Journal: Nature

Article Title: Autoimmunity in Down’s syndrome via cytokines, CD4 T cells and CD11c + B cells

doi: 10.1038/s41586-023-05736-y

Figure Lengend Snippet: a , PCA analysis of the HuProt IgG dataset for adults with DS ( n = 5), age-matched HC individuals ( n = 4), and patients with IPEX ( n = 3) and APS-1 ( n = 1). b , The number of IgG autoantigens enriched at least twofold in individuals with DS, IPEX and APS-1 compared with HC individuals. c , Enriched IgG autoantigens overlapping between disease groups. d , Enriched IgG autoantigens in HC individuals and in individuals with DS, IPEX and APS-1. The colour intensity corresponds to the log 2 -transformed fold change expression value relative to the mean of healthy adult controls. F, female; M, male; NA, unknown. e , Chromosomal expression pattern of IgG autoantigens enriched in DS. f , Gene expression pattern of IgG autoantigens enriched in DS ( n = 5) according to the Human Protein Atlas. g , GO analysis of IgG autoantigens enriched in DS ranked by the number of autoantigens found to be enriched in the associated gene set. The dot size and colour intensity correspond to the FDR-adjusted P value. Med., mediated; NK, natural killer; reg., regulation; sig, signalling; surf, surface; sys., system. h , The surface expression of CD64 in monocytes, natural killer cells from individuals with DS ( n = 14) and age-matched HC individuals ( n = 8). Mono, monocytes. i , ELISA analysis of anti-IFNGR2 autoantibodies in the plasma from adults with DS ( n = 4) and age-matched HC individuals ( n = 7). j , Neutralizing IFNγ signalling in THP-1 cells by IgG fraction of plasma from adults with DS ( n = 3), age-matched HC individuals ( n = 3) or recombinant anti-IFNGR2 antibody. Significance was assessed using one-way ANOVA with Tukey’s post hoc analysis. For h and i , significance was assessed using two-tailed unpaired t -tests. For h and j , data are mean ± s.d. For i , the whiskers denote the minimum and maximum values, the box limits denote quartile 1 to quartile 3, and the centre bar denotes the mean.

Article Snippet: F, female; M, male; NA, unknown. e , Chromosomal expression pattern of IgG autoantigens enriched in DS. f , Gene expression pattern of IgG autoantigens enriched in DS ( n = 5) according to the Human Protein Atlas. g , GO analysis of IgG autoantigens enriched in DS ranked by the number of autoantigens found to be enriched in the associated gene set.

Techniques: Immunopeptidomics, Transformation Assay, Expressing, Gene Expression, Enzyme-linked Immunosorbent Assay, Clinical Proteomics, Recombinant, Two Tailed Test

Journal: Nature

Article Title: Autoimmunity in Down’s syndrome via cytokines, CD4 T cells and CD11c + B cells

doi: 10.1038/s41586-023-05736-y

Figure Lengend Snippet: ( A ) Principal component analysis of HuProt IgA dataset for adult HCs (n = 4), adults with DS (n = 5), and patients, Immunodysregulation polyendocrinopathy enteropathy X-linked syndrome (IPEX) (n = 3) and Autoimmune polyglandular syndrome type 1 (APS-1) (n = 1). ( B ) Number of IgA autoantigens enriched at least 2-fold in DS, IPEX, and APS-1 compared to HCs. ( C ) Venn diagram of enriched IgA autoantigens overlapping between disease groups. ( D ) Heatmap of enriched IgA autoantigens in HCs, DS, IPEX, and APS-1. Colour intensity corresponds to the log2FC expression value relative to the mean of healthy adult controls. ( E ) Component loadings (PC1 and PC2) from Principal component analysis of HuProt IgG dataset for adults with DS (n = 5) and age-matched HCs (n = 4). ( F ) ELISA of anti-MSTN and anti-ATP6V1G2 autoantibodies in plasma from HCs (n = 6) and individuals with DS (n = 6). Significance assessed by two-tailed unpaired t tests, * denotes p ≤ 0.05. Whiskers denote min and max values, bounds of box denote Q1–Q3, and centre bar denotes mean. ( G ) Heatmap of IgG type I IFN autoantigens in HCs, DS, IPEX, and APS-1. Colour intensity corresponds to the log2FC expression value relative to the mean of healthy adult controls. ( H ) Quantification of antibodies against IFNα2 and IFNω in serum from HCs (n = 32), DS without COVID-19 (n = 10), DS with COVID-19 (n = 6), and APS-1 (n = 1) by Gyros assay. ( I ) Neutralization of IFNα2 and IFNω activity by serum from HCs (n = 32), DS without COVID-19 (n = 10), DS with COVID-19 (n = 6), and APS-1 (n = 1) by Gyros assay. (H-I) Significance assessed by One-way ANOVA with Tukey’s post-hoc analysis, ns denotes p > 0.05, *p ≤ 0.05; **p ≤ 0.005; ***p ≤ 0.0005; ****p ≤ 0.0001.

Article Snippet: F, female; M, male; NA, unknown. e , Chromosomal expression pattern of IgG autoantigens enriched in DS. f , Gene expression pattern of IgG autoantigens enriched in DS ( n = 5) according to the Human Protein Atlas. g , GO analysis of IgG autoantigens enriched in DS ranked by the number of autoantigens found to be enriched in the associated gene set.

