Disease genes and chromosomes: disease maps of the human genome. Chromosome 9

"Desert" gene (Chr9p21) variants as novel markers for coronary artery disease

OBJECTIVE

Previous reports have denoted to the possible link of Chr9p21 locus to the incidence of coronary artery disease (CAD). The entire core of chr9p21 is covered by "ANRIL" (Antisense noncoding RNA in INK4 Locus) and lies in a region that is free from any coding proteins; therefore, it is called the desert gene. The major objectives of this study were to examine the association of rs10757278 and rs2383206 SNPs on Chr9p21 with the incidence of CAD in the presence and absence of type 2 diabetes (T2D) in Egyptians and to correlate these genetic variants with several disease biomarkers (TC, CRP, and HbA1c).

METHODS

The study subjects consisted of 150 subjects; 50 healthy controls and 100 patients that were divided into two groups; CAD patients and CAD T2D patients. The genotyping of SNPs was performed using qPCR.

RESULTS

Genotype distribution for both SNPs were found to be significantly different (p=0.0009 for rs10757278 and p=0.001 for rs2383206) between patients and controls. The allele frequency was also different for rs10757278.

CONCLUSION

The current study showed that rs10757278/rs2383206-G allele increases the risk for CAD in Egyptians. Moreover, AA variant appeared as a protective genotype. However, SNPs did not noticeably contribute in the elevation of TC, hs-CRP, and HbA1c in non-diabetic and diabetic CAD patients.

Comparison of microRNA expression profiles in K562-cells-derived microvesicles and parental cells, and analysis of their roles in leukemia

Microvesicles (MVs) are 30-1,000-nm extracellular vesicles that are released from a multitude of cell types and perform diverse cellular functions, including intercellular communication, antigen presentation, and transfer of proteins, messenger RNA and microRNA (also known as miR). MicroRNAs have been demonstrated to be aberrantly expressed in leukemia, and the overall microRNA expression profile may differentiate normal blood cells vs. leukemia cells. MVs containing microRNAs may enable intercellular cross-talk in vivo. This prompted us to investigate specific variations of microRNA expression patterns in MVs derived from leukemia cells. The present study examined the microRNA expression profile of MVs from chronic myeloid leukemia K562 cells and that of MVs from normal human volunteers' peripheral blood cells. The potential targets of the differentially expressed microRNAs were predicted using computational searches. Bioinformatic analyses of the predicted target genes were performed for further evaluation. The present study analyzed microRNAs of MVs derived from leukemia and normal cells, and characterized specific microRNAs expression. The results revealed that MVs derived from K562 cells expressed 181 microRNAs of the 888 microRNAs assessed. Further analysis revealed that 16 microRNAs were downregulated, while 7 were upregulated in these MVs. In addition, significant differences in microRNA expression profiles between MVs derived from K562 cells and K562 cells were identified. The present results revealed that 77 and 122 microRNAs were only expressed in MVs derived from K562 cells and in K562 cells, respectively. There were 104 microRNAs co-expressed in MVs derived from K562 cells and in K562 cells. Target gene-related pathway analyses demonstrated that the majority of the dysregulated microRNAs were involved in pathways associated with leukemia, particularly the mitogen-activated protein kinase (MAPK) and the p53 signaling pathways. By further conducting microRNA gene network analysis, the present study revealed that the miR-15a/b, miR-16, miR-17 and miR-30 families were likely to play a role in the regulation of the MAPK signaling pathway. Since K562 cells presented the t(9;22) translocation, the current study further examined the predicted function of 12 microRNAs located in chromosomes 9 [Homo sapiens (hsa)-let-7a, hsa-let-7f, miR-126, miR-126*, miR-23b, miR-24, miR-27b and miR-7] and 22 (hsa-let-7b, miR-1249, miR-130b and miR-185), which were expressed both in MVs derived from K562 cells and in K562 cells. The present study identified microRNAs of MVs from leukemia and normal cells, and characterized the expression of specific microRNAs. The current study is also the first to identify and characterize distinct microRNA expression between MVs derived from K562 cells and K562 cells. These findings highlight that a number of microRNAs from leukemia-derived MVs may contribute to the development of hematopoietic malignancies. Further investigation may reveal the function of these differentially expressed microRNAs and may provide potential targets for novel therapeutic strategies.

