Single-Cell Epigenomics and Functional Fine-Mapping of Atherosclerosis GWAS Loci

Rationale: Genome-wide association studies have identified hundreds of loci associated with coronary artery disease (CAD). Many of these loci are enriched in cisregulatory elements but not linked to cardiometabolic risk factors nor to candidate causal genes, complicating their functional interpretation. Objective: Single-nucleus chromatin accessibility profiling of the human atherosclerotic lesions was used to investigate cell type-specific patterns of cisregulatory elements, to understand transcription factors establishing cell identity, and to interpret CAD-relevant, noncoding genetic variation. Methods and Results: We used single-nucleus ATAC-seq (assay for transposase-accessible chromatin with sequencing) to generate DNA accessibility maps in >7000 cells derived from human atherosclerotic lesions. We identified 5 major lesional cell types including endothelial cells, smooth muscle cells, monocyte/macrophages, natural killer/T cells, and B cells and further investigated subtype characteristics of macrophages and smooth muscle cells transitioning into fibromyocytes. We demonstrated that CAD-associated genetic variants are particularly enriched in endothelial and smooth muscle cell-specific open chromatin. Using single-cell coaccessibility and cis-expression quantitative trait loci information, we prioritized putative target genes and candidate regulatory elements for approximate to 30% of all known CAD loci. Finally, we performed genome-wide experimental fine-mapping of the CAD variants identified in genome-wide association studies using epigenetic quantitative trait loci analysis in primary human aortic endothelial cells and self-transcribing active regulatory region sequencing (STARR-Seq) massively parallel reporter assay in smooth muscle cells. This analysis identified potential causal single-nucleotide polymorphisms (SNPs) and the associated target gene for over 30 CAD loci. We present several examples where the chromatin accessibility and gene expression could be assigned to one cell type predicting the cell type of action for CAD loci. Conclusions: These findings highlight the potential of applying single-nucleus ATAC-seq to human tissues in revealing relative contributions of distinct cell types to diseases and in identifying genes likely to be influenced by noncoding genome-wide association study variants.</p

Bakteerien mikrobilääkeresistenssi Suomessa : Finres 2020

Vuosittainen Finres-raportti kuvaa kattavasti Suomen resistenssitilannetta ja sen kehittymistä viimeisen kymmenenvuoden ajalta. Raportissa on koottu yhteen kliinisten mikrobiologianlaboratorioiden ja THL:n Mykobakteerilaboratorion vuosittain rutiinisti tuottamaa mikrobilääkeherkkyystietoa. Finres-raportin resistenssiseurantatiedot koostuvat pääosin kliinisistä infektioista eristettyjen bakteerien resistenssitiedoista

Loss of NRF-2 and PGC-1α genes leads to retinal pigment epithelium damage resembling dry age-related macular degeneration

Age-related macular degeneration (AMD) is a multi-factorial disease that is the leading cause of irreversible and severe vision loss in the developed countries. It has been suggested that the pathogenesis of dry AMD involves impaired protein degradation in retinal pigment epithelial cells (RPE). RPE cells are constantly exposed to oxidative stress that may lead to the accumulation of damaged cellular proteins, DNA and lipids and evoke tissue deterioration during the aging process. The ubiquitin-proteasome pathway and the lysosomal/autophagosomal pathway are the two major proteolytic systems in eukaryotic cells. NRF-2 (nuclear factor-erythroid 2-related factor-2) and PGC-1 alpha (peroxisome proliferator-activated receptor gamma coactivator-1 alpha) are master transcription factors in the regulation of cellular detoxification. We investigated the role of NRF-2 and PGC-1 alpha in the regulation of RPE cell structure and function by using global double knockout (dKO) mice. The NRF-2/PGC-1 alpha dKO mice exhibited significant age-dependent RPE degeneration, accumulation of the oxidative stress marker, 4-HNE (4-hydroxynonenal), the endoplasmic reticulum stress markers GRP78 (glucose-regulated protein 78) and ATF4 (activating transcription factor 4), and damaged mitochondria. Moreover, levels of protein ubiquitination and autophagy markers p62/SQSTM1 (sequestosome 1), Beclin-1 and LC3B (microtubule associated protein 1 light chain 3 beta) were significantly increased together with the Iba-1 (ionized calcium binding adaptor molecule 1) mononuclear phagocyte marker and an enlargement of RPE size. These histopathological changes of RPE were accompanied by photoreceptor dysmorphology and vision loss as revealed by electroretinography. Consequently, these novel findings suggest that the NRF-2/PGC-1 alpha dKO mouse is a valuable model for investigating the role of proteasomal and autophagy clearance in the RPE and in the development of dry AMD.Peer reviewe

Common Inflammation-Related Candidate Gene Variants and Acute Kidney Injury in 2647 Critically Ill Finnish Patients

