Sulev Koks

Objective
Our study investigates the impact of copy number variations (CNVs) on Parkinson’s disease (PD) pathogenesis using genome-wide data, aiming to uncover novel genetic mechanisms and improve the understanding of the role of CNVs in sporadic PD.

Methods
We applied a sliding window approach to perform CNV-GWAS and conducted genome-wide burden analyses on CNV data from 11,035 PD patients (including 2,731 early-onset PD (EOPD)) and 8,901 controls from the COURAGE-PD consortium.

Results
We identified 14 genome-wide significant CNV loci associated with PD, including one deletion and 13 duplications. Among these, duplications in 7q22.1, 11q12.3 and 7q33 displayed the highest effect. Two significant duplications overlapped with PD-related genes SNCA and VPS13C, but none overlapped with recent significant SNP-based GWAS findings. Five duplications included genes associated with neurological disease, and four overlapping genes were dosage-sensitive and intolerant to loss-of-function variants. Enriched pathways included neurodegeneration, steroid hormone biosynthesis, and lipid metabolism. In early-onset cases, four loci were significantly associated with EOPD, including three known duplications and one novel deletion in PRKN. CNV burden analysis showed a higher prevalence of CNVs in PD-related genes in patients compared to controls (OR=1.56 [1.18-2.09], p=0.0013), with PRKN showing the highest burden (OR=1.47 [1.10-1.98], p=0.026). Patients with CNVs in PRKN had an earlier disease onset. Burden analysis with controls and EOPD patients showed similar results.

Interpretation
This is the largest CNV-based GWAS in PD identifying novel CNV regions and confirming the significant CNV burden in EOPD, primarily driven by the PRKN gene, warranting further investigation.

Selecting high quality preimplantation embryo for transfer has been the most difficult task when producing embryos in vitro. To date the most used non-invasive method is based on visual observation. Developing a non-invasive method for embryo assessment is essential to have a profitable in vitro embryo production (IVP) and embryo transfer system. Molecular characterization of embryo growth media has been proposed as an complementary method to visual assessment of embryo morphology. In this study we are demonstrating a novel method, allowing sample collection at different embryo development stages, without compromising embryo quality, to determine potential viability markers for bovine IVP. Single bovine embryos were cultured in 60µl SOF+0.4% BSA droplets under mineral oil. Twenty µl of culture media was removed at day 2, 5 and 8 post-fertilization. A total of 58 samples were analyzed using liquid chromatography-mass spectrometry (Q-Trap 3200), followed by principal component analysis. Our results indicate that there are significant differences (p<0,00001) in concentrations for proline (m/z = 116), inositol (m/z of sodium adduct = 203) and citrate (m/z of sodium adduct = 215) also in the amino acid group of leucine and isoleucine (m/z = 132), phenylalanine (m/z = 165) and arginine (m/z = 211) between the normally developed and retarded in development embryo culture media. Platelet activating factor (m/z = 524) (PAF) was roughly 3 fold increased in day 5 to day 8 embryo culture media. Unfortunately the increase of PAF was not statistically significant between normally developing and retarded embryos. These results demonstrate that it is possible to remove culture media samples from droplets and not significantly affect embryo development. Applying this method for embryo selection provides a possibility to identify well-developing embryos and provides an opportunity for improving the herds genetic value.

Psoriasis is a common, debilitating immune-mediated skin disease. Genetic studies have identified biological mechanisms of psoriasis risk, including those targeted by effective therapies. However, the genetic liability to psoriasis is not fully explained by variation at robustly identified risk loci. To move towards a saturation map of psoriasis susceptibility we meta-analysed 18 GWAS comprising 36,466 cases and 458,078 controls and identified 109 distinct psoriasis susceptibility loci, including 45 that have not been previously reported. These include susceptibility variants at loci in which the therapeutic targets IL17RA and AHR are encoded, and deleterious coding variants supporting potential new drug targets (including in STAP2, CPVL and POU2F3). We conducted a transcriptome-wide association study to identify regulatory effects of psoriasis susceptibility variants and cross-referenced these against single cell expression profiles in psoriasis-affected skin, highlighting roles for the transcriptional regulation of haematopoietic cell development and epigenetic modulation of interferon signalling in psoriasis pathobiology.