Rapid and sensitive detection of point mutations and DNA polymorphisms using the polymerase chain reaction

Diversity and consequences of structural variation in the human genome

The biomedical community is increasingly invested in capturing all genetic variants across human genomes, interpreting their functional consequences and translating these findings to the clinic. A crucial component of this endeavour is the discovery and characterization of structural variants (SVs), which are ubiquitous in the human population, heterogeneous in their mutational processes, key substrates for evolution and adaptation, and profound drivers of human disease. The recent emergence of new technologies and the remarkable scale of sequence-based population studies have begun to crystalize our understanding of SVs as a mutational class and their widespread influence across phenotypes. In this Review, we summarize recent discoveries and new insights into SVs in the human genome in terms of their mutational patterns, population genetics, functional consequences, and impact on human traits and disease. We conclude by outlining three frontiers to be explored by the field over the next decade.

Reticulate Evolution in Japanese Sceptridium (Ophioglossaceae), including diploid, tetraploid, and hexaploid species

Homospory represents an intriguing reproductive strategy, including the potential for gametophytic selfing, considered the ultimate form of selfing. The plants of the fern genus Sceptridium (Ophioglossaceae) are generally considered to be predominantly selfing, making them suitable for analyzing speciation patterns and intraspecific variation characteristic of homosporous plants. The Sceptridium species in Japan not only exhibit variations in ploidy, including diploids, tetraploids, and hexaploids, but also pose taxonomic challenges due to morphologically distinctive forms that are difficult to be assigned to previously described species. We developed multiple single-copy nuclear markers and aimed to identify ancestral species of the polyploids and to elucidate the evolutionary entity of an undescribed species. Chromosome counts and analyses of individual gene trees confirmed that S. japonicum, S. atrovirens, and the undescribed species are allohexaploids originating through hybridization between a maternal tetraploid ancestor closely related to S. formosanum and a paternal diploid ancestor closely related to extant diploid species. By identifying homoeologs derived from the diploid ancestor, we successfully analyzed the phylogenetic relationship between the diploid ancestor of the hexaploid species and extant diploid species using the multispecies coalescent model. The examined undescribed species could not be distinguished from S. atrovirens by multiple nuclear markers or by SNP data obtained from multiplexed ISSR genotyping by sequencing. This species appears to represent one of the polymorphisms of S. atrovirens, which was fixed through gametophytic selfing.

Current approaches in CRISPR-Cas systems for diabetes

In the face of advancements in health care and a shift towards healthy lifestyle, diabetes mellitus (DM) still presents as a global health challenge. This chapter explores recent advancements in the areas of genetic and molecular underpinnings of DM, addressing the revolutionary potential of CRISPR-based genome editing technologies. We delve into the multifaceted relationship between genes and molecular pathways contributing to both type1 and type 2 diabetes. We highlight the importance of how improved genetic screening and the identification of susceptibility genes are aiding in early diagnosis and risk stratification. The spotlight then shifts to CRISPR-Cas9, a robust genome editing tool capable of various applications including correcting mutations in type 1 diabetes, enhancing insulin production in T2D, modulating genes associated with metabolism of glucose and insulin sensitivity. Delivery methods for CRISPR to targeted tissues and cells are explored, including viral and non-viral vectors, alongside the exciting possibilities offered by nanocarriers. We conclude by discussing the challenges and ethical considerations surrounding CRISPR-based therapies for DM. These include potential off-target effects, ensuring long-term efficacy and safety, and navigating the ethical implications of human genome modification. This chapter offers a comprehensive perspective on how genetic and molecular insights, coupled with the transformative power of CRISPR, are paving the way for potential cures and novel therapeutic approaches for DM.

Comparative efficiency of differential diagnostic methods for the identification of BRAF V600E gene mutation in papillary thyroid cancer (Review)

V-Raf murine sarcoma viral oncogene homolog B1 (BRAF) encodes a serine-threonine kinase. The V600E point mutation in the BRAF gene is the most common mutation, predominantly occurring in melanoma, and colorectal, thyroid and non-small cell lung cancer. Particularly in the context of thyroid cancer research, it is routinely employed as a molecular biomarker to assist in diagnosing and predicting the prognosis of papillary thyroid cancer (PTC), and to formulate targeted therapeutic strategies. Currently, several methods are utilized in clinical settings to detect BRAF V600E mutations in patients with PTC. However, the sensitivity and specificity of various detection techniques vary significantly, resulting in diverse detection outcomes. The present review highlights the advantages and disadvantages of the methods currently employed in medical practice, with the aim of guiding clinicians and researchers in selecting the most suitable detection approach for its high sensitivity, reproducibility and potential to develop targeted therapeutic regimens for patients with BRAF gene mutation-associated PTC.

Frequency of the DI*A, DI*B and Band 3 Memphis polymorphism among distinct groups in Brazil

INTRODUCTION

The Band 3 is a red blood cell protein that carries the Dia and Dib antigens from the Diego blood system. The SLC4A1 gene encodes Band 3; Band 3 Memphis is a polymorphism of normal Band 3 and has two variants, but only the variant II carries the Dia antigen.

OBJECTIVES

Describe the frequencies of the DI*A and DI*B alleles and the Band 3 Memphis among blood donors, sickle cell disease (SCD) patients and Amazonian Indians.

METHODS

A total of 427 blood samples were collected and separated into three groups: 206 unrelated blood donors, 90 patients with SCD and 131 Amazonian Indians. We performed DI*A/B, normal Band 3 and Band 3 Memphis genotyping, using the Polymerase Chain Reaction Restriction Fragment Length Polymorphism (PCR-RFLP).