Acute kidney injury (AKI) is a syndrome with high incidence among the critically ill. Because the clinical variables and currently used biomarkers have failed to predict the individual susceptibility to AKI, candidate gene variants for the trait have been studied. Studies about genetic predisposition to AKI have been mainly underpowered and of moderate quality. We report the association study of 27 genetic variants in a cohort of Finnish critically ill patients, focusing on the replication of associations detected with variants in genes related to inflammation, cell survival, or circulation. In this prospective, observational Finnish Acute Kidney Injury (FINNAKI) study, 2647 patients without chronic kidney disease were genotyped. We defined AKI according to Kidney Disease: Improving Global Outcomes (KDIGO) criteria. We compared severe AKI (Stages 2 and 3, n = 625) to controls (Stage 0, n = 1582). For genotyping we used iPLEX(TM) Assay (Agena Bioscience). We performed the association analyses with PLINK software, using an additive genetic model in logistic regression. Despite the numerous, although contradictory, studies about association between polymorphisms rs1800629 in TNFA and rs1800896 in IL10 and AKI, we found no association (odds ratios 1.06 (95% CI 0.89-1.28, p = 0.51) and 0.92 (95% CI 0.80-1.05, p = 0.20), respectively). Adjusting for confounders did not change the results. To conclude, we could not confirm the associations reported in previous studies in a cohort of critically ill patients.Peer reviewe

Heme oxygenase-1 repeat polymorphism in septic acute kidney injury

Acute kidney injury (AKI) is a syndrome that frequently affects the critically ill. Recently, an increased number of dinucleotide repeats in the HMOX1 gene were reported to associate with development of AKI in cardiac surgery. We aimed to test the replicability of this finding in a Finnish cohort of critically ill septic patients. This multicenter study was part of the national FINNAKI study. We genotyped 300 patients with severe AKI (KDIGO 2 or 3) and 353 controls without AKI (KDIGO 0) for the guanine-thymine (GTn) repeat in the promoter region of the HMOX1 gene. The allele calling was based on the number of repeats, the cut off being 27 repeats in the S-L (short to long) classification, and 27 and 34 repeats for the S-M-L2 (short to medium to very long) classification. The plasma concentrations of heme oxygenase-1 (HO-1) enzyme were measured on admission. The allele distribution in our patients was similar to that published previously, with peaks at 23 and 30 repeats. The S-allele increases AKI risk. An adjusted OR was 1.30 for each S-allele in an additive genetic model (95% CI 1.01-1.66; p = 0.041). Alleles with a repeat number greater than 34 were significantly associated with lower HO-1 concentration (p<0.001). In septic patients, we report an association between a short repeat in HMOX1 and AKI risk

Automaattileikkurin ja kaavoitusohjelmistojen hankinnan alkuselvitys

Tämä opinnäytetyö käsittelee hankintaprosessia, automaattileikkureita, kaavoitusja asetelmaohjelmistoja. Opinnäyteyön tavoitteena on tehdä kattava alkuselvitys ohjelmistojen ja automaattileikkurin hankintaa varten Insofa Oy:lle. Teoriaosa pohjautuu hankinnasta kertovaan kirjallisuuteen. Teoriaosassa käsitellään hankintaprosessia yleisesti. Hankintaprosessia kuvattaessa on keskitytty niihin vaiheisiin, joissa alkuselvityksestä on hyötyä. Teoriaosassa käsitellään myös automaattileikkuuseen kuuluvat vaiheet sekä kankaiden ominaisuuksien vaikutukset leikkuuseen. Automaattileikkuun vaiheet on käsitelty, jotta saadaan kuva missä vaiheissa ohjelmistoja käytetään. Automaattileikkuun vaiheisiin kuuluvat kaavoitus kaavaohjelmalla, asetelmien valmistus asetelmaohjelmalla, kankaiden laakaus ja varsinainen leikkaus automaattileikkurilla. Tutkimusosa perustuu yrityksen henkilökunnan haastatteluihin sekä ohjelmisto- ja automaattileikkureiden toimittajien haastatteluihin. Henkilökunnan haastatteluilla haettiin tietoa käytössä olevista ohjelmista ja automaattileikkurista samalla kartoittaen, mitä ominaisuuksia uusilta ohjelmistoilta ja automaattileikkurilta haetaan. Toimittajien haastatteluilla hankittiin tietoa tarjolla olevista ohjelmista ja leikkureista. Haastattelujen perusteella pohdittiin, mitkä ominaisuudet ovat tärkeitä hankintaa ajatellen. Näiden perusteella laadittiin hankintakriteerit, joita käytettiin eri vaihtoehtojen vertailussa. Tavoitteena oli etsiä paras ratkaisu yritykselle. Tuloksena päädyttiin siihen, että helpoin ratkaisu on hankkia uusi automaattileikkuri vanhalta toimittajalta ja päivittää ohjelmistot. Jos ratkaisussa päädytään pelkän automaattileikkurin hankintaan, on hinta ratkaisevin tekijä ja toimittaja ratkaistaan tarjouksien hintojen perusteella.This thesis deals with multiply cutting machines, pattern and marker making programs and a purchasing process. This thesis was commissioned by Insofa Ltd for their upcoming purchasing process and selection of an importer. The theoretical part of this thesis focuses on dealing with the purchasing process in general, on the cutting process and on the fabric cutting properties. This part is based on the books that handle purchasing processes. In the theory, it is told what purchasing is and how the process works. One part of the theoretical part focuses on the manufacturing process from pattern and marker making to cutting fabrics. The research part of this thesis consists of a description of the cutting process, programs and a cutting machine in Insofa Ltd and of comparing the purchasing possibilities. One part of the research was done by interviewing the workers that are a part of the process in the company and the other part by interviewing the importers of the programs and multiply cutting machines. Based on the first part of the interviews, reasons for the purchasing process were established. The second part tells what kind of products there are on the market. The last part of the research deals with comparing the different programs and cutting machine combinations. The results show that it is easier to stay with the old familiar importer/ producer when purchasing new programs and machinery. The easiest option is to purchase new multiply cutting machines and to update the existing programs. One reason for this is that companies already have a relationship. The result of this thesis can be used to ease the purchasing process of pattern and marker making programs and multiply cutting machines

