MicroRNAs (miRNAs) are a form of single-stranded RNA molecules with a length that varies between 18 and 23 nucleotides and which are synthesized in the nucleus but function in the cytoplasm. miRNAs function endogenously and bind to complementary sequences in either the coding regions or the 3' untranslated regions (UTRs) of target messenger RNAs (mRNAs). This indicates that miRNAs operate in a post-transcriptional manner.
View Article and Find Full Text PDFDrugs Today (Barc)
May 2019
Onpattro, also commonly known as patisiran, is a small interfering RNA (siRNA) molecule packaged within a lipid nanoparticle and is transported into the cell to target transthyretin gene (TTR) messenger mRNA (mRNA) by attaching to its complementary sequence. The target mRNA is degraded and both mutant and wild-type amyloid transthyretin (ATTR) protein production becomes suppressed. This drug was developed by Alnylam Pharmaceuticals to treat a rare disease called hereditary ATTR (hATTR) amyloidosis.
View Article and Find Full Text PDFTo help characterize the FDFT1 gene and protein expression in cancer. Cholesterol represents an important structural component of lipid rafts. These specializations can be involved in pathways stimulating cell growth, survival and other processes active in cancer.
View Article and Find Full Text PDFPharmgenomics Pers Med
November 2017
RNA interference (RNAi) is a naturally existing endogenous mechanism for post-transcriptional gene regulation, nowadays commonly utilized for functional characterization of genes and development of potential treatment strategies for diseases. RNAi-based studies for therapy, after being examined for over a decade, are finally in the pipeline for developing a potential treatment for the mutated transthyretin (TTR) gene, which gives rise to a dysfunctional TTR protein. This dysfunctional protein causes TTR amyloidosis (ATTR), an inherited, progressively incapacitating, and often fatal genetic disorder.
View Article and Find Full Text PDFRecent molecular studies provide important clues into treatment of [Formula: see text]-thalassemia, sickle-cell anaemia and other [Formula: see text]-globin disorders revealing that increased production of fetal hemoglobin, that is normally suppressed in adulthood, can ameliorate the severity of these diseases. In this paper, we present a novel approach for drug prediction for [Formula: see text]-globin disorders. Our approach is centered upon quantitative modeling of interactions in human fetal-to-adult hemoglobin switch network using hybrid functional Petri nets.
View Article and Find Full Text PDFJ Bioinform Comput Biol
April 2015
p16 is recognized as a tumor suppressor gene due to the prevalence of its genetic inactivation in all types of human cancers. Additionally, p16 gene plays a critical role in controlling aging, regulating cellular senescence, detection and maintenance of DNA damage. The molecular mechanism behind these events involves p16-mediated signaling pathway (or p16- Rb pathway), the focus of our study.
View Article and Find Full Text PDFAscorbyl chitosan was synthesized by heating chitosan with ascorbic acid in isopropanol. The products were characterized by FTIR and C-13 NMR spectroscopies, SEM, and elemental analysis. Blood contact properties of ascorbyl chitosans were evaluated.
View Article and Find Full Text PDFTumor-suppressor genes (TSGs) have been classically defined as genes whose loss of function in tumor cells contributes to the formation and/or maintenance of the tumor phenotype. TSGs containing nonsense mutations may not be expressed because of nonsense-mediated RNA decay (NMD). We combined inhibition of the NMD process, which clears transcripts that contain nonsense mutations, with the application of high-density single-nucleotide polymorphism arrays analysis to discriminate allelic content in order to identify candidate TSGs in five breast cancer cell lines.
View Article and Find Full Text PDFSimvastatin and lovastatin are statins traditionally used for lowering serum cholesterol levels. However, there exists evidence indicating their potential chemotherapeutic characteristics in cancer. In this study, we used bioinformatic analysis of publicly available data in order to systematically identify the genes involved in resistance to cytotoxic effects of these two drugs in the NCI60 cell line panel.
View Article and Find Full Text PDFThe thalassemia syndromes are a diverse group of inherited disorders that can be characterized according to their insufficient synthesis or absent production of one or more of the globin chains. They are classified in to α, β, γ, δβ, δ, and εγδβ thalassemias depending on the globin chain(s) affected. The β-thalassemias refer to that group of inherited hemoglobin disorders, which are characterized by a reduced synthesis (β(+)-thalassemia) or absence (β(0)-thalassemia) of beta globin (β-globin) chain production (1).
View Article and Find Full Text PDFExperimental alteration of gene expression is a powerful technique for functional characterization of disease genes. RNA interference (RNAi) is a naturally occurring mechanism of gene regulation, which is triggered by the introduction of double-stranded RNA into a cell. This phenomenon can be synthetically exploited to down-regulate expression of specific genes by transfecting mammalian cells with synthetic short interfering RNAs (siRNAs).