Techniques: Immunopeptidomics, Expressing, Enzyme-linked Immunosorbent Assay, Clinical Proteomics, Two Tailed Test, Neutralization, Activity Assay

Journal: Scientific Reports

Article Title: STK4 protein expression pattern follows different trends in endometrioid and serous endometrial adenocarcinoma upon tumor progression

doi: 10.1038/s41598-022-26391-9

Figure Lengend Snippet: Representative images of the STK4 protein staining in EC tissue. Expression of STK4 was assessed by immunohistochemistry, using a specific antibody. The signal (shown in green and black) was detected mainly in nuclei and in the cytoplasm. Nuclei were counterstained with DAPI. The top row—highly differentiated endometrial carcinoma, the bottom row—middle-low differentiated endometrioid carcinoma. Notice that the STK4 protein signal decreased with tumor progression. CV crystal violet, DNA deoxyribonucleic acid, STK4 serine/threonine-protein kinase 4.

Article Snippet: Figure 4 The STK4 gene expression pattern, obtained at the Broad Institute portal. ( A ) STK4 mRNA expression in various tumor cell lines, according to RNAseq.

Techniques: Staining, Expressing, Immunohistochemistry

Journal: Scientific Reports

Article Title: STK4 protein expression pattern follows different trends in endometrioid and serous endometrial adenocarcinoma upon tumor progression

doi: 10.1038/s41598-022-26391-9

Figure Lengend Snippet: STK4 protein expression in relation to tumor clinicopathological characteristics. The Kruskal-Walli’s test was applied in all cases with respective exact p-values reported in the figure. ( A ) STK4 is expressed at higher levels in Type 1 tumors, than in Type 2 samples; ( B ) STK4 protein levels are decreasing with the advanced tumor grade; ( C ) This observation (in B ) became more clear when serous tumors were included in statistical calculations; ( D ) No significant differences were observed in SKT4 expression, when it was related to the tumor stage; ( E ) A slight decrease in STK4 expression upon tumor progression was detected, when serous tumors were included in calculations.

Article Snippet: Figure 4 The STK4 gene expression pattern, obtained at the Broad Institute portal. ( A ) STK4 mRNA expression in various tumor cell lines, according to RNAseq.

Techniques: Expressing

Journal: Scientific Reports

Article Title: STK4 protein expression pattern follows different trends in endometrioid and serous endometrial adenocarcinoma upon tumor progression

doi: 10.1038/s41598-022-26391-9

Figure Lengend Snippet: STK4 gene expression pattern, obtained at the Oncomine portal. ( A ) STK4 mRNA expression in endometrioid tumors in relation to the grade; ( B ) as in ( A ), related to the stage; ( C ) STK4 gene copy number related to the different stages of endometrioid ECs; ( D ) as in ( C ), but of serous cancers.

Article Snippet: Figure 4 The STK4 gene expression pattern, obtained at the Broad Institute portal. ( A ) STK4 mRNA expression in various tumor cell lines, according to RNAseq.

Techniques: Gene Expression, Expressing

Journal: Scientific Reports

Article Title: STK4 protein expression pattern follows different trends in endometrioid and serous endometrial adenocarcinoma upon tumor progression

doi: 10.1038/s41598-022-26391-9

Figure Lengend Snippet: The STK4 gene expression pattern, obtained at the Broad Institute portal. ( A ) STK4 mRNA expression in various tumor cell lines, according to RNAseq.; ( B ) STK4 mRNA expression according to microarray studies; ( C ) the STK4 gene copy number ratio, calculated based on mRNA expression in normal tissue and cancer cell lines (16). Note that the highly expressed STK4 in Burkitt lymphoma has only 2 copies (20 × 2 = 2), while in solid tumors there is a gain in copy number values (up to 3 copies in EC cell lines: 20.75 × 2 = 3.3); ( D ) methylation of the STK4 promoter, obtained by reduced representation bisulfite sequencing (RRBS). The STK4 promoter methylation is quite high in EC, prostate cancer, and breast cancer cell lines, i.e., in hormone-driven cancers of the human reproductive system. RMA robust multichip averaging, relative units of the signal intensity (see detailed description at https://portals.broadinstitute.org/ccle ). AML acute myeloid leukemia, T-cell ALL acute T-cell lymphocytic leukemia, NSC lung non-small cell lung tumor.

Article Snippet: Figure 4 The STK4 gene expression pattern, obtained at the Broad Institute portal. ( A ) STK4 mRNA expression in various tumor cell lines, according to RNAseq.

Techniques: Gene Expression, Expressing, Microarray, Methylation, Methylation Sequencing

Journal: Scientific Reports

Article Title: STK4 protein expression pattern follows different trends in endometrioid and serous endometrial adenocarcinoma upon tumor progression

doi: 10.1038/s41598-022-26391-9

Figure Lengend Snippet: STK4 expression and 5-year survival of patients with EC. ( A ) STK4 protein expression shows a trend to decrease in Type 2 EC samples of deceased patients, i.e., in poorly differentiated cancers; bars in solid colors represent living individuals, bars with patterns—deceased patients; ( B ) as in ( A ), however, this phenomenon is better recognized in individuals with the Type 2 EC; ( C ) overall survival of patients with endometrioid (left two bars) and serous (right two bars) EC; high (above median) STK4 expression is associated with poor prognosis for patients with serous tumors (pink—% of living patients, blue—% of deceased patients).

Article Snippet: Figure 4 The STK4 gene expression pattern, obtained at the Broad Institute portal. ( A ) STK4 mRNA expression in various tumor cell lines, according to RNAseq.

Techniques: Expressing

Journal: Scientific Reports

Article Title: STK4 protein expression pattern follows different trends in endometrioid and serous endometrial adenocarcinoma upon tumor progression

doi: 10.1038/s41598-022-26391-9

Figure Lengend Snippet: A survival analysis, based on the intensity of a STK4 protein signal.

Article Snippet: Figure 4 The STK4 gene expression pattern, obtained at the Broad Institute portal. ( A ) STK4 mRNA expression in various tumor cell lines, according to RNAseq.

Techniques: Expressing