RESULTS

The frequency of the DI*A/DI*A genotype was 0.5% in blood donors and it was not found in other groups. The frequency of the DI*A/DI*B was higher in Amazonian Indians (33.6%) and the frequency of the DI*B/DI*B was highest in blood donors (92.2%). All 105 individuals tested were positive for the presence of normal Band 3 and of these individuals, only 5/105 (4.8%) presented the Band 3 Memphis mutation.

CONCLUSION

We observed a higher frequency of the DI*B allele in blood donors and a low frequency of the DI*A/DI*A genotype in all groups studied. The Band 3 Memphis was found in a higher frequency in the blood donor group. Our findings highlight the importance of analyzing different population groups to gain a better understanding of the genetic association of blood group antigens.

Rapid Detection of SARS-CoV-2 Genetic Targets Using Nanoporous Waveguide Based Competitive Displacement Assay

Rapid detection of unlabeled SARS-CoV-2 genetic target was demonstrated using a competitive displacement hybridization assay made by a nanostructured anodized alumina oxide (AAO) membrane. The assay applied the toehold-mediated strand displacement reaction. The nanoporous surface of the membrane was functionalized with a complementary pair consisting of Cy3-labeled probe and quencher-labeled nucleic acids through a chemical immobilization process. In the presence of the unlabeled SARS-CoV-2 target, the quencher-tagged strand of the immobilized probe-quencher duplex was separated from the Cy3-modifed strand. A stable probe-target duplex formed and regained a strong fluorescence signal, thus enabling real-time and label-free SARS-CoV-2 detection. Assay designs with different numbers of base pair (bp) matches were synthesized to compare their affinities. Because of the large surface of a free-standing nanoporous membrane, two orders enhancement of the fluorescence was observed, where the detection limit of the unlabeled concentration can be improved to 1 nM. The assay was miniaturized by integrating a nanoporous AAO layer onto an optical waveguide device. The detection mechanism and the sensitivity improvement of the AAO-waveguide device were illustrated from the finite difference method (FDM) simulation and the experimental results. Light-analyte interaction was further improved due to the presence of the AAO layer, which created an intermediate refractive index and enhanced the waveguide's evanescent field. Our competitive hybridization sensor is an accurate and label-free testing platform applicable to the deployment of compact and sensitive virus detection strategies.

Allele mining through TILLING and EcoTILLING approaches in vegetable crops

MAIN CONCLUSION

The present review illustrates a comprehensive overview of the allele mining for genetic improvement in vegetable crops, and allele exploration methods and their utilization in various applications related to pre-breeding of economically important traits in vegetable crops. Vegetable crops have numerous wild descendants, ancestors and terrestrial races that could be exploited to develop high-yielding and climate-resilient varieties resistant/tolerant to biotic and abiotic stresses. To further boost the genetic potential of economic traits, the available genomic tools must be targeted and re-opened for exploitation of novel alleles from genetic stocks by the discovery of beneficial alleles from wild relatives and their introgression to cultivated types. This capability would be useful for giving plant breeders direct access to critical alleles that confer higher production, improve bioactive compounds, increase water and nutrient productivity as well as biotic and abiotic stress resilience. Allele mining is a new sophisticated technique for dissecting naturally occurring allelic variants in candidate genes that influence important traits which could be used for genetic improvement of vegetable crops. Target-induced local lesions in genomes (TILLINGs) is a sensitive mutation detection avenue in functional genomics, particularly wherein genome sequence information is limited or not available. Population exposure to chemical mutagens and the absence of selectivity lead to TILLING and EcoTILLING. EcoTILLING may lead to natural induction of SNPs and InDels. It is anticipated that as TILLING is used for vegetable crops improvement in the near future, indirect benefits will become apparent. Therefore, in this review we have highlighted the up-to-date information on allele mining for genetic enhancement in vegetable crops and methods of allele exploration and their use in pre-breeding for improvement of economic traits.

Listeria monocytogenes in foods-From culture identification to whole-genome characteristics

Listeria monocytogenes is an important foodborne pathogen, which is able to persist in the food production environments. The presence of these bacteria in different niches makes them a potential threat for public health. In the present review, the current information on the classical and alternative methods used for isolation and identification of L. monocytogenes in food have been described. Although these techniques are usually simple, standardized, inexpensive, and are routinely used in many food testing laboratories, several alternative molecular-based approaches for the bacteria detection in food and food production environments have been developed. They are characterized by the high sample throughput, a short time of analysis, and cost-effectiveness. However, these methods are important for the routine testing toward the presence and number of L. monocytogenes, but are not suitable for characteristics and typing of the bacterial isolates, which are crucial in the study of listeriosis infections. For these purposes, novel approaches, with a high discriminatory power to genetically distinguish the strains during epidemiological studies, have been developed, e.g., whole-genome sequence-based techniques such as NGS which provide an opportunity to perform comparison between strains of the same species. In the present review, we have shown a short description of the principles of microbiological, alternative, and modern methods of detection of L. monocytogenes in foods and characterization of the isolates for epidemiological purposes. According to our knowledge, similar comprehensive papers on such subject have not been recently published, and we hope that the current review may be interesting for research communities.

Absence of significant genetic alterations in the VSX1, SOD1, TIMP3, and LOX genes in Brazilian patients with Keratoconus

PURPOSE

To identify inherited or acquired mutations in the VSX1, SOD1, TIMP3 and LOX genes from the combined analysis of corneal and blood samples from patients with Keratoconus.

