The altered expression of long non-coding RNAs: GHET1, BACE1-AS, PANDA, UCA1 associated with non-small cell lung cancer

Objective: Long non-coding RNAs (lncRNAs) are characterized as non-coding transcripts greater than 200 nucleotides. lncRNAs have extensive molecular connections with proteins and microRNAs, which are important in the regulation of gene expression in physiologic and pathologic states including cancer. About 18% of human LncRNAs were recently found to be associated with tumours. Many studies indicated that aberrant expression of LncRNAs play key roles in the progression and metastasis of NSCLC. In this study we evaluated the expression of long non-coding RNAs: GHET1, BACE1-AS, PANDA, UCA1 in non-small cell lung cancer. Material & Methods: In this study, RNA was extracted from tumor tissues of NSCLC and paired adjacent normal lung tissues. After cDNA synthesis, the relative expression level of lncRNA GHET1, BACE1-AS, PANDA, and UCA1 genes was studied by TaqMan Real-Time PCR, and the data were analyzed by 2-∆∆CT. The t-test was used to compare the values and P-value < 0.05 was considered statistically significant. Results: The data of qRT-PCR analysis revealed that the expression level of GHET1 gene in patients with NSCLC is increased (P= 0.0032) and BACE1-AS showed down-regulation (P= 0.0093). There was no significant change in the expression of PANDA and UCA1 genes. Conclusion: Our study sheds lights on the expression signature of several crucial lncRNAs in human lung cancer. This data not only could be further be utilized for different therapeutic approaches but also reveal the changes in biological processes of human lung tumors. &nbsp

A novel 355-357delGAG mutation and frequency of connexin-26 (GJB2) mutations in Iranian patients

The common form of autosomal recessive non-syndromic deafness is caused by the mutation in gap junction beta 2 (GJB2) gene (GenBank M86849, OMIM# 121011) which is located at the DFNB1 locus at 13q11. GJB2 is a small gene about 5500-bp length with two exons, of which only one contains the coding region (Kelley et al. 2000). The sequence of the coding region consists of 681 bp, encoding a gap-junction protein with 226 amino acids (Schrijver 2004). The genetics of hearing loss is highly heterogeneous and more than 100 mutations in connexin 26 (GJB2) genes are reported to be responsible for 30%–40% of hereditary hearing loss in deaf subjects (Ballana et al. 2001; Schrijver 2004). The most frequent mutation 35delG has been detected in different populations; especially in European countries where it is established to be due to founder effect (Van Laer et al. 2001; Rothrock et al. 2003). In this study, we performed mutation screening in 33 families who met clinical criteria of non-syndromic hereditary hearing loss (NSHHL) to evaluate the type and frequency of GJB2 mutations in Iranian population

Mitochondrial DNA Copy Number Variations in Gastrointestinal Tract Cancers: Potential Players

International audienceAlterations of mitochondria have been linked to several cancers. Also, the mitochondrial DNA copy number (mtDNA-CN) is altered in various cancers, including gastrointestinal tract (GIT) cancers, and several research groups have investigated its potential as a cancer biomarker. However, the exact causes of mtDNA-CN variations are not yet revealed. This review discussed the conceivable players in this scheme, including reactive oxygen species (ROS), mtDNA genetic variations, DNA methylation, telomere length, autophagy, immune system activation, aging, and infections, and discussed their possible impact in the initiation and progression of cancer. By further exploring such mechanisms, mtDNA-CN variations may be effectively utilized as cancer biomarkers and provide grounds for developing novel cancer therapeutic agents

Promoter Hypermethylation of Estrogen Receptor Alpha Gene Is Correlated to Estrogen Receptor Negativity in Iranian Patients with Sporadic Breast Cancer

Objective: Breast Cancer is the most common cancer in Iranian women. Breast tumors are classified based on the estrogen receptor alpha (ERα) expression status into ER negative and ER positive tumors. ER negative tumors tend to have worse prognosis and less likely to respond to endocrine therapy. Aberrant methylation of gene promoter is one of the mechanisms for gene silencing in breast tumors. Because of its reversible nature, promoter methylation is a good target for new therapeutic strategies. We aimed to evaluate the frequency of this epigenetic event in ERα gene and its association to clinicopathological features in Iranian breast cancer patients.Materials and Methods: In this case control study the patient series consisted of 100 sporadic primary breast cancer cases (51 ER negative and 49 ER positive tumors). None of the participants had chemo or radiotherapy before surgery. In breast tumors ERα promoter methylation were assessed with methylation specific polymerase chain reaction (MSP). Data was collected on clinicopathological features of the patients. Correlation between ERα methylation and clinicopathological characteristics of the patients was investigated by Pearson Chi-Square and Fisher’s exact test.Results: ERα methylation was detected in 98% of ER negative and 65% of ER positive breast tumors. A strong correlation was found between ERα methylation and ER negativity in tumors (p<0.0001). Also, ERα methylation has associated to progesterone receptor negativity (p<0.008) and double receptor negative status (p<0.0001) in breast tumors.Conclusion: ERα methylation occurs with high frequency in the breast tumors of Iranian breast cancer patients and may play a considerable role in pathogenesis of ERα negative tumors as a poor prognosis and more aggressive category. The reversible nature of DNA methylation may provide new therapeutic possibilities in ER negative breast tumors

Dynamic Changes of Mitochondrial DNA Copy Number in Gastrointestinal Tract Cancers: A Systematic Review and Meta-Analysis

