Paired-end Sequencing of Transcriptomes of human cells expressing the human gene LY6S

We discovered a new human gene, LY6S, coding for an LY6-like protein. TransMap and phylogenetic studies reveal that LY6S is the homolog of the murine Ly6a gene known as Ly6A.2/Ly6E.1, Sca1 (Stem Cell Antigen-1) and TAP (T-cell activating protein) which codes for a cell-surface protein used extensively as a hematopoietic stem cell marker. LY6S is interferon-inducible and codes for both GPI-linked membrane and secreted proteins. The LY6S cell-surface protein, contains only 9 cysteines distinguishing it from all other LY6-like proteins that have 10 consensus cysteine residues. LY6S is most highly expressed in cells of the human spleen that constitute a unique spleen cell lineage. Expression of the GPI-linked LY6S protein in various human cell lines leads to profound changes in cell morphology and cell growth, neither of which are affected by expression of the secreted LY6S protein. RNA-Seq analyses presented here show distinct shifts in patterns of gene expression, particularly of genes coding for inflammatory and immune response proteins, were associated with these changes. Our findings reveal the presence of a previously non-annotated human gene, LY6S, which is the Ly6a homolog and that codes for proteins expressed in spleen cells representing a new cell lineage, are associated with a florid inflammatory phenotype and regulate immune responses and cell growth. Overall design: mRNA profiles of human U87 glioblastoma cells that were stably transfected with either control pQCXIP expression vector or with the same vector coding for the GPI-linked, cell membrane located human LY6-iso1 protein were generated by deep sequencing, in triplicate, ??using Illumina GAIIx??.