METHODS

The casuistry was consisted of samples of peripheral blood and corneal epithelium from 35 unrelated patients with Keratoconus who were submitted to corneal crosslink treatment. Also, blood and corneal epithelium samples from 89 non-keratoconic patients were used to compose the control group. Ophthalmologic evaluations included a clinical examination, topography and tomography. DNA samples were extracted from peripheral blood and from corneal epithelium in both groups and all coding regions of the VSX1, SOD1, TIMP3 and LOX genes were amplified by polymerase chain reaction, denatured and subjected to polyacrylamide gel electrophoresis. Mutational screening was performed by single-strand conformation polymorphism and direct DNA sequencing.

RESULTS

No pathogenic variant was found in all coding regions of VSX1, SOD1, TIMP3 and LOX genes, we detected only few SNPs (single-nucleotide polymorphisms). Among the polymorphisms stand out three of them, corresponding to the synonymous exchange of amino acids: exon 3 of VSX1 Ala182Ala and exon 3 of TIMP3 His83His and Ser87Ser; in patients with Keratoconus and also in control subjects. All the polymorphisms were found in samples of corneal epithelium and corresponding blood.

CONCLUSION

There is absence of KC pathogenic related to mutations in the VSX1, SOD1, TIMP3 and LOX genes in the studied patients.

Single-Strand Conformation Polymorphism Fingerprint Method for Dictyostelids

Dictyostelid social amoebae are a highly diverse group of eukaryotic soil microbes that are valuable resources for biological research. Genetic diversity study of these organisms solely relies on molecular phylogenetics of the SSU rDNA gene, which is not ideal for large-scale genetic diversity study. Here, we designed a set of PCR–single-strand conformation polymorphism (SSCP) primers and optimized the SSCP fingerprint method for the screening of dictyostelids. The optimized SSCP condition required gel purification of the SSCP amplicons followed by electrophoresis using a 9% polyacrylamide gel under 4°C. We also tested the optimized SSCP procedure with 73 Thai isolates of dictyostelid that had the SSU rDNA gene sequences published. The SSCP fingerprint patterns were related to the genus-level taxonomy of dictyostelids, but the fingerprint dendrogram did not reflect the deep phylogeny. This method is rapid, cost-effective, and suitable for large-scale sample screening as compared with the phylogenetic analysis of the SSU rDNA gene sequences.

A review of methods for detecting single-nucleotide polymorphisms in the Toll-like receptor gene family

The Toll-like receptors play an essential role in immunity through targeting the pathogen-associated molecular patterns. Nucleotide variations in TLR genes, especially single-nucleotide polymorphisms, have been shown to alter host immune susceptibility to several infections and diseases. Since TLR genes' polymorphisms can be a promising biomarker, ongoing investigations aim to develop, optimize and validate SNP detection methods. This review discusses various TLR SNP detection methods, either used extensively or occasionally, but having a vast potential in high-throughput settings. Methods such as PCR-restriction fragment length polymorphism, TaqMan^® assay, direct sequencing and matrix-assisted laser desorption ionization - time of flight mass spectroscopy MS are frequently used methods whereas Illumina GoldenGate^® assay, reverse hybridization technology, PCR-confronting two-pair primers, KBiosciences KASPar^® SNP assay, SNP stream^®, PCR-fluorescence hybridization and SNaPshot^® are powerful but sporadically used methods. We suggest that, for individual laboratories, the detection method of choice depends on a combination of factors such as throughput volume, reproducibility, feasibility and cost-effectiveness.

Sensitivity and applications of the PCR Single-Strand Conformation Polymorphism method

PCR Single-Strand Conformation Polymorphism is a method used to identify and detect mutations and is now well known for its many applications on living beings. This paper will discuss the experimental details, limitations and sensitivity of the PCR Single-Strand Conformation Polymorphism method in relation to all existing literature available to us until today. Genomic DNA extraction, PCR amplification and Single-Strand Conformation Polymorphism conditions (concentration of polyacrylamide slab gel electrophoresis, dissociation treatment of double- stranded DNA) and comparison with PCR Restriction Fragment Length Polymorphism are presented. Since its discovery in 1989, there have been many variations, innovations, and modifications of the method, which makes it very easy, safe, fast and for this reason widely applied in clinical diagnostic, forensic medicine, biochemical, veterinary, microbiological, food and environmental laboratories. One of the possible applications of the method is the diagnosis and identification of mutations in new strains of coronaviruses, because science needs more tools to tackle the problem of this pandemic. The PCR Single-Strand Conformation Polymorphism method can be applied in many cases provided that control samples are available and the required conditions of the method are achieved.

Familial Hypercholesterolemia in Russia: Three Decades of Genetic Studies

The first studies of familial hypercholesterolemia (FH) in Russia go back to late 1980-ies. For more than 10 years the research in this field was carried out in Saint-Petersburg, the megapolis in the North-West Russia. Studies were focused on the search for causative mutations in low-density lipoprotein receptor gene (LDLR). Gradually the research was spread to Petrozavodsk in Karelia and in the XXI century two more centers contributed in investigations of genetics of FH, i.e., in Moscow and Novosibirsk. The best studied is the spectrum of mutations in LDLR, though genetic abnormalities in APOB and PCSK9 genes were also considered. Despite that some 40% mutations in LDLR found in Saint-Petersburg and Moscow are referred to as specific for Russian population, and this proportion is even higher in Karelia (ca. 70%), rapid introduction of NGS and intensifying genetic research all over the world result in continuous decrease of these numbers as "Slavic" mutations become documented in other countries. The samplings of genetically characterized patients in Russia were relatively small, which makes difficult to specify major mutations reflecting the national specificity of FH. Moreover, the majority of studies accomplished so far did not explore possible associations of certain mutations with ethnic origin of patients. By now the only exception is the study of Karelian population showing the absence of typical Finnish mutations in the region that borders on Finland. It can be concluded that the important primary research partly characterizing the mutation spectrum in FH patients both in the European and Siberian parts of Russia has been done. However, it seems likely that the most interesting and comprehensive genetic studies of FH in Russia, concerning various mutations in different genes and the variety of ethnic groups in this multi-national country, are still to be undertaken.

