗

Dietary fiber content in clinical ketogenic diets modifies the gut microbiome and seizure resistance in mice

The gut microbiome is emerging as an important modulator of the anti-seizure effects of the classic ketogenic diet. However, many variations of the ketogenic diet are used clinically to treat refractory epilepsy, and how different dietary formulations differentially modify the gut microbiome in ways that impact seizure outcome is poorly understood. We find that clinically prescribed ketogenic infant formulas vary in macronutrient ratio, fat source, and fiber content and also in their ability to promote resistance to 6-Hz psychomotor seizures in mice. By screening specific dietary variables for their effects on a model human infant microbial community, we observe that dietary fiber, rather than fat ratio or source, drives substantial metagenomic shifts. Addition of dietary fiber to a fiber-deficient ketogenic formula restores seizure resistance, and supplementing protective ketogenic formulas with excess dietary fiber further potentiates seizure resistance. By screening 13 fiber sources and types, we identify distinct subsets of metagenomic responses in the model human infant microbial community that correspond with increased seizure resistance in mice. In particular, supplementation with seizure-protective fibers enriches microbial representation of genes related to queuosine biosynthesis and preQ0 biosynthesis and decreases representation of microbial genes related to sucrose degradation, which is also seen in seizure-protected mice that are fed fiber-containing ketogenic infant formulas. Overall, this study reveals that different formulations of clinical ketogenic diets, and dietary fiber content in particular, differentially impact seizure outcome in mice, likely through modification of the gut microbiome. Understanding interactions between dietary components of the ketogenic diet, the gut microbiome, and host susceptibility to seizures could inform novel microbiome-guided approaches to treat refractory epilepsy.

microbiology↗

Atf4 protects islet beta-cell identity and function under acute glucose-induced stress but promotes beta-cell failure in the presence of free fatty acid

Glucolipotoxicity, caused by combined hyperglycemia and hyperlipidemia, results in {beta}-cell failure and type 2 diabetes (T2D) via cellular stress-related mechanisms. Activating transcription factor 4 (Atf4) is an essential effector of stress response. We show here that Atf4 expression in {beta}-cells is dispensable for glucose homeostasis in young mice, but it is required for {beta}-cell function during aging and under obesity-related metabolic stress. Henceforth, aged Atf4-deficient {beta}-cells display compromised secretory function under acute hyperglycemia. In contrast, they are resistant to acute free fatty acid-induced loss-of identity and dysfunction. At molecular level, Atf4-deficient {beta}-cells down-regulate genes involved in protein translation, reducing {beta}-cell identity gene products under high glucose. They also upregulate several genes involved in lipid metabolism or signaling, likely contributing to their resistance to free fatty acid-induced dysfunction. These results suggest that Atf4 activation is required for {beta}-cell identity and function under high glucose, but this paradoxically induces {beta}-cell failure in the presence of high levels of free fatty acids. Different branches of Atf4 activity could be manipulated for protecting {beta}-cells from metabolic stress-induced failure. HighlightsO_LIAtf4 is dispensable in {beta}-cells in young mice C_LIO_LIAtf4 protects {beta}-cells under high glucose C_LIO_LIAtf4 exacerbate fatty acid-induced {beta}-cell defects C_LIO_LIAtf4 activates translation but depresses lipid-metabolism C_LI

genetics↗

Low-dose cryo-electron ptychography of proteins at sub-nanometer resolution

Cryo-transmission electron microscopy (cryo-EM) of frozen hydrated specimens is an efficient method for the structural analysis of purified biological molecules. However, cryo-EM and cryo-electron tomography are limited by the low signal-to-noise ratio (SNR) of recorded images, making detection of smaller particles challenging. For dose-resilient samples often studied in the physical sciences, electron ptychography - a coherent diffractive imaging technique using 4D scanning transmission electron microscopy (4D-STEM) - has recently demonstrated excellent SNR and resolution down to tens of picometers for thin specimens imaged at room temperature. Here we applied 4D-STEM and ptychographic data analysis to frozen hydrated proteins, reaching sub-nanometer resolution 3D reconstructions. We employed low-dose cryo-EM with an aberration-corrected, convergent electron beam to collect 4D-STEM data for our reconstructions. The high frame rate of the electron detector allowed us to record large datasets of electron diffraction patterns with substantial overlaps between the interaction volumes of adjacent scan positions, from which the scattering potentials of the samples were iteratively reconstructed. The reconstructed micrographs show strong SNR enabling the reconstruction of the structure of apoferritin protein at up to 5.8 [A] resolution. We also show structural analysis of the Phi92 capsid and sheath, tobacco mosaic virus, and bacteriorhodopsin at slightly lower resolutions.

