Molecular Biology Research Communications (2322181X)6(1)pp. 1-11
Stem cell factor (SCF) is a critical protein with key roles in the cell such as hematopoiesis, gametogenesis and melanogenesis. In the present study a comparative analysis on nucleotide sequences of SCF was performed in Humanoids using bioinformatics tools including NCBI-BLAST, MEGA6, and JBrowse. Our analysis of nucleotide sequences to find closely evolved organisms with high similarity by NCBI-BLAST tools and MEGA6 showed that human and Chimpanzee (Pan troglodytes) were placed into the same cluster. By using JBrowse, we found that SCF in Neanderthal had a single copy number similar to modern human and partly conserved nucleotide sequences. Together, the results approved the gene flow and genetics similarity of SCF among human and P. troglodytes. This may suggest that during evolution, SCF gene transferred partly intact either on the basis of sequence or function from the same ancestors to P. troglodytes, the ancient human like Neanderthal, and then to the modern human.
Genetic Testing and Molecular Biomarkers (19450265)18(12)pp. 820-825
Background and Aims: SLC26A4 gene mutations are the second currently identifiable genetic cause of autosomal recessive nonsyndromic hearing loss after GJB2 mutations. Because of the extensive size of the SLC26A4 gene and the variety of mutations, indirect diagnosis using linkage analysis has been suggested. Therefore, in this investigation three potential short tandem repeat (STR) markers related to this region including D7S2420, D7S496, and D7S2459 were selected for further analysis. Methods: The characteristics and haplotype frequency of the markers were examined for the first time in five ethnic groups of the Iranian population including Fars, Azari, Turkmen, Gilaki, and Arab using the polymerase chain reaction followed by fluorescent capillary electrophoresis. Results were analyzed by GeneMarker HID Human STR Identity, GenePop, Microsatellite tools, PowerMarker 3.25, and Arlequin 3.5 software.
Iranian Journal Of Public Health (22516085)41(5)pp. 97-104
Background: Genetic diversity of three polymorphic markers in the phenylalanine hydroxylase (PAH) gene region including PvuII (a), PAHSTR and MspI were investigated. Methods: Unrelated individuals (n=139) from the Iranian populations were genotyped using primers specific to PAH gene markers including PvuII(a), MspI and PAHSTR. The amplified products for PvuII(a), MspI were digested using the appropriate restriction enzymes and separated on 1.5% agarose. The PAHSTR alleles were identified using polyacrylamide gel electrophoresis followed by silver staining. The exact size of the STR alleles was determined by sequencing. The allele frequency and population status of the alleles were estimated using PHASE, FBAT and GENEPOP software. Results: The estimated degree of heterozygosity for PAHSTR, MspI and PvuII (a) was 66%, 56% and 58%, respectively. The haplotype estimation analysis of the markers resulted in nine informative haplotypes with frequencies ≥5%. Moreover, the results obtained from Ewens-Watterson test for neutrality suggested that the markers were under balancing selection in the Iranian population. Conclusion: These findings suggested the presence of genetic diversity at these three markers in the PAH gene region. Therefore, the markers could be considered as functional markers for linkage analysis of the PAH gene mutations in the Iranian families with the PKU disease.
The estimation of genetic distance between populations could improve our viewpoint about human migration and its genetic origin. In this study, we used allele frequency data of 12 polymorphic markers on 250 individuals (500 alleles) from the Iranian population to estimate genetic distance between the Iranians and other world populations. The phylogenetic trees for three different sets of allele frequency data were constructed. Our results revealed the genetic similarity between the Iranians and European populations. The lowest genetic distance was observed between the Iranians and some populations reside in Russia. Furthermore, the high genetic distance was observed between the Iranians and East Asian populations. The data suggested that the Iranians might have relatively close evolutionary history with Europeans, but historically independent from East Asian populations. The evaluation of genetic distance between Indians populations and Iranians was also performed. The Indian groups showed low genetic distance with others, but high genetic distance with the Iranians. This study could provide a new insight into the evolutionary history of the Iranian population.
Iranian Journal Of Biotechnology (23222921)9(3)pp. 163-172
Phenylketonuria (PKU) is the most common autosomal recessive disorder of amino acid metabolism. The disease is caused mainly by mutations in the phenylalanine hydroxylase (PAH) gene, encoding phenylalanine hydroxylase (PAH) enzyme. The PAH enzyme deficiency results in the elevation of phenylalanine in the blood, which may cause severe irreversible mental retardation in the affected individuals. More than 500 different disease causing mutations have been identified in the PAH gene. Direct and indirect molecular approaches have been developed for carrier detection and prenatal diagnosis of PKU disease. Population distribution of the PAH gene mutations and the PKU disease varies in different countries. In view of relatively high prevalence of the disease in Iranian population, investigations toward the elucidation of molecular aspects of the disease were required. In the present article, clinical and molecular basis of the PKU disease, with emphasis on the studies performed in Iranian population, were reviewed.
