Biology subjects

Cheng, P.

Publications and source records attributed to Cheng, P..

At least 19 recordsLinked to original sources

bioRxiv2026

An in vitro System for Studying Osteochondrogenic Differentiation of Smooth Muscle Cells and Modeling Intimal Vascular Calcification

Objective: Smooth muscle cells (SMCs) undergo phenotypic transitions during atherosclerosis, including towards a chondromyocyte (CMC) state associated with intimal calcification. Although standard in vitro calcification assays robustly reproduce mineral deposition, it remains unclear how well they recapitulate these disease-associated SMC states. We sought to define the CMC transcriptional phenotype in atherosclerosis and develop an in vitro system that faithfully reproduces it. Approach and Results: We firstly identified a CMC transcriptional signature in murine and human atherosclerotic plaque through single-cell RNA-sequencing, and spatial transcriptomics. CMCs showed a conserved osteochondrogenic program which localized within plaques and adjacent to calcified regions. We then developed an osteochondrogenic differentiation (OCD) assay by combining well-established calcification components with a high-density SMC micromass culture and TGF-{beta}1 supplementation and benchmarked it against a standard calcification (SC) assay using calcium quantification and bulk RNA-sequencing. Despite comparable calcification, OCD and SC resulted in distinct transcriptional states, with OCD showing preferential upregulation of osteochondrogenic programs, and a higher CMC signature score. Additionally, OCD upregulated genes with a stronger enrichment near coronary artery disease (CAD)-associated loci. These responses were reproducible across several primary human SMC lines. Timecourse analysis also showed that chondrogenic programs preceded calcification and showed directional concordance with the inferred in vivo SMC-to-CMC trajectory. To interrogate regulatory pathways controlling this process, we overexpressed the chondrogenic regulator SOX9, which enhanced cartilage and extracellular matrix programs while repressing inflammatory pathways. Finally, we examined 552 CAD-associated genes nominated across five genome-wide association studies. Of these, 240 were differentially expressed by day 12, and included established SMC regulators as well as a number of candidates not previously characterized in osteochondrogenic SMC transition. Conclusions: The OCD assay results in a strong calcification phenotype together with a disease-associated CMC-like transcriptional state, providing a reliable in vitro model for mechanistic investigation of SMC phenotypic transition and prioritization of candidate regulators.

cell biology↗

bioRxiv2026

Transcriptomic, Specific Marker, and Pathway Analysis of Smooth Muscle Cell Foam Cells Compared to Macrophage Foam Cells in Human Atherosclerosis