Yhteisiä leikkihetkiä Nuppulassa: Leikkikansio ryhmäperhepäiväkotiin

Leikki on hyvin tärkeää lapsille, ja se edistää heidän kehitystään, kasvuaan ja oppimistaan monipuolisesti. Leikeissä lasten tiedot ja taidot edistyvät, ja sen tulisikin olla keskeisessä roolissa varhaiskasvatuksen eri toimintaympäristöissä. Opinnäytetyössä tehtiin tuotteistettuna kehittämistyönä leikkikansio, joka sisälsi 3–5-vuotiaille suunnattuja ohjattuja yhteisleikkejä. Toimeksiantajana oli yksityinen ryhmäperhepäiväkoti Nuppula Iisalmesta. Heillä oli haasteita keksiä yhteisleikkejä eri-ikäisille lapsille. Tavoitteena oli luoda leikkikansio toimeksiantajan tarpeisiin. Tämän pohjalta selvitettiin eri tavoin, millaisia yhteisleikkejä voi järjestää 3–5-vuotiaille lapsille ryhmäperhepäiväkodissa. Kansiota varten etsittiin ajankohtaista teoriatietoa, vanhemmille ja työntekijöille tehtiin kyselyt, leikkejä kokeiltiin lasten kanssa ja niitä havainnoitiin. Teoreettisena viitekehyksenä opinnäytetyön taustalla toimivat varhaiskasvatussuunnitelman perusteiden ja varhaiskasvatuslain lisäksi erityisesti leikin teoria ja leikki-ikäisten lasten kehitys. Valmis leikkikansio sisältää 70 kuvitettua leikkiä. Kaikissa leikeissä on mainittu tavoitteet, ohjeet ja tarvikkeet sekä osasta löytyy vinkkejä leikin kehittämiseen ja muokkaamiseen. Kansion leikit ovat eri kirjoista ja Internet-lähteistä sekä opinnäytetyön tekijöiden itse keksimiä. Vaikka leikkikansio on suunniteltu ja toteutettu Nuppulan tarpeiden mukaan, voivat muutkin varhaiskasvatuksen parissa työskentelevät hyötyä siitä. Kansiota voi jatkokehittää esimerkiksi pitämällä se ajan tasalla, ottamalla huomioon 6-vuotiaat, osallistamalla lapsia enemmän kansion suunnittelussa sekä jakamalla leikit eri tavoin. Leikkikansiota voisi myös tutkia sen hyödyllisyyden ja käytön perusteell

The angiopoietin receptor Tie2 is atheroprotective in arterial endothelium

Leukocytes and resident cells in the arterial wall contribute to atherosclerosis, especially at sites of disturbed blood flow. Expression of endothelial Tie1 receptor tyrosine kinase is enhanced at these sites, and attenuation of its expression reduces atherosclerotic burden and decreases inflammation. However, Tie2 tyrosine kinase function in atherosclerosis is unknown. Here we provide genetic evidence from humans and from an atherosclerotic mouse model to show that TIE2 is associated with protection from coronary artery disease. We show that deletion of Tie2, or both Tie2 and Tie1, in the arterial endothelium promotes atherosclerosis by increasing Foxo1 nuclear localization, endothelial adhesion molecule expression and accumulation of immune cells. We also show that Tie2 is expressed in a subset of aortic fibroblasts, and its silencing in these cells increases expression of inflammation-related genes. Our findings indicate that unlike Tie1, the Tie2 receptor functions as the dominant endothelial angiopoietin receptor that protects from atherosclerosis.Peer reviewe