Differentially expressed genes in human peripheral blood as potential markers for statin response

Alzheimer's disease-associated inflammatory pathways might contribute to osteoporosis through the interaction between PROK2 and CSF3

This study aimed to explore the potential molecular pathways and targets of Alzheimer's disease leading to osteoporosis using bioinformatics tools. The Alzheimer's and osteoporosis microarray gene expression data were retrieved from the Gene Expression Omnibus, and differentially expressed genes in the blood microenvironment related to Alzheimer's disease and osteoporosis were identified. The intersection of the three datasets (GSE97760, GSE168813, and GSE62402) was used to obtain 21 co-expressed targets in the peripheral blood samples in patients with Alzheimer's disease and osteoporosis. Based on the degree algorithm, the top 10 potential core target genes related to these diseases were identified, which included CLEC4D, PROK2, SIGLEC7, PDGFB, PTCRA, ECH1, etc. Two differentially expressed mRNAs, Prokineticin 2 (PROK2) and three colony-stimulating factor 3 (CSF3), were screened in the GSE62402 dataset associated with osteoporosis. Protein–protein rigid docking with ZDOCK revealed that PROK2 and CSF3 could form a stable protein docking model. The interaction of PROK2 and CSF3, core genes related to osteoporosis inflammation, plays an important role in the mechanism of osteoporosis in patients with Alzheimer's. Therefore, abnormalities or alterations in the inflammatory pathways in the peripheral blood samples of Alzheimer's patients may affect the course of osteoporosis.

Intensive Statin Treatment in Acute Ischaemic Stroke Patients with Intracranial Atherosclerosis: a High-Resolution Magnetic Resonance Imaging study (STAMINA-MRI Study)

OBJECTIVE

Intracranial atherosclerosis is a major cause of ischaemic stroke worldwide. A number of studies have shown the effects of statin treatment on coronary and carotid artery plaques, but there is little evidence on the effects of statin treatment on intracranial atherosclerotic plaques.

METHODS

The Intensive Statin Treatment in Acute Ischaemic Stroke Patients with Intracranial Atherosclerosis - High-Resolution Magnetic Resonance Imaging (STAMINA-MRI) Trial is a single-arm, prospective, observational study monitoring imaging and clinical outcomes of high-dose statin treatment among statin-naive patients with acute ischaemic stroke caused by symptomatic intracranial atherosclerosis. The primary outcome was the change in vascular remodelling and plaque characteristics before and after 6 months (median: 179 days, IQR 163-189 days) of statin treatment measured by high-resolution MRI (HR-MRI).

RESULTS

A total of 77 patients (mean age: 62.6±13.7 years, 61.0% women) were included in this study. Low-density lipoprotein cholesterol (LDL-C) levels (mg/dL) at initial and follow-up assessments were 125.81±35.69 and 60.95±19.28, respectively. Overall, statin treatment significantly decreased enhancement of plaque volume (mm³, 32.07±39.15 vs 17.06±34.53, p=0.013), the wall area index (7.50±4.28 vs 5.86±4.05, p=0.016) and stenosis degree (%, 76.47±20.23 vs 64.05±21.29, p<0.001), but not the remodelling index (p=0.195). However, 35% patients showed no change or increased enhancement volume and stenosis degree after statin treatment. Higher reduction of LDL-C and longer duration of statin treatment were associated with decreased enhancement volume after statin treatment.

CONCLUSIONS

High-dose statin treatment effectively stabilised symptomatic intracranial atherosclerotic plaques as documented by HR-MRI. Further study is needed to determine laboratory and genetic factors associated with poor response to statins and alternative therapeutic options, such as proprotein convertase subtilisin-kexin type 9 inhibitors, for these patients.

TRIAL REGISTRATION NUMBER

ClinicalTrials.gov NCT02458755.

Endometriosis risk alleles at 1p36.12 act through inverse regulation of CDC42 and LINC00339

Genome-wide association studies (GWAS) have identified markers within the WNT4 region on chromosome 1p36.12 showing consistent and strong association with increasing endometriosis risk. Fine mapping using sequence and imputed genotype data has revealed strong candidates for the causal SNPs within these critical regions; however, the molecular pathogenesis of these SNPs is currently unknown. We used gene expression data collected from whole blood from 862 individuals and endometrial tissue from 136 individuals from independent populations of European descent to examine the mechanism underlying endometriosis susceptibility. Association mapping results from 7,090 individuals (2,594 cases and 4,496 controls) supported rs3820282 as the SNP with the strongest association for endometriosis risk (P = 1.84 × 10−5, OR = 1.244 (1.126-1.375)). SNP rs3820282 is a significant eQTL in whole blood decreasing expression of LINC00339 (also known as HSPC157) and increasing expression of CDC42 (P = 2.0 ×10−54 and 4.5x10−4 respectively). The largest effects were for two LINC00339 probes (P = 2.0 ×10−54; 1.0 × 10−34). The eQTL for LINC00339 was also observed in endometrial tissue (P = 2.4 ×10−8) with the same direction of effect for both whole blood and endometrial tissue. There was no evidence for eQTL effects for WNT4. Chromatin conformation capture provides evidence for risk SNPs interacting with the promoters of both LINC00339 and CDC4 and luciferase reporter assays suggest the risk SNP rs12038474 is located in a transcriptional silencer for CDC42 and the risk allele increases expression of CDC42. However, no effect of rs3820282 was observed in the LINC00339 expression in Ishikawa cells. Taken together, our results suggest that SNPs increasing endometriosis risk in this region act through CDC42, but further functional studies are required to rule out inverse regulation of both LINC00339 and CDC42.