BACKGROUNDSmooth muscle cells (SMCs) are reported to contribute the majority of cholesterol-overloaded foam cells in human and mouse atheromas. However, the transcriptome, specific markers, and biologic itinerary of SMC foam cells relative to macrophage foam cells have not been determined. METHODSTranscriptomic analysis by single cell RNA sequencing (scRNA-seq) was performed on fresh coronary segments from heart transplant recipients with early to intermediate stage atherosclerosis. The gene expression pattern of a putative cluster of SMC foam cells was compared to those of cultured SMCs loaded with either aggregated low density lipoprotein (agLDL) or cholesterol bound to methyl-{beta}-cyclodextrin (Chol-M{beta}CD). Candidate markers of SMC foam cells not expressed by macrophage foam cells were validated in ours and publicly available datasets, by spatial transcriptomics and by immunofluorescence microscopy of human atheromas. Pathway analysis was performed using Gene Set Enrichment Analysis Hallmark gene sets. RESULTSSMC foam cells derived from fibromyocytes were tentatively identified using a panel of markers upregulated with in vitro cholesterol loading of SMCs. agLDL loading reproduced the same transcriptional profile, whereas Chol-M{beta}CD did not reproduce any in vivo SMC state. Top genes highly represented in SMC foam cells included SERPINE1, encoding plasminogen activator inhibitor 1 (PAI-1) and CFH, complement factor H, which were validated in further human coronary scRNA-seq datasets, by Xenium spatial transcriptomics, and by immunofluorescence microscopy. Relative to macrophage foam cells, SMC foam cells exhibit a distinct biologic itinerary, including activation of extracellular matrix, coagulation and angiogenesis pathways. CONCLUSIONSSMC foam cells, which are derived from fibromyocytes ("lipomyocytes"), exhibit unique markers and biologic programs that differ markedly from macrophage foam cells in atherosclerotic plaque development. Further understanding of the role of lipomyocytes and their expression of CFH and PAI-1 expression in plaque biology may offer novel therapeutic options to reduce ischemic cardiovascular disease. Novelty and SignificanceO_ST_ABSWhat is Known?C_ST_ABSO_LISingle-cell transcriptomic studies have demonstrated vascular SMCs undergo extensive phenotypic modulation during atherosclerosis, giving rise to fibromyocytes and other intermediate cell states. C_LIO_LISMC-derived foam cells constitute a major proportion of plaque foam cells. C_LIO_LIPrevious studies have shown that SMC-derived foam cells differ from macrophage-derived foam cells in cholesterol handling and lipid metabolism, making their identification using conventional macrophage-associated foam-cell markers challenging, and highlighting the need for SMC foam cell-specific molecular markers. C_LI What New Information Does This Article ContributeO_LIBy integrating published transcriptomic datasets with bulk RNA-sequencing of agLDL-loaded human SMCs, we identify the transcriptional program of human SMC-derived foam cells and demonstrate that these cells are embedded within the fibromyocyte population rather than forming a distinct cell cluster. C_LIO_LIagLDL loading in vitro reproduces the in vivo SMC foam-cell phenotype, whereas loading with cholesterol bound to cyclodextrin induces an inflammatory state not found in any in vivo SMC state in human atherosclerosis. C_LIO_LICFH and SERPINE1 were identified as specific markers of SMC-derived foam cells and validated by immunostaining and Xenium spatial transcriptomics, providing robust markers for identification of these cells in human atherosclerotic plaques. C_LIO_LIThe top transcriptional programs activated in SMC foam cells differ completely from macrophage foam cells and include extracellular matrix remodeling, complement regulation, coagulation and angiogenesis. C_LI In this study, we mapped smooth muscle foam cells to the fibromyocyte cluster of arterial SMC subtypes in human coronary artery atheromas. In vitro loading of smooth muscle cells with aggregated low-density lipoprotein, the presumed physiologic substrate for foam cell formation during plaque development, induced a gene expression pattern that localized to the same fibromyocyte cluster. The proposed sequence of SMC foam cell formation is that fibromyocytes present in human pre-atherosclerotic intima generate the proteoglycans that bind lipoproteins and allow their uptake by fibromyocytes to generate cholesterol-loaded "lipomyocytes". Lipid loading of fibromyocytes drives expression of specific markers and transcriptional programs, but with an overall gene expression pattern that continues to resemble fibromyocytes. We demonstrate here that lipomyocytes express the specific markers CFH and SERPINE1, and exhibit activation of a completely different set of pathways relative to macrophage foam cells in the plaque. These findings provide evidence for the unique phenotype and specific markers of lipomyocytes relative to macrophage foam cells in human atherosclerosis, which will be critical in evaluating the response of these different types of foam cell to novel therapies.

genomics↗

bioRxiv2026

MYC pathway reprogramming through a TIP60 coactivator switch in neuroendocrine lineage transition in prostate cancer

