Biology subjects

Tan, S. Y.

Publications and source records attributed to Tan, S. Y..

8 recordsLinked to original sources

bioRxiv2025

Dissecting regulatory syntax in human development with scalable multiomics and deep learning

Transcription factors (TFs) establish cell identity during development by binding regulatory DNA in a sequence-specific manner, often promoting local chromatin accessibility, and regulating gene expression. Mapping accessible chromatin offers critical insights into transcriptional control, but available datasets for human development are restricted to bulk tissue, single organs, or single modalities. Here, we present the Human Development Multiomic Atlas (HDMA), a single-cell atlas of chromatin accessibility and gene expression from 817,740 fetal cells across 12 organs, spanning 203 cell types and over 1 million candidate cis-regulatory elements, many of which exhibit organ-specific in vivo enhancer activity. Deep learning models trained to predict accessibility from local DNA sequence unravel a comprehensive lexicon of motifs which influence accessibility, including composite motifs exhibiting distinct syntactic constraints predicted to mediate TF cooperativity. We identify "hard" syntactic rules requiring precise motif spacing and orientation, "soft" rules allowing flexible motif arrangements, and ubiquitous motifs that inhibit accessibility. Model-based interpretation of genetic variants reveals that disruption of motifs with positive and negative effects is associated with concordant effects on gene expression. Our work delineates how motif syntax governs cell type-specific chromatin accessibility and provides a foundational resource for decoding cis-regulatory logic and interpreting genetic variation during human development.

genomics↗

bioRxiv2024

sc-SPLASH provides ultra-efficient reference-free discovery in barcoded single-cell sequencing

Typical high-throughput single-cell RNA-sequencing (scRNA-seq) analyses are primarily conducted by (pseudo)alignment, through the lens of annotated gene models, and aimed at detecting differential gene expression. This misses diversity generated by other mechanisms that diversify the transcriptome such as splicing and V(D)J recombination, and is blind to sequences missing from imperfect reference genomes. Here, we present sc-SPLASH, a highly efficient pipeline that extends our SPLASH framework for statistics-first, reference-free discovery to barcoded scRNA-seq (10x Chromium) and spatial transcriptomics (10x Visium); we also provide its optimized module for preprocessing and k-mer counting in barcoded data, BKC, as a standalone tool. sc-SPLASH rediscovers known biology including V(D)J recombination and cell-type-specific alternative splicing in human and trans-splicing in tunicate (Ciona) and when applied to spatial datasets, detects sequence variation including tumor-specific somatic mutation. In sponge (Spongilla) and tunicate (Ciona), we uncover secreted repeat proteins expressed in immune-type cells and regulated during development; the sponge genes were absent from the reference assembly. sc-SPLASH provides a powerful alternative tool for exploring transcriptomes that is applicable to the breadth of lifes diversity.

bioinformatics↗

bioRxiv2024

IFNγ-Expressing Myeloid Cells Localize within Lipoproteinosis during Drug-Associated Pulmonary Alveolar Proteinosis occurring in Systemic Juvenile Idiopathic Arthritis

In the United States, approximately one in 1000 children are diagnosed with the autoinflammatory disease, Juvenile Idiopathic Arthritis (JIA). A subset of JIA cases manifests as Systemic JIA (sJIA), which is characterized by joint pain, fevers, rashes, and systemic inflammation. Severe pulmonary complications have not historically been associated with sJIA. Since 2010, inhibitors of interleukin-1 and interleukin 6 (IL-1i/IL-6i) are the recommended course of treatment for sJIA, yet recently studies show evidence of a severe drug hypersensitivity reaction implicating these medications in a subset of those treated. With this reaction, sJIA patients can develop severe lung disease, including pulmonary alveolar proteinosis (PAP). As this drug-associated lung disease has only recently been identified, the etiology of sJIA drug-associated PAP (sJIA-daPAP) is poorly understood. We used multiplexed ion beam imaging by time-of-flight (MIBI-TOF) to define the cellular immune infiltrate and describe pathological features of PAP in sJIA-daPAP patients. We found an enrichment of eosinophils, neutrophils, and M2 macrophages within regions of lipoproteinosis. These enriched subsets all upregulate IFN{gamma} within lipoproteinosis, a signature specific to sJIA-daPAP samples compared to non-sJIA-PAP samples. In a cellular neighborhood analysis, we identified that eosinophils, neutrophils and M2 macrophages frequently co-localize within the same cellular microenvironment, especially in lipoproteinosis regions. Therefore, this spatial coordination may be involved in clearance or persistence of lipoproteinosis in sJIA-daPAP. This study provides a comprehensive overview of sJIA-daPAP immune pathology and suggests cellular mechanisms that drive inflammation in sJIA patients experiencing pulmonary complications associated with delayed drug hypersensitivity during IL-1i/IL-6i treatment.

