Solanum nigrum Anticancer Effect Through Epigenetic Modulations in Breast Cancer Cell Lines

Background:

DNA methylation plays an important role in the regulation of gene expression in mammalian cells and often occurs at CpG islands in the genome. It is more reversible than genetic variations and has therefore attracted much attention for the treatment of many diseases, especially cancer. In the present study, we investigated the effect of Solanum nigrum Extract (SNE) on the methylation status of the VIM and CXCR4 genes in breast cancer cell lines.

Methods:

The Trypan blue assay was used to study the effect of SNE at various concentrations of 0, 0.1, 1.5, 2.5, 3.5 and 5 mg/ml for 48 h on the survival of three human breast cancer cell lines MCF7, MDA-MB-468, MDA-MB-231. Methylation status of VIM and CXCR4 genes in breast cancer cell lines was assessed by Methylation-Specific PCR (MSP) method. Also, methylation changes of VIM and CXCR4 genes in breast cancer cell lines after treatment with 0.1 mg/ml of SNE for 6 days were analyzed by MSP method. To confirm the effect of SNE on methylation of VIM and CXCR4 genes, Real-Time PCR was performed.

Results:

The Trypan blue assay results indicated that treatment with SNE reduced cell viability in a dose-dependent manner in breast cancer cells. Our results showed that treatment of breast cancer cells with 0.1 mg/ml of SNE hypermethylated the VIM, CXCR4 genes and significantly reduced the expression levels of their mRNA (P<0.05).

Conclusion:

Our findings reveal for the first time the impact of SNE on the methylation of breast cancer cells.

Examination of methylation changes of VIM, CXCR4, DOK7, and SPDEF genes in peripheral blood DNA in breast cancer patients

BACKGROUND

Studying whole blood DNA methylation as a risk marker has valuable applications in either diagnosis or staging of breast cancer. We investigated whole blood DNA methylation status of VIM, CXCR4, DOK7, and SPDEF genes in breast cancer patients in comparison to healthy control subjects.

MATERIALS AND METHODS

60 patients with breast cancer and 40 healthy controls were examined. Genomic DNA isolated from peripheral blood and restriction enzyme polymerase chain reaction (REP) method was applied for analysis. Real-time PCR was used to confirm methylation status of the aforementioned genes and therefore to find out the methylation differences between normal and breast cancer subjects.

RESULTS

Level of DOK7 promoter hypomethylation in normal and breast cancer samples was significant (P-value = 0.001). The study, also, showed that hypomethylation of VIM and CXCR4 genes are significant in patients compared with normal cases (P-value < 0.05). Furthermore, SPDEF promoter hypomethylation was not significantly differed between normal and breast cancer samples (P-value = 0.2).

CONCLUSIONS

Hypermethylation of DOK7 gene in DNA from patients affected with breast cancer offers a biomarker for diagnosis of the breast cancer. This study indicates that methylation status of VIM and CXCR4 genes changes in breast cancer; so, they can be used as molecular biomarkers in breast cancer prognosis.

Impact of a Missense Variation (p.S150R:AGC>AGG) in the XRCC2 Gene on Susceptibility to Colorectal Cancer

BACKGROUND

The X-ray repair complementing defective repair in Chinese hamster cells 2 (XRCC2) is an important protein in response to DNA double-strand breaks (DSBs) in human cells. XRCC2, as a functional protein in the homologous recombination repair (HRR) process, has been identified to have several polymorphisms which might be associated with the risk of cancer. Therefore, we aimed to investigate a novel missense variation (AGC>AGG, p.Ser150Arg) in the XRCC2 gene for colorectal cancer susceptibility.

METHODS

We studied 291 colorectal cancer (CRC) patients and 140 healthy individuals. ARMS PCR method was used to detect the AGC>AGG (p.Ser150Arg) variation in the XRCC2 gene.

RESULTS

The results showed that there was a significant differential among CRC and controls in the genotypic and allelic frequencies (p < 0.001) of XRCC2; AGC>AGG, p.Ser150Arg. Our results demonstrated that the G allele of XRCC2; AGC>AGG, p.Ser150Arg was associated with increased CRC risk (odds ratio = 59.04, 95% confidence interval = 18.6 - 186). This variation also influenced CRC cancer susceptibility in smokers (p < 0.001).

CONCLUSIONS

The G allele of XRCC2; AGC>AGG, p.Ser150Arg, may be a potential marker for CRC in Iranians and investigations in other populations are warranted for further universal application in CRC detection and prediction.

Comprehensive analysis via exome sequencing uncovers genetic etiology in autosomal recessive nonsyndromic deafness in a large multiethnic cohort

Purpose

Autosomal recessive non-syndromic deafness (ARNSD) is characterized by a high degree of genetic heterogeneity with reported mutations in 58 different genes. This study was designed to detect deafness causing variants in a multiethnic cohort with ARNSD by using whole-exome sequencing (WES).

