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Molecular diagnosis of haemoglobin disorders.

The haemoglobinopathies refer to a diverse group of inherited disorders characterized by a reduced synthesis of one or more globin chains (thalassaemias) or the synthesis of a structurally abnormal haemoglobin (Hb). In prevalent regions, the thalassaemias often coexist with a variety of structural Hb variants giving rise to complex genotypes and an extremely wide spectrum of clinical and haematological phenotypes. An appreciation of these phenotypes is needed to facilitate the definitive diagnosis of the causative mutations to inform management and counselling. Haematological and biochemical investigations, and family studies provide essential clues to the different interactions and are fundamental to DNA diagnostics of the Hb disorders. With the exception of a few rare deletions and rearrangements, the molecular lesions causing haemoglobinopathies are all identifiable by PCR-based techniques. Although a full spectrum of >1000 mutations causing haemoglobinopathies has been documented, in practice only a limited number are associated with disease states and clinical significance. Furthermore, each at-risk ethnic group has its own combination of common Hb variants and thalassaemia mutations. Prior identification of the ethnic origin is thus an important part of the diagnostic strategy which becomes less reliable in the UK because of the large ethnic mix. Although the current approach using a combination of different PCR-based techniques seems to work in most laboratories, practice pressures with the imminent implementation of universal antenatal screening for clinically significant Hb disorders in the UK will require a higher throughput approach for DNA diagnostics in the near future. The complex mutational spectrum and the compactness of the globin genes places them in an ideal position for the different non-gel based analytical platforms.

Anemia, Sickle Cell↗

Eight novel MICB alleles, including a null allele, identified in gastric MALT lymphoma patients.

MICA and MICB, as members of the major histocompatibility complex (MHC) class I-chain-related genes (MIC), encode stress-inducible glycoproteins that act as activating ligands for NKG2D and gammadelta T-cell receptor-bearing cells. We here describe the identification of eight novel MICB variants, including a null allele, which were identified in peripheral blood leukocytes of gastric MALT lymphoma patients. Only two of the novel alleles are characterized by point mutations, whereas the other variants display a recombination of known exonic MICB sequences that may be best explained by intragenic conversions. The novel MICB null allele is characterized by a Cytosin (C) deletion in a stretch of four Cs beginning from nucleotide 135 of exon 2 that leads to a premature stop codon (TGA) at codon 66.

Alleles↗

Antigenic analysis of rabies-virus isolates from Latin America and the Caribbean.

A total of 288 rabies-virus samples from 17 Latin American and Caribbean countries were reacted with an array of monoclonal antibodies. Identification of eight distinct antigenic variants among these samples permitted epidemiologic studies of the geographic distribution of different concentrations of rabies in the region and of the animal species serving as maintenance sources for rabies within a concentrated area. Two variants were broadly distributed and associated with enzootic disease in dogs and vampire bats. All isolates from cases of human rabies contained one of these two variants. Two variants had a limited distribution: an outbreak in Brazil, primarily affecting dogs and believed to be maintained by dog-to-dog transmission, and nine cases of rabies in cattle in Venezuela, animal reservoir unknown. A reservoir of rabies in insectivorous bats was identified and the associated variant was found in a rabid domestic cat. The remaining three rabies variants were found in single isolates only, but due to inference from antigenic-typing data from North American samples, were believed to be maintained by reservoirs of rabies in hoary bats, foxes, and skunks.

Animals↗

New approaches for the molecular characterization of canine parvovirus type 2 strains.

Characterization of the canine parvovirus type 2 (CPV-2) is sometimes ambiguous, frequently requiring more than one technique for definitive prediction of the viral type. Taking into account the single-nucleotide polymorphisms encountered in the VP2-protein gene between types 2a and 2b and between type 2b and Glu-426 mutant (type 2c), two different minor groove binder (MGB) probe assays were developed for rapid identification of the CPV-2 variants. A total of 315 samples collected from dogs with diarrhoea were screened for CPV-2 by a real-time polymerase chain reaction (PCR) assay capable of detecting all CPV-2 types. In order to compare the type-specific assays with the traditional techniques [haemagglutination inhibition with monoclonal antibodies, PCR-restriction fragment-length polymorphism (RFLP), sequence analysis] for prediction of CPV-2 antigen specificity, the 203 samples tested CPV-2 positive were analysed using the different methods. The results showed a 100% concordance between the MGB probe assays and the combined conventional methods, with 116 samples characterized as type 2a, 32 as type 2b and 55 as type 2c. Therefore, the MGB probe assays represent a quick, reliable tool for prediction of CPV-2 antigen specificity, with regard to the more time-consuming assays currently used.

