Use of capillary electrophoresis for accurate determination of CAG repeats causing Huntington disease. An oligonucleotide design avoiding shadow bands

Neurodegenerative Diseases and Flavonoids: Special Reference to Kaempferol

Neurodegenerative diseases like Alzheimer's disease, Parkinson's disease, Huntington's disease, Multiple Sclerosis and Ischemic stroke have become a major health problem worldwide. Pre-clinical studies have demonstrated the beneficial effects of flavonoids on neurodegenerative diseases and suggest them to be used as therapeutic agents. Kaempferol is found in many plants such as tea, beans, broccoli, strawberries, and neuroprotective effects against the development of many neurodegenerative diseases such as Parkinson, Alzheimer's disease and Huntington's disease. The present study summarizes the neuroprotective effects of kaempferol in various models of neurodegenerative diseases. Kaempferol delays the initiation as well as the progression of neurodegenerative disorders by acting as a scavenger of free radicals and preserving the activity of various antioxidant enzymes. Kaempferol can cross the Blood-Brain Barrier (BBB), and therefore results in an enhanced protective effect. The multi-target property of kaempferol makes it a potential dietary supplement in preventing and treating neurodegenerative diseases.

A Novel Triplet-Primed PCR Assay to Detect the Full Range of Trinucleotide CAG Repeats in the Huntingtin Gene (HTT)

The expanded CAG repeat number in HTT gene causes Huntington disease (HD), which is a severe, dominant neurodegenerative illness. The accurate determination of the expanded allele size is crucial to confirm the genetic status in symptomatic and presymptomatic at-risk subjects and avoid genetic polymorphism-related false-negative diagnoses. Precise CAG repeat number determination is critical to discriminate the cutoff between unexpanded and intermediate mutable alleles (IAs, 27–35 CAG) as well as between IAs and pathological, low-penetrance alleles (i.e., 36–39 CAG repeats), and it is also critical to detect large repeat expansions causing pediatric HD variants. We analyzed the HTT-CAG repeat number of 14 DNA reference materials and of a DNA collection of 43 additional samples carrying unexpanded, IAs, low and complete penetrance alleles, including large (>60 repeats) and very large (>100 repeats) expansions using a novel triplet-primed PCR-based assay, the AmplideX PCR/CE HTT Kit. The results demonstrate that the method accurately genotypes both normal and expanded HTT-CAG repeat numbers and reveals previously undisclosed and very large CAG expansions >200 repeats. We also show that this technique can improve genetic test reliability and accuracy by detecting CAG expansions in samples with sequence variations within or adjacent to the repeat tract that cause allele drop-outs or inaccuracies using other PCR methods.

Improved high sensitivity screen for Huntington disease using a one-step triplet-primed PCR and melting curve assay

Molecular diagnosis of Huntington disease (HD) is currently performed by fluorescent repeat-flanking or triplet-primed PCR (TP-PCR) with capillary electrophoresis (CE). However, CE requires multiple post-PCR steps and may result in high cost in high-throughput settings. We previously described a cost-effective single-step molecular screening strategy employing the use of melting curve analysis (MCA). However, because it relies on repeat-flanking PCR, its efficiency in detecting expansion mutations decreases with increasing size of the repeat, which could lead to false-negative results. To address this pitfall, we have developed an improved screening assay coupling TP-PCR, which has been shown in CE-based assays to detect all expanded alleles regardless of size, with MCA in a rapid one-step assay. A companion protocol for rapid size confirmation of expansion-positive samples is also described. The assay was optimized on 30 genotype-known DNAs, and two plasmids pHTT(CAG)26 and pHTT(CAG)33 were used to establish the threshold temperatures (TTs) distinguishing normal from expansion-positive samples. In contrast to repeat-flanking PCR MCA, TP-PCR MCA displayed much higher sensitivity for detecting large expansions. All 30 DNAs generated distinct melt peak Tms which correlated well with each sample's larger allele. Normal samples were clearly distinguished from affected samples. The companion sizing protocol accurately sized even the largest expanded allele of ~180 CAGs. Blinded analysis of 69 clinical samples enriched for HD demonstrated 100% assay sensitivity and specificity in sample segregation. The assay targets the HTT CAG repeat specifically, tolerates a wide range of input DNA, and works well using DNA from saliva and buccal swab in addition to blood. Therefore, rapid, accurate, reliable, and high-throughput detection/exclusion of HD can be achieved using this one-step screening assay, at less than half the cost of fluorescent PCR with CE.

