Jay Woo Shin

Background: Mast cells (MCs) are crucial in allergic and inflammatory responses, including in skin disorders. However, the transcriptional landscape of resting and stimulated skin MCs and the role of long non‐coding RNAs (lncRNAs) remain poorly characterized. Objective: To define FcεRI‐induced gene and promoter regulation in primary mast cells from human foreskin ( n = 5 cultures) and breast skin ( n = 2 cultures), assess tissue‐origin effects, identify novel lncRNAs, and evaluate MALAT1 function. Methods: Skin‐derived MCs were stimulated by FcεRI aggregation and subjected to Low Quantity single‐strand Cap Analysis of Gene Expression (LQ‐ssCAGE) sequencing. MALAT1 knockdown was achieved via antisense oligonucleotides. Functional evaluations included flow cytometry, caspase‐3 activity, cytokine secretome studies, and histamine release assays. Results: FcεRI cross‐linking induced considerable changes, with over 5000 genes and 6400 promoters being differentially regulated, also encompassing many novel MC‐enriched lncRNAs, e.g., CATG00000075668, CATG00000072979, and CATG00000048788. Selected cytokines were among the strongest responders, and their pattern was largely reproduced at the secretome level (e.g., GM‐CSF, IL‐5, TNF, LIF). Cell surface receptors like NTRK were likewise boosted. Moderate differences were noted between MCs from breast and foreskin, mainly affecting cytokines and tryptase isoenzymes. MALAT1 influenced the transcription of only few genes, but contributed to FcεRI‐triggered histamine release. Conclusion: FcεRI aggregation triggered widespread transcriptional reprogramming in skin MCs, also encompassing novel MC‐selective lncRNAs. The skin source made a modest contribution to FcεRI responsiveness, while MALAT1 fine‐tuned MC function. The study shows that lncRNAs can be successfully manipulated in primary tissue MCs to further determine the function of this new class of biomolecules.

Blood provides an accessible window into human health, yet the absence of a peripheral blood mononuclear cells (PBMCs) reference with standardized immune cell annotations has constrained comparisons between single-cell RNA sequencing (scRNAseq) studies. Here, we present HARP ( H uman Cell A tlas R eference for P BMCs), an integrated atlas of ∼9 million PBMCs from >2,600 donors across 15 studies spanning four continents, encompassing diverse populations, neonates to 97 years, across health and diverse immune-related diseases. We developed optimized integration workflows, including novel label-free metrics to assess integration quality, and generated community-driven consensus annotations for 192 immune cell subsets, identifying rare populations representing as few as 0.004% of PBMCs. HARP reveals coordinated cellular modules associated with age, sex, and disease, identifies female-biased interferon and inflammatory gene programs and their perturbation by COVID-19, and uncovers a novel sexual dimorphism in prostaglandin signaling. Finally, we introduce scTiger, a hierarchical label-transfer framework that accurately projects these 192 cell annotations onto ∼18 million additional PBMCs, providing a robust and transferable reference for harmonizing future PBMC studies. HARP provides a high-resolution community-driven reference atlas for PBMC annotation and analysis, as a basis for emerging clinical applications of single-cell genomics.

More than twenty years ago, the FANTOM consortium uncovered that mammalian genomes are pervasively transcribed, revealing multitudes of RNAs with unknown functions. A subset of these transcripts has since then been linked to transcriptional control and to chromatin organization via their ability to interact with DNA, suggesting that chromatin-associated RNAs could be key players in genome regulation. Although recent technological advances now enable the mapping of genome-wide RNA-DNA contacts, a lack of analyses integrating these methods with other genomic features and across multiple cellular contexts hinders our comprehensive understanding of the principles underlying RNA-DNA interactions and of their biological importance. As part of the FANTOM6 project, we thus generated RNA-DNA interaction maps in 16 different human cell types, then combined these contacts with multiple layers of other genomic data to investigate how patterns of interaction between RNA and DNA relate to chromatin organization and function. We show that the RNA-DNA interactome is highly dynamic yet reproducibly organized in cell-type specific networks, constituted of a great diversity of interactions that vary in function of their distance, the nature of their sources and the chromatin state of their targets. In particular, we detected numerous regulatory elements that exhibit marked changes in activity when differentially bound by transcripts, implying that thousands of RNA-DNA interactions can play a mechanistic role in gene expression. This regulatory function correlates with RNA-protein interactions and significantly associates with cell type-relevant and disorder-related traits. In addition to providing essential resources for future research in RNA-mediated chromatin regulation, cellular biology and human diseases, our study thus establishes the RNA-DNA interactome as a new genome regulatory layer that defines and maintains cellular identity and behavior.

Mainland Southeast Asia (MSEA) remains under-represented in global immunogenomic references despite its extensive genetic heterogeneity. We present the first single-cell immune atlas of an MSEA population, utilizing Thai individuals from the Asian Immune Diversity Atlas (AIDA) as a representative cohort. We demonstrate that the Thai population is highly genetically diverse, reflecting its history as a geographic nexus for Asian admixture. By integrating single-cell transcriptomics with high-resolution genotyping, we show that genetic ancestry significantly shapes innate immune profiles, specifically CD14⁺ monocytes, highlighting potential evolutionary adaptations to regional pathogens. We identify specific sex-by-ancestry interactions that may drive the baseline activation of pro-inflammatory pathways in females, providing a long-sought cellular rationale for the high prevalence of autoimmune disorders observed in Southeast Asian populations. Ultimately, our study reveals that population-specific genetic architecture dictates immune heterogeneity often missed by self-reported ethnicity or country of origin, providing a critical immunogenomic reference for precision medicine in MSEA regions.

