Genetic Evidence Supporting the Association of Protease and Protease Inhibitor Genes with Inflammatory Bowel Disease: A Systematic Review

As part of the European research consortium IBDase, we addressed the role of proteases and protease inhibitors (P/PIs) in inflammatory bowel disease (IBD), characterized by chronic mucosal inflammation of the gastrointestinal tract, which affects 2.2 million people in Europe and 1.4 million people in North America. We systematically reviewed all published genetic studies on populations of European ancestry (67 studies on Crohn's disease [CD] and 37 studies on ulcerative colitis [UC]) to identify critical genomic regions associated with IBD. We developed a computer algorithm to map the 807 P/PI genes with exact genomic locations listed in the MEROPS database of peptidases onto these critical regions and to rank P/PI genes according to the accumulated evidence for their association with CD and UC. 82 P/PI genes (75 coding for proteases and 7 coding for protease inhibitors) were retained for CD based on the accumulated evidence. The cylindromatosis/turban tumor syndrome gene (CYLD) on chromosome 16 ranked highest, followed by acylaminoacyl-peptidase (APEH), dystroglycan (DAG1), macrophage-stimulating protein (MST1) and ubiquitin-specific peptidase 4 (USP4), all located on chromosome 3. For UC, 18 P/PI genes were retained (14 proteases and 4protease inhibitors), with a considerably lower amount of accumulated evidence. The ranking of P/PI genes as established in this systematic review is currently used to guide validation studies of candidate P/PI genes, and their functional characterization in interdisciplinary mechanistic studies in vitro and in vivo as part of IBDase. The approach used here overcomes some of the problems encountered when subjectively selecting genes for further evaluation and could be applied to any complex disease and gene family

Assessing the state of marine biodiversity in the Northeast Atlantic

The Northeast Atlantic, a highly productive maritime area, has been exposed to a wide range of direct human pressures, such as fishing, shipping, coastal development, pollution, and non-indigenous species (NIS) introductions, in addition to anthropogenically-driven global climate change. Nonetheless, this regional sea supports a high diversity of species and habitats, whose functioning provides a variety of ecosystem services, essential for human welfare. In 2017, OSPAR, the Northeast Atlantic Regional Seas Commission, delivered an assessment of marine biodiversity for the Northeast Atlantic. This assessment examined biodiversity indicators separately to identify changes in Northeast Atlantic biodiversity, but stopped short of determining the status of biodiversity for many species and habitats. Here, we expand on this work and for the first time, a semi-quantitative approach is applied to evaluate holistically the state of Northeast Atlantic marine biodiversity across marine food webs, from plankton to top predators, via fish, pelagic and benthic habitats, including xeno-biodiversity (i.e. NIS). Our analysis reveals widespread degradation in marine ecosystems and biodiversity, particularly for marine birds and coastal bottlenose dolphins, as well as for benthic habitats and fish in some regions. The poor biodiversity status of these ecosystem components is likely the result of cumulative effects of human activities, such as habitat destruction or disturbance, overexploitation, eutrophication, the introduction of NIS, and climate change. Bright spots are also revealed, such as recent signs of recovery in some fish and marine bird communities and recovery in harbour and grey seal populations and the condition of coastal benthic communities in some regions. The status of many indicators across all ecosystem components, but particularly for the novel pelagic habitats, food webs and NIS indicators, however, remains uncertain due to gaps in data, unclear pressure-state relationships, and the non-linear influence of some pressures on biodiversity indicators. Improving monitoring and data access and increasing understanding of pressure-state relationships, including those that are non-linear, is therefore a priority for enabling future assessments, as is consistent and stable resourcing for expert involvement

SNP Assoziationsstudien multifaktorieller Erkrankungen auf Chromosom 6p.

Kopplungsregionen multifaktorieller Erkrankungen umfassen meist mehrere Megabasen und können ein oder mehrere Suszeptibilitätsgene beinhalten. Assoziationsanalysen zur Identifizierung der relevanten Gene sind kosten- und zeitintensiv. In der vorliegenden Arbeit wurden SNP-Assoziationsanalysen auf Chromosom 6p21 für Asthma, erhöhtes Immunglobulin E, atopische Dermatitis, Morbus Crohn, Schizophrenie und Typ 1 Diabetes durchgeführt. Hierfür wurde eine neu entwickelte Methode der Allelfrequenzbestimmung an gepoolter DNA mittels MALDI-TOF MS etabliert. Allelfrequenzen von 546 SNPs wurden durch Mehrfachmessungen an 8 Erkrankungspools und einem populationsbasierten Kontrollpool bestimmt. Die Allelfrequenzdifferenzen verschiedener Pools zeigen die genetische Verwandtschaft assoziierter Phänotypen und bestätigen die Validität des Kontrollpools. Typ 1 Diabetes Proben dienten als Positivkontrolle des Pooling-Ansatzes, da die Assoziation von T1D zu HLA-DR und HLA-DQ bereits bekannt war. Darüber hinaus konnten die Ergebnisse durch Einzelgenotypisierung bestätigt werden. Ferner konnten neue Gene identifiziert werden, wie die HLA Klasse IV Region für extrinsisches Asthma und atopische Dermatitis, die distale HLA Klasse I Region für Schizophrenie sowie die proximale HLA Klasse I Region und HLA Klasse II Region für Morbus Crohn. Aufgrund des durchschnittlichen Detektionslimits von 5% Allelfrequenz und einer mittleren Abweichung der Allelfrequenzdifferenz von 2% eignet sich die Methode damit unter Voraussetzung eines Kopplungsungleichgewichts von häufigen SNPs zum indirekten bzw. direkten Nachweis assoziierter SNPs. Die Allelfrequenzdifferenzbestimmung verschiedener Pools ist zudem eine kostengünstige Screening-Methode. Da Hardy-Weinberg-Gleichgewichtsabweichungen im Pool nicht ersichtlich sind bzw. genotypische Effekte nicht zuordenbar sind, sollten signifikante Ergebnisse durch Einzelgenotypisierung verifiziert werden. Die familiäre Transmission der im Pooling-Ansatz identifizierten und mittels Einzelgenotypisierung validierten Asthmamarker zeigen nur geringe Signifikanz. Es konnte jedoch als Verifizierung der Ergebnisse die Assoziation von MICB, LST1 und AIF1 zu allergischem Asthma nachgewiesen werden. Alle drei Gene könnten durch immunmodulatorische Funktionen oder Einfluss auf die Proliferation der Blutgefäße und Polymerisierung von F-Aktin bei der Ausprägung der Phänotypen involviert sein. Weitere Analysen dieser ca. 150 kb umfassenden Region, für welche zurzeit über 900 weitere SNP-Datenbankeinträge existieren, sollten die funktionelle Beteiligung der dort lokalisierenden Gene an der komplexen Pathophysiologie zeigen

