Our New Publication: Nature Genetic Cover Story
Tittle: “Single-cell RNA-seq of peripheral blood links cell-type-specific regulation of splicing to autoimmune and inflammatory diseases”
Alternative splicing is a critical process that transforms primary mRNA into mature mRNA, allowing the generation of distinct mRNA isoforms. These isoforms are subsequently translated into proteins with diverse functions. Understanding and quantifying alternative splicing events can provide valuable insights into their role in complex diseases. Splicing quantitative trait loci (sQTLs) are identified through linear models that assess whether single nucleotide polymorphisms (SNPs) are significantly associated with specific splicing events in the transcriptome [1].
To date, bulk RNA-sequencing in various tissues or organs has been widely applied to identify sQTLs, including studies on lymphoblastoid cell lines (LCLs), adipose tissue, and pancreatic islets [2-4]. Moreover, multi-tissue studies, such as the BLUEPRINT and DICE databases for blood cells and the GTEx database for 52 body tissues, have also focused on sQTL identification. However, there are still two significant gaps in sQTL research: the lack of studies on immune cell-type-specific sQTLs and the underrepresentation of Asian populations in sQTL studies, which primarily focus on European populations.
On November 21, 2024, our team published a landmark study in Nature Genetics titled “Single-cell RNA-seq of peripheral blood links cell-type-specific regulation of splicing to autoimmune and inflammatory diseases.” This study addresses the aforementioned gaps by analyzing over one million peripheral blood mononuclear cells (PBMCs) from 474 healthy donors of diverse Asian ancestries, including East, Southeast, and South Asian populations (Figure 1). The research provides a comprehensive map of cell-type-specific, sex-biased, and ancestry-biased alternative splicing events in Asian populations, offering guidance for understanding the role of splicing in complex diseases.
Figure 1
Through the analysis of 21 PBMC subtypes, the study identified 48 sex-biased splicing events, including the female-biased isoform ENST00000498491 of FLNA. Additionally, 1,031 ancestry-biased splicing events were discovered, such as SPSB2, where rs11064437 disrupts the 3' splice site of exon 2. The team also mapped 10,874 cis-sQTLs affecting protein-coding genes and 703 cis-sQTLs affecting lncRNAs, many of which exhibit cell-type specificity or sex bias. Furthermore, 865 dynamic intron usage events and 107 dynamic splicing genetic effects along B cell differentiation trajectories were identified.
The study revealed 607 trans-sGenes and genetic co-regulation between a trans-sQTL of PTPRC (a key regulator of T cell development) and a cis-eQTL of hnRNPLL (a master regulator of alternative splicing in T cell activation). Notably, cis-sQTL effects showed significant enrichment in heritability for autoimmune and inflammatory disease GWAS loci, with colocalization analysis identifying 563 potential risk genes. The team functionally validated an East Asian-specific sQTL (rs74416240~TCHP) associated with Graves' disease. This SNP disrupts the 5' splice site of exon 4 in TCHP, leading to intron retention and nonsense-mediated mRNA decay, thereby increasing the risk of Graves' disease specifically in East Asian populations.
In summary, this study establishes a cell-type-specific sQTL map for Asian populations and underscores the importance of ancestry diversity. It provides a crucial resource for understanding splicing mechanisms in complex diseases at the cellular level.
Professor Liu Boxiang from NUS Pharmacy is the corresponding author of this study. PhD students Chi Tian, Yuntian Zhang, and Yihan Tong are co-first authors of this groundbreaking research.
References
Li, Y.I. et al. RNA splicing is a primary link between genetic variation and disease. Science 352, 600–604 (2016).
Brotman, S.M. et al. Subcutaneous adipose tissue splice quantitative trait loci reveal differences in isoform usage associated with cardiometabolic traits. Am J Hum Genet 109, 66–80 (2022).
Atla, G. et al. Genetic regulation of RNA splicing in human pancreatic islets. Genome Biol 23, 196 (2022).
Qi, T. et al. Genetic control of RNA splicing and its distinct role in complex trait variation. Nat Genet (2022).