Relationships of FOXE1 and ATM genetic polymorphisms with papillary thyroid carcinoma risk: a meta-analysis

We conducted the meta-analysis of all relevant case-control studies aiming to evaluate the relationships of common polymorphisms in forkhead box E1 (FOXE1) and ataxia telangiectasia mutated (ATM) genes to the risk of papillary thyroid carcinoma (PTC). A range of electronic databases were searched without language restrictions: Web of Science (1945 ~ 2013), the Cochrane Library Database (Issue 12, 2013), PubMed (1966 ~ 2013), EMBASE (1980 ~ 2013), CINAHL (1982 ~ 2013), and the Chinese Biomedical Database (CBM) (1982 ~ 2013). This meta-analysis was conducted using the STATA 12.0 software. Crude odds ratio (OR) with their 95 % confidence interval (CI) were calculated. Eight case-control studies with 2,085 PTC patients and 10,341 healthy controls were included. Fourteen common polymorphisms were evaluated, including rs3758249 A > G, rs907577 G > A, rs1867277 G > A, rs3021526 C > T, rs1443434 G > T, rs907580 G > A, rs965513 A > G, rs944289 C > T, and rs189037 G > A polymorphisms in the FOXE1 gene and rs373759 G > A, rs4988099 A > G, rs1801516 G > A, rs664677 T > C, and rs609429 G > C polymorphisms in the ATM gene. Our results demonstrated that the FOXE genetic polymorphisms might be closely related to an increased risk of developing PTC under five genetic models (all P < 0.005), especially for rs3758249, rs907577, rs1867277, rs3021526, rs1443434, rs907580, rs704839, rs894673, and rs10119760 polymorphisms. Nevertheless, no positive associations were found between the ATM genetic polymorphisms and the development of PTC (all P > 0.05). The current meta-analysis provided evidence that FOXE1 genetic polymorphisms may contribute to increased PTC risk, especially for rs3758249, rs907577, rs1867277, rs3021526, rs1443434, rs907580, rs704839, rs894673, and rs10119760 polymorphisms. However, the ATM genetic polymorphisms may not be important dominants of susceptibility to PTC.

Correlation of RECK with matrix metalloproteinase-2 in regulation of trophoblast invasion of early pregnancy

To study the role of the reversion-inducing-cysteine-rich protein with Kazal motifs (RECK) gene and matrix metalloproteinase-2 (MMP-2) in the regulation of trophoblast invasion of early pregnancy. Immunohistochemistry, Western blot and gelatin zymography were used to detect the RECK protein expression localization, expression level and MMP-2 activation level in the placental tissues harvested from 52 normal pregnant women (27 in the early pregnancy, 25 in the term pregnancy). Immunohistochemistry showed that RECK expression was found both in villous tissues of early pregnancy group and term pregnancy group and was mainly observed in cell membrane and cytoplasm of cytotrophoblasts and syncytiotrophoblasts. RECK expression increased with gestational time. RECK expression of early pregnancy group was significantly lower than that of term pregnancy group (P<0.05). RECK expression was significantly lower in cellular column (CC) with invasion ability. Western blot showed that the RECK protein expression in early pregnancy group was significantly lower than that in term pregnancy (P<0.05). The optical density values of RECK protein expression in early pregnancy group and term pregnancy group were 1.35-0.14 and 2.68+/-0.26, respectively, while MMP-2 activation ratio was contrary to RECK protein expression and decreased with the gestation time (P<0.01). The MMP-2 activation ratios of early pregnancy group and term pregnancy group were 0.46 +/- 0.05 and 0.10+/-0.02, respectively. The expression of the tumor inhibitory gene RECK was positively related with the invasion ability of trophoblasts, while the invasion gene MMP-2 was negatively related with the ability. The interaction between RECK and MMP-2 may play an important role in the regulation of the trophoblast invasion in early pregnancy.

Cloning and characterization of a human novel gene C9orf19 encoding a conserved putative protein with an SCP-like extracellular protein domain

A novel human transcript, C9orf19, mapped to the genomic region involved in hereditary inclusion body myopathy (IBM2) at chromosome 9p12-p13, has been cloned and characterized. A single cDNA clone consisting of the full-length 1.9 kb transcript has been isolated from a human placenta cDNA library and further analyzed. Genomic characterization of the C9orf19 gene identified five exons extending over 27.2 kb of genomic DNA, located 12 kb centromeric to the tumor suppressor RECK gene. C9orf19 mRNA is expressed in a wide range of adult tissues as a single transcript, most abundantly in lung and peripheral blood leukocytes. The predicted protein contains the SCP-like extracellular protein signature classified to IPR001283, a family of evolutionary related proteins with extracellular domains, which includes the human glioma pathogenesis-related protein (GliPR), the human testis specific glycoprotein (TPX-1), and several other extracellular proteins from rodents (SCP), insects venom allergens (Ag5, Ag3), plants pathogenesis proteins (PR-1) and yeast hypothetical proteins. Homology searches with the deduced 154 amino acid protein sequence of C9orf19 revealed highly similar proteins in mouse, drosophila, nematode and yeast. Mutation analysis of C9orf19 in IBM2 patients excluded it as the disease causing gene and revealed four single nucleotide polymorphisms within and in the vicinity of the gene, which will certainly be useful tools to study its potential role in several human diseases mapped to chromosome 9p12-p13. Parallel to this study, the gene termed GNE, approximately 50 kb centromeric to C9orf19, was shown to be the disease causing gene in IBM2.