Iranian Journal Of Biotechnology (23222921)7(3)pp. 137
In the present study, genotyping of six short tandem repeat (STR) loci including CSF1PO, D16S539, F13A01, F13B, LPL and HPRTB was performed on genomic DNA from 127 unrelated individuals from the Iranian province of Isfahan. The results indicated that the allele and genotype distributions were in accordance with Hardy-Weinberg expectations. The observed heterozygosity (Ho), expected heterozygosity (He) as well as forensic and paternity indices including power of discrimination (PD) and exclusion (PE), polymorphism information content (PIC), typical paternity index (PItypical) and probability of paternity (W) were determined for the examined STR alleles. In addition, genetic diversity index (GD) and population parameter (θ) were calculated for the six loci. The combined power of discrimination (Pd combined) and combined probability of exclusion (PE typical) were 0.9999998 and 0.999856 over the six loci, respectively. Together, the examined STR loci in this study have proven a relatively high genetic variation in Iranian population. The data could be used for construction of a forensic genetic database for Iranian population.
Iranian Journal Of Public Health (22516085)38(4)pp. 136-139
Background: The haplotype phasing is more useful than genotyping markers independently at carrier detection and prenatal diagnosis of diseases. The PAH gene region contains several markers used in detection of PKU disease. In the present study, the efficiency of BglII-EcoRI-VNTR haplotype phasing in Iranian family trios was investigated. Then, this information was compared with those obtained for unrelated individuals. Methods: Blood samples were collected from 20 healthy family trios and 60 unrelated individuals. The genomic DNA was extracted by use of salting-out procedure. The two markers BglII and EcoRI were genotyped by use of PCR-RFLP. The genotype of VNTR marker was identified by use of PCR and electrophoresis. The genotyping data obtained from family trios was used to infer haplotype phase. We also compared this data with results obtained from a widely used method for haplotype frequency inference from unrelated individuals, the PHASE program. Results: The haplotype phase of all members was only ascertained at eight family trios. The comparison of this data with the results obtained by use of PHASE program showed that eight haplotypes [211, 221, 215, 216, 214, 121, 225 and 111] were informative haplotypes in Iranian population. Conclusion: Since diversity of BglII-EcoRI-VNTR haplotypes was high in Iranian population, haplotype phasing at family trios was difficult. The results of this study showed that the genotyping data obtained from family trios could not provide enough information for BglII-EcoRI-VNTR haplotype phasing at Iranian PKU families and the genotyping of other family members was necessary at most cases.
Iranian Journal Of Biotechnology (23222921)6(3)pp. 151-156
A single nucleotide polymorphism (SNP) in CD24 has been associated with multiple sclerosis (MS) in a population based study. This SNP results in the replacement of alanine (CD24A) by valine (CD24V) at amino acid 57 in the resulting polypeptide chain. In the current study, the genotyping of this SNP and its contribution to MS in 217 patients and 200 healthy individuals of an Iranian population was investigated. The correlation of the SNP alleles with the progression of the disease was determined using the expanded disability status scale (EDSS) and progression index (PI). The data revealed that individuals with the CD24V/V genotype showed a 2-fold increase in the relative risk of MS compared to patients with the CD24A/V (0.27) and CD24A/A (0.25) genotypes (P = 0.0193, Odds Ratio 2.4882, 95% CI: 1.416-4.3722). Moreover, the progression of the disease in patients with CD24V/V was much faster than other patients that were examined by ANOVA and the least significant difference (LSD) test. However, in the CD24V/V patients LSD analysis was statistically significant (p<0.05 and p<0.01). These results support the hypothesis that CD24 may function as a genetic modifier for susceptibility and progression of MS through the CD24V/V genotype.