Dynamic Role of trans Regulation of Gene Expression in Relation to Complex Traits

Identifying causal genetic variants and understanding their mechanisms of effect on traits remains a challenge in genome-wide association studies (GWASs). In particular, how genetic variants (i.e., trans-eQTLs) affect expression of remote genes (i.e., trans-eGenes) remains unknown. We hypothesized that some trans-eQTLs regulate expression of distant genes by altering the expression of nearby genes (cis-eGenes). Using published GWAS datasets with 39,165 single-nucleotide polymorphisms (SNPs) associated with 1,960 traits, we explored whole blood gene expression associations of trait-associated SNPs in 5,257 individuals from the Framingham Heart Study. We identified 2,350 trans-eQTLs (at p < 10^-7); more than 80% of them were found to have cis-associated eGenes. Mediation testing suggested that for 35% of trans-eQTL-trans-eGene pairs in different chromosomes and 90% pairs in the same chromosome, the disease-associated SNP may alter expression of the trans-eGene via cis-eGene expression. In addition, we identified 13 trans-eQTL hotspots, affecting from ten to hundreds of genes, suggesting the existence of master genetic regulators. Using causal inference testing, we searched causal variants across eight cardiometabolic traits (BMI, systolic and diastolic blood pressure, LDL cholesterol, HDL cholesterol, total cholesterol, triglycerides, and fasting blood glucose) and identified several cis-eGenes (ALDH2 for systolic and diastolic blood pressure, MCM6 and DARS for total cholesterol, and TRIB1 for triglycerides) that were causal mediators for the corresponding traits, as well as examples of trans-mediators (TAGAP for LDL cholesterol). The finding of extensive evidence of genome-wide mediation effects suggests a critical role of cryptic gene regulation underlying many disease traits.

Study on Certain Biomarkers of Inflammation in Psoriasis Through "OMICS" Platforms

Background:

In recent years, research on psoriasis has focused on the identification of biomarkers for the diagnosis, pathogenesis, prognosis, or therapeutic response of the disease. These studies could provide insights into the susceptibility and natural history of psoriasis. The identification of biomarkers related to comorbidities in psoriasis, such as arthritis, cardiovascular disease, and the metabolic syndrome, is of special clinical interest.

Materials and Methods:

We performed an extensive review on psoriasis biomarkers, including cytokine and growth factors, in the literature published between 1997 and 2013, including cross-references of any retrieved articles. We also included some data from our own studies.

Results:

This review presents current knowledge of soluble biomarkers in psoriasis, including cytokines, chemokines, proangiogenic mediators, growth factors, antimicrobial proteins, neuropeptides, and oxidative stress markers.

Conclusion:

In conclusion, a number of studies have been conducted with the aim of establishing soluble biomarkers for psoriasis. Most of the biomarkers that have been studied do not meet the criteria for a clinically useful biomarker. Further work is needed to establish a role for soluble biomarkers in the diagnosis and treatment of psoriasis, with a special focus on biomarkers for psoriasis comorbidities, such as arthritis, cardiovascular disease, and the metabolic syndrome.

Meta-analysis derived (MAD) transcriptome of psoriasis defines the "core" pathogenesis of disease

The cause of psoriasis, a common chronic inflammatory skin disease, is not fully understood. Microarray experiments have been widely used in recent years to identify genes associated with psoriasis pathology, by comparing expression levels of lesional (LS) with adjacent non-lesional (NL) skin. It is commonly observed that the differentially expressed genes (DEGs) differ greatly across experiments, due to variations introduced in the microarray experiment pipeline. Therefore, a statistically based meta-analytic approach, which combines the results of individual studies, is warranted. In this study, a meta-analysis was conducted on 5 microarray data sets, including 193 LS and NL pairs. We termed this the Meta-Analysis Derived (MAD) transcriptome. In “MAD-5” transcriptome, 677 genes were up-regulated and 443 were down-regulated in LS skin compared to NL skin. This represents a much larger set than the intersection of DEGs of these 5 studies, which consisted of 100 DEGs. We also analyzed 3 of the studies conducted on the Affymetrix hgu133plus2 chips and found a greater number of DEGs (1084 up- and 748 down-regulated). Top canonical pathways over-represented in the MAD transcriptome include Atherosclerosis Signaling and Fatty Acid Metabolism, while several “new” genes identified are involved in Cardiovascular Development and Lipid Metabolism. These findings highlight the relationship between psoriasis and systemic manifestations such as the metabolic syndrome and cardiovascular disease. Then, the Meta Threshold Gradient Descent Regularization (MTGDR) algorithm was used to select potential markers distinguishing LS and NL skin. The resulting set (20 genes) contained many genes that were part of the residual disease genomic profile (RDGP) or “molecular scar” after successful treatment, and also genes subject to differential methylation in LS tissues. To conclude, this MAD transcriptome yielded a reference list of reliable psoriasis DEGs, and represents a robust pool of candidates for further discovery of pathogenesis and treatment evaluation.