Microbial and autoantibody immunogenic repertoires in TIF1? autoantibody positive dermatomyositis

Spyridon Megremis; Thomas Walker; Xiaotong He; James O'Sullivan; William E.R. Ollier; Hector Chinoy; Neil Pendleton; Antony Payton; Lynne Hampson; Ian Hampson; Janine Lamb

To describe the accumulated antibodies present in dermatomyositis we use the SARA pipeline which integrates an Escherichia coli FliTrxTM random 12 amino acid (AA) peptide display system with epitope signature enrichment through competitive bio-panning and high-throughput DNA sequencing ( Figure 1 ). Competitive bio-panning was applied to pooled total immunoglobulin fractions (IgA, IgG, IgM) purified from the plasma of twenty anti-TIF1 positive adult-onset dermatomyositis patients (DM) and twenty healthy controls (HC) ( Table S1 ). Four sample pools were generated and paired: the first pair contained 10 pooled samples (P10) of DM (DM P10) used for competitive biopanning against 10 pooled samples of HC (HC P10) ( Table S1 ). The second pair included 20 pooled samples (P20) of DM (DM P20) used for competitive biopanning against 20 pooled samples of HC (HC P20) (Table S1 ). Figure 1 and figure S1 detail achieved metrics while defining the microbial and autoantibody immunogenic repertoires in DM and HC. We retrieved ≈36 million (DM) and ≈24 million (HC) next generation sequencing (NGS) reads which represent 8.7 million (DM) and 4.7 million (HC) expressed epitopes. Cohorts presented highly enriched epitope sequences that are unique to DM (15, 522) and HC (4,817) respectively. Our epitope cohorts retrieved 6.75 million (DM) and 2.25 million (HC) microbial or human protein annotations respectively which mapped to 9,111 (DM) and 4,994 (HC) Distinct species. 6,202 Unique species were identified in DM while 2,085 Unique species were identified in HC.