Prostate adenocarcinomas (PRAD) can acquire resistance to androgen receptor signaling inhibitors through lineage transition to a cell state known as neuroendocrine prostate cancer (NEPC). Using a panel of isogenic PRAD and NEPC mouse tumoroids, we show that NEPC cells acquire new transcription factor (TF) dependencies that function in a previously undefined network. Through selective perturbation of each TF, we identify ASCL1 as a key regulator of NE lineage fate whereas MYCL functions downstream to drive NEPC growth/survival by recruitment of the TIP60/KAT5 acetyltransferase. Interestingly, while dependencies on specific TF family paralogs can vary across NEPC models, all show markedly enhanced dependency on TIP60. Moreover, the H2A.Z-acetyltransferase activity of the TIP60 complex (TIP60-C) is required for NEPC as well as the acetyl-reader BRD8, which is newly incorporated as a TIP60-C subunit with the NEPC transition. Targeted degradation studies in isogenic tumoroids reveal increased dependence on MYCL in NEPC relative to its paralog MYC in PRAD. In addition to a paralog switch (MYC to MYCL), the MYC pathway-addicted NE state is accompanied by a chaperone switch (from TIP60-C to SRCAP) for H2A.Z histone exchange and a coactivator switch (to TIP60) for MYC target gene expression. The NE-specific coupling of MYCL with TIP60 reveals a previously unappreciated opportunity to target MYC-driven NE diseases through pharmacological inhibition of TIP60.

cancer biology↗

bioRxiv2026

Functional Landscape of Motifs within the Sarbecovirus Spike Cytoplasmic Tail

Sarbecoviruses exhibit extensive diversity in host range and zoonotic potential. Although the ectodomain of the viral spike protein has been well characterized, the functional landscape of the cytoplasmic tail (CT) remains poorly defined. To address this gap, we systematically generated CT truncation variants of representative spike proteins from all major ACE2-utilizing clades to define the roles of conserved host factor-interacting motifs associated with COPI, COPII, FERM, and SNX27. Using vesicular stomatitis virus (VSV)- and lentivirus-based pseudotyping systems, we evaluated viral entry in cells expressing varying levels of ACE2 and TMPRSS2. Our results demonstrate that CT-associated motifs differentially regulate viral infectivity. Specifically, truncation of the COPI- or SNX27-binding motifs markedly reduces entry efficiency, whereas disruption of the COPII-binding motif produces the opposite outcome. By contrast, removal of the FERM-binding motif consistently enhances infectivity across lineages. Mechanistically, truncation of this motif increases spike expression, cell surface localization, incorporation into virions, and particle stability. Importantly, despite these pronounced effects on viral infectivity, deletion of the FERM-binding motif does not affect antigenicity, receptor dependence, or sensitivity to protease inhibitors, as demonstrated by neutralization and inhibition assays. In addition, this approach substantially increases spike protein density on virus-like particles (VLPs). Collectively, by extending the analysis beyond SARS-CoV-1 and SARS-CoV-2, our study reveals a generalizable mechanism in which cytoskeletal anchoring mediated by the FERM-binding motif acts as a limiting determinant of viral assembly. These findings provide a practical framework for optimizing pseudovirus platforms and guiding vaccine development against emerging viral threats.

microbiology↗

bioRxiv2026

Z-RNA-ZBP1 axis drives Tau-mediated neurodegeneration

Although the causes of Tau aggregates vary, once Tau aggregates are formed, their neurotoxicity significantly contributes to neuronal death and cognitive decline in tauopathies, with Alzheimers disease (AD) being the most well-known example. Despite its central pathogenic role, however, effective therapeutic strategies targeting neurotoxicity of Tau remain poor. Here we demonstrate the pathogenic role of neuronal cell death in Tau-related neurodegeneration. Tau-expressing neurons undergo cell death through Z-DNA-binding protein 1 (ZBP1) activation triggered by endogenous Z-RNAs. These Z-RNAs are derived from reactivated transposable elements (TEs) that are typically silenced within heterochromatin. Tau aggregates show a strong affinity for H3K9me3-modified chromatin, effectively sequestering these epigenetic marks from Heterochromatin Protein 1 (HP1), thereby disrupting the condensation of constitutive heterochromatin. Clinically, an inverse correlation between ZBP1 expression levels in excitatory neurons and cognitive performance in AD patients was observed. Importantly, Zbp1 haploinsufficiency significantly ameliorated cognitive deficits in aged Tau-transgenic mice (24-month-old), highlighting the therapeutic potential of ZBP1 inhibition to strive against neurodegeneration in tauopathies.

