Pathway trajectory analysis with tensor imputation reveals drug-induced single-cell transcriptomic landscape.

Genome-wide identification of single-cell transcriptomic responses of drugs in various human cells is a challenging issue in medical and pharmaceutical research. Here we present a computational method, tensor-based imputation of gene-expression data at the single-cell level (TIGERS), which reveals the drug-induced single-cell transcriptomic landscape. With this algorithm, we predict missing drug-induced single-cell gene-expression data with tensor imputation, and identify trajectories of regulated pathways considering intercellular heterogeneity. Tensor imputation outperformed existing imputation methods for data completion, and provided cell-type-specific transcriptomic responses for unobserved drugs. For example, TIGERS correctly predicted the cell-type-specific expression of maker genes for pancreatic islets. Pathway trajectory analysis of the imputed gene-expression profiles of all combinations of drugs and human cells identified single-cell-specific drug activities and pathway trajectories that reflect drug-induced changes in pathway regulation. The proposed method is expected to expand our understanding of the single-cell mechanisms of drugs at the pathway level.

Integration of genetics and miRNA-target gene network identified disease biology implicated in tissue specificity.

MicroRNAs (miRNAs) modulate the post-transcriptional regulation of target genes and are related to biology of complex human traits, but genetic landscape of miRNAs remains largely unknown. Given the strikingly tissue-specific miRNA expression profiles, we here expand a previous method to quantitatively evaluate enrichment of genome-wide association study (GWAS) signals on miRNA-target gene networks (MIGWAS) to further estimate tissue-specific enrichment. Our approach integrates tissue-specific expression profiles of miRNAs (∼1800 miRNAs in 179 cells) with GWAS to test whether polygenic signals enrich in miRNA-target gene networks and whether they fall within specific tissues. We applied MIGWAS to 49 GWASs (nTotal = 3 520 246), and successfully identified biologically relevant tissues. Further, MIGWAS could point miRNAs as candidate biomarkers of the trait. As an illustrative example, we performed differentially expressed miRNA analysis between rheumatoid arthritis (RA) patients and healthy controls (n = 63). We identified novel biomarker miRNAs (e.g. hsa-miR-762) by integrating differentially expressed miRNAs with MIGWAS results for RA, as well as novel associated loci with significant genetic risk (rs56656810 at MIR762 at 16q11; n = 91 482, P = 3.6 × 10-8). Our result highlighted that miRNA-target gene network contributes to human disease genetics in a cell type-specific manner, which could yield an efficient screening of miRNAs as promising biomarkers.

Contribution of a Non-classical HLA Gene, HLA-DOA, to the Risk of Rheumatoid Arthritis.

Despite the progress in human leukocyte antigen (HLA) causal variant mapping, independent localization of major histocompatibility complex (MHC) risk from classical HLA genes is challenging. Here, we conducted a large-scale MHC fine-mapping analysis of rheumatoid arthritis (RA) in a Japanese population (6,244 RA cases and 23,731 controls) population by using HLA imputation, followed by a multi-ethnic validation study including east Asian and European populations (n = 7,097 and 23,149, respectively). Our study identified an independent risk of a synonymous mutation at HLA-DOA, a non-classical HLA gene, on anti-citrullinated protein autoantibody (ACPA)-positive RA risk (p = 1.4 × 10(-9)), which demonstrated a cis-expression quantitative trait loci (cis-eQTL) effect on HLA-DOA expression. Trans-ethnic comparison revealed different linkage disequilibrium (LD) patterns in HLA-DOA and HLA-DRB1, explaining the observed HLA-DOA variant risk heterogeneity among ethnicities, which was most evident in the Japanese population. Although previous HLA fine-mapping studies have identified amino acid polymorphisms of the classical HLA genes as driving genetic susceptibility to disease, our study additionally identifies the dosage contribution of a non-classical HLA gene to disease etiology. Our study contributes to the understanding of HLA immunology in human diseases and suggests the value of incorporating additional ancestry in MHC fine-mapping.

Significant impact of miRNA-target gene networks on genetics of human complex traits.

The impact of microRNA (miRNA) on the genetics of human complex traits, especially in the context of miRNA-target gene networks, has not been fully assessed. Here, we developed a novel analytical method, MIGWAS, to comprehensively evaluate enrichment of genome-wide association study (GWAS) signals in miRNA-target gene networks. We applied the method to the GWAS results of the 18 human complex traits from >1.75 million subjects, and identified significant enrichment in rheumatoid arthritis (RA), kidney function, and adult height (P < 0.05/18 = 0.0028, most significant enrichment in RA with P = 1.7 × 10(-4)). Interestingly, these results were consistent with current literature-based knowledge of the traits on miRNA obtained through the NCBI PubMed database search (adjusted P = 0.024). Our method provided a list of miRNA and target gene pairs with excess genetic association signals, part of which included drug target genes. We identified a miRNA (miR-4728-5p) that downregulates PADI2, a novel RA risk gene considered as a promising therapeutic target (rs761426, adjusted P = 2.3 × 10(-9)). Our study indicated the significant impact of miRNA-target gene networks on the genetics of human complex traits, and provided resources which should contribute to drug discovery and nucleic acid medicine.

TRIM28 prevents autoinflammatory T cell development in vivo.

TRIM28 is a component of heterochromatin complexes whose function in the immune system is unknown. By studying mice with conditional T cell-specific deletion of TRIM28 (CKO mice), we found that TRIM28 was phosphorylated after stimulation via the T cell antigen receptor (TCR) and was involved in the global regulation of CD4(+) T cells. The CKO mice had a spontaneous autoimmune phenotype that was due in part to early lymphopenia associated with a defect in the production of interleukin 2 (IL-2) as well as incomplete cell-cycle progression of their T cells. In addition, CKO T cells showed derepression of the cytokine TGF-ß3, which resulted in an altered cytokine balance; this caused the accumulation of autoreactive cells of the T(H)17 subset of helper T cells and of Foxp3(+) T cells. Notably, CKO Foxp3(+) T cells were unable to prevent the autoimmune phenotype in vivo. Our results show critical roles for TRIM28 in both T cell activation and T cell tolerance.

Gene organization of human transporter associated with antigen processing-like (TAPL, ABCB9): analysis of alternative splicing variants and promoter activity.

The gene organization of human TAPL (TAP-like, ABCB9) was determined. The TAPL gene consists of 12 exons including the first non-coding exon on human chromosome 12q23.34. Three alternative splicing variants of the 12th exon have been identified by 3(')RACE using RNA from human cell lines and isolated lymphocytes. As expected from the similarity of the amino acid sequences of TAP1, TAP2, and TAPL, the intron insertion points in these three genes are essentially the same. However, the TAP2 and TAPL genes are closely related, since each has common non-coding exon and splicing isoforms. The novel splicing variants of TAPL termed 12B and 12C have shorter carboxyl terminal amino acid sequences than 12A, reportedly a conserved isoform in rodents and human. The proximal promoter region of the TAPL gene lacks a canonical TATA-box but contains several GC-box elements. The 60bp upstream sequence containing two GC-boxes from the human TAPL transcriptional start site confers basal promoter activity.