ZnO Nanolower-Based NanoPCR as an Efficient Diagnostic Tool for Quick Diagnosis of Canine Vector-Borne Pathogens

Polymerase chain reaction (PCR) is a unique technique in molecular biology and biotechnology for amplifying target DNA strands, and is also considered as a gold standard for the diagnosis of many canine diseases as well as many other infectious diseases. However, PCR still faces many challenges and issues related to its sensitivity, specificity, efficiency, and turnaround time. To address these issues, we described the use of unique ZnO nanoflowers in PCR reaction and an efficient ZnO nanoflower-based PCR (nanoPCR) for the molecular diagnosis of canine vector-borne diseases (CVBDs). A total of 1 mM of an aqueous solution of ZnO nanoflowers incorporated in PCR showed a significant enhancement of the PCR assay with respect to its sensitivity and specificity for the diagnosis of two important CVBDs, Babesia canis vogeli and Hepatozoon canis. Interestingly, it drastically reduced the turnaround time of the PCR assay without compromising the yield of the amplified DNA, which can be of benefit for veterinary practitioners for the improved management of diseases. This can be attributed to the favorable adsorption of ZnO nanoflowers to the DNA and thermal conductivity of ZnO nanoflowers. The unique ZnO nanoflower-assisted nanoPCR greatly improved the yield, purity, and quality of the amplified products, but the mechanism behind these properties and the effects and changes due to the different concentrations of ZnO nanoflowers in the PCR system needs to be further studied.

Polymorphism of lactoferrin gene in Egyptian goats and its association with milk composition traits in Zaraibi breed

The objectives of this study were to identify polymorphisms in the lactoferrin gene among three Egyptian goat breeds (Barki, Zaraibi, and Damascus) and to investigate the effect of LF genotype, parity, and lactation stage on milk composition traits of Zaraibi goats. One hundred and thirty-two blood samples were collected for DNA extraction, with 53 from Zaraibi, 40 from Damascus, and 39 from Barki breeds. Fat, protein, total solids, solids-not-fat, and lactose percentages were determined in Zaraibi goat milk using an automatic milk analyzer. Two genotypes, GG and GA, in the lactoferrin gene were identified using single-strand conformation polymorphism and were confirmed by direct sequencing technique. The Zaraibi breed recorded the highest heterozygosity (0.272) and effective number of alleles (1.369), while the Damascus breed recorded the lowest values. The G/A SNP showed a significant association with protein, solids-not-fat, and total solid content of Zaraibi goat milk. Protein, solids-not-fat, and total solid content in our study were significantly higher at early and late parities. Lactose percentage decreased significantly from early to late parity. Fat, protein, solids-not-fat, and total solid content were significantly higher at early and late stages of lactation, and our results encourage the utilization of Zaraibi goat milk in cheese and butter processing at these stages. Moreover, the G/A SNP of the LF gene may be a useful marker for assisted selection programs to improve goat milk composition.

Digital polymerase chain reaction technology - recent advances and future perspectives

Digital polymerase chain reaction (dPCR) technology has remained a "hot topic" in the last two decades due to its potential applications in cell biology, genetic engineering, and medical diagnostics. Various advanced techniques have been reported on sample dispersion, thermal cycling and output monitoring of digital PCR. However, a fully automated, low-cost and handheld digital PCR platform has not been reported in the literature. This paper attempts to critically evaluate the recent developments in techniques for sample dispersion, thermal cycling and output evaluation for dPCR. The techniques are discussed in terms of hardware simplicity, portability, cost-effectiveness and suitability for automation. The present paper also discusses the research gaps observed in each step of dPCR and concludes with possible improvements toward portable, low-cost and automatic digital PCR systems.

Transitions and Transversions in Ki-Ras Gene in Colorectal Cancers in Mexican Patients

Aims & Background

An important increase in the incidence of colorectal cancers has been detected in the last 15 years in Mexico. This fact has been attributed to several causes, including the change in diet acquired from industrialized countries. Various groups have studied the mutational pattern of oncogenes, including Ki-ras gene, in colorectal cancers from different human populations. The aim of this work was to study the prevalence of mutations at codons 12, 13 and 61 of the Ki-ras gene in 37 colorectal tumors from Mexican patients and to correlate them with clinical data.

Methods

Point mutations were studied in 37 colorectal cancers at codons 12 and 13 of the Ki-ras gene, using PCR followed by RFLP. We also performed PCR-SSCP to identify mutations at codon 61. We confirmed mutations by sequence analysis in all the altered codons.

Results

Our results indicated that 24.3% of the tumors presented mutations at codon 12, 5.4% at codon 13, and 2.7% at codon 61 of the Ki-ras gene. We found that 75% of these mutations were transitions and 25% transversions. The overall results indicated that the frequency of Ki-ras mutations in colorectal cancers in a sample of a Mexican population (Mexico City) was 32.4%, which is similar to that reported in other populations. We did not find a correlation between the Ki-ras mutations and gender, location of the tumor, or Dukes’ stage, but survival of the patient without recurrence was statistically significant.

Conclusions

The study of colorectal cancer indicated that in a Mexican population Ki-ras mutations were present in tumors of patients who survived without tumor recurrence. Most of them were transitions in the first and second base of codon 12.