biophysics↗

Scalable single-cell pooled CRISPR screens with conventional knockout vector libraries

Current methods for single-cell RNA profiling of pooled CRISPR screens are limited, either by indirect capture of single guide RNAs (sgRNAs) or by custom modification of plasmid libraries. Here, we present a direct sgRNA capture platform called Native sgRNA Capture and sequencing (NSC-seq) that enables single-cell CRISPR screens using common knockout plasmid libraries, facilitating genotype-phenotype mapping at multiple scales in vitro and in vivo. Additionally, we characterize sgRNA expression in three whole-genome knockout libraries, revealing a substantial subset of truncated (isoform) spacer reads. We provide this dataset as a reference of expressed sgRNA isoforms that may potentially have compromised CRISPR gene editing efficacy and precision.

genomics↗

Temporal recording of mammalian development and precancer

Key to understanding many biological phenomena is knowing the temporal ordering of cellular events, which often require continuous direct observations [1, 2]. An alternative solution involves the utilization of irreversible genetic changes, such as naturally occurring mutations, to create indelible markers that enables retrospective temporal ordering [3-8]. Using NSC-seq, a newly designed and validated multi-purpose single-cell CRISPR platform, we developed a molecular clock approach to record the timing of cellular events and clonality in vivo, while incorporating assigned cell state and lineage information. Using this approach, we uncovered precise timing of tissue-specific cell expansion during murine embryonic development and identified new intestinal epithelial progenitor states by their unique genetic histories. NSC-seq analysis of murine adenomas and single-cell multi-omic profiling of human precancers as part of the Human Tumor Atlas Network (HTAN), including 116 scRNA-seq datasets and clonal analysis of 418 human polyps, demonstrated the occurrence of polyancestral initiation in 15-30% of colonic precancers, revealing their origins from multiple normal founders. Thus, our multimodal framework augments existing single-cell analyses and lays the foundation for in vivo multimodal recording, enabling the tracking of lineage and temporal events during development and tumorigenesis.

developmental biology↗

Single-cell transcriptomics reveals heterogenous thymic dendritic cell subsets with distinct functions and requirements for thymocyte-regulated crosstalk

Dendritic cells are essential for establishing thymic central tolerance; however, mechanisms supporting their homeostasis and activation remain unresolved. Through single-cell transcriptomics and functional assays, we identify seven thymic conventional dendritic cell (cDC) subsets and discriminate their abilities to present self-antigens and induce regulatory T cells. Mice blocked at different stages of T-cell development reveal that CD4+ single-positive (SP) and CD8SP thymocytes differentially support homeostasis and activation of cDC1s versus cDC2s/plasmacytoid DCs (pDCs), respectively. CD8SPs indirectly support pDC survival and cDC2 thymic immigration, and they induce interferon signaling in cDCs, partly by promoting Type III interferon expression by medullary thymic epithelial cells (mTECs). In contrast, CD4SPs undergo cognate interactions with cDCs, inducing CD40 signaling required for activation of cDC1s. Activated cDC1s make non-redundant contributions to central tolerance. Altogether, this study comprehensively identifies distinct thymic DC subsets and elucidates requirements for crosstalk with thymocyte subsets that support their homeostasis, activation, and function.

immunology↗

ACE2 mimetic antibody potently neutralizes all SARS-CoV-2 variants and fully protects in XBB.1.5 challenged monkeys