neuroscience↗

bioRxiv2025

A Hybridization-Based Novel DNA Storage Technology with Rapid Read Performance

The development of traditional silicon-based microelectronic storage media has increasingly lagged behind the rapidly growing demands of contemporary data storage. DNA storage, with its ultra-high information density and long-term preservation advantages, has rapidly become a research hotspot for next-generation storage technologies. However, current mainstream DNA storage methods based on synthesis and sequencing suffer from slow read/write speeds, hindering practical applications. To address this limitation, we propose an innovative hybridization-based DNA storage scheme. Through principle validation experiments, short-text read/write and error-correction tests, and high-density multi-format file storage experiments, we verify the feasibility of this approach. The proposed method exhibits high parallelism, rapid read speeds, and robust encryption capabilities, demonstrating promising application prospects in scenarios such as confidential data storage.

synthetic biology↗

bioRxiv2025

Chronic Electronic Cigarette Exposure Promotes Atherosclerosis and Chondrogenic Modulation of Smooth Muscle Cells

BackgroundElectronic cigarette (E-cig) use has reached epidemic proportions worldwide, yet its cardiovascular consequences remain poorly defined. While several lines of evidences in human epidemiological and animal studies suggest chronic aerosol exposure accelerates atherosclerosis; the cellular and molecular mechanisms underlying this pathological remain unknown. MethodsWe exposed hyperlipidemic mice to chronic e-cigarette aerosol inhalation and characterized the plaque cellular landscape by coupling SMC lineage tracing with single-cell transcriptomic/epigenomic profiling and histologic phenotyping. We subsequently leveraged human coronary artery smooth muscle cells (HCASMCs) to validate in vivo discovery and identified E-cig specific pathological signaling pathways relevant to human vascular disease risk. ResultsChronic E-cig aerosol exposure accelerated atherosclerosis, increasing both SMC phenotypic modulation and plaque macrophage burden in a lipid-independent manner. Transcriptomically, SMCs are particularly more sensitive to E-cig than other vascular cell types. E-cig exposure reprogrammed SMCs toward a pro-calcifying, chondrogenic phenotype, thereby enhancing vascular ossification in vivo and in HCASMCs in vitro. Mechanistically, E-cig mediated SMC fate alteration occurs through activation of a glutamatergic/NMDAR signaling program, that increased NMDAR-dependent Ca2+ influx in a GRIN2A dependent manner. Notably, inhibition of GRIN2A mediated signaling reversed E-cig-induced pathological shifts in SMC phenotype. ConclusionsSMC chondrogenic reprogramming and subsequent vascular calcification are central to the detrimental cardiovascular consequences of E-cig exposure. Our findings implicate a GRIN2A-dependent glutamatergic/NMDAR signaling axis in SMC as a primary driver of this calcifying remodeling program. These findings define a SMC-specific vulnerability to E-cig aerosols and establish the GRIN2A/NMDAR pathway as potential therapeutic targets for mitigating E-cig-associated cardiovascular disease.