Chimeric antigen receptor (CAR)-T cell therapy has transformed the treatment of B-cell malignancies, but its success in acute myeloid leukemia (AML) remains limited. Durable responses depend on the formation of long-lived memory T cells, whereas T cell exhaustion contributes to non-response and relapse. In patients with AML who achieved remission after cord blood transplantation, we here first observe enrichment of memory T cells with high expression of the chemokine receptor CXCR4. Next, we show that engineering CAR-T cells to co-express CXCR4 enhances their persistence and anti-leukemic activity in patient-derived xenograft models. Using single-cell profiling and metabolic analysis, we find that CXCR4 promotes memory-associated transcriptional programs, reduces exhaustion, and supports oxidative metabolism. These effects are observed with CAR-T cells targeting CD25 or CD96 as AML-associated targets. Our results indicate that CXCR4 strengthens CAR-T cell memory and durability, offering a strategy to improve immunotherapy outcomes in AML and beyond.

Dravet syndrome (DS) is a severe neurodevelopmental disorder associated with physical and cognitive impairments, often attributed to mutations in the SCN1A gene. However, gene regulatory features that modulate SCN1A expression found in vivo and in vitro models remain elusive. This study elucidates cell type-specific cis-regulatory elements (CRE) regulating SCN1A expression in cortical fast-spiking GABAergic inhibitory interneurons, the predominantly affected cell type in DS. We establish a differentiation protocol from human induced pluripotent stem cells (iPSCs) for both healthy control and DS patient-derived lines, followed by single-cell 5' RNA-seq at different stages of interneuron maturation. Through this analysis, we identify interneuron-enriched transcriptional start sites (TSSs) in cell type-restricted promoters regulated by a distinct set of transcription factors. Furthermore, we investigate SCN1A anti-sense (AS) transcripts and emphasize the importance of accurate 5' gene annotation in the context of developing targeted gene therapeutics. This work highlights the complexities and dynamics of studying DS at the molecular level and the need for comprehensive gene regulation analysis in vitro and ex vivo to enable precision medicine therapeutic approaches for DS.

Cell differentiation towards neurons is accompanied by widespread changes in three-dimensional (3D) genome organization and gene expression. Chromatin-associated RNAs have been proposed to be important regulators of such changes; however, the type, abundance, and role of these RNAs during neuronal differentiation remain largely unexplored. Here, we integrate multi-omic data generated in the frame of the Functional ANnoTation Of the Mammalian genome (FANTOM6) to chart 3D genome, RNA-DNA contactome, and transcriptome changes occurring during in vitro differentiation of human induced pluripotent stem cells to neural stem cells and neurons. We reveal a previously unreported phenomenon, in which intronic RNAs engage in long-distance contacts with DNA loci distributed all over the genome. These trans-contacting intronic RNAs (TIRs) are produced from exceptionally long (mean length: 750 kilobases, kb) protein-coding genes that carry ultra-long introns and are selectively expressed in neurons. We show that TIRs do not undergo rapid co-transcriptional degradation but rather accumulate in the nucleus of neuronal cells, forming large ‘dot clouds’ around their source loci and spreading across the nucleus, as visualized by single-molecule RNA fluorescence in situ hybridization. TIRs engage in contacts with a set of genomic regions (TIR-contacted regions or TIRCs) that carry much shorter (mean length: ∼30 kb) neuronally expressed genes forming high-connectivity hubs. We also show that the expression of genes within TIRCs contacted by the same set of TIRs is highly co-varied, and that TIR source genes, especially their introns, are enriched in genetic risk loci for neurodevelopmental and neuropsychiatric disorders. Our findings point to a functional role of the persistence of long intronic RNAs in the nucleus of neuronal cells and might contribute to explain why neurons uniquely express many ultra-long genes. We propose a model in which TIRs form pan-nuclear scaffolds—which we propose to name introsomes—that constitute a dynamically self-renewing regulatory layer, where transcription itself continuously regenerates the very scaffold that organizes genome function in neurons, and that might be involved in the pathogenesis of neurodevelopmental and neuropsychiatric disorders.

Single cell and spatial transcriptomics have dramatically changed how we can profile RNA from heterogenous biological samples. Combining single cell and spatial profiling with long read RNA-Seq promises to enable the discovery and quantification of individual RNA isoforms at the single-cell level. However, highly multiplexed data such as from a single cell experiment only generates a limited number of reads for each cell, constituting a major challenge for transcript discovery and quantification with existing approaches that usually have limited power for samples with low sequencing depth. Here we present Bambu-Clump, a computational method that performs transcript discovery and quantification from single cell and spatial long read RNA-Seq data using information from both each cell and the cell cluster. Using this approach, Bambu-Clump provides the most accurate transcript discovery compared to other existing methods, and improves transcript quantification compared to methods that rely on estimates derived from single cells. We apply Bambu-Clump to identify fusion transcripts in single-cells, compare 5’ and 3’ selection protocols, and identify novel isoform cell-type markers in spatial mouse brain data. Together, Bambu-Clump provides an easy-to-use, efficient, and accurate method for analysing individual isoform expression for single cells and cell clusters across multiple datasets and replicates from long read RNA-Seq.