Immune Isoform Atlas: Landscape of alternative splicing in human immune cells

Abstract

Alternative splicing events are a major causal mechanism for complex traits, but they have been understudied due to the limitation of short-read sequencing. Here, we generated a comprehensive full-length isoform annotation of human immune cells, Immune Isoform Atlas, by long-read sequencing for 29 cell subsets. Our atlas contained a number of unannotated transcripts and isoforms such as a read-through transcript of TOMM40-APOE. We profiled functional characteristics of isoforms including encoded domains, inserted repetitive elements, and translational efficiency, and we showed that repetitive elements significantly explained the diversity of unannotated isoforms. Some of the isoforms are expressed in a cell-type specific manner, whose alternative 3'-UTRs usage contributed to their specificity. Further, we identified a number of disease-associated isoforms by isoform switch analysis and by integration of several quantitative trait loci analyses with genome-wide association study data. Our findings will promote the elucidation of the pathomechanism of diseases via alternative splicing.

Uncovering the Localization and Function of a Novel Read-Through Transcript ‘TOMM40-APOE’

“…Finally, we confirmed the expression of read-through transcripts from the TO APOE locus in the hippocampus of human brains from eight AD and 10 non-AD subje ure 4). Inter-individual variation in expression suggests underlying genetic variant ef demonstrated in a previous study [4].…”

“…Although the existence of the TOMM40-APOE transcript is known [ 4 ], the nature of the protein and how it is involved in cellular phenomena have not been analyzed at the protein level, which we clarified in this study. In addition, since there are APOE alleles, the normal types E3 and E4 , with a higher risk of Alzheimer’s disease, we analyzed the differences between TOMM40-APOE3 and TOMM40-APOE4 .…”

“…In recent years, genome analysis technology has made remarkable progress, enabling long-read sequencing [ 1 , 2 , 3 ]. As a result, many unannotated transcripts and isoforms have been found [ 4 ]. Among them, there are read-through transcripts in which transcription continues by skipping the polyA signal, which originally serves as a stop codon, and fusion mRNA containing downstream gene sequences is produced [ 5 ].…”

“…One such read-through transcript is a fusion transcript of TOMM40 , a gene encoding the mitochondrial outer membrane protein TOMM40, and APOE , encoding the secreted protein APOE. They are neighboring genes and are considered risk genes for Alzheimer’s disease [ 4 , 6 , 7 ] because their SNPs are strongly correlated with the accumulation and aggregation of amyloid-β and the disease severity of Alzheimer’s disease [ 8 , 9 , 10 , 11 ]. Therefore, the read-through transcript of TOMM40-APOE may also influence the pathogenesis of Alzheimer’s disease.…”

Multi-omic profiling of pathogen-stimulated primary immune cells

“…Long-read mRNA sequencing has provided insight into regulatory mechanisms of immune responses, for instance in alternative splicing in macrophages 18 , and allows for accurate sequencing of complex transcripts in immune cells 19 . Further work on cell-type specific long-read transcriptomes have shown preferential expression of transcripts in specific cell types 20 . The impact of the newly discovered transcripts as well as post-transcriptional processes can only be fully understood by observing the proteome.…”