Journal of Applied Genetics (12341983)47(1)pp. 79-83
Phenylketonuria is an inherited metabolic disease, which is characterized by increased level of serum phenylalanine (Phe). The quantitative measurement of Phe in the serum is necessary to confirm the disease, and to distinguish phenylketonuria from other forms of hyperphenylalaninemia. In this study, we report a rapid and inexpensive micro-assay for simultaneous detection and quantitative measurement of serum Phe in dry blood-spots. Analysis of the standard curve showed a broad linear Phe range of 120-1800 μmol L -1. Application of this method in conjunction with the standard Guthrie bacterial inhibition assay and high-pressure liquid chromatography in analyzing 34 samples from phenylketonuria patients and control samples produced comparable results, with the regression equation of Y= 0.994 + 0.996. The advantage of this method over the Guthrie bacterial inhibition assay is its ability to measure the serum Phe quantitatively without false positive results. The method was successfully applied to dried blood-spots as well as serum and whole blood samples. The cost per sample is about 20-50 US cents, which is much less than those of high-pressure liquid chromatography and enzymatic commercial kits. The method can be automated, which is suitable for neonatal and mass phenylketonuria screening, especially in developing countries, where funding is a limiting factor.
Obstetrics and Gynecology (00297844)91(3)pp. 319-323
Objective: To determine whether the mechanism for the retention of interstitial fluid in trisomy 21 fetuses presenting with nuchal translucency at 10-14 weeks' gestation is an alteration in the composition of collagen type VI, which is normally a triple helix formed of three single chains, α1, α2, and α3. The genes responsible for the α1 and α2 chains, COL6A1 and COL6A2, are located on chromosome 21 and therefore may be overexpressed in trisomy 21, whereas COL6A3 is located in chromosome 2. Methods: Skin tissue was obtained after termination of pregnancy at 11-16 weeks' gestation in five fetuses with trisomy 21 and five normal controls. Total RNA was extracted and the steady-state levels of COL6A1 and COL6A3 mRNA expression of the gene transcripts were determined. Additionally, the distribution of collagen type VI in the skin of trisomy 21 and normal fetuses was analyzed using an immunohistochemical method. Results: The ratio of the normalized densitometric scores for the mRNA expression of COL6A1 to COL6A3 in the skin of trisomy 21 fetuses was twice as high as in normal fetuses. Immunohistochemistry demonstrated that in trisomy 21 fetuses collagen type VI formed a dense network extending from the epidermal basement membrane to the subcutis, whereas in normal fetuses dense staining was confined to the upper region of the dermis. Conclusion: The distribution for collagen type VI is different from normal in the skin of trisomy 21 fetuses, and there is overexpression of COL6A1 compared with COL6A3.
Vallian borujeni, S., Gäken, J.A., Gingold, E.B., Kouzarides, T., Chang k.-s., K., Farzaneh, F.
Oncogene (14765594)16(22)pp. 2843-2853
The growth and transformation suppressor function of promyelocytic leukemia (PML) protein are disrupted in acute promyelocytic leukemia (APL) as a result of its fusion to the RARα gene by t(15;17) translocation. There is significant sequence homology between the dimerization domain of PML and the Fos family of proteins, which imply that PML may be involved in AP-1 activity. Here we show that PML can cooperate with Fos to stimulate its AP-1-mediated transcriptional activity. Cotransfection of PML, with GAL4/Fos strongly induced Fos-mediated activation of GAL4-responsive reporters, indicating a functional interaction between Fos and PML in vivo. Deletion analysis of Fos and PML demonstrated that the intact C-terminal domain of Fos (containing the dimerization domain), and the RING-finger, B1 box and nuclear localization domains of PML are involved in the cooperative activity of Fos and PML. Immunoprecipitation and electrophoretic mobility shift assay showed that PML is associated with the AP-1 complex. PMLRARα was also found to enhance the transcriptional activity of GAL4/Fos. The addition of retinoic acid abrogated the PMLRARα, but not PML-induced stimulation of GAL4/Fos activity in a dose-dependent manner. This study demonstrated that PML is involved in the AP-1 complex and can modulate Fos-mediated transcriptional activity, which may contribute to its growth suppressor function.