View Article and Find Full Text PDFThe technique of site-directed mutagenesis has been used to characterize gene and protein structure-function relationships, protein-protein interactions, binding domains of proteins, or active sites of enzymes for the last three decades. In this technique, a nucleotide sequence of interest is experimentally altered using synthetic oligonucleotides. The most commonly used approach is to use an oligonucleotide that is complementary to part of a single-stranded DNA template, but containing an internal mismatch to direct the mutation.
View Article and Find Full Text PDFProtein kinase C betaII (PKCβII) represents a novel potential target for anticancer therapies in breast cancer. In order to identify patient subgroups which might benefit from PKC-targeting therapies, we investigated the expression of PKCβII in human breast cancer cell lines and in a tissue microarray (TMA). We first screened breast cancer cell line representatives of breast cancer subtypes for PKCβII expression at the mRNA and at the protein levels.
View Article and Find Full Text PDFChemotherapy is a major treatment modality for individuals affected by cancer. Currently, a number of genome-based technologies are being adopted to identify genes associated with drug response; however, large-scale genetic association applications are still limited. Here we describe a novel strategy based on the genetic and drug response data of the NCI60 cell lines to discover potential candidate genetic variants associated with variable response to chemotherapy.
View Article and Find Full Text PDFMethods Mol Biol
April 2007
RNA interference (RNAi) is a natural mechanism, that is triggered by the introduction of double-stranded RNA into a cell. The long double-stranded RNA is then processed into short interfering RNA (siRNA) that mediates sequence-specific degradation of homologous transcripts. This phenomenon can be exploited to experimentally trigger RNAi and downregulate gene expression by transfecting mammalian cells with synthetic siRNA.
View Article and Find Full Text PDFPancreatic cancer is a highly aggressive disease characterized by poor prognosis and vast genetic instability. Recent microarray-based, genome-wide surveys have identified multiple recurrent copy number aberrations in pancreatic cancer; however, the target genes are, for the most part, unknown. Here, we characterized the 19q13 amplicon in pancreatic cancer to identify putative new drug targets.
View Article and Find Full Text PDFSingle nucleotide polymorphisms (SNPs) constitute the most common type of genetic variation in humans. SNPs introducing premature termination codons (PTCs), herein called X-SNPs, can alter the stability and function of transcripts and proteins and thus are considered to be biologically important. Initial studies suggested a strong selection against such variations/mutations.
View Article and Find Full Text PDFThe identification of tumor-suppressor genes in solid tumors by classical cancer genetics methods is difficult and slow. We combined nonsense-mediated RNA decay microarrays and array-based comparative genomic hybridization for the genome-wide identification of genes with biallelic inactivation involving nonsense mutations and loss of the wild-type allele. This approach enabled us to identify previously unknown mutations in the receptor tyrosine kinase gene EPHB2.
View Article and Find Full Text PDFIn this report we describe the molecular analysis of 795 chromosomes derived from unrelated Turkish beta-thalassemia and sickle cell anemia carriers identified in hematology clinics in Istanbul, Ankara, Izmir, Adana, and Antalya. The determination of the molecular pathology of 754 beta-thalassemia and 42 abnormal hemoglobin genes and analysis of the frequency distribution in six distinct regions of Turkey was accomplished. The experimental strategy, based on PCR amplification of the beta-globin gene, included dot-blot hybridization with 18 probes specific for the Mediterranean populations, denaturing gradient gel electrophoresis, and genomic sequencing.
View Article and Find Full Text PDFGenotypes and phenotypes were studied in 31 Turkish HbS-beta-thalassemia patients. In 19 patients the beta-thalassemia mutations were beta+ and in 12 the beta 0 phenotype. The IVSI-110 mutation was found in 45% of the patients.
View Article and Find Full Text PDFWe describe the rare beta-thalassemia mutation at codons 36/37 (-T) for the first time in Turkey. The propositus is a Turkish patient with beta-thalassemia major who originated in Adana but now resides in Istanbul. Molecular analysis revealed a compound heterozygosity for the common eastern Mediterranean mutation IVS-I-110 (G-A) along with mutation FSC-36/37 (-T).
View Article and Find Full Text PDFThis paper reports our experience of molecular analysis and diagnosis of beta-thalassaemia and sickle cell anaemia (HbS) in 70 prospective parents of Turkish descent and their fetuses. Molecular screening was carried out by allele-specific oligonucleotide (ASO) hybridization of amplified DNA to the 12 most common mutations in the Turkish population. By using this approach, we were able to define the mutation in 95 per cent of chromosomes investigated.
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