Identification of the hybrid gene <i>LILRB5-3</i> by long-read sequencing and implication of its novel signaling function

Leukocyte immunoglobulin (Ig)-like receptors (LILRs) on human chromosome 19q13.4 encode 11 immunoglobulin superfamily receptors, exhibiting genetic diversity within and between human populations. Among the <i>LILR</i> genes, the genomic region surrounding <i>LILRB3</i> and <i>LILRA6</i> has yet to be fully characterized due to their significant sequence homology, which makes it difficult to differentiate between them. To examine the <i>LILRB3</i> and <i>LILRA6</i> genomic region, a tool named JoGo-LILR CN Caller, which can call copy number from short-read whole genome sequencing (srWGS) data, was applied to an extensive international srWGS dataset comprising 2,504 samples. During this process, a previously unreported loss of both <i>LILRB3</i> and <i>LILRA6</i> was detected in three samples. Using long-read sequencing of these samples, we have discovered a novel large deletion (33,692 bp) in the <i>LILRB3</i> and <i>LILRA6</i> genomic regions in the Japanese population. This deletion spanned three genes, <i>LILRB3</i>, <i>LILRA6</i>, and <i>LILRB5</i>, resulting in <i>LILRB3</i> exons 12-13 being located immediately downstream of <i>LILRB5</i> exons 1-12 with the loss of <i>LILRA6</i>, suggesting the potential expression of a hybrid gene between <i>LILRB5</i> and <i>LILRB3</i> (<i>LILRB5-3</i>). Transcription and subsequent translation of the <i>LILRB5-3</i> hybrid gene were also verified. The hybrid junction was located within the intracellular domain, resulting in an LILRB5 extracellular domain fused to a partial LILRB3 intracellular domain with three immunoreceptor tyrosine-based inhibitory motifs (ITIMs), suggesting that LILRB5-3 acquired a novel signaling function. Further application of the JoGo-LILR tool to srWGS samples suggested the presence of the <i>LILRB5-3</i> hybrid gene in the CEU population. Our findings provide insight into the genetic and functional diversity of the LILR family.