Our previous studies demonstrated that the promyelocytic leukemia gene, PML which involved in the 15;17 translocation in acute promyelocytic leukemia (APL) is a growth and transformation suppressor. In this study, recombinant PML adenovirus, Ad-PML was constructed and used to infect human breast cancer cells in vitro and in vivo, the anti-oncogenic function of PML and its mechanism of growth suppressing effect in breast cancer cells were examined. We showed that Ad-PML effectively infected the MCF-7 and SK-BR-3 cells. A high level of PML protein was expressed within 24 h post-infection and a detectable level remained at day 16. Ad-PML significantly suppressed the growth rate, clonogenicity, and tumorigenicity of breast cancer cells. Intratumoral injections of MCF-7-induced tumors by high titer Ad-PML suppressed tumor growth in nude K mice by about 80%. The injection sites expressed high level of PML and associated with a massive apoptotic cell death. To elucidate the molecular mechanism of PML's growth suppressing function, we examined the effect of Ad-PML on cell cycle distribution in MCF-7 and SK-BR-3 cells. We found that Ad-PML infection caused a cell cycle arrest at the G1 phase. We further showed that G1 arrest of MCF-7 cells is associated with a significant decrease in cyclin D1 and CDK2. An increased expression of p53, p21 and cyclin E was found. The Rb protein became predominantly hypophosphorylated 48 h post-infection. These findings indicate that PML exerts its growth suppressing effects by modulating several key G1 regulatory proteins. Our study provides important insight into the mechanism of tumor suppressing function of PML and suggests a potential application of Ad-PML in human cancer gene therapy.
Molecular and Cellular Biology (02707306)18(12)pp. 7147-7156
The promyelocytic leukemia protein (PML) is a nuclear phosphoprotein with growth- and transformation-suppressing ability. Having previously shown it to be a transcriptional repressor of the epidermal growth factor receptor (EGFR) gene promoter, we have now shown that PML's repression of EGFR transcription is caused by inhibition of EGFR's Sp1-dependent activity. On functional analysis, the repressive effect of PML was mapped to a 150-hp element (the sequences between -150 and -16, relative to the ATG initiation site) of the promoter. Transient transfection assays with Sp1-negative Drosophila melanogaster SL2 cells showed that the transcription of this region was regulated by Sp1 and that the Sp1-dependent activity of the promoter was suppressed by PML in a dose-dependent manner. Coimmunoprecipitation and mammalian two-hybrid assays demonstrated that PML and Sp1 were associated in vivo. In vitro binding by means of the glutathione S-transferase (GST) pull-down assay, using the full-length and truncated GST- Sp1 proteins and in vitro-translated PML, showed that PML and Sp1 directly interacted and that the C-terminal (DNA-binding) region of Sp1 and the coiled-coil (dimerization) domain of PML were essential for this interaction. Analysis of the effects of PML on Sp1 DNA binding by electrophoretic mobility shift assay (EMSA) showed that PML could specifically disrupt the binding of Sp1 to DNA. Furthermore, cotransfection of PML specifically repressed Sp1, but not the E2F1-mediated activity of the dihydrofolate reductase promoter. Together, these data suggest that the association of PML and Sp1 represents a novel mechanism for negative regulation of EGFR and other Sp1 target promoters.
Our previous studies demonstrated that PML is a growth suppressor that suppresses oncogenic transformation of NIH/3T3 cells and rat embryo fibroblasts. PML is a nuclear matrix-associated phosphoprotein whose expression is regulated during the cell cycle. Disruption of PML function by t(15;17) in acute promyelocytic leukemia (APL) plays a critical role in leukemogenesis. To further study the role of PML in the control of cell growth, we have stably overexpressed PML protein in the HeLa cell line. This overexpression of PML significantly reduced the growth rate of HeLa cells and suppressed anchorage-independent growth in soft agar. We consequently investigated several parameters correlated with cell growth and cell cycle progression. We found that, in comparison with the parental HeLa cells, HeLa/PML stable clones showed proportionally more cells in G1 phase, fewer cells in S phase and about the same number in G2/M phase. The HeLa/PML clones showed a significantly longer doubling time as a result of a lengthening of the G1 phase. No effect on apoptosis was found in HeLa cells overexpressing PML. This observation indicates that PML suppresses cell growth by increasing cell cycle duration as a result of G1 elongation. To further understand the mechanism of the effect of PML on HeLa cells, expression of cell cycle-related proteins in HeLa/PML and parental HeLa cells was analyzed. We found that Rb phosphorylation was significantly reduced in PML stable clones. Expression of cyclin E, Cdk2 and p27 proteins was also significantly reduced. These studies indicate that PML affects cell cycle progression by mediating expression of several key proteins that normally control cell cycle progression. These results further extend our current understanding of PML function in human cells and its important role in cell cycle regulation.
Vallian borujeni, S., Gäken, J.A., Trayner, I.D., Gingold, E.B., Kouzarides, T., Chang k.-s., K., Farzaneh, F.