genomics↗

bioRxiv2025

C/EBPβ-mediated PARP1 Suppression Drives Tumor Progression of Aneuploid Cells

Aneuploidy--defined as gains and losses of chromosomes--is frequently observed in cancer and has been implicated in promoting tumor progression and metastasis. However, the molecular mechanisms underlying this phenomenon remain poorly understood. By generating new models of aneuploidy, we found that aneuploidy confers remarkable resistance to reactive oxygen species (ROS)-mediated cell death. This resistance is a general consequence of aneuploidy, independent of the specific chromosomes gained or lost. Mechanistically, Poly(ADP-Ribose) Polymerase 1 (PARP1) is suppressed in aneuploid cells, which inhibits PARP1-mediated cell death after ROS (parthanatos). We validated aneuploidy-associated PARP1 suppression across 15 cell models and human tumors, with pronounced effects in metastatic tumors. Importantly, decreased PARP1 levels promote tumor metastasis while increased PARP1 suppresses it. Through a genome-wide CRISPR screen and functional validation, we identified the transcription factor CCAAT/enhancer-binding protein beta (CEBPB) as a critical mediator of PARP1 downregulation and ROS resistance in aneuploid cells. Furthermore, we found that lysosomal dysfunction serves as the upstream mediator of CEBPB activation in aneuploid cells. We propose that aneuploidy-driven CEBPB activation promotes PARP1 suppression, fostering ROS resistance and cancer progression. HighlightsO_LIAneuploidy confers resistance to oxidative stress independent of p53 status, karyotype and cell lineage through inhibition of PARP1 expression and activity C_LIO_LISuppressed PARP1 enhances metastatic potential, while PARP1 restoration suppresses metastatic spread, revealing a novel mechanism linking aneuploidy to cancer progression. C_LIO_LIPARP1 suppression compromises DNA damage repair and cell death to multiple genotoxic stressors, including reactive oxygen species, alkylating agents, and UV radiation. C_LIO_LIA genome-wide CRISPR screen and a CRISPRa screen identifies CEBPB as a critical transcription factor mediating PARP1 regulation and ROS resistance. C_LIO_LINuclear CEBPB increases significantly after aneuploidization in experimental systems and in primary human cancers. C_LI O_FIG O_LINKSMALLFIG WIDTH=195 HEIGHT=200 SRC="FIGDIR/small/670212v2_ufig1.gif" ALT="Figure 1"> View larger version (63K): org.highwire.dtl.DTLVardef@1bf4edforg.highwire.dtl.DTLVardef@d3311eorg.highwire.dtl.DTLVardef@13daf25org.highwire.dtl.DTLVardef@b5e65f_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

Metrics for studying the porous void space of packed particles

Characterizing porosity in packed particle assemblies is a complex task that requires advanced analytical tools. We present a visually rich and extensive library of global, pore-based, and other metrics for analyzing features of porosity in such assemblies. Our library includes over 25 descriptors of "3D pores" that are identified using our LOVAMAP software. By applying our metrics to a set of simulated packings that vary by particle size, shape, and stiffness, we reveal predictable relationships between particle and void space characteristics. We identify two fundamental parameters of a monodisperse particle system - particle diameter ({delta}) and void volume fraction ({phi}) - that govern several void space features, such as the total number of bottlenecks (i.e., doors between pores), the median value of the largest enclosed sphere across all pores in a packing, and the fraction of reaction-center "hotspots." Through regression analyses on transformations of{delta} and{phi} , we quantify multiple packing-descriptor relationships, demonstrating, for example, that packing properties scale linearly with the median values of length-based descriptors across assemblies. We further introduce approaches for computing the number of vertices, edges, and faces of 3D pores, allowing for approximation to simpler polyhedra. Additional metrics explore surface entrances into the particle scaffold, traversable paths through the void space, and size-based accessibility. Together, these descriptors, which have been bundled into LOVAMAP, offer new insights into particle-pore architecture and spatial organization.

bioengineering↗

bioRxiv2025

NLRP1 inflammasome activation in skin equivalents revealsmechanistic insights into the roles of keratinocytes in psoriasis

Psoriasis is a major inflammatory skin disease for which a causal therapy is still not available. The pro-inflammatory cytokines interleukin(IL)-1{beta} and IL-36{gamma} are key drivers of the disease phenotype, but the mechanisms underlying their regulation in psoriasis remain poorly understood. Generation of IL-1{beta} activity is regulated by protein complexes, termed inflammasomes. We activated the NLRP1 inflammasome in human keratinocytes cultivated in three-dimensional skin equivalents. NLRP1 activation induced histological and molecular features that are highly reminiscent of psoriasis. Mechanistically, the phenotype was dependent on IL-1, which triggered a pro-inflammatory epidermal-dermal crosstalk. This included induction of expression of IL-36{gamma}, which, together with IL-1{beta}, was released from keratinocytes through NLRP1-induced gasdermin D pores. The in vivo relevance of these findings is reflected by the expression of the NLRP1 sensor and signs of inflammasome activation in lesional skin of psoriatic patients. Finally, we discovered endogenous cytoplasmic double stranded (ds) RNA, recently associated with cellular perturbations in psoriasis, as a novel activator of the NLRP1 inflammasome in human keratinocytes. Our results identify a novel endogenous double-stranded RNA-mediated NLRP1-IL-1-IL-36{gamma} signaling axis relevant in psoriasis and suggest targeting of this pathway as a promising treatment strategy.

