The balance of expression of PTPN22 splice forms is significantly different in rheumatoid arthritis patients compared with controls

Complex disease is characterized by the interplay of multiple genetic and environmental factors. Rheumatoid arthritis (RA) is a complex autoimmune disease with a pronounced genetic component, mainly due to HLA-DRB1 gene, but also a multitude of loci outside the HLA region. In this work we strive to contribute to the understanding of the functional involvement of these susceptibility loci in the pathogenesis of RA. This study is based on a large material of whole blood samples and peripheral blood mononuclear cells (PBMCs) from RA patients and matched healthy controls from Sweden. The main methods used in this work included probe-based genotyping and gene-expression assays, cell cultures, RNA-sequencing, gene-gene interaction and pathway analysis, as well as a plethora of common molecular genetics and bioinformatics methods. We investigated the role of expression of known genetic risk factors PTPN22 and PTPN2 in RA, with a special attention to the splicing profile of these genes. Our data indicates significant differences in the expression ratio of splice variants for PTPN22 in whole blood samples from RA patients and healthy controls. For PTPN2 we demonstrate a significant difference in the relative mRNA expression of' transcript TC48 in PBMCs of healthy controls and RA patients. Additionally, we identified new susceptibility SNPs in the PTPN2 locus: rs657555 and rs11080606, by addressing the interaction of PTPN2 variants with HLA-DRB1 shared-epitope (SE) alleles in autoantibody positive RA patients in two independent cohorts. In this work, we also address the functional genetic role of the members of the MAP signaling pathway upstream of p38 and JNK – crucial enzymes in RA – with a regard to splicing profile and their connection to HLA-DRB1. We found a significant statistical interaction for rs10468473 from MAP2K4 locus with SE alleles in autoantibody-positive RA. Importantly, individuals heterozygous for rs10468473 demonstrated higher expression of total MAP2K4 mRNA in blood, compared to A-allele homozygous. We also describe a novel, putatively translated RNA splice form of MAP2K4, that is differentially expressed in peripheral blood mononuclear cells from 88 RA cases and controls, and is modulated in response to TNF in Jurkat cell line. Finally, we performed an expression analysis of multiple validated RA risk loci, and pathway analysis to assess functional relationship between RA susceptibility genes and predict new potential study candidates. New candidate molecules suggested by the pathway analysis, genes ERBB2 and HSPB1, as well as HLA-DRB1, were differentially expressed between RA patients and healthy individuals in RNA-seq data. ERBB2 expression profile was similar in whole blood of both treated and untreated patients compared to healthy individuals. A similar expression profile was replicated for ERBB2 in PBMCs in an independent material. In this work, we approached the task of elucidating the functional aspects of genetic susceptibility of RA, by integrating genetic epidemiology, transcriptomics, proteomics, cellmodels, and bioinformatics. We maintain, that such integrative approach provides the rationale to prioritize genes and genetic events for further functional studies. Our findings also outline the need to consider potential clinical significance of alternative splicing in gene expression studies

Assessing agonistic potential of a candidate therapeutic anti-IL21R antibody

<p>Abstract</p> <p>Background</p> <p>Selective neutralization of the IL21/IL21R signaling pathway is a promising approach for the treatment of a variety of autoimmune diseases. Ab-01 is a human neutralizing anti-IL21R antibody. In order to ensure that the activities of Ab-01 are restricted to neutralization even under <it>in vitro </it>cross-linking and <it>in vivo </it>conditions, a comprehensive assessment of agonistic potential of Ab-01 was undertaken.</p> <p>Methods</p> <p><it>In vitro </it>antibody cross-linking and cell culture protocols reported for studies with a human agonistic antibody, TGN1412, were followed for Ab-01. rhIL21, the agonist ligand of the targeted receptor, and cross-linked anti-CD28 were used as positive controls for signal transduction. <it>In vivo </it>agonistic potential of Ab-01 was assessed by measuring expression levels of cytokine storm-associated and IL21 pathway genes in blood of cynomolgus monkeys before and after IV administration of Ab-01.</p> <p>Results</p> <p>Using a comprehensive set of assays that detected multiple activation signals in the presence of the positive control agonists, <it>in vitro </it>Ab-01-dependent activation was not detected in either PBMCs or the rhIL21-responsive cell line Daudi. Furthermore, no difference in gene expression levels was detected in blood before and after <it>in vivo </it>Ab-01 dosing of cynomolgus monkeys.</p> <p>Conclusions</p> <p>Despite efforts to intentionally force an agonistic signal from Ab-01, none could be detected.</p

A Search for Technosignatures Around 31 Sun-like Stars with the Green Bank Telescope at 1.15-1.73 GHz

We conducted a search for technosignatures in April of 2018 and 2019 with the L-band receiver (1.15-1.73 GHz) of the 100 m diameter Green Bank Telescope. These observations focused on regions surrounding 31 Sun-like stars near the plane of the Galaxy. We present the results of our search for narrowband signals in this data set as well as improvements to our data processing pipeline. Specifically, we applied an improved candidate signal detection procedure that relies on the topographic prominence of the signal power, which nearly doubles the signal detection count of some previously analyzed data sets. We also improved the direction-of-origin filters that remove most radio frequency interference (RFI) to ensure that they uniquely link signals observed in separate scans. We performed a preliminary signal injection and recovery analysis to test the performance of our pipeline. We found that our pipeline recovers 93% of the injected signals over the usable frequency range of the receiver and 98% if we exclude regions with dense RFI. In this analysis, 99.73% of the recovered signals were correctly classified as technosignature candidates. Our improved data processing pipeline classified over 99.84% of the ~26 million signals detected in our data as RFI. Of the remaining candidates, 4539 were detected outside of known RFI frequency regions. The remaining candidates were visually inspected and verified to be of anthropogenic nature. Our search compares favorably to other recent searches in terms of end-to-end sensitivity, frequency drift rate coverage, and signal detection count per unit bandwidth per unit integration time.Comment: 20 pages, 8 figures, in press at the Astronomical Journal (submitted on Sept. 9, 2020; reviews received Nov. 6; re-submitted Nov. 6; accepted Nov. 17

Australian Vietnam veterans: Factors contributing to psychosocial problems

Objective: The objective of the present paper is to present comprehensive models of the current psychosocial morbidity of Australian Vietnam veterans. Seldom has research in this area attempted to 'untangle' direct and indirect influences on current functioning via possible pre-army, Vietnam and homecoming pathways, Method: The Australian Vietnam Veterans' Health Study gathered data on a sample of 641 veterans throughout Australia drawn randomly from army Vietnam tour lists of the era. The data arose from interview and army records of the era, and fall into four temporal categories: pre-army, Vietnam service, homecoming after Vietnam, and current state. Path analysis models of the veterans' current psychological morbidities and social wellbeing are used to identify direct aetiological influences of earlier era constructs on current state, free of confounding by indirect (often selection) effects. Results: Our results indicate that psychological morbidity (particularly posttraumatic stress disorder) is largely influenced by combat and poor homecoming experiences, although pre-military characteristics do play some direct roles in symptomatology. Social dysfunction measures show smaller effects of the Vietnam War, which may be accounted for by an indirect association with Vietnam-related psychological morbidity. Some social measures show evidence of compensatory influences of combat, high combat leading to social dysfunction because of morbidity, but simultaneously being associated with healthier social disposition (possibly because of increased ex-service activity). Conclusions: For Australian Vietnam veterans, combat-related and homecoming effects persist on a range of psychosocial endpoints 20-30 years after exposure. These effects are not explicable in terms of veterans' pre-Vietnam characteristics