Additional file 1: Mapping of differentially expressed ir-lncRNAs to protein coding genes. (A) Diagram representation of the random walk with restart global propagation network algorithm. (B) Walkscore distribution of protein-coding genes in TCGA-BRCA, with cutoff set at walkscore ≥ 0.01 to generate a ranked list of protein-coding genes in proximity of differentially expressed ir-lncRNAs.

Additional file 9: Correlation of 3 ir-lncRNA signature with immune subpopulations across tumor types. Pearson correlation heatmap between immune cell subpopulation enrichment scores and 3 ir-lncRNA scores.

DNA methylation and blood circulating proteins have been associated with many complex disorders, but the underlying disease-causing mechanisms often remain unclear. Here, we report an epigenome-wide association study of 1123 proteins from 944 participants of the KORA population study and replication in a multi-ethnic cohort of 344 individuals. We identify 98 CpG-protein associations (pQTMs) at a stringent Bonferroni level of significance. Overlapping associations with transcriptomics, metabolomics, and clinical endpoints suggest implication of processes related to...

Breast cancer largely dominates the global cancer burden statistics; however, there are striking disparities in mortality rates across countries. While socioeconomic factors contribute to population-based differences in mortality, they do not fully explain disparity among women of African ancestry (AA) and Arab ancestry (ArA) compared to women of European ancestry (EA). In this study, we sought to identify molecular differences that could provide insight into the biology of ancestry-associated disparities in clinical outcomes. We applied...

Breast cancer largely dominates the global cancer burden statistics; however, there are striking disparities in mortality rates across countries. While socioeconomic factors contribute to population-based differences in mortality, they do not fully explain disparity among women of African ancestry (AA) and Arab ancestry (ArA) compared to women of European ancestry (EA). In this study, we sought to identify molecular differences that could provide insight into the biology of ancestry-associated disparities in clinical outcomes. We applied...

Failure of the heat shock response is a key event that leads to insulin resistance and type 2 diabetes. We recently showed that DNAJB3 co-chaperone is downregulated in obese and diabetic patients and that physical exercise restores its normal expression with a significant improvement of the clinical outcomes. In 3T3-L1 adipocytes, DNAJB3 has a role in improving the sensitivity to insulin and glucose uptake. In co-immunoprecipitation assays, DNAJB3 interacts with both JNK1 and IKKβ kinases....

Additional file 5: Spearman correlation coefficients of ir-lncRNAs with immune checkpoint expression in TCGA-BRCA.

Abstract Objectives To examine the hypothesis that obesity complicated by the metabolic syndrome, compared to uncomplicated obesity, has distinct molecular signatures and metabolic pathways. Methods We analyzed a cohort of 39 participants with obesity that included 21 with metabolic syndrome, age-matched to 18 without metabolic complications. We measured in whole blood samples 754 human microRNAs (miRNAs), 704 metabolites using unbiased mass spectrometry metabolomics, and 25,682 transcripts, which include both protein coding genes (PCGs) as well...

Poster by Bushra Memon (Hamad Bin Khalifa University), Ihab Younis (Carnegie Mellon University in Qatar), Fadhil Abubaker (Carnegie Mellon University in Qatar), and Essam M. Abdelalim (Hamad Bin Khalifa University) Background: Human pluripotent stem cells (hPSCs) are excellent tools for studying early human pancreatic development, modeling diabetes and cell therapy. hPSCs have been differentiated in vitro to functional pancreatic beta cells, however, the hPSC-derived beta cells are transcriptionally and functionally dissimilar to adult beta...

Additional file 5: Spearman correlation coefficients of ir-lncRNAs with immune checkpoint expression in TCGA-BRCA.

Additional file 6: Prognostic value of ICR classifier across solid cancers. Forest plot showing HRs for death (overall survival) and corresponding 95%-confidence interval for the continuous ICR score and number of patients for each TCGA cancer cohort and RAQA breast cancer cohort. Significant positive HRs are visualized in blue and significant negative HRs are visualized in red. ICR enabled (HR < 1, p-value < 0.05) cancer types are indicated with orange asterisks and ICR disabled...

Additional file 8: Survival curves of 3 ir-lncRNA signature. Overall survival Kaplan-Meier curves in which the 3 ir-lncRNAs signature did not show any significant prognostic value. Dichotomization cutoff of ‘high’ (red) and ‘low’ (cyan) subgroups was based on the optimal cut-off point as determined by a 5-fold cross-validation analysis. Censor points are indicated by vertical lines. P-values were determined by logrank test.

Additional file 8: Survival curves of 3 ir-lncRNA signature. Overall survival Kaplan-Meier curves in which the 3 ir-lncRNAs signature did not show any significant prognostic value. Dichotomization cutoff of ‘high’ (red) and ‘low’ (cyan) subgroups was based on the optimal cut-off point as determined by a 5-fold cross-validation analysis. Censor points are indicated by vertical lines. P-values were determined by logrank test.