immunology↗

bioRxiv2025

Vascular smooth muscle cell atherosclerosis trajectories characterized at single cell resolution identify causal transcriptomic and epigenomic mechanisms of disease risk

Vascular smooth muscle cells (SMC) contribute to heritable coronary artery disease (CAD) risk and undergo complex cell state transitions to multiple disease related phenotypes. To investigate the genetic basis of SMC state trajectories that underlie the SMC component of CAD causality we have developed a dense timecourse single cell transcriptomic and epigenetic map of atherosclerosis in a murine disease animal model. Cellular trajectories were derived from the temporal data and probabilistic fate modeling with Waddington-Optimal Transport (WOT). We created transcription factor (TF) centered regulons mapped across the developmental timeline and through network-based prioritization with WOT predicted TFs and in silico TF perturbation, identified key drivers of cell state changes associated with EMT, vascular development, and circadian clock functions. Integration of mouse disease data with human CAD genetic findings identified transition SMC phenotypes that mediate disease risk and point to causal disease mechanisms. Parallel studies using knockout of the validated CAD gene Tcf21 revealed its impact on SMC transition cellular phenotypes and disease risk genes, due in part to a role regulating the transition of SMC precursor cells in the secondary heart field. Together, these studies characterize atherosclerosis trajectories at single cell resolution and identify genetic causal transcriptomic and epigenomic mechanisms of CAD risk.

genomics↗

bioRxiv2025

National Scale Genomic Engine for Precision Medicine: Singapore PRECISE-SG100K Experience

The whole-of-nation National Precision Medicine (NPM) programme in Singapore aims to integrate a genomics backbone into standard healthcare. Phase II recently completed the sequencing of 102,202 genomes from the diverse Asian population of Singapore, generating the PRECISE-SG100K dataset. The scaling from the pilot SG10K_Health phase to national production scale demanded a central shift: from earlier generation workflows to an integrated, industrial grade "Genomic Engine". The initiative was co-developed under a public-private partnership model. Our Genomic Engine was designed with an automation-first approach, as a modular platform linking a purpose-built, centralized biospecimen processing and DNA extraction facility (EXTRACT Lab), a high-throughput sequencing operation (Illumina Data Generation Infrastructure, IDGI), with the cloud-native analytics (GRIDS) running on a fully integrated PRECISE Sample Tracking System (STS). Here we describe the key design features of our Genomic Engine. Highlighting the Stress Test phase where the automated DNA extraction yields failed to meet expectations. We share the operational adjustments which were implemented to stabilize production and resulted in a three-fold reduction in sample triage due to improved DNA recovery. Without establishing the operational guardrails during the Stress Test, the Engine would not have reached a steady-state production evidenced by >3,000 genomes per month, median turnaround time 11 days, 99.6% operational success, within in six months. This framework offers a practical blueprint for other population-scale initiatives seeking to bridge the gap between scientific piloting and industrial delivery.

genomics↗

bioRxiv2025

Targeting Modulated Vascular Smooth Muscle Cells in Atherosclerosis via FAP-Directed Immunotherapy

Vascular smooth muscle cell (VSMC) and immune cell diversification play a central role in driving atherosclerotic coronary artery disease (CAD)1-3. However, the molecular mechanisms governing cell state transitions within the neo-intima in human CAD remain poorly understood, and no lipid-independent therapies are currently approved for its treatment. Here, we performed multi-omic single-cell gene expression profiling, epitope mapping, and spatial transcriptomics from 27 human coronary arteries. Our analysis identified fibroblast activation protein (FAP) as a marker of modulated VSMCs within the neo-intima. Genetic lineage tracing in mice confirmed that FAP cells in the plaque originate from medial VSMCs. Additionally, non-invasive positron emission tomography (PET) imaging in patients with CAD revealed focal FAP uptake in atherosclerotic lesions. Spatial transcriptomics further delineated the distinct localization of VSMC and immune cell subsets within plaques, with FAP states enriched in the neo-intima. To explore the therapeutic potential of targeting de-differentiated VSMCs, we developed an anti-FAP bispecific T-cell engager (BiTE) and demonstrated that it significantly reduced the plaque burden in multiple mouse models of atherosclerosis. Collectively, our study provides the first single-cell and spatially resolved map of human CAD, establishes FAP as a marker of modulated smooth muscle cells, and demonstrates the broader potential of immunotherapeutics for lipid independent targets in atherosclerotic CAD.

