We present the software Condition-specific Regulatory Units Prediction (CRUP) to infer from epigenetic marks a list of regulatory units consisting of dynamically changing enhancers with their target genes. The workflow consists of a novel pre-trained enhancer predictor that can be reliably applied across cell types and species, solely based on histone modification ChIP-seq data. Enhancers are subsequently assigned to different conditions and correlated with gene expression to derive regulatory units. We thoroughly test and then apply CRUP to a rheumatoid arthritis model, identifying enhancer-gene pairs comprising known disease genes as well as new candidate genes.

The LIM and SH3 domain protein 1 (Lasp1) was originally cloned from metastatic breast cancer and characterised as an adaptor molecule associated with tumourigenesis and cancer cell invasion. However, the regulation of Lasp1 and its function in the aggressive transformation of cells is unclear. Here we use integrative epigenomic profiling of invasive fibroblast-like synoviocytes (FLS) from patients with rheumatoid arthritis (RA) and from mouse models of the disease, to identify Lasp1 as an epigenomically co-modified region in chronic inflammatory arthritis and a functionally important binding partner of the Cadherin-11/β-Catenin complex in zipper-like cell-to-cell contacts. In vitro, loss or blocking of Lasp1 alters pathological tissue formation, migratory behaviour and platelet-derived growth factor response of arthritic FLS. In arthritic human TNF transgenic mice, deletion of Lasp1 reduces arthritic joint destruction. Therefore, we show a function of Lasp1 in cellular junction formation and inflammatory tissue remodelling and identify Lasp1 as a potential target for treating inflammatory joint disorders associated with aggressive cellular transformation.

BackgroundPodocytes are postmitotic visceral epithelial cells, located at the Bowmans capsule of the kidney building up the slit diaphragm with their foot processes to filtrate the blood and keep valuable large proteins in the vessels.In Systemic Lupus Erythematosus (SLE) different organs are affected by autoantibodies which results in chronic inflammation and a high percentage of patients develop Lupus nephritis (LN) resulting in podocyte damage and disruption of the slit diaphragm. The risk for LN correlates directly with the level of anti-double stranded DNA antibodies (adsDNAabs).In this study, we wanted to identify the direct effect of adsDNAabs on podocytes.MethodsWe established an in vitro system to investigate the specific impact of monoclonal antibodies and their immune complexes directly on podocytes (AB8 cell line). Monoclonal antibodies were generated by transfecting HEK293T cell line with Ig heavy and corresponding light chain encoding plasmid DNA obtained from single B cells of patients with SLE and LN. Podocytes were incubated with the produced monoclonal antibodies and the internalisation process and functional consequences were analysed by immunofluorescence, Western Blot, FACS and electron microscopy. For comparison, primary human podocytes were isolated from LN patient urine and analysed by immunofluorescence.ResultsThe recombinantly produced adsDNAabs from LN patients were specific against nuclear structures and build complexes with double stranded DNA, essential for the internalisation by cultivated podocytes. Interestingly, viability and migratory capacity were not influenced by the exposure to adsDNAabs for 48 hour. The internalised antibodies were enclosed by membranous structures and reach the cytosol via clathrin dependent endocytosis. The process of internalisation was time and dose dependent and reversible. Furthermore, internalised antibody complexes could also be detected in primary human LN podocytes.ConclusionIn our in vitro model the specific uptake of adsDNAabs was observed, in line with human LN data. Podocytes from patients with LN show IgG positive aggregates in the cytosol. The internalisation depends on the complex formation of the antibodies with dsDNA and could be important part of the LN pathogenesis.