Animals↗

Stable azole drug resistance associated with a substrain of Candida albicans from an HIV-infected patient.

Oral candidiasis is one of the earliest and most frequent complications of a failing immune system in HIV-infected individuals. For several years, oral candidiasis has been treated effectively with azole drugs, the one most frequently used is fluconazole. Unfortunately, extensive use of the drug for treatment and prophylaxis has led to treatment failure in an increasing number of patients. In most of these cases, strains of C. albicans isolated from the infection are less susceptible to fluconazole. The development of azole resistance in strains of C. albicans has been studied biochemically and more recently with molecular techniques. One excellent example of the development of azole resistance in C. albicans has been documented in a series of 17 C. albicans isolates from a single patient over a 2-year period. During this time, the patient experienced 14 episodes of oral candidiasis and was treated with increasing doses of fluconazole. Molecular and biochemical analyses confirms that the isolates are the same strain of C. albicans and that the resistance in these isolates is stable over 600 generations, suggesting that the changes in this strain are genetic in nature. In addition, the development of resistance is correlated with the identification of a substrain or variant of the original strain, as identified by restriction fragment length polymorphism (RFLP) analysis with the moderately repetitive probe, Ca3. The analysis of this series of isolates demonstrates that azole drug resistance is associated with several small genetic changes, each of which contributes to the overall resistance of the strain. Clearly, continual use of azole drugs by a patient can select for genetic changes that render oral candidiasis refractory to treatment.

AIDS-Related Opportunistic Infections↗

Review: Creutzfeldt-Jakob disease.

The clinicopathological spectrum of Creutzfeldt-Jakob disease has recently been extended by the identification of an apparently new variant of this disorder in the UK. The hypothesis that this new disorder is causally related to the transmissible agent responsible for bovine spongiform encephalopathy has prompted re-evaluation of the relationships between human and animal transmissible spongiform encephalopathies, and reinforced the need for adequate experimental models to investigate this field. Recent experimental transmission studies of bovine spongiform encephalopathy into primates have supported the hypothesis, and reinforced the central role of neuropathology in the investigation of this group of diseases. Whilst clearly of distinctive etiology, Creutzfeldt-Jakob disease shares both clinical and neuropathological features with other human dementias; renewed evaluation of potentially similar disease mechanisms in these devastating conditions might provide new information of both scientific and therapeutic value.

Animals↗

Evaluation of molecular typing for epidemiological study of Chlamydia trachomatis genital infections.

Molecular typing and serotyping were compared for 150 Chlamydia trachomatis strains isolated from genital sources, belonging to 10 different serovars. Because of the general agreement of the two methods, molecular omp1 genotyping was applied to the epidemiological study of C. trachomatis isolates from genital infections in Bordeaux (France), during a 29-month period. The most prevalent omp1 genotypes were E (51.7%), F (17.3%), D (8.8%), and G (8.4%). Restriction enzyme analysis allowed identification of a serovar D variant (Dv), whereas serovar E strains were homogeneous.

Bacterial Outer Membrane Proteins↗

The use of two-dimensional electrophoresis to detect mutations induced in mouse spermatogonia by ethylnitrosourea.

Two-dimensional electrophoresis should, in theory, be a suitable method for the measurement of induced mutation rates in the germ cells of mice. Not only can the polypeptide products of a large number of genes be resolved on a single gel but the detection of mutations which lead to proteins with altered electrophoretic properties (but not necessarily altered function) is possible. Our attempts to apply two-dimensional electrophoresis to the detection of mutation in vivo have involved three stages: (i) the rapid production of gels of high resolution and reproducibility; (ii) the identification of eight interstrain protein variants and demonstration of their simple genetic basis; and (iii) a pilot experiment using the powerful germ-cell mutagen ethylnitrosourea. It was found that although interstrain protein variants could be detected and shown to be inherited in a codominant manner, induced variants were rarely detected even on high quality gels. Only 2 variants were detected among 67 offspring of male mice treated with 150 mg/kg ethylnitrosourea. This represented a mutation rate of 0.88 X 10(-4) mutations per locus per gamete.

Animals↗

Partial cloning and characterization of Slc12a2: the gene encoding the secretory Na+-K+-2Cl- cotransporter.