Ethidium Bromide Modifies The Agarose Electrophoretic Mobility of CAG•CTG Alternative DNA Structures Generated by PCR

The abnormal expansion of unstable simple sequence DNA repeats can cause human disease through a variety of mechanisms, including gene loss-of-function, toxic gain-of-function of the encoded protein and toxicity of the repeat-containing RNA transcript. Disease-associated unstable DNA repeats display unusual biophysical properties, including the ability to adopt non-B-DNA structures. CAG•CTG trinucleotide sequences, in particular, have been most extensively studied and they can fold into slipped-stranded DNA structures, which have been proposed as mutation intermediates in repeat size expansion. Here, we describe a simple assay to detect unusual DNA structures generated by PCR amplification, based on their slow electrophoretic migration in agarose and on the effects of ethidium bromide on the mobility of structural isoforms through agarose gels. Notably, the inclusion of ethidium bromide in agarose gels and running buffer eliminates the detection of additional slow-migrating DNA species, which are detected in the absence of the intercalating dye and may be incorrectly classified as mutant alleles with larger than actual expansion sizes. Denaturing and re-annealing experiments confirmed the slipped-stranded nature of the additional DNA species observed in agarose gels. Thus, we have shown that genuine non-B-DNA conformations are generated during standard PCR amplification of CAG•CTG sequences and detected by agarose gel electrophoresis. In contrast, ethidium bromide does not change the multi-band electrophoretic profiles of repeat-containing PCR products through native polyacrylamide gels. These data have implications for the analysis of trinucleotide repeat DNA and possibly other types of unstable repetitive DNA sequences by standard agarose gel electrophoresis in diagnostic and research protocols. We suggest that proper sizing of CAG•CTG PCR products in agarose gels should be performed in the presence of ethidium bromide.

A Case of Previously Unsuspected Huntington Disease Diagnosed at Autopsy

Huntington disease (HD) is a neurodegenerative disorder with a worldwide prevalence of four to ten per 100 000. It is characterized by choreiform movements, behavioral/psychiatric disturbances, and eventual cognitive decline. Symptoms usually present between 30 and 50 years of age and the diagnosis is based on the combination of clinical symptoms, family history, and genetic testing. A variation of HD, juvenile Huntington disease (JHD), presents earlier, with more severe symptoms and with a worse prognosis. Symptoms are different in JHD, with personality changes and learning difficulties being the predominant presenting features. Seizures are common in JHD, and chorea is uncommon; movement disorders at presentation of JHD are predominantly nonchoreiform. The inheritance pattern for both HD and JHD is autosomal dominant and the disease is caused by an elongation of the CAG repeat in the huntingtin gene. There are many published case reports of Huntington disease that were confirmed at autopsy, but to our knowledge, there are no reports in the literature where the diagnosis of Huntington disease was first made at autopsy. We present a case of a 28-year-old African-American male who was in a state of neglect due to a lifetime of abuse, cognitive difficulties, and seizures, whose cause of death was pneumonia. The gross autopsy findings included bilateral caudate nucleus atrophy and lateral ventricular dilation. Microscopically, severe bilateral neuronal loss and gliosis of the caudate and putamen nuclei were seen. Genetic testing for the number of CAG repeats confirmed the diagnosis and was consistent with JHD.

Polyphenols: multipotent therapeutic agents in neurodegenerative diseases

Aging leads to numerous transitions in brain physiology including synaptic dysfunction and disturbances in cognition and memory. With a few clinically relevant drugs, a substantial portion of aging population at risk for age-related neurodegenerative disorders require nutritional intervention. Dietary intake of polyphenols is known to attenuate oxidative stress and reduce the risk for related neurodegenerative diseases such as Alzheimer's disease (AD), stroke, multiple sclerosis (MS), Parkinson's disease (PD), and Huntington's disease (HD). Polyphenols exhibit strong potential to address the etiology of neurological disorders as they attenuate their complex physiology by modulating several therapeutic targets at once. Firstly, we review the advances in the therapeutic role of polyphenols in cell and animal models of AD, PD, MS, and HD and activation of drug targets for controlling pathological manifestations. Secondly, we present principle pathways in which polyphenol intake translates into therapeutic outcomes. In particular, signaling pathways like PPAR, Nrf2, STAT, HIF, and MAPK along with modulation of immune response by polyphenols are discussed. Although current polyphenol researches have limited impact on clinical practice, they have strong evidence and testable hypothesis to contribute clinical advances and drug discovery towards age-related neurological disorders.

Clinical profile, BRCA2 expression, and the androgen receptor CAG repeat region in Egyptian and Moroccan male breast cancer patients

INTRODUCTION

Male breast cancer (MBC) is a rare disease. Rates of MBC in Northern Africa vary by region. The age-standardized incidence for MBC is higher in Morocco than in Egypt, and the Egyptian rate is similar to the U.S of approximately 1/10(5)This study aimed at investigating the clinical and molecular characteristics of MBC in Egypt and Morocco.