immunology↗

bioRxiv2023

Dysregulated expression of Hoxa1 isoforms in hematopoietic stem and progenitor cells causes myelodysplastic syndromes.

The homeobox gene, Hoxa1, has two different isoforms generated by alternative splicing: a full-length homeodomain-containing Hoxa1 (Hoxa1-FL), and a truncated Hoxa1 (Hoxa1-T), that lacks the homeodomain. The effects of the distinct Hoxa1 isoforms in hematopoiesis have not been investigated. Oncoretroviral studies revealed that Hoxa1-T acts in a dominant negative manner, regulating transcriptionally active Hoxa1. Oncoretroviral overexpression of wildtype Hoxa1 (WT-Hoxa1), which generates both Hoxa1 isoforms, in murine hematopoietic stem and progenitor cells (HSPCs) perturbed hematopoiesis, resulting in transplantable myelodysplastic syndromes (MDS) in mice. Overexpression of a mutated Hoxa1 cDNA (MUT-Hoxa1) that generates Hoxa1-FL, but not Hoxa1-T, led to a more severe MDS that transformed to secondary acute myeloid leukemia (sAML). DNA damage repair pathways were downregulated in Hoxa1-overexpressing hematopoietic progenitor cells, accompanied by increased {gamma}H2AX foci. In silico analyses revealed that CD34+ cells from approximately 50% of patients with MDS had elevated HOXA1-FL expression. Conditional knock-in WT-Hoxa1 and MUT-Hoxa1 mice were generated and had features of pre-MDS, developing altered hematopoiesis within 4 months of Hoxa1 isoform overexpression in HSPCs. HSPCs were significantly reduced in all knock-in mice, accompanied by significantly increased apoptosis in WT-Hoxa1 HSPCs. Healthy wildtype recipients transplanted with bone marrow cells from Hoxa1 knock-in mice developed trilineage MDS, with Hoxa1 isoform and gene dosage dependent phenotypes. Collectively our data identify a role for HOXA1 in the pathogenesis of MDS. Our Hoxa1 mouse models capture different stages of progression of disease from pre-MDS to MDS to sAML and provide novel, clinically relevant tools to study MDS. Key pointsHOXA1 is upregulated in approximately 50% of MDS patient CD34+ BM cells, highlighting a potential role for HOXA1 in the pathogenesis of MDS. Dysregulated expression of Hoxa1 isoforms in murine hematopoietic stem and progenitor cells predisposes mice to pre-MDS and MDS.

cancer biology↗

bioRxiv2021

Transcriptomic Analysis of 3D Vasculature-On-A-Chip Reveals Paracrine Factors Affecting Vasculature Growth and Maturation

In vitro models of vasculature are of great importance for modelling vascular physiology and pathology. However, there is usually a lack of proper spatial patterning of interacting heterotypic cells in conventional vasculature dish models, which might confound results between contact and non-contact interactions. We use a microfluidic platform with structurally defined separation between human microvasculature and fibroblasts to probe their dynamic, paracrine interactions. We also develop a novel, versatile technique to retrieve cells embedded in extracellular matrix from the microfluidic device for downstream transcriptomic analysis, and uncover growth factor and cytokine expression profiles associated with improved vasculature growth. Paired receptor-ligand analysis further reveals paracrine signaling molecules that could be supplemented into the medium for vasculatures models where fibroblast co-culture is undesirable or infeasible. These findings also provide deeper insights into the molecular cues for more physiologically relevant vascular mimicry and vascularized organoid model for clinical applications such as drug screening and disease modeling.