The rapid evolution of SARS-CoV-2 to variants with improved transmission efficiency and reduced sensitivity to vaccine-induced humoral immunity has abolished the protective effect of licensed therapeutic human monoclonal antibodies (mAbs). To fill this unmet medical need and protect vulnerable patient populations, we isolated the P4J15 mAb from a previously infected, vaccinated donor, with <20 ng/ml neutralizing activity against all Omicron variants including the latest XBB.2.3 and EG.1 sub-lineages. Structural studies of P4J15 in complex with Omicron XBB.1 Spike show that the P4J15 epitope shares [~]93% of its buried surface area with the ACE2 contact region, consistent with an ACE2 mimetic antibody. Although SARS-CoV-2 mutants escaping neutralization by P4J15 were selected in vitro, these displayed lower infectivity, poor binding to ACE2, and the corresponding escape mutations are accordingly rare in public sequence databases. Using a SARS-CoV-2 XBB.1.5 monkey challenge model, we show that P4J15 confers complete prophylactic protection. We conclude that the P4J15 mAb has potential as a broad-spectrum anti-SARS-CoV-2 drug.

microbiology↗

The histone lysine demethylase KDM5C fine-tunes gene expression to regulate dendritic cell heterogeneity and function

The functional and phenotypic heterogeneity of dendritic cells (DCs) plays a crucial role in facilitating the development of diverse immune responses that are essential for providing host protection. We found that KDM5C, a histone lysine demethylase of the KDM5 family regulates several aspects of conventional DC (cDC) and plasmacytoid DC (pDC) population heterogeneity and function. Using mice conditionally deficient in KDM5C in DCs, we found that loss of KDM5C results in an increase in Ly6C- pDCs compared to Ly6C+ pDCs. We found that Ly6C- pDCs, compared to Ly6C+ pDCs, have increased expression of cell cycle genes, decreased expression of activation markers and limited ability to produce type I interferon (IFN). Both KDM5C-deficient Ly6C- and Ly6C+ pDCs have increased expression of activation markers, however, are dysfunctional and have limited ability to produce type I IFN. For conventional cDCs, KDM5C deficiency resulted in increased proportions of cDC2Bs (CLEC12A+, ESAM-) and cDC1s, which was partly dependent on type I IFN and pDCs. Using ATAC-seq, RNA-seq, and CUT&RUN for histone marks, we found that KDM5C regulates epigenetic programming of cDC1. In the absence of KDM5C, we found an increased expression of inflammatory markers, consistent with our previous results in bone marrow-derived DCs. However, we also found a decrease in mitochondrial metabolism genes and altered expression of cDC lineage-specific genes. In response to Listeria infection, KDM5C-conditionally deficient mice mounted reduced CD8+ T cell responses, indicating that KDM5C expression in DCs is necessary for their function. Thus, KDM5C is a key regulator of DC heterogeneity by modulating the balance of DC subsets and serves as a critical driver of the epigenetic programming and functional properties of DCs.

immunology↗

Uncovering and engineering the mechanical properties of the adhesion GPCR ADGRG1 GAIN domain

Key cellular functions depend on the transduction of extracellular mechanical signals by specialized membrane receptors including adhesion G-protein coupled receptors (aGPCRs). While recently solved structures support aGPCR activation through shedding of the extracellular GAIN domain, the molecular mechanisms underpinning receptor mechanosensing remain poorly understood. When probed using single-molecule atomic force spectroscopy and molecular simulations, ADGRG1 GAIN dissociated from its tethered agonist at forces significantly higher than other reported signaling mechanoreceptors. Strong mechanical resistance was achieved through specific structural deformations and force propagation pathways under mechanical load. ADGRG1 GAIN variants computationally designed to lock the alpha and beta subdomains and rewire mechanically-induced structural deformations were found to modulate the GPS-Stachel rupture forces. Our study provides unprecedented insights into the molecular underpinnings of GAIN mechanical stability and paves the way for engineering mechanosensors, better understanding aGPCR function, and informing drug-discovery efforts targeting this important receptor class.

biophysics↗