METHODS

This case-case study included 211 cases from Egypt and 132 from Morocco. Tumor tissues were available for 47 Egyptian and 18 Moroccan patients. Medical record information was abstracted for patients' demographics, medical history, and treatment. BRCA2 protein expression status was examined in Egyptian and Moroccan tumors. Androgen receptor CAG repeat length was analyzed using the tissue samples in Egyptian MBC tumors and controls. Limited amount of tissues from Morocco did not allow for the analysis of CAG repeats.

RESULTS

Egyptian MBC patients had a significantly lower age at diagnosis (Egypt: 57.5 ± 15.1, Morocco: 63.9 ± 14.4, P=0.0002) and a higher prevalence of liver cirrhosis (Egypt: 28.0%, Morocco: 0.8%, P=< 0.0001). MBC patients also had higher tumor grades [I (0.9%), II (81.0%), III (18.1%)] in Egypt vs. [I (10.7%), II (81.0%), III (8.3%)] in Morocco (P=0.0017). The clinical and molecular characteristics of the groups from the 2 countries did not significantly differ. There was no significant difference with respect to BRCA2 expression amongst countries (Egypt: 28.9% non-wild type, Morocco: 27.8% non-wild type, P=0.9297) or CAG lengths amongst BRCA2 expression types in Egyptians (Wild type: 54.6% with CAG repeat lengths of 20+, Non-wild type: 50% with CAG repeat lengths of 20+, P=0.7947).

CONCLUSIONS

Differences in MBC between Egypt and Morocco are more likely due to differences in other risk factors such as consanguinity and use of xenoestrogenic pesticides.

Androgen receptor polyglutamine tract length in Egyptian male breast cancer patients

Male breast cancer (MBC) is a rare disease in the U.S., accounting for less than 1% of all breast cancers. Rates of MBC in Africa are more variable than in the U.S., therefore, understanding the risk factors involved in a population like Egypt can clarify the nature of MBC. The polyglutamine tract (QT) is a variable region of the androgen receptor (AR), a nuclear receptor which is important in modulating androgen actions and generally inhibits growth in breast tissue. It is hypothesized that a long QT results in weaker AR activity over the lifetime, resulting in less AR mediated control over cellular division and higher risk of MBC. As a corollary, we expect to see a distribution skewed toward longer QTs in MBC patients compared to controls and overall relatively longer QT's in populations with higher rates of MBC. This study aimed to investigate for the first time the distribution of AR QT lengths among MBC patients in Egypt. Paraffin-embedded tumor tissues from 44 Egyptian MBC patients were analyzed for this polymorphism. Amplification followed by fragment length analysis revealed QT length. For the control series, blood from 43 Egyptian males without a family or personal history of breast or prostate cancers was collected and analyzed similarly. There was no significant difference between patients and controls with respect to mean QT length (P = 0.84; means were 19.5 ± 2.8 and 19.3 ± 4.2, for patients and controls, respectively). Though, short QT lengths were more prevalent among controls (14.0%), but almost absent in cases (2.3%). Although the mean lengths were not different in cases and controls, the near absence of short tracts in cases suggests a possible protective effect of very short QT lengths against MBC. In populations in which there is variable incidence of MBC by region, investigations of the distribution of AR QT lengths are warranted to further delineate its role as a risk factor in MBC.

A unified rapid PCR method for detection of normal and expanded trinucleotide alleles of CAG repeats in huntington chorea and CGG repeats in fragile X syndrome

We report on a unified rapid betaine-based-PCR protocol for amplification of the (CAG)n region in Huntington disease (HD) and the (CGG)n region in Fragile X syndrome (FXS), followed by an electrophoretic separation on automated sequencer for precise determination of the triplet numbers. The high betaine concentration (2.5 M betaine) permits precise amplification of the CAG and CGG repeats. Ten HD affected patients and 10 healthy individuals from HD families were re-evaluated. For FXS the CGG region in normal individuals and premutations of about 100 repeats were precisely amplified by this protocol. Ten unrelated FXS premutation carriers and 24 mentally retarded non-FXS affected boys were re-examined by this method. The results totally coincided with the previous ones. This protocol is a good choice as a fast screening test. Within 24 h we can have preliminary information on the patient's genetic status. Normal individuals, CGG premutation carriers up to 100 repeats, as well as HD patients carrying an expansion up to 50 CAG repeats can be easily clarified. This accounts for a relatively large proportion (about 90%) of the suspected HD and FXS patients, referred to our laboratory for genetic analysis. The calculation of the repeat's number is more accurate for the correct interpretation of the results, screening tests and genetic counselling.