Papers by Gerli R Pielberg
European Journal of Human Genetics, 2018
PLoS genetics, May 1, 2016
Gliomas are the most common form of malignant primary brain tumors in humans and second most comm... more Gliomas are the most common form of malignant primary brain tumors in humans and second most common in dogs, occurring with similar frequencies in both species. Dogs are valuable spontaneous models of human complex diseases including cancers and may provide insight into disease susceptibility and oncogenesis. Several brachycephalic breeds such as Boxer, Bulldog and Boston Terrier have an elevated risk of developing glioma, but others, including Pug and Pekingese, are not at higher risk. To identify glioma-associated genetic susceptibility factors, an across-breed genome-wide association study (GWAS) was performed on 39 dog glioma cases and 141 controls from 25 dog breeds, identifying a genome-wide significant locus on canine chromosome (CFA) 26 (p = 2.8 x 10-8). Targeted re-sequencing of the 3.4 Mb candidate region was performed, followed by genotyping of the 56 SNVs that best fit the association pattern between the re-sequenced cases and controls. We identified three candidate gene...
<p><b>(A)</b> The haplotype made of SNPs 3:57432981–3:57546568 is best associat... more <p><b>(A)</b> The haplotype made of SNPs 3:57432981–3:57546568 is best associated with expression changes of <i>WHAMM</i> (1.5-fold up-regulation in the risk, <i>P<0</i>.<i>0001</i>), while <i>AP3B2</i> was not altered in this haplotype. <b>(B)</b> The frequencies of the haplotypes made of the top SNPs that represent three independently associated regions. <b>(C)</b> The second risk haplotype (3:57432981–3:57484486) is stronger associated with up-regulation of <i>AP3B2</i> (1.5-fold, <i>P = 0</i>.<i>007</i>) and to a lesser extent with <i>WHAMM</i> (1.2-fold up-regulation, <i>P = 0</i>.<i>016</i>, <b><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005248#pgen.1005248.s004" target="_blank">S4 Fig</a></b>). <b>(D)</b> The schematic structure of the HOMER2 protein with the EVH1 domain and a coiled coil region. The amino acid sequence is shown below for the region from β4 to β6 strands. The nonsynonymous variant 3:57546568 changes Thr (blue color, protective) to Ala (red color, risk) in the HOMER2 protein. An asterisk marks the hydrophobic core residue and the two amino acids critical for the peptide binding site are marked with diamonds.</p
<p>ANAs directed against specific nuclear antigens reveal different patterns on stained cel... more <p>ANAs directed against specific nuclear antigens reveal different patterns on stained cells. <b>A)</b> Speckled ANA pattern. Arrows point at mitotic cells with negatively stained chromosomes surrounded by positive nucleosome staining. <b>B)</b> Homogeneous ANA pattern. The positive staining of chromatin in dividing cells is shown by arrows.</p
<p>S = Speckled, H = Homogeneous</p><p>Bold indicate between what groups the la... more <p>S = Speckled, H = Homogeneous</p><p>Bold indicate between what groups the largest allele frequency difference occurred and where statistics were performed (OR and P-values).</p><p>Genotype frequencies in the NSDTR population indicate an increased frequency for ANA<sup>S</sup> dogs homozygous for haplotype 2 (DLA-DRB1*00601/DQA1*005011/DQB1*02001) compared to controls and an increase in frequency for ANA<sup>H</sup> dogs with a homozygous haplotype (No 1.1 and 3.3) compared to controls.</p
<p><b>(A)</b> Two independent strong association signals were observed for SRMA... more <p><b>(A)</b> Two independent strong association signals were observed for SRMA affected dogs (8:68726546) and ANA<sup>H</sup> dogs with DLA risk allele DLA-DQA1*00601(8:68712185 and 8:68708503). The only closest gene, <i>VRK1</i>, is located over 100 kb upstream of the associated region while there are no protein-coding genes for more than 1.9 Mb downstream. The black circle indicates the SRMA SNP not associated with expression changes of <i>VRK1</i>, the red circles—SNPs associated with <i>VRK1</i> expression. <b>(B)</b> No SNPs were in LD with the top SRMA SNP. <b>(C)</b> The SNP 8:68708503 for ANA<sup>H</sup> dogs with DLA risk allele DLA-DQA1*00601 is not in LD with any other genotyped variants, but have a strong regulatory potential. The 1 kb region aligned with the corresponding human fragment is shown below with several tracks for gene regulation and conservation displayed. <b>(D)</b> Expression levels of the <i>VRK1</i> gene in the blood cells of healthy NSDTRs stratified by SNP 8:68708503. Only one dog homozygous for the risk A allele was available. <b>(E)</b> The DNA fragment with the SNP 8:68708503 was cloned in the luciferase reporter vector and following transfection in K562 cells the protein lysate was assayed for enzyme activity. The risk allele A enhances luciferase expression comparing to the protective C allele in both unstimulated and stimulated with PMA cells.</p