Asthma is associated with single-nucleotide polymorphisms in ADAM33.

Background The ADAM33 gene has recently been associated with asthma and bronchial hyper-reactivity. It codes for a disintegrin and metalloproteinase that triggers intra- and extracellular signalling by protein shedding. Objective We examined whether polymorphisms in ADAM33 are associated with asthma and related traits in two German populations. Methods We genotyped 15 intragenic single-nucleotide polymorphisms (SNPs) by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of allele-specific primer extension products. The transmission disequilibrium test was used for association analysis in the German asthma family study. Additionally, we tested for association of these SNPs in a case–control sample from the European Community Respiratory Health Study using Armitage's trend test. Results In both studies, we found SNPs that were significantly associated with asthma and related traits. In the family study, significant associations were observed for the SNPs F+1, ST+4 and ST+5 (with the lowest P-value for F+1, P=0.005). Remarkably, this association is seen even in the absence of linkage with two microsatellite markers from a previous genome scan either 3.1 million bases (Mb) up- or 5.6 Mb downstream. In the case–control study, SNP ST+7 (P=0.008) was significantly associated with asthma. Some of these SNPs overlapped with those found to be associated with elevated total IgE levels and bronchial hyper-responsiveness. Conclusion This study replicates the recently published association between asthma and ADAM33 gene variants. However, most of the associated SNPs were at non-identical positions in the German, UK and US samples. As linkage disequilibrium is high among the tested SNPs, and there is no known functional polymorphism, either not-tested variants in ADAM33, unknown regulatory elements or a gene in close proximity is responsible for this association

STAT6 as an asthma candidate gene : Polymorphism-screening, association and haplotype analysis in a Caucasian sib-pair study.

The human signal transducer and activator of transcription 6 (STAT6) gene represents one of the most promising candidate genes for asthma and other inflammatory diseases on the chromosomal region 12q13-q24. Therefore we screened all 23 exons, including parts of the neighbouring introns, as well as the promoter region for common polymorphisms and tested them for linkage/association with asthma and related traits (total serum IgE level, eosinophil cell count and SLOPE of the dose-response curve after bronchial challenge) in a Caucasian sib-pair study (108 families with at least two affected children). We could identify 13 single nucleotide polymorphisms (SNPs), which are all non-coding. A recently described dinucleotide (GT) repeat in exon 1 was also examined. Besides the confirmation of the four alleles described elsewhere we could identify a new one, named allele A5. Neither the SNPs nor the GT repeat showed linkage/association to asthma. Two intronic SNPs and one SNP in the 3'untranslated region of the gene showed weak association to total IgE levels (P = 0.0200, 0.0260 and 0.0280, respectively), whereas a significant association was found between a SNP in intron 18 and an increase in total IgE levels (P = 0.0070). However, the most promising effect was seen between allele A4 of the GT repeat polymorphism and an increase in eosinophil cell count (P = 0.0010). From these findings we conclude that the human STAT6 gene is rather involved in the development of eosinophilia and changes in total IgE levels than contributing to the pathogenesis of asthma

Association of the interleukin-1 receptor antagonist gene with asthma

The interleukin-1 cluster on human chromosome 2q12-2q14 harbors various promising candidate genes for asthma and other inflammatory diseases. We conducted a systematic association study with single-nucleotide polymorphisms (SNPs) located in candidate genes situated in this cluster. Single-marker, two-locus and three-locus haplotype analysis of SNPs yielded several significant results (p < 0.05\u20130.0021) for the human IL1RN gene encoding the IL-1 receptor antagonist protein, an antiinflammatory cytokine that plays an important role in maintaining the balance between inflammatory and antiinflammatory cytokines. These findings were replicated and confirmed in an independent Italian family sample in which significant, although weaker, association with asthma was detected. A sequencing approach to the coding region of the human IL1RN gene revealed additional DNA variants, from which a selection was also associated with the disease in German and Italian samples. Calculation of the linkage disequilibrium for the human IL1RN gene showed strong linkage disequilibrium for nearly all analyzed SNPs. Further haplotype analysis indicated that six SNPs are sufficient for tagging all haplotypes with a prevalence of more than 1%. The most frequent haplotype constructed from these SNPs was 1.4-fold overtransmitted in the German family sample