A novel method of multiplex SNP genotyping assay through variable fragment length allele-specific polymerase chain reaction: Multiplex VFLASP-ARMS

Variable Fragment Length Allele-Specific Polymerase Chain Reaction (VFLASP) and Amplification Refractory Mutation System (ARMS) are reliable methods for detecting allelic variations resulting from single base changes within the genome. Due to their widespread application, allele variations caused by Single Nucleotide Polymorphisms (SNPs) can be readily detected using allele-specific primers. In the context of the current study, VFLASP was combined with ARMS method as a novel strategy to enhance the efficacy of both techniques. Clinically important base variations within SNP regions used in the study were detected by a fragment analysis method. To validate the accuracy of the developed VFLASP-ARMS method, specifically designed synthetic sequences were tested using a capillary electrophoresis system. Allele-specific primers exhibit differences solely at the 3' end based on the sequence of the SNP. Additionally, to increase the specificity of the primers, a base was intentionally added for incompatibility. Therefore, allele discrimination on fragment analysis has been made possible through the 3-6 bp differences in the amplicons. With the optimization of the system, designed synthetic sequences provided reliable and reproducible results in wild-type, heterozygous, and homozygous genotypes using the VFLASP-ARMS method. Hence, our results demonstrated that VFLASP-ARMS method, offers a novel design methodology that can be included in the content of SNP genotyping assays.

Development of super-specific epigenome editing by targeted allele-specific DNA methylation

BACKGROUND

Epigenome editing refers to the targeted reprogramming of genomic loci using an EpiEditor which may consist of an sgRNA/dCas9 complex that recruits DNMT3A/3L to the target locus. Methylation of the locus can lead to a modulation of gene expression. Allele-specific DNA methylation (ASM) refers to the targeted methylation delivery only to one allele of a locus. In the context of diseases caused by a dominant mutation, the selective DNA methylation of the mutant allele could be used to repress its expression but retain the functionality of the normal gene.

RESULTS

To set up allele-specific targeted DNA methylation, target regions were selected from hypomethylated CGIs bearing a heterozygous SNP in their promoters in the HEK293 cell line. We aimed at delivering maximum DNA methylation with highest allelic specificity in the targeted regions. Placing SNPs in the PAM or seed regions of the sgRNA, we designed 24 different sgRNAs targeting single alleles in 14 different gene loci. We achieved efficient ASM in multiple cases, such as ISG15, MSH6, GPD1L, MRPL52, PDE8A, NARF, DAP3, and GSPT1, which in best cases led to five to tenfold stronger average DNA methylation at the on-target allele and absolute differences in the DNA methylation gain at on- and off-target alleles of > 50%. In general, loci with the allele discriminatory SNP positioned in the PAM region showed higher success rate of ASM and better specificity. Highest DNA methylation was observed on day 3 after transfection followed by a gradual decline. In selected cases, ASM was stable up to 11 days in HEK293 cells and it led up to a 3.6-fold change in allelic expression ratios.

CONCLUSIONS

We successfully delivered ASM at multiple genomic loci with high specificity, efficiency and stability. This form of super-specific epigenome editing could find applications in the treatment of diseases caused by dominant mutations, because it allows silencing of the mutant allele without repression of the expression of the normal allele thereby minimizing potential side-effects of the treatment.

Blastocystis subtype 1 (allele 4); Predominant subtype among tuberculosis patients in Iran

BACKGROUND

Blastocystis and tuberculosis are two public health issues that are frequently reported in regions with low level of hygiene. Therefore, the current study aimed to investigate Blastocystis subtype and allele distribution in TB patients.

METHODS

Totally, 161 stool samples were taken from TB patients who were undergoing anti-MTB treatment. Stool samples were concentrated using conventional formalin-ether technique and examined using Lugol's iodine staining under light microscopy. DNA extraction was carried out and discriminative fragment was amplified and sequenced. With comparison in GenBank database, relevant subtypes and alleles were characterized and phylogenetically analyzed using MEGA v.7 and Tamura 3-parameter model.

RESULTS

In total, from 161 stool samples, 19 samples were suspected to be Blastocystis-positive. The expected fragment was amplified in 13 (8.07%) of samples. Accordingly, 11/13 (84.62%) of Blastocystis cases settled in urban and 2/13 (15.38%) were villagers. Close-contact with animals was also seen among 7/13 (53.84%) of samples. Subtype 1 (7/13; 53.84%) was the most prevalent followed by subtype 2 (5/13; 38.46%) and subtype 3 (1/13, 7.69%). All ST1 were allele 4, while alleles 9, 11 and 12 were seen in ST2 and allele 34 was the only allele observed in ST3. All three subtypes were clearly separated, while there was no separation between sequences from TB and non-TB patients.

CONCLUSION

Blastocystis ST1 was the most prevalent subtype in TB patients and there was no difference between Blastocystis isolates from TB and non-TB human subjects.

Genetic diversity analysis of Blastocystis subtypes from both symptomatic and asymptomatic subjects using a barcoding region from the 18S rRNA gene

Blastocystis is the most prevalent protozoa found in human stool samples. This study aimed to evaluate genetic diversity among Blastocystis subtypes isolated from both symptomatic and asymptomatic subjects as well as the potential correlation between subtypes and symptoms. A total of 55 Blastocystis-positive isolates were included in this study. A barcoding region of the small subunit rDNA was amplified and genetically assessed using MEGA6 and DnaSP regarding the presence of symptoms. BLAST analyses revealed the presence of 5 different subtypes (ST1, ST2, ST3, ST6 and ST7) among the samples. ST3 was the most prevalent subtype (25/55, 45%) while only one ST7 isolate was detected. Moreover, alleles 4 and 86 for ST1; alleles 9, 11 and 12 for ST2; alleles 31, 34, 36, 37 and 52 for ST3; allele 122 for ST6 and allele 137 for ST7 were detected. No statistically significant association was found between gender and symptoms with certain subtypes. Analysis of the intra-subtype variability in both symptomatic and asymptomatic subjects revealed highest similarity among ST1 isolates while lowest similarity was seen among ST3 isolates. Neutrality indices, Tajima's D and Fu's Fs, were negative but only statistically significant for ST3. Furthermore, highest values of Hd, π and S were observed among ST1, ST2 and ST3 isolated from symptomatic patients indicating high level of diversity among isolates obtained from these subjects. In addition, inter-subtype analysis showed the highest similarity between ST1 and ST2 isolates and the lowest similarity between ST2 and ST7 isolates. This is the first study revealing the presence of both ST6 and ST7 isolates in human from Iran. Phylogenetic analysis did not suggest any significant correlation between clinical manifestations and certain subtypes although genetic analysis showed highest value of diversity and significant neutrality indices among ST3 isolates obtained from symptomatic patients.