Methods

After excluding mutations in the most common gene, GJB2, we performed WES in 160 multiplex families with ARNSD from Turkey, Iran, Mexico, Ecuador and Puerto Rico to screen for mutations in all known ARNSD genes.

Results

We detected ARNSD-causing variants in 90 (56%) families, 54% of which had not been previously reported. Identified mutations were located in 31 known ARNSD genes. The most common genes with mutations were MYO15A (13%), MYO7A (11%), SLC26A4 (10%), TMPRSS3 (9%), TMC1 (8%), ILDR1 (6%) and CDH23 (4%). Nine mutations were detected in multiple families with shared haplotypes suggesting founder effects.

Conclusion

We report on a large multiethnic cohort with ARNSD in which comprehensive analysis of all known ARNSD genes identifies causative DNA variants in 56% of the families. In the remaining families, WES allows us to search for causative variants in novel genes, thus improving our ability to explain the underlying etiology in more families.

Relation between serum ferritin and liver and heart MRI T2* in beta thalassaemia major patients

There is a need for higly accurate non-invasive methods for assessing organ iron content in thalassaemia patients. This study evaluated the relation between serum ferritin level, liver enzyme levels and hepatitis C antibody and liver and heart iron deposition assessed by MRI T2*. Data were obtained from the medical records of 156 thalassemia major patients in Tehran. There was a moderate negative correlation between serum ferritin and liver MRI T2* relaxation time (r = -0.535) and a weak negative correlation between serum ferritin and heart MRI T2* relaxation time (r = -0.361). Hepatitis C infection and liver enzyme levels did not confound or modify the relation between ferritin and liver or heart MRI T2*. Liver and heart MRI T2* readings were poorly correlated (r = 0.281). Routine evaluation of liver and heart iron content using MRI T2* is suggested to better evaluate the haemosiderosis status in thalassemia patients.

A transversion mutation in non-coding exon 3 of the TMC1 gene in two ethnically related Iranian deaf families from different geographical regions; evidence for founder effect

OBJECTIVES

Transmembrane channel-like 1 (TMC1) gene is a member of the transmembrane channel-like (TMC) gene family that encodes an integral membrane protein of the inner ear. It is suggested that mutation in this gene is one of the main causes of autosomal recessive non-syndromic hearing loss (ARNSHL) in different populations. The aim of this study was to determine the contribution of the TMC1 gene mutations in causing hearing loss in Iran.

METHODS

In total 54 unrelated Iranian families containing 159 affected individuals with ARNSHL detected by audiometric and otologic examinations were analyzed. Haplotype analysis of all members of 45 GJB2- & GJB6-negative families, using four microsatellite markers linked to DFNB7/11 was performed.

RESULTS

Co-segregation of hearing loss with all investigated markers for the DFNB7/11 locus was found in one family. DNA sequencing of all coding and non-coding exons and intron boundaries of the TMC1 gene identified c.-258A>C mutation in non-coding exon 3 only in individuals with hearing loss. This mutation has been previously reported in another Iranian family (G9) that share similar ethnicity. This variant was not detected in 300 ethnically matched healthy controls.

CONCLUSIONS

These results increase the probability that this nucleotide variation may be a pathogenic mutation. This study showed that the ethnicity may be more useful than geographical location to design research strategy for determining which genes should be considered when a heterogeneous disorder is under investigation.

Screening of OTOF mutations in Iran: a novel mutation and review

OBJECTIVE

Mutations in OTOF have been reported to cause nonsyndromic hearing loss in different populations. The purpose of this study is screening of OTOF mutations in Iranian population.

METHODS

Thirty-eight consanguineous families affected with autosomal recessive nonsyndromic hearing loss (ARNSHL) and negative for GJB2 or GJB6 mutations were screened by autozygosity mapping and Sanger sequencing to find OTOF mutations.

RESULTS

A novel homozygous frameshift mutation (c.1981dupG) was found to cause hearing loss in one family and no other OTOF variants were detected in the remaining families. The affected individuals were homozygous forp. D661GfsX2 causing defect in long isoform of otoferlin.

CONCLUSIONS

We conclude that OTOF mutations are not the major cause of ARNSHL in the Iranian population but still may play an important role in HL; therefore evaluation the OTOF gene is of concern.

Design of a biological method for rapid detection of presence of PCR inhibitors in aged bone DNA

BACKGROUND

Molecular human identification is one of the most important tests performed in forensic laboratories. Some of these tests are applied for identification of human remains from natural disasters, wars, etc., but problems may occur as a result of DNA degradation and external DNA contamination. We investigated effects of bacterial DNA on identifying the presence or absence of PCR inhibitors in aged bone DNA.

