Fig. 2
L1Hs expressed at elevated levels in SLE neutrophils. A Average normalized read counts of the transcripts uniquely mapping to full-length L1Hs loci that are increased in neutrophils from SLE patients (n = 15) and healthy donors (HC; n = 12). The loci are identified by their chromosomal location and genomic coordinates. B. Heat map representation of individual patient patterns of L1Hs expression. The normalized read counts were adjusted to 100 for the highest expression of each locus. C The predicted translation products of the indicated L1Hs element on chromosome 4 and the normalized read counts for it in the healthy controls (HC) in the SLE patients segregated by SLEDAI score into low versus high disease activity (left panel) or by low versus high ISG levels (right panel). Red letters ‘x’ denote premature stop codons, red boxes represent ORF1 translatable into full-length 338-amino acid residue ORF1p. Purple boxes represent ORF2p; full-length is 1275aa. Note that ORF2 in this locus has a frame-shift mutation followed by a stop codon that terminates the protein after 870aa residues, which includes intact endonuclease (EN) and reverse transcriptase (RT) domains, but lacks the C-terminal Cys-rich domain (CR), the sequence of which can be found in a different reading frame (pale blue box) and therefore not translated. D same data for the indicated L1Hs on chromosome 20, which is full-length and has intact ORF1 and ORF2. E Same data for the indicated L1Hs on chromosome 7. F Side-by-side data from the present study (left panel) and similarly retrieved data from data set GSE139360 (n = 30 SLE, n = 29 HC) for the same L1Hs as in panel C. G Schematic illustration of the location of the same L1Hs (chr4:87347104–87353146) within the 5th intron of the HSD17B11 gene. The L1Hs element must be independently transcribed from its 5’ UTR to be poly-adenylated and translated. H Normalized read counts for the processed mRNA of HSD17B11 in HC and SLE patients segregated by disease activity. Bars indicate mean ± standard deviation. * denotes p values < 0.05, ** p < 0.01, and *** p < 0.005