bioengineering↗

bioRxiv2021

RNA splicing programs define tissue compartments and cell types at single cell resolution

More than 95% of human genes are alternatively spliced. Yet, the extent splicing is regulated at single-cell resolution has remained controversial due to both available data and methods to interpret it. We apply the SpliZ, a new statistical approach that is agnostic to transcript annotation, to detect cell-type-specific regulated splicing in > 110K carefully annotated single cells from 12 human tissues. Using 10x data for discovery, 9.1% of genes with computable SpliZ scores are cell-type specifically spliced. These results are validated with RNA FISH, single cell PCR, and in high throughput with Smart-seq2. Regulated splicing is found in ubiquitously expressed genes such as actin light chain subunit MYL6 and ribosomal protein RPS24, which has an epithelial-specific microexon. 13% of the statistically most variable splice sites in cell-type specifically regulated genes are also most variable in mouse lemur or mouse. SpliZ analysis further reveals 170 genes with regulated splicing during sperm development using, 10 of which are conserved in mouse and mouse lemur. The statistical properties of the SpliZ allow model-based identification of subpopulations within otherwise indistinguishable cells based on gene expression, illustrated by subpopulations of classical monocytes with stereotyped splicing, including an un-annotated exon, in SAT1, a Diamine acetyltransferase. Together, this unsupervised and annotation-free analysis of differential splicing in ultra high throughput droplet-based sequencing of human cells across multiple organs establishes splicing is regulated cell-type-specifically independent of gene expression.

bioinformatics↗

bioRxiv2020

Neutralizing antibodies from early cases of SARS-CoV-2 infection offer cross-protection against the SARS-CoV-2 D614G variant.

The emergence of a SARS-CoV-2 variant with a point mutation in the spike (S) protein, D614G, has taken precedence over the original Wuhan isolate by May 2020. With an increased infection and transmission rate, it is imperative to determine whether antibodies induced against the D614 isolate may cross-neutralize against the G614 variant. In this report, profiling of the anti-SARS-CoV-2 humoral immunity reveals similar neutralization profiles against both S protein variants, albeit waning neutralizing antibody capacity at the later phase of infection. These findings provide further insights towards the validity of current immune-based interventions. IMPORTANCERandom mutations in the viral genome is a naturally occurring event that may lead to enhanced viral fitness and immunological resistance, while heavily impacting the validity of licensed therapeutics. A single point mutation from aspartic acid (D) to glycine (G) at position 614 of the SARS-CoV-2 spike (S) protein, termed D614G, has garnered global attention due to the observed increase in transmissibility and infection rate. Given that a majority of the developing antibody-mediated therapies and serological assays are based on the S antigen of the original Wuhan reference sequence, it is crucial to determine if humoral immunity acquired from the original SARS-CoV-2 isolate is able to induce cross-detection and cross-protection against the novel prevailing D614G variant.

immunology↗

bioRxiv2019

Digital phenotyping by consumer wearables identifies sleep-associated markers of cardiovascular disease risk and biological aging

Despite growing adoption of consumer wearables, the potential for sleep metrics from these devices to contribute to sleep-related biomedical research remains largely uncharacterized. Here we analyze sleep tracking data, along with questionnaire responses and multi-modal phenotypic data, generated from 482 normal volunteers. First, we provide a detailed comparison of wearable-derived and self-reported sleep metrics, particularly total sleep time (TST) and sleep efficiency (SE). We then identified demographic, socioeconomic and lifestyle factors associated with wearable-derived sleep duration. We also analyzed our multi-modal phenotypic data and showed that wearable-derived TST and SE are associated with various cardiovascular disease risk markers, whereas self-reported measures were not. Using whole-genome sequencing data, we estimated leukocyte telomere length and showed that volunteers with insufficient sleep also exhibit premature telomere attrition. Our study highlights the potential for sleep metrics generated by consumer wearables to provide novel insights into data generated from population cohort studies.

epidemiology↗