METHODS

DNA samples were extracted from blood, bone remains and Escherichia coli. These DNA were amplified using human and bacterial specific primers.

RESULTS

Using different blood, aged bone, and bacterial DNA dilutions along with PCR based methods; we checked their positive, negative effects, or detecting presence of inhibitors in aged bone DNA by PCR method.

CONCLUSIONS

Our observation indicated that the addition of bacterial DNA could be a valid biological method for testing the quality of bone DNA to enable us to obtain a usable profile for the identification of human remains. This method will help to test the presence of inhibitors, quantity or even quality of DNA which are of importance in profiling archeological remains. Our method will help to determine if PCR failure is due to presence of inhibitors or lack of amplifiable DNA either because of degradation, minute amount or absence of human DNA.

High level of intrafamilial phenotypic variability of non-syndromic hearing loss in a Lur family due to delE120 mutation in GJB2 gene

Hearing loss is the most common sensory defect in the world. The genetic basis of this condition is very complex. Molecular variations in GJB2 gene are the common cause of hearing impairment in Caucasians. One expects that affected members of a family with same mutation have similar phenotype. Here, we report phenotypic variability in hearing loss among the members of a Lur family. Two brothers from a Lur family from Lurestan province in western Iran with variable degrees of nonsyndromic sensorineural hearing loss were evaluated for genetic counseling. Clinical examinations, audiological tests and molecular studies including GJB2 gene sequencing and detection of Delta(GJB6-D13S1830) deletion were performed. Sequencing analysis of GJB2 gene revealed delE120 mutation in both brothers in homozygous form. Since one of them was profoundly deaf and the other was mild hearing loss and had normal conversation, we were expecting different genotypes or other causative effects. Delta(GJB6-D13S1830) was not found. Phenotypic variability between members of different families with the same type of mutation can be expected which may be due to the role of different modifying factors, unrecognized gap junction isoforms, or polymorphism effects.

Investigation of GJB6 large deletions in Iranian patients using quantitative real-time PCR

BACKGROUND

Hearing loss is a serious sensory defect in the world. Mutations in the GJB2 and GJB6 genes are the major causes of autosomal recessive nonsyndromic hearing loss (NSHL). Recently, three major large deletions in the GJB6 gene including del(GJB6-D13S1830), del(GJB6-D13S1854), and a > 920 kb deletion have been reported to form double heterozygosity with GJB2. This may suggest that deletions involving GJB6 may be responsible for some NSHL.

METHODS

We designed a real time SYBR green-based PCR to quantify a common deleted region in GJB6 gene. The amplified region covers the area which has been seen to be deleted in all of the above reports. We selected nine families heterozygous for different mutations in GJB2 gene to investigate the presence of deletions in the GJB6 gene. The samples were run along with controls for normal hearing and heterozygous and homozygous for GJB2 mutations to optimize our method. As a reference gene or external standard, a segment of the CLCN7 gene was also quantified as well.

RESULTS

We did not detect any deletion in the GJB6 gene.

CONCLUSIONS

Using this method, any deletion involving GJB6 gene can be detected in a rapid and sensitive way.

Lipid profile in minor thalassemic patients: a historical cohort study

Minor beta thalassemia is a disorder without any special symptom which only causes mild anemia. In thalassemic patients accelerated erythropoiesis and enhanced cholesterol consumption have been suggested as the dominant mechanism for low level of lipoproteins. Hyperlipidemia is a risk factor for cardiovascular diseases and hence, low level of serum lipids can act as a protective factor. Because of the differences between social, economic, cultural conditions, dietary habits and genetics patterns among Iranians with other nations, this survey was conducted to verify these parameters among our thalassemia minor subjects. This study was carried out on 100 thalassemia carriers and 200 normal controls. Blood samples were collected and the biochemical evaluation was performed for measuring serum total cholesterol, LDL, HDL, TG, VLD. Descriptive statistical tables, independent t-test, Mann- Whitney and Chi-square were used for analyzing the data. The average values of serum total cholesterol, TG, LDL, HDL and VLDL in thalassemia minor subjects were 163.63±34.28, 159.74±157.54, 90.97±23.94, 34.97±8.07 and 73.44±72.43 mg/dl respectively. Moreover, the mean levels of total cholesterol, TG, LDL, HDL and VLDL in normal subjects were 192.77±37.27, 155.67±109.58, 123.42±33.57, 38.02±15.6 and 71.57±50.5 mg/dl respectively. The amount of serum total cholesterol and LDL in thalassemia carriers was significantly lower than normal subjects that shows the potential decline of cardiovascular and brain vessels diseases among thalassemia minor subjects compared to control group while other factors between the two groups did not show any significant difference. DOI:  http://dx.doi.org/10.3329/bmrcb.v37i1.7795 Bangladesh Med Res Counc Bull 2011; 37: 24 - 27