The effects of allospecific mitochondrial genome on the fitness of northern redbelly dace (Chrosomus eos)

Instantaneous mitochondrial introgression events allow the disentangling of the effects of hybridization from those of allospecific mtDNA. Such process frequently occurred in the fish Chrosomus eos, resulting in cybrid individuals composed of a C. eos nuclear genome but with a C. neogaeus mtDNA. This provides a valuable model to address the fundamental question: How well do introgressed individuals perform in their native environment? We infer where de novo production of cybrids occurred to discriminate native environments from those colonized by cybrids in 25 sites from two regions (West-Qc and East-Qc) in Quebec (Canada). We then compared the relative abundance of wild types and cybrids as a measure integrating both fitness and de novo production of cybrids. According to mtDNA variation, 12 introgression events are required to explain the diversity of cybrids. Five cybrid lineages could not be associated with in situ introgression events. This includes one haplotype carried by 93% of the cybrids expected to have colonized West-Qc. These cybrids also displayed a nearly complete allopatric distribution with wild types. We still inferred de novo production of cybrids at seven sites, that accounted for 70% of the cybrids in East-Qc. Wild-type and cybrid individuals coexist in all East-Qc sites while cybrids were less abundant. Allopatry of cybrids restricted to the postglacial expansion suggests the existence of higher fitness for cybrids in specific conditions, allowing for the colonization of different environments and expanding the species' range. However, allospecific mtDNA does not provide a higher fitness to cybrids in their native environment compared to wild types, making the success of an introgressed lineage uncertain.

Engineered nickel oxide nanoparticles affect genome stability in Allium cepa (L.)

Indiscriminate uses of engineered nickel oxide nanoparticles (NiO-NPs) in heavy industries have ushered their introduction into the natural environment, ensuing novel interactions with biotic components of the ecosystem. Though much is known about the toxicity of NiO-NPs on animals, their phytotoxic potential is not well elucidated. NiO-NP hinders intra-cellular homeostasis by producing ROS in excess, having profound effect on the antioxidant profile of exposed animal and plant tissues. In the present study, bulbs of the model plant Allium cepa were treated with varying concentrations of NiO-NP (10 mg L^-1 - 500 mg L^-1) to study changes in ROS production and potential genotoxic effect. The data generated proved a concomitant upsurge in intracellular ROS accumulation with NiO-NP dosage that could be correlated with increased genotoxicity in A. cepa. Augmented in situ ROS production was revealed through DCFH-DA assay, with highest increase in fluorescence (70% over control) in bulbs exposed to 125 mg L^-1 NiO-NP. Effect of NiO-NP on genomic DNA was studied through detailed analyses of RAPD profiles which allows detection of even slightest changes in DNA sequence of treated plants. Significant differences in band intensity, loss and appearance of bands as well as genomic template stability and band sharing indices of treated plants revealed increased vulnerability of genomic DNA to NiO-NP, at even lowest concentration (10 mg L^-1). This is the first report of NiO-NP induced genotoxicity on A. cepa, which confirms the nanoparticle as a potent environmental hazard.

Simultaneous Profiling of DNA Mutation and Methylation by Melting Analysis Using Magnetoresistive Biosensor Array

Epigenetic modifications, in particular DNA methylation, are gaining increasing interest as complementary information to DNA mutations for cancer diagnostics and prognostics. We introduce a method to simultaneously profile DNA mutation and methylation events for an array of sites with single site specificity. Genomic (mutation) or bisulphite-treated (methylation) DNA is amplified using nondiscriminatory primers, and the amplicons are then hybridized to a giant magnetoresistive (GMR) biosensor array followed by melting curve measurements. The GMR biosensor platform offers scalable multiplexed detection of DNA hybridization, which is insensitive to temperature variation. The melting curve approach further enhances the assay specificity and tolerance to variations in probe length. We demonstrate the utility of this method by simultaneously profiling five mutation and four methylation sites in human melanoma cell lines. The method correctly identified all mutation and methylation events and further provided quantitative assessment of methylation density validated by bisulphite pyrosequencing.

Association of CYP1A1 and CYP1B1 polymorphisms with bone mineral density variations in postmenopausal Mexican-Mestizo women

Herein, we investigated potential associations between polymorphisms of genes related to estrogen metabolism and bone mineral density (BMD) in postmenopausal women. This was a cross-sectional study, in which two hundred and ninety postmenopausal Mexican-Mestizo women were studied. The BMD of the lumbar spine (LS), total hip (TH), and femoral neck (FN) was measured. The distribution of the genetic polymorphisms, including rs1799814 and rs1048943 at CYP1A1 as well as rs1056836 at CYP1B1, were analyzed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), single-stranded conformational polymorphism (SSCP), and DNA sequencing. Deviations from Hardy-Weinberg equilibrium (HWE) were tested, and linkage disequilibrium (LD) was calculated by direct correlation (r²). Moreover, haplotype analysis was performed. All polymorphisms were in HWE. The genotype and allele distributions of the three single nucleotide polymorphisms (SNPs) studied showed no significant differences. However, statistical significance was reached when constructing haplotypes. The CG haplotype in CYP1A1 was associated with variations in LS and FN BMD after adjustment for covariates (p = 0.021 and 0.045, respectively), but the association with TH BMD was not significant. These results suggested that the CG haplotype in CYP1A1 may play an important role in the mechanism of osteoporosis and may be useful as a genetic marker.