<p><b>(A)</b> The strongest association signals were observed in all ANA-positi... more <p><b>(A)</b> The strongest association signals were observed in all ANA-positive dogs in the <i>AP3B2</i> and in the intergenic region between <i>AP3B2</i> and <i>FSD2</i> genes, followed by a single SNP peak in the <i>HOMER2</i> gene (3:57546568) associated ANA<sup>H</sup> dogs with the risk allele DLA-DQA1*00601. <b>(B)</b> The top SNP for ANA-positive dogs (3:57432981) occurs in a four SNP haplotype with strong LD (r<sup>2</sup>>0.9). <b>(C)</b> Another associated region was identified for ANA-positive dogs (top SNP 3:57484486) in an 18 SNP haplotype with strong LD (r<sup>2</sup>>0.9). <b>(D)</b> ANA<sup>H</sup> dogs with the risk DLA-DQA1*00601 show one top SNP (3:57546568) independent of other variants.</p
<p><b>(A)</b> The strongest association was observed for the ANA<sup>H<... more <p><b>(A)</b> The strongest association was observed for the ANA<sup>H</sup> dogs with a homozygous DLA haplotype (14 patient dogs) in the region that contains <i>WFDC3</i> and <i>DNTTIP1</i> genes. Differentially expressed gene <i>WFDC3</i> is labeled with bold font. <b>(B)</b> r<sup>2</sup> analysis was performed on the top SNP (24:36087012) and revealed a seven SNP risk haplotype (r<sup>2</sup>>0.9) overlapping the <i>WFDC3</i> and <i>DNTTIP1</i> genes. <b>(C)</b> Haplotype frequencies in cases and controls. <b>(D)</b> The increased transcript level of <i>WFDC3</i> in the risk haplotype made of two synonymous SNPs (24:36066098, 24:36075761) and the top SLE variant.</p
<p>The strongest genetic association to a phenotype marked with bold “<b>+</b>”... more <p>The strongest genetic association to a phenotype marked with bold “<b>+</b>”, regular “+” means the gene is associated with a particular phenotype. <sup>1</sup>-we observed also a trend towards down-regulation of <i>HOMER2</i> in the risk haplotype, although it did not reach statistical significance due to small sample size. <sup>2</sup>-the strong genetic association signal with SRMA on chromosome 8 was not associated with <i>VRK1</i> expression levels</p><p>Genes associated with IMRD and SRMA phenotypes.</p
<p><b>(A)</b> Strong association to the locus was observed in ANA and independe... more <p><b>(A)</b> Strong association to the locus was observed in ANA and independently in SRMA-affected dogs. The signal for ANA dogs is located between the <i>MTTP</i> and <i>DAPP1</i> gene. SRMA dogs show multiple strong signals spread over a 1.3 Mb region. <b>(B)</b> ANA<sup>S</sup> dogs homozygous for DLA haplotype 2 show a narrow eight SNP risk haplotype with complete LD (r<sup>2</sup> = 1) with the top SNP (32:24542001). <b>(C)</b> No strong LD was identified for the top SNP (32:24827518) in SRMA dogs, but r<sup>2</sup> of 0.6–0.8 occurs throughout the region. <b>(D)</b> Haplotype frequencies in cases and controls in ANA<sup>S</sup> dogs. <b>(E-I)</b> Genes with differential expression in the blood cells associated with two top variants (32:24542001 for ANA<sup>S</sup>-DLA 2.2) with <i>BANK1</i><b>(E)</b>, and (32:24827518 for SRMA) with <i>DAPP1</i><b>(F)</b>, <i>LAMTOR3</i><b>(G)</b>, <i>DDIT4L</i><b>(H)</b>, <i>PPP3CA</i><b>(I)</b>.</p
<p>* Muscle pain and fever occur in both ANA-positive groups, but were slightly more freque... more <p>* Muscle pain and fever occur in both ANA-positive groups, but were slightly more frequent in ANA<sup>S</sup> dogs in the study cohort. ANA<sup>S</sup> showed an earlier onset of disease than ANA<sup>H</sup> (2 versus 3 years), while SRMA affected dogs at even a younger age (4–19 months).</p
<p><b>(A)</b> The strongest association signal was observed for the ANA-positiv... more <p><b>(A)</b> The strongest association signal was observed for the ANA-positive IMRD phenotype and overlaps with the <i>PTPN3</i> gene. The red circles show the SNPs that correlate with gene expression and indicated for all associated sub-phenotypes. The gene structure is shown below with exons as vertical bars, the direction of transcription is indicated by red arrowhead. <b>(B)</b> A 15 SNP risk haplotype identified for ANA-positive cases, all SNPs in almost complete LD (r<sup>2</sup> >0.9 for all pairs) with the top associated variant (11:67537177). <b>(C)</b> Haplotype frequencies in cases and controls. The SNPs used for expression studies are shown in bold and their risk alleles in red. <b>(D)</b> The log-transformed mRNA levels of <i>PTPN3</i> in the PBMCs of dogs with different haplotypes comprised of SNPs in the 3’-UTR and intron 18 and two synonymous SNPs in exons 18 and 3. The protective haplotype is T/T-C/C-A/A-C/C is shown in blue color, the associated risk haplotypes T/C-C/A-A/G-T/T and C/C-A/A-G/G-T/T—in red color. The <i>PTPN3</i> gene is down-regulated 7-fold in the heterozygous risk haplotype compared to the protective haplotype. Boxes represent interquartile range 25–75% with median, and 5–95 percentile range with maximum and minimum values. The dog number in each group is shown next to the haplotypes. The gene expression was normalized to the levels of the reference gene <i>TBP</i> and analyzed using a one-way ANOVA. All phenotypes and SNP labels as well as gene structures, expression and normalization presented here are unified with the figures for other loci.</p
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Papers by Gerli R Pielberg