International audienceWe have performed a systematic review and meta-analysis for evaluation of mitochondrial DNA copy number (mtDNA-CN) alterations in peripheral blood leukocytes (PBL), and tumor tissues of gastrointestinal tract (GIT) cancers. Analysis of the PBL demonstrated a significant decrease [OR: 0.6 (0.5, 0.8)] and increase [OR: 1.4 (1.1, 1.9)] prior to and following GIT cancer development, respectively. This trend was more evident in CRC, and GC subgroups. Analysis of tissue yielded high levels of heterogeneity. However, the mean difference for the CRC subgroup was statistically significant [1.5 (1.0, 2.2)]. Our analysis suggests mtDNA-CN deserves further investigations as a GIT-cancer screening tool

Molecular Analysis of HS-111 and 3`HS1 Variations in β-Thalassemia Intermedia Patients with High Levels of HbF

Objective: To study the possible association between high levels of fetal haemoglobin(HbF) in β-thalassemia intermedia patients and HS-111 and 3`HS1 sequence variations.Materials and Methods: In this study, the 3' HS-1 and HS-111 regions of 30 ß-thalassaemiaintermedia patients (ß°/ß°) with high levels of HbF, 21 ß-thalassemia major patientsand 40 normal Iranian individuals were analyzed by single-strand conformation polymorphism(SSCP) and polymerase chain reaction (PCR) sequencing.Results: Two nucleotide variations in 3' HS111 (-21A>G) and 3`HS1 (179C>T) wereidentified. The most frequent sequence variation was 3' HS111 (-21A) in the intermediapatients and 3`HS111 (-21G) in the major thalassemia patients. In contrast to the 3`HS1marker, both 3'HS111 A and G variants showed a correlation with each studied group.Conclusion: The HS111 marker in conjunction with other parameters could be used asappropriate genetic markers to discriminate β-thalassemia intermedia patients (β°/β°) withhigh levels of HbF from β-thalassemia major patients

Assessing Methylation of Mir-146b in Patients with Non-Small Cell Lung Cancer

Background: One of the most important epigenetic factors in lung cancer is aberrant DNA methylation. So far, many studies have been performed on the methylation of various genes and microRNAs in various cancers, especially lung cancer. So because of the high importance of microRNAs in cancer. In this study, mir-146b methylation was checked in NSCLC tissues.Method: Analysis methylation of mir146b was investigated in 30 samples NSCLC tissues and 30 adjacent normal tissues using by MS-HRM method.Results: Study on mir146b methylation showed that there was no significant difference between the methylation levels of this microRNA in tumor samples compared with healthy samples (P>0.05). However, this study was designed as a pilot study, and further investigations are required to confirm our findings

Expression analysis data of BCL11A and γ-globin genes in KU812 and KG-1 cell lines after CRISPR/Cas9-mediated BCL11A enhancer deletion

The data presented in this article are related to the research article entitled as "Targeted deletion of the BCL11A gene by CRISPR-Cas9 system for fetal hemoglobin reactivation: A promising approach for gene therapy of beta-thalassemia disease " [1]. BCL11A is a master regulator of γ-globin gene silencing, and suppresses fetal hemoglobin expression by association with other γ-globin suppressors, and also interacts with human beta-globin locus control region as well as intergenic region between the Aγ and δ-globin genes to reconfigure beta-globin cluster. Thus, HbF reactivation has been proposed to be an approach for the treatment of β-thalassemia through knockout of BCL11A. Accordingly, an erythroid enhancer sequence was identified that, when inactivated, led to repression of BCL11A and induction of γ-globin in the erythroid lineage [2-7]. This article describes data that obtained from BCL11A gene enhancer modification in KU812 and KG-1 cell lines using the CRISPR-Cas9 genome editing system in order to reactivate γ-globin gene expression

Structural Insight into Anaphase Promoting Complex 3 Structure and Docking with a Natural Inhibitory Compound

Background: Anaphase promoting complex (APC) is the biggest Cullin-RING E3 ligase and is very important in cell cycle control; many anti-cancer agents target this. APC controls the onset of chromosome separation and mitotic exit through securin and cyclin B degradation, respectively. Its APC3 subunit identifies the APC activators-Cdh1 and Cdc20. Materials and Methods: The structural model of the APC3 subunit of APC was developed by means of computational techniques; the binding of a natural inhibitory compound to APC3 was also investigated. Results: It was found that APC3 structure consists of numerous helices organized in anti-parallel and the overall model is superhelical of tetratrico-peptide repeat (TPR) domains. Furthermore, binding pocket of the natural inhibitory compound as APC3 inhibitor was shown. Conclusion: The findings are beneficial to understand the mechanism of the APC activation and design inhibitory compounds

Improvement of K562 Cell Line Transduction by FBS Mediated Attachment to the Cell Culture Plate

Lentiviral vectors have been used for gene therapy in the clinical phase in recent years. These vectors provide a tool for gene insertion, deletion, or modification in organisms. The K562 human cell line has been used extensively in hematopoietic research. Despite its broad application, it is hard-to-transfection and transduction. So, this study presents a simple method to increase the transduction efficiency of K562 cells with a low multiplicity of infection (MOI) of the virus particle. For this purpose, 24-well plate was coated by 300 μl fetal bovine serum (FBS) before seeding. Then 2×104 K562 cells were seeded in each FBS coated plate. After 24h, K562 cells were attached and doubled. Different amount of lentivirus-based GFP vector according to MOI (5, 10, 15, and 20) along with 8 μg polybrene was added to the attached K562 cells and after 6h cells and viral particle complex were spinfected. Then cells were returned to the plate and incubated in 37°C overnight. After 48h transduction efficiency was established by measuring the GFP-expressing cells by flow cytometry. Flow cytometry analysis showed that, after plate treatment by FBS, 64.5% transduction rate in K562 cells was achieved at MOI=20. Therefore, this method can be an effective and simple way to increase the lentiviral transduction rate for suspended cells such as K562