Genomic and Transcriptomic Resources for Marker Development in Synchytrium endobioticum, an Elusive but Severe Potato Pathogen

Synchytrium endobioticum is an obligate biotrophic fungus that causes wart diseases in potato. Like other species of the class Chytridiomycetes, it does not form mycelia and its zoospores are small, approximately 3 μm in diameter, which complicates the detection of early stages of infection. Furthermore, potato wart disease is difficult to control because belowground organs are infected and resting spores of the fungus are extremely durable. Thus, S. endobioticum is classified as a quarantine organism. More than 40 S. endobioticum pathotypes have been reported, of which pathotypes 1(D1), 2(G1), 6(O1), 8(F1), and 18(T1) are the most important in Germany. No molecular methods for the differentiation of pathotypes are available to date. In this work, we sequenced both genomic DNA and cDNA of the German pathotype 18(T1) from infected potato tissue and generated 5,422 expressed sequence tags (EST) and 423 genomic contigs. Comparative sequencing of 33 genes, single-stranded confirmation polymorphism (SSCP) analysis with polymerase chain reaction fragments of 27 additional genes, as well as the analysis of 41 simple sequence repeat (SSR) loci revealed extremely low levels of variation among five German pathotypes. From these markers, one sequence-characterized amplified region marker and five SSR markers revealed polymorphisms among the German pathotypes and an extended set of 11 additional European isolates. Pathotypes 8(F1) and 18(T1) displayed discrete polymorphisms which allow their differentiation from other pathotypes. Overall, using the information of the six markers, the 16 isolates could be differentiated into three distinct genotype groups. In addition to the presented markers, the new collection of EST from genus Synchytrium might serve in the future for molecular taxonomic studies as well as for analyses of the host-pathogen interactions in this difficult pathosystem. [Formula: see text] Copyright © 2017 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Sensitive and selective detection of the p53 gene based on a triple-helix magnetic probe coupled to a fluorescent liposome hybridization assembly via rolling circle amplification

Developing a sensitive and selective sensing platform for the p53 gene and its mutation analysis is essential and may aid in early cancer screening and assessment of prognosis.

Label-free electrochemical aptasensor for adenosine detection based on cascade signal amplification strategy

In this work, a simple and highly sensitive label-free electrochemical aptasensor for adenosine detection was developed based on target-aptamer binding triggered nicking endonuclease-assisted strand-replacement DNA polymerization and rolling circle amplification (RCA) strategy. The magnetic beads (MB) probe, which was attached the aptamer of adenosine and mDNA, was firstly fabricated. In the presence of adenosine, mDNA was released from MB upon recognition of the aptamer to target adenosine. The released mDNA as the primer activated autonomous DNA polymerization/nicking process and accompanied by the continuous release of replicated DNA fragments. Subsequently, numerous released DNA fragments were captured on the working electrode, and then as initiators to trigger the downstream RCA process leading to the formation of a long ssDNA concatemer for loading large amounts of Ru(NH₃)₆³⁺. Therefore, a conspicuously amplified electrochemical signal through the developed dual-amplification strategy could be achieved. This method exhibited a high sensitivity toward adenosine with a detection limit of 0.032nM. Also, it exhibited high selectivity to different nucleoside families and good reproducibility. This design opens new horizons for integrating different disciplines, presenting a versatile tool for ultrasensitive detecting organic small molecules in medical research and clinical diagnosis.

Genetic markers for antimony resistant clinical isolates differentiation from Indian Kala-azar

Visceral Leishmaniasis or Kala-azar is caused by the protozoan parasites belonging to the Genus Leishmania. Once thought eradicated from the Indian subcontinent, the disease came back with drug resistance to almost all prevalent drugs. Molecular epidemiological studies revealed the polymorphic nature of the population of the main player of the disease, Leishmania donovani and involvement of other species (L. tropica) and other genus (Leptomonas) with the disease. This makes control measures almost futile. It also strongly demands the characterization of each and every isolate mandatory which is not done. In this background, the present study has been carried out to assess the genetic attributes of each clinical isolates (n=26) of KA and PKDL patients from India and Bangladesh. All the isolates were characterized through Restriction Fragment Length Polymorphism (RFLP) analysis to ascertain their species identity. 46.2% of the isolates were found to be Sodium Stibogluconate (SSG) resistant by amastigote-macrophage model. When the clinical isolates were subjected to Single Stranded Conformation Polymorphism (SSCP) of Internal Transcribed Spacer 1 (ITS1), Internal Transcribed Spacer 2 (ITS2) and some anonymous markers, the drug resistant Leishmania isolates of SSG can be distinguished from the sensitive isolates distinctly. This study showed for the first time, the genetic markers for SSG drug resistance of Indian Kala-azar clinical isolates.

Inconsistent phylogeographic pattern between a sperm dependent fish and its host: in situ hybridization vs dispersal

Background

Co-dispersal of sperm-dependent hybrids and their sexual relatives is expected to result in consistent spatial patterns between assemblages of hybrids and genetic structure of parental species. However, local hybridization events may blur this signal as assemblages could be organized under different connectivity constraints. This study aims at testing the hypothesis of local hybridization events by comparing the assemblage of hybrid fish Chrosomus eos-neogaeus to the genetic diversity of one of its parental species, Chrosomus eos.

Results

An extensive survey performed on a total of 132 sites located in two regions of Southern Quebec (West-Qc and East-Qc) revealed a distinct organization of hybrid lineages. One of the six hybrid lineages detected in West-Qc is widespread throughout this region resulting in a low α-diversity (1.38) and β-diversity (4.35). On the other hand, 36 hybrid lineages were detected in East-Qc and displayed narrow geographic distributions leading to a high α-diversity (2.30) and β-diversity (15.68). In addition, the C. eos multilocus haplotype of several of these hybrids is assigned to their respective sympatric C. eos population. Finally, contrasting with hybrids, the paternal species C. eos displayed a higher ρ_ST in West-Qc (0.2300) than in East-Qc (0.0734).