The Slc12a2 gene encodes a widely expressed bumetanide-sensitive Na+-K+-2Cl- cotransporter that participates in various functions such as Cl- secretion and cell volume regulation. We isolated and characterized 75 kilobases of the murine gene encoding the cotransporter. The cotransport protein is encoded by 27 exons. Ribonuclease protection assay and primer extension demonstrated tissue-specific transcription initiation sites located within 270 base pairs upstream of the start codon. Nucleotide sequence analysis of the proximal 5'-flanking region revealed the presence of a weak TATA box, multiple Sp1/GC consensus sites, and the consensus sequence of a putative transcriptional initiator. Transfection of luciferase reporter gene constructs in mouse inner medullary collecting duct (mIMCD-3) cells confirmed the location of the minimal promoter within a 120-base pair fragment upstream of the cDNA. We also report the identification of an alternatively spliced variant of the cotransporter, expressed primarily in brain. This new spliced variant lacks exon 21, which encodes a 16-amino acid peptide located in the COOH-terminal tail of the protein. The absence of this exon causes the loss of the single protein kinase A consensus site of the cotransport protein.

Animals↗

Costs and benefits of diagnosing familial breast cancer.

Based on results from our surveillance program for women at risk for inherited breast cancer, we have calculated cost per year earned. Norwegian National Insurance Service reimbursement fees were used in the calculations. The calculated costs are based on empirical figures for expanding already established medical genetic departments and diagnostic outpatient clinics to undertake the work described. Cost per year earned was estimated at Euro 753 using our current practice of identifying the high-risk women through a traditional cancer family clinic. A strategy of identifying the high-risk families through genetic testing of all incident breast and ovarian cancers for founder mutations in BRCA1, will increase the cost to Euro 832. Costs related more to genetic counseling and clinical follow-up than to laboratory procedures. This potential economic limiting factor coincides with a shortage of personnel trained in genetic counseling. The number of relatives counseled to identify one healthy female mutation carrier (i.e. the uptake of genetic testing) is more important to cost-effectiveness than family size. Costs will vary depending upon the penetrance of the mutations detected and the prevalence of founder mutations in the population examined. Prevalences of BRCA1 founder mutations in some high incidence areas of Norway may be sufficiently high to consider population screening. Unlike mutation screening of cancer genes, founder mutation analysis will not identify DNA variants of uncertain clinical significance. Identification of high-risk families through founder mutation analysis of BRCA1 ensures that families with maximum risks are given first access to the limited resources of the high-risk clinics. This may be the greatest contribution to increased cost effectiveness of such a strategy. The assumptions underlying the calculations are discussed. The conclusion is that inherited breast cancer may be managed effectively for the cost of Euro 750-1,600 per year earned.

Biopsy↗

Microarray comparative genomic hybridization profile of a murine model for epithelial ovarian cancer reveals genomic imbalances resembling human ovarian carcinomas.

Microarray comparative genomic hybridization (mCGH) is emerging as a high-resolution technology to detect gene dosage alterations in numerous pathologies, including cancer. We optimized cDNA microarrays to identify genome-wide imbalances in spontaneously transformed mouse ovarian surface epithelial cell lines, an in vitro murine model for ovarian cancer. Amplification of chromosome 19 and a more variable gain pattern of chromosomes 15 and 5 were detected and independently validated using conventional metaphase CGH. In addition, cryptic aberrations in segments of chromosomes 4, 7, 8, 9, 11, 17, and X, allowed identification of 2 related genomic variants among six cell lines studied. Mouse-human synteny revealed an overall early transformation stage with approximately 80% conservation relative to human ovarian malignancies of epithelial origin including low malignant potential tumors, serous carcinoma, and carcinoma cell lines. Importantly, three of the cells bear gained segments 13 and 41 Mbp length of chromosomes 5 and 15, respectively, which are syntenic to human 22q11-13, 8q24 and 12p11-q24, the two latter chromosomal regions thought to define one pathway of karyotypic changes in the development of human ovarian tumors. Our findings support the utility of mouse ovarian surface epithelial (MOSE) cells in studying initiation and progression of human ovarian cancer and as a suitable model to evaluate therapeutic approaches.

Animals↗

Characterizing exons 11 and 1 promoters of the mu opioid receptor (Oprm) gene in transgenic mice.