genomics↗

bioRxiv2025

Epigenome and transcriptome changes in KMT2D-related Kabuki syndrome Type 1 iPSCs, neuronal progenitors and cortical neurons

Kabuki syndrome type 1 (KS1) is a neurodevelopmental disorder caused by loss-of-function variants in KMT2D which encodes a H3K4 methyltransferase. The mechanisms underlying neurodevelopmental problems in KS1 are still largely unknown. Here, we track the epigenome and transcriptome across three stages of neuronal differentiation using patient-derived induced pluripotent stem cells (iPSCs) to gain insights into the disease mechanism of KS1. In KS1 iPSCs we detected significantly lower levels of functional KMT2D transcript and KMT2D protein, and lower global H3K4me1 and H3K4me2 levels. We identify loss of thousands of H3K4me1 peaks in iPSCs, neuronal progenitors (NPs) and early cortical neurons (CNs) in KS1. We show that the number of lost peaks increase as differentiation progresses. We also identify hundreds of differentially expressed genes (DEGs) in iPSCs, NPs and CNs in KS1. In contrast with the epigenomic changes, the number of DEGs decrease as differentiation progresses. Our analysis reveals significant enrichment of differentially downregulated genes in areas containing putative enhancer regions with H3K4me1 loss. We also identify a set of distinct transcription factor binding sites in differentially methylated regions and a set of DEGs related to KS1 phenotypes. We find that genes regulated by SUZ12, a subunit of Polycomb Repressive complex 2, are over-represented in KS1 DEGs at early stages of differentiation. In conclusion, we present a disease-relevant human cellular model for KS1 that provides mechanistic insights for the disorder and could be used for high throughput drug screening for KS1.

genetics↗

bioRxiv2024

A cell and transcriptome atlas of the human arterial vasculature

Contiguous arterial segments show different propensities for different vascular pathologies, yet mechanisms explaining these fundamental differences remain unknown. We sought to build a transcriptomic, cellular, and spatial atlas of human arterial cells across multiple different arterial segments to understand these underlying differences. Analysis of multiple isogenic arterial segments from healthy donors reveals a significant stereotyped pattern of cell type-specific segmental heterogeneity in healthy arteries. Combining single cell analysis with spatial transcriptomic data reveals cellular heterogeneity not captured by commonly used cell-type marker genes. Determinants of arterial transcriptomic identities are predominantly encoded in fibroblasts and smooth muscle cells (SMC), and their differentially expressed genes are particularly enriched for different vascular disease-associated genetic risk- loci and risk-genes. Adventitial fibroblast-specific heterogeneity in gene expression coincides with a disproportionally large number of vascular disease genetic signals, suggesting a previously unrecognized role for this cell type in disease risk. Adult arterial cells from different segments cluster not by anatomical proximity, but by embryonic origin. Global regulon analysis of disease related segment-specific gene expression program in fibroblast and SMC enriches for binding sites of transcription factors that are developmental master regulators whose expression persists into adulthood, suggesting an important functional role of the same developmental master regulators in adult gene expression and disease. Lastly, non-coding transcriptomes across arterial cells contain extensive variation in lncRNAs expressed in cell type- and segment-specific patterns, rivaling heterogeneity in protein coding transcriptomes. Differentially expressed LncRNA demonstrate enrichment for non-coding genetic signals for vascular diseases, suggesting a potential global role of segmental specific LncRNAs in regulating inherited human vascular disease risk.