Conclusion

The unusually high diversity of hybrid lineages in East-Qc as well as the spatial organization and the close genetic relationship with C. eos sympatric populations support the hypothesis that multiple hybridization events occurred in situ. These findings coupled to the near absence of the maternal species Chrosomus neogeaus suggest that the decline of this species could be the trigger event at the origin of the high rates of spontaneous hybridization in this region.

Electronic supplementary material

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A New Mutation of the p53 Gene in Human Neuroblastoma, Not Correlated with N-myc Amplification

N-myc gene amplification and/or loss of heterozygosity of chromosome 1 (LOH lp) are important criteria for prognosis and progression in human neuroblastoma (NB). Despite the high incidence of alterations of the p53 gene in human cancers, very few p53 mutations have been reported in NB. The objective of our study was to search for p53 mutations in NB and their correlation with N-myc amplification and clinical or pathologic parameters. We analyzed 14 selected cases of NB from the Spanish Protocol N-II-92. We found a missense mutation in codon 248 CGG to GGG (Arg/Gly) in one case of stage 4 NB with no N-myc amplification. Our results confirm the low incidence of p53 gene mutation in neuroblastoma and the absence of correlation with histopathologic parameters.

Primary Rhabdomyosarcoma Mimicking a Small Cell Sarcoma of Bone: A Nude Mice Xenograft, Cytogenetic, and Molecular Approach

Small cell sarcomas of bone are difficult to classify and diagnose. The present case deals with such a tumor in which the original biopsy and the resected specimen, studied by histology before chemotherapy, provided no final information about its real nature. Thus several techniques were applied to discern its histogenesis and biology. Myogenin proved positive in isolated cells of the primary neoplasm but was extensively expressed in nude mice xenografts. Electron microscopy confirmed the existence of myofilaments. The cytogenetic analysis revealed a large number of chromo somal abnormalities, but not those found in the Ewing's/PNET (peripheral neuroectodermal tumor) family of tumors. This was confirmed by polymerase chain reaction (RT-PCR) wherein no EWS/Fli 1 or PAX3/FKHR gene rearrangements were detected. Based upon these studies, a rhabdomyosarcoma of bone was diagnosed. Clinically the neoplasm showed a highly aggressive behavior, causing death of the patient within 2 years after diagnosis.

Genetic relationship between the Echinococcus granulosus sensu stricto cysts located in lung and liver of hosts

G1 genotype of Echinococcus granulosus sensu stricto is the major cause of hydatidosis in Northern Africa, Tunisia included. The genetic relationship between lung and liver localization were studied in ovine, bovine and human hydatid cysts in Tunisia. Allozyme variation and single strand conformation polymorphism were used for genetic differentiation. The first cause of genetic differentiation was the host species and the second was the localization (lung or liver). The reticulated genetic relationship between the liver or the lung human isolates and isolates from bovine lung, is indicative of recombination (sexual reproduction) or lateral genetic transfer. The idea of two specialized populations (one for the lung one for the liver) that are more or less successful according to host susceptibility is thus proposed.

Effective screen of CRISPR/Cas9-induced mutants in rice by single-strand conformation polymorphism

A method based on DNA single-strand conformation polymorphism is demonstrated for effective genotyping of CRISPR/Cas9-induced mutants in rice. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) has been widely adopted for genome editing in many organisms. A large proportion of mutations generated by CRISPR/Cas9 are very small insertions and deletions (indels), presumably because Cas9 generates blunt-ended double-strand breaks which are subsequently repaired without extensive end-processing. CRISPR/Cas9 is highly effective for targeted mutagenesis in the important crop, rice. For example, homozygous mutant seedlings are commonly recovered from CRISPR/Cas9-treated calli. However, many current mutation detection methods are not very suitable for screening homozygous mutants that typically carry small indels. In this study, we tested a mutation detection method based on single-strand conformational polymorphism (SSCP). We found it can effectively detect small indels in pilot experiments. By applying the SSCP method for CRISRP-Cas9-mediated targeted mutagenesis in rice, we successfully identified multiple mutants of OsROC5 and OsDEP1. In conclusion, the SSCP analysis will be a useful genotyping method for rapid identification of CRISPR/Cas9-induced mutants, including the most desirable homozygous mutants. The method also has high potential for similar applications in other plant species.

Identification of point mutations in exon 2 of GDF9 gene in Kermani sheep

Screening the fertile ewes from national herds to detect the major genes for prolificacy is an effective way to create the fertile flocks. Growth differentiation factor (GDF) 9 is a member of the transforming growth factor β superfamily that is essential for folliculogenesis and female fertility. The aim of this study was to detect single nucleotide polymorphisms (SNPs) in exon 2 of GDF9 gene in Kermani sheep breed using PCR-SSCP. Genomic DNA was extracted from whole blood of collected samples using salting-out method. Whole exon 2 of GDF9 gene was amplified (634 bp and 647 bp fragments) using designed specific primers. The single stranded conformation polymorphism (SSCP) patterns of PCR products were studied using electrophoresis on acrylamide gel and silver-nitrate staining method. Finally, 4 banding patterns for the first primer pair and 4 banding patterns for the second primer pair were obtained. Also, indices of population genetic per SNP were calculated using Gen Alex 6.41 software. The sequencing results showed the presence of 3 mutations (SNP) (443, 477 and 721 positions) in the studied population.

Strong synergy with APR-246 and DNA-damaging drugs in primary cancer cells from patients with TP53 mutant High-Grade Serous ovarian cancer

BACKGROUND

Mutation in the tumor suppressor gene TP53 is an early event in the development of high-grade serous (HGS) ovarian cancer and is identified in more than 96 % of HGS cancer patients. APR-246 (PRIMA-1(MET)) is the first clinical-stage compound that reactivates mutant p53 protein by refolding it to wild type conformation, thus inducing apoptosis. APR-246 has been tested as monotherapy in a Phase I/IIa clinical study in hematological malignancies and prostate cancer with promising results, and a Phase Ib/II study in combination with platinum-based therapy in ovarian cancer is ongoing. In the present study, we investigated the anticancer effects of APR-246 in combination with conventional chemotherapy in primary cancer cells isolated from ascitic fluid from 10 ovarian, fallopian tube, or peritoneal cancer patients, 8 of which had HGS cancer.