BACKGROUND: The complexity of the mouse mu opioid receptor (Oprm) gene was demonstrated by the identification of multiple alternatively spliced variants and promoters. Our previous studies have identified a novel promoter, exon 11 (E11) promoter, in the mouse Oprm gene. The E11 promoter is located approximately 10 kb upstream of the exon 1 (E1) promoter. The E11 promoter controls the expression of nine splice variants in the mouse Oprm gene. Distinguished from the TATA-less E1 promoter, the E11 promoter resembles a typical TATA-containing eukaryote class II promoter. The aim of this study is to further characterize the E11 and E1 promoters in vivo using a transgenic mouse model. RESULTS: We constructed a approximately 20 kb transgenic construct in which a 3.7 kb E11 promoter region and an 8.9 kb E1 promoter region controlled expression of tau/LacZ and tau/GFP reporters, respectively. The construct was used to establish a transgenic mouse line. The expression of the reporter mRNAs, determined by a RT-PCR approach, in the transgenic mice during embryonic development displayed a temporal pattern similar to that of the endogenous promoters. X-gal staining for tau/LacZ reporter and GFP imaging for tau/GFP reporter showed that the transgenic E11 and E1 promoters were widely expressed in various regions of the central nervous system (CNS). The distribution of tau/GFP reporter in the CNS was similar to that of MOR-1-like immunoreactivity using an exon 4-specific antibody. However, differential expression of both promoters was observed in some CNS regions such as the hippocampus and substantia nigra, suggesting that the E11 and E1 promoters were regulated differently in these regions. CONCLUSION: We have generated a transgenic mouse line to study the E11 and E1 promoters in vivo using tau/LacZ and tau/GFP reporters. The reasonable relevance of the transgenic model was demonstrated by the temporal and spatial expression of the transgenes as compared to those of the endogenous transcripts. We believe that these transgenic mice will provide a useful model for further characterizing the E11 and E1 promoter in vivo under different physiological and pathological circumstances such as chronic opioid treatment and chronic pain models.

Animals↗

Characterisation of silent and active genes for a variable large protein of Borrelia recurrentis.

BACKGROUND: We report the characterisation of the variable large protein (vlp) gene expressed by clinical isolate A1 of Borrelia recurrentis; the agent of the life-threatening disease louse-borne relapsing fever. METHODS: The major vlp protein of this isolate was characterised and a DNA probe created. Use of this together with standard molecular methods was used to determine the location of the vlp1B. recurrentis A1 gene in both this and other isolates. RESULTS: This isolate was found to carry silent and expressed copies of the vlp1B. recurrentis A1 gene on plasmids of 54 kbp and 24 kbp respectively, whereas a different isolate, A17, had only the silent vlp1B. recurrentis A17 on a 54 kbp plasmid. Silent and expressed vlp1 have identical mature protein coding regions but have different 5' regions, both containing different potential lipoprotein leader sequences. Only one form of vlp1 is transcribed in the A1 isolate of B. recurrentis, yet both 5' upstream sequences of this vlp1 gene possess features of bacterial promoters. CONCLUSION: Taken together these results suggest that antigenic variation in B. recurrentis may result from recombination of variable large and small protein genes at the junction between lipoprotein leader sequence and mature protein coding region. However, this hypothetical model needs to be validated by further identification of expressed and silent variant protein genes in other B. recurrentis isolates.

Antigens, Bacterial↗

Exploring the use of machine and deep learning in genome-wide association studies: a comprehensive review.

The advent of high-throughput sequencing technologies has generated increasingly large and complex genomic datasets, necessitating analytical approaches capable of capturing high-dimensional and potentially nonlinear genetic interactions. This situation has significantly impacted the entire field of Genome-Wide Association Study (GWAS), whose primary goal is the identification of genomic traits and variants that are statistically associated with the risk of a disease. However, traditional GWAS methods may show reduced performance when applied to highly polygenic and nonlinear genetic architectures. Computational strategies from Artificial Intelligence (AI) and, in particular, from machine- and deep-learning may provide a powerful tool to overcome such limitations, especially by capturing nonlinear interactions and complex hidden regularities in large-scale data, which traditional GWAS approaches might overlook. To date, only a few approaches have been introduced and systematically assessed. In this review, we describe the main characteristics and limitations of standard statistical approaches for GWAS, the main uses of AI methods in computational genomics, and recent attempts to leverage AI strategies in GWAS. Particular attention will be devoted to key issues, such as the interpretability of methods and results, and the curse of dimensionality. More specifically, the review presents 30 methods designed to leverage AI in GWAS, as well as presenting a comprehensive set of evaluation metrics for their performance, also providing references to the most frequently used databases, and biobanks. Overall, this work may serve as a starting point for both dry- and wet-lab researchers, aiming to extract deeper insights from genomic data by moving beyond traditional linear additive assumptions, and leveraging large-scale datasets through AI-driven approaches.