The association of salivary α-amylase activity (SAA) activity or low copy number of its coding gene AMY1 with diabetes remains controversial. We aimed to reinvestigate the association of these factors with diabetes in Qatar, where diabetes prevalence is about 16%. We obtained cross-sectional data of 929 Qataris (age > 18 years) from the Qatar Biobank. We estimated AMY1 copy number variants (CNV) from whole-genome data, and quantified the SAA activity in plasma (pSAA). We used...

Genomics has the potential to revolutionize medical approaches to disease prevention, diagnosis, and treatment, but it does not come without challenges. The success of a national population-based genome program, like the Qatar Genome Program (QGP), depends on the willingness of citizens to donate samples and take up genomic testing services. This study explores public attitudes of the Qatari population toward genetic testing and toward participating in the QGP. A representative sample of 837 adult Qataris...

Clinical laboratory tests play a pivotal role in medical decision making, but little is known about their genetic variability between populations. We report a genome-wide association study with 45 clinically relevant traits from the population of Qatar using a whole genome sequencing approach in a discovery set of 6218 individuals and replication in 7768 subjects. Trait heritability is more similar between Qatari and European populations (r = 0.81) than with Africans (r = 0.44). We...

Genetic research of elite athletic performance has been hindered by the complex phenotype and the relatively small effect size of the identified genetic variants. The aims of this study were to identify genetic predisposition to elite athletic performance by investigating genetically-influenced metabolites that discriminate elite athletes from non-elite athletes and to identify those associated with endurance sports. By conducting a genome wide association study with high-resolution metabolomics profiling in 490 elite athletes, common variant metabolic...

Genetic research of elite athletic performance has been hindered by the complex phenotype and the relatively small effect size of the identified genetic variants. The aims of this study were to identify genetic predisposition to elite athletic performance by investigating genetically-influenced metabolites that discriminate elite athletes from non-elite athletes and to identify those associated with endurance sports. By conducting a genome wide association study with high-resolution metabolomics profiling in 490 elite athletes, common variant metabolic...

The NAD+-dependent deacetylase SIRT1 controls key metabolic functions by deacetylating target proteins and strategies that promote SIRT1 function such as SIRT1 overexpression or NAD+ boosters alleviate metabolic complications. We previously reported that SIRT1-depletion in 3T3-L1 preadipocytes led to C-Myc activation, adipocyte hyperplasia, and dysregulated adipocyte metabolism. Here, we characterized SIRT1-depleted adipocytes by quantitative mass spectrometry-based proteomics, gene-expression and biochemical analyses, and mitochondrial studies. We found that SIRT1 promoted mitochondrial biogenesis and respiration in adipocytes and...

Despite the potential value of graduate-level research ethics training, most Middle East countries, including Jordan, do not routinely offer formal research ethics training. In students enrolled in Jordanian master’s level graduate program in pharmacy, the current study assessed: 1- differences in pre- and post-enrollment exposure to research ethics core themes, 2- whether this exposure was through a formal course or in an informal setting, and 3- student attitudes towards research ethics education and the need...

Additional file 1: Mapping of differentially expressed ir-lncRNAs to protein coding genes. (A) Diagram representation of the random walk with restart global propagation network algorithm. (B) Walkscore distribution of protein-coding genes in TCGA-BRCA, with cutoff set at walkscore ≥ 0.01 to generate a ranked list of protein-coding genes in proximity of differentially expressed ir-lncRNAs.

Additional file 3: Propagation walkscores of 127 proxy protein-coding genes in the TCGA-BRCA cohort.

Additional file 7: Akaike information criterion (AIC), delta AIC, and HRs for death (overall survival) and corresponding 95%-confidence interval for ICR and 3 ir-lncRNA signature in 18 solid cancer TCGA datasets and RAQA cohort.

FOXA2 has been identified as an essential factor for pancreas development and emerging evidence supports an association between FOXA2 and diabetes. Although the role of FOXA2 during pancreatic development is well-studied in animal models, its role during human islet cell development remains unclear. Here, we generated induced pluripotent stem cells (iPSCs) from a patient with FOXA2 haploinsufficiency (FOXA2+/− iPSCs) followed by beta-cell differentiation to understand the role of FOXA2 during pancreatic beta-cell development. Our results...

Prostate cancer (PC) castration resistance has been linked to the differentiation of PC luminal cells into hormone-refractory neuroendocrine (NE) cells. However, the molecular mechanisms controlling the emergence of lethal NE prostate cancer (NEPC) remain unclear. The present study aimed to investigate the mechanisms underlying the transition from prostate adenocarcinoma to NEPC. The microRNA miR-708 was involved in NE differentiation and was downregulated in NEPC cells and tumor specimens. miR-708 targeted Sestrin-3 to inhibit Forkhead Box...