Experimental Cell Research (10902422)237(2)pp. 371-382
Acute promyelocytic leukemia is characterized by the presence of a t(15; 17) chromosomal translocation which results in the expression of a chimeric gene product, PMLRARα, consisting of an N-terminal-truncated retinoic acid receptor-α fused to a C-terminal-truncated PML. Several structural features, and regions of homology to known transcription factors, suggest that PML may be involved in the regulation of gene expression. In this study we have analyzed the transcriptional regulatory activity of PML using chimeric GAL4/PML constructs and GAL4-responsive reporter plasmids. The data presented demonstrate that PML, when fused to the DNA-binding domain of GAL4 (GAL4/PML), inhibits transcription from GAL4-responsive promoters. The magnitude of this repression is cell type and promoter dependent, and deletion studies show that the putative coiled-coil and part of the serine- rich regions of PML are required for this activity. These regions are also shown to be responsible for the repression of transcription activity from the EGFR promoter. The data presented also demonstrate that GAL4/PML can recruit PMLRARα resulting in the retinoid-inducible transcriptional activation of a GAL4-responsive promoter, a function dependent on the presence of the coiled- coil region of PMLRARα.
Gäken, J.A., Tavassoli, M., Gan, S., Vallian borujeni, S., Giddings, I., Darling, D.C., Galea-lauri, J., Thomas, M.G., Abedi, H., Schreiber, V.
Journal of Virology (10985514)70(6)pp. 3992-4000
Integration of proviral DNA into the host cell genome is a characteristic feature of the retroviral life cycle. This process involves coordinate DNA strand break formation and rejoining reactions. The full details of the integration process are not yet fully understood. However, the endonuclease and DNA strand-joining activities of the virus-encoded integrase protein (IN) are thought to act in concert with other, as-yet-unidentified, endogenous nuclear components which are involved in the DNA repair process. The nuclear enzyme poly(ADP-ribose) polymerase (PARP), which is dependent on DNA strand breaks for its activity, is involved in the efficient repair of DNA strand breaks, and maintenance of genomic integrity, in nucleated eukaryotic cells. In the present work, we examine the possible involvement of PARP in the retroviral life cycle and demonstrate that inhibition of PARP activity, by any one of three independent mechanisms, blocks the infection of mammalian cells by recombinant retroviral vectors. This requirement for PARP activity appears to be restricted to processes involved in the integration of provirus into the host cell DNA. PARP inhibition does not affect viral entry into the host cell, reverse transcription of the viral RNA genome, postintegration synthesis of viral gene products, synthesis of the viral RNA genome, or the generation of infective virions. Therefore, efficient retroviral infection of mammalian cells is blocked by inhibition of PARP activity.
Arif, S., Vallian borujeni, S., Farzaneh, F., Zanone, M.M., James, S.L., Pietropaolo, M., Hettiarachchi, S., Vergani, D., Conway, G.S., Peakman, M.
Journal of Clinical Endocrinology and Metabolism (0021972X)81(12)pp. 4439-4445
Autoantibodies directed against steroid hormone-producing cells (SCA) detectable by immunofluorescence are typically found in a small proportion of patients with premature ovarian failure (POF) as well as in other endocrine autoimmune diseases. The SCA pattern stains cells in the outer zones of the adrenal cortex, ovary, and testis. To identify the molecular target of SCA, an adrenal complementary DNA expression library was screened using SCA- positive serum, and the steroid enzyme 3β-hydroxysteroid dehydrogenase (3βHSD) was identified. Only 1 of 48 (2%) patients with idiopathic POF, not preselected for the presence of other autoimmune diseases, had SCA by immunofluorescence, whereas 10 of 48 (21%) had anti-3βHSD autoantibodies detectable by immunoblot using recombinant human enzyme compared with 6 of 115 (5%) control subjects (P = 0.002). Absorption of SCA-positive serum with recombinant human 3βHSD abolished the immunofluorescence pattern. We also examined the prevalence of anti-3βHSD autoantibodies in other endocrine autoimmune diseases. Two of 112 (2%) diabetic patients, but none of the thyroid or Addisonian patients, had SCA by immunofluorescence. Twenty-six (23%) diabetic subjects (P < 0.001 vs. controls), 3 of 18 thyroid patients (P > 0.05 vs. controls), and none of 4 Addisonian patients had anti-3βHSD autoantibodies. 3βHSD is the first steroid cell autoantigen defined at the molecular level to be associated with idiopathic POF occurring in the absence of other polyglandular diseases. Autoantibodies to 3βHSD in patients with other organ-specific autoimmune diseases indicate that the enzyme behaves as a typical target of polyendocrine autoimmunity. Anti-3βHSD autoantibodies in patients with POF may provide a marker of those subjects whose ovarian failure is autoimmune in origin and, as recent studies suggest, may be salvageable with glucocorticoid treatment.