METHODS

Cell viability was assessed with fluorometric microculture cytotoxicity assay (FMCA) and Combination Index was calculated using the Additive model. p53 status was determined by Sanger sequencing and single strand conformation analysis, and p53 protein expression by western blotting.

RESULTS

We observed strong synergy with APR-246 and cisplatin in all tumor samples carrying a TP53 missense mutation, while synergistic or additive effects were found in cells with wild type or TP53 nonsense mutations. Strong synergy was also observed with carboplatin or doxorubicin. Moreover, APR-246 sensitized TP53 mutant primary ovarian cancer cells, isolated from a clinically platinum-resistant patient, to cisplatin; the IC50 value of cisplatin decreased 3.6 fold from 6.5 to 1.8 μM in the presence of clinically relevant concentration of APR-246.

CONCLUSION

These results suggest that combination treatment with APR-246 and DNA-damaging drugs could significantly improve the treatment of patients with TP53 mutant HGS cancer, and thus provide strong support for the ongoing clinical study with APR-246 in combination with carboplatin and pegylated liposomal doxorubicin in patients with recurrent HGS cancer.

Strong synergy with APR-246 and DNA-damaging drugs in primary cancer cells from patients with TP53 mutant High-Grade Serous ovarian cancer

BACKGROUND

Mutation in the tumor suppressor gene TP53 is an early event in the development of high-grade serous (HGS) ovarian cancer and is identified in more than 96 % of HGS cancer patients. APR-246 (PRIMA-1(MET)) is the first clinical-stage compound that reactivates mutant p53 protein by refolding it to wild type conformation, thus inducing apoptosis. APR-246 has been tested as monotherapy in a Phase I/IIa clinical study in hematological malignancies and prostate cancer with promising results, and a Phase Ib/II study in combination with platinum-based therapy in ovarian cancer is ongoing. In the present study, we investigated the anticancer effects of APR-246 in combination with conventional chemotherapy in primary cancer cells isolated from ascitic fluid from 10 ovarian, fallopian tube, or peritoneal cancer patients, 8 of which had HGS cancer.

METHODS

Cell viability was assessed with fluorometric microculture cytotoxicity assay (FMCA) and Combination Index was calculated using the Additive model. p53 status was determined by Sanger sequencing and single strand conformation analysis, and p53 protein expression by western blotting.

RESULTS

We observed strong synergy with APR-246 and cisplatin in all tumor samples carrying a TP53 missense mutation, while synergistic or additive effects were found in cells with wild type or TP53 nonsense mutations. Strong synergy was also observed with carboplatin or doxorubicin. Moreover, APR-246 sensitized TP53 mutant primary ovarian cancer cells, isolated from a clinically platinum-resistant patient, to cisplatin; the IC50 value of cisplatin decreased 3.6 fold from 6.5 to 1.8 μM in the presence of clinically relevant concentration of APR-246.

CONCLUSION

These results suggest that combination treatment with APR-246 and DNA-damaging drugs could significantly improve the treatment of patients with TP53 mutant HGS cancer, and thus provide strong support for the ongoing clinical study with APR-246 in combination with carboplatin and pegylated liposomal doxorubicin in patients with recurrent HGS cancer.

Strong synergy with APR-246 and DNA-damaging drugs in primary cancer cells from patients with TP53 mutant High-Grade Serous ovarian cancer

Background

Mutation in the tumor suppressor gene TP53 is an early event in the development of high-grade serous (HGS) ovarian cancer and is identified in more than 96 % of HGS cancer patients. APR-246 (PRIMA-1^MET) is the first clinical-stage compound that reactivates mutant p53 protein by refolding it to wild type conformation, thus inducing apoptosis. APR-246 has been tested as monotherapy in a Phase I/IIa clinical study in hematological malignancies and prostate cancer with promising results, and a Phase Ib/II study in combination with platinum-based therapy in ovarian cancer is ongoing. In the present study, we investigated the anticancer effects of APR-246 in combination with conventional chemotherapy in primary cancer cells isolated from ascitic fluid from 10 ovarian, fallopian tube, or peritoneal cancer patients, 8 of which had HGS cancer.

Methods

Cell viability was assessed with fluorometric microculture cytotoxicity assay (FMCA) and Combination Index was calculated using the Additive model. p53 status was determined by Sanger sequencing and single strand conformation analysis, and p53 protein expression by western blotting.

Results

We observed strong synergy with APR-246 and cisplatin in all tumor samples carrying a TP53 missense mutation, while synergistic or additive effects were found in cells with wild type or TP53 nonsense mutations. Strong synergy was also observed with carboplatin or doxorubicin. Moreover, APR-246 sensitized TP53 mutant primary ovarian cancer cells, isolated from a clinically platinum-resistant patient, to cisplatin; the IC₅₀ value of cisplatin decreased 3.6 fold from 6.5 to 1.8 μM in the presence of clinically relevant concentration of APR-246.

Conclusion

These results suggest that combination treatment with APR-246 and DNA-damaging drugs could significantly improve the treatment of patients with TP53 mutant HGS cancer, and thus provide strong support for the ongoing clinical study with APR-246 in combination with carboplatin and pegylated liposomal doxorubicin in patients with recurrent HGS cancer.