cell biology↗

bioRxiv2024

Putting computational models of immunity to the test - an invited challenge to predict B. pertussis vaccination outcomes

Systems vaccinology studies have been used to build computational models that predict individual vaccine responses and identify the factors contributing to differences in outcome. Comparing such models is challenging due to variability in study designs. To address this, we established a community resource to compare models predicting B. pertussis booster responses and generate experimental data for the explicit purpose of model evaluation. We here describe our second computational prediction challenge using this resource, where we benchmarked 49 algorithms from 53 scientists. We found that the most successful models stood out in their handling of nonlinearities, reducing large feature sets to representative subsets, and advanced data preprocessing. In contrast, we found that models adopted from literature that were developed to predict vaccine antibody responses in other settings performed poorly, reinforcing the need for purpose-built models. Overall, this demonstrates the value of purpose-generated datasets for rigorous and open model evaluations to identify features that improve the reliability and applicability of computational models in vaccine response prediction.

immunology↗

bioRxiv2024

A natural language processing system for the efficient extraction of cell markers

1.BackgroundIn the last few years, single-cell RNA sequencing (scRNA-seq) has been widely used in various species and tissues. The construction of the cellular landscape for a given species or tissue requires precise annotation of cell types, which relies on the quality and completeness of existing empirical knowledge or manually curated cell marker databases. The natural language processing (NLP) technique is a potent tool in text mining that enables the rapid extraction of entities of interest and relationships between them by parsing the syntax structure. Methods and resultsWe developed MarkerGeneBERT, an NLP-based system designed to automatically extract information about species, tissues, cell types and cell marker genes by parsing the full texts of the literature from single-cell sequencing studies. As a result, 8873 cell markers of 1733 cell types in 435 human tissues/subtissues and 9064 cell markers of 1832 cell types in 492 mouse tissues/subtissues were collected from 3987 single-cell sequencing-related studies. By comparison with the marker genes of existing manual curated cell marker databases, our method achieved 76% completeness and 75% accuracy. Furthermore, within the same literature, we found 89 cell types and 183 marker genes for which the cell marker database was not available. Finally, we annotated brain tissue single-cell sequencing data directly using the compiled list of brain tissue marker genes from our software, and the results were consistent with those of the original studies. Taken together, the results of this study illustrate for the first time how systematic application of NLP-based methods could expedite and enhance the annotation and interpretation of scRNA-seq data.

bioinformatics↗

bioRxiv2023

Mitochondrial complex I as a diagnostic and therapeutic target in a mouse model of tauopathy

Dysfunction of the energy producing organelle of the cell, mitochondria, plays a pivotal role in Alzheimers disease (AD). We have recently used a novel positron emission tomographic (PET) imaging tracer targeting mitochondrial complex I (MC-I) to visualize mitochondrial abnormalities in the brains of living tau transgenic (TauTg) mice. MC-I mediates the first and limiting step in oxidative phosphorylation, the primary source of neuronal energy production. Here we used MC-I-PET to test if inhibition of mutant tau expression through transgene suppression with doxycycline could reverse mitochondrial defects in a mouse model of tauopathy and evaluate the efficacy of a MC-I-targeted candidate therapeutic, Mdivi-1. We found that late-stage suppression of mutant tau did not rescue mitochondrial deficits measured in vivo by MC-I-PET, despite reduced burden of tauopathy and neuroinflammation. These findings demonstrate that mitochondrial dysfunction may continue even if tauopathy is halted, particularly if initiated at late-stage disease. Further, we demonstrate the potential application of MC-I-PET for monitoring therapeutic efficacy, surprisingly finding detrimental effects of the mitochondrial-targeted candidate therapeutic, Mdivi-1, in TauTg mice. These findings directly contrast with the beneficial effects of Mdivi-1 observed in other models of neurodegeneration. Together, our findings highlight the need for clinical endpoints measuring mitochondrial damage in addition to markers of tauopathy in the assessment of disease prognosis and efficacy of candidate therapeutics and demonstrates the potential application of MC-I-PET to meet this need.

neuroscience↗