Artificial intelligence↗

Beta1PIX, the PAK-interacting exchange factor, requires localization via a coiled-coil region to promote microvillus-like structures and membrane ruffles.

PIX is a Rho-family guanine nucleotide exchange factor that binds PAK. We previously described two isoforms of PIX that differ in their N termini. Here, we report the identification of a new splice variant of betaPIX, designated beta2PIX, that is the dominant species in brain and that lacks the region of approximately 120 residues with predicted coiled-coil structure at the C terminus of beta1PIX. Instead, beta2PIX contains a serine-rich C terminus. To determine whether these splice variants differ in their cellular function, we studied the effect of expressing these proteins in HeLa cells. We found that the coiled-coil region plays a key role in the localization of beta1PIX to the cell periphery and is also responsible for PIX dimerization. Overexpression of beta1, but not beta2PIX, drives formation of membrane ruffles and microvillus-like structures (via activation of Rac1 and Cdc42, respectively), indicating that its function requires localized activation of these GTPases. Thus, beta1PIX, like other RhoGEFs, exerts specific morphological functions that are dependent on its intracellular location and are mediated by its C-terminal dimerization domain.

3T3 Cells↗

Properties of the double substituted hemoglobin C Ziguinchor alpha2A beta 2 6 Glu replaced by Val 58 Pro replaced by Arg.

We have previously described the structural identification of the sickle hemoglobin variant Hb C Ziguinchor (alpha2A beta2 6 Glu replaced by Val, 58 Pro replaced by Arg). This hemoglobin was found in two generations (three members) of an African family. In two family members, the clinical picture resembled that typical of a sickle cell trait, while the third member showed a more extreme clinical condition due to complication by an iron deficiency anemia. The functional properties of Hb C Zig. in red blood cells or in dilute solutions were identical to those of Hb S. The gelling behaviour of deoxy Hb C Zig. was also indistinguishable from that of Hb S. These findings suggest that, in contrast to the case of Hb C Harlem, the second substitution in position beta58 in Hb C Zig. does not interfere with the intermolecular interactions determined by the sickle substitution.

Adult↗

Cytologic findings of cervicovaginal smears in women with uterine papillary serous carcinoma.

The goal of this study was to evaluate the cytomorphologic features of histologically confirmed uterine papillary serous carcinomas (UPSC) of the endometrium. We reviewed cervicovaginal smears from 12 patients with UPSC who had done their cervical smears at six months to a year earlier before the time of diagnosis; nine smears (75%) were diagnosed as positive for malignancy and three smears (25%) were diagnosed as negative. The cervical smears of patients with UPSC revealed frequent papillary clusters that were composed of large pleomorphic tumor cells with prominent nucleoli in a background of necrosis. Other findings revealed from the tests were relatively frequent single malignant cells and bare nuclei. Although the Pap smear is not a sensitive screening test for endometrial carcinoma, we could depend on it to reveal the cytologic features of UPSC which are fairly characteristic and reliable for a preoperative diagnosis of UPSC. Preoperative identification of this poor prognostic variant of endometrial carcinoma may influence the surgical management of these cases and the choice of adjuvant therapy.

Adenocarcinoma↗

Rabies postexposure prophylaxis. Human and domestic animal considerations.

The emphasis on rabies control and prevention in the United States seems to be a function of our perception of proximity of the threat. Wildlife rabies epizootics within a state may be of little concern to the uninformed urban dweller. Additionally, many parts of the western United States are free of terrestrial rabies; were it not for the presence of bat rabies, people in those areas would likely interpret rabies control as a minor public health concern. It is essential that federal, state, and local public health programs emphasize the importance of rabies control through activities that include rabies education, sponsorship of legislated requirements for domestic animal vaccination, support for local animal control programs, and the promotion of recommendations that encourage the appropriate use of PEP. We are almost guaranteed that rabies is going to remain a major public health issue well into the next century because of expanding wildlife rabies epizootics, identification of new rabies viral variants with increased public health concern, emotional and legal concerns associated with rabies exposure, and increasing national cost associated with rabies control and prevention. Nevertheless, the development of new laboratory technology that allows an understanding of the epidemiologic nature of the rabies virus based on an evolving genetic history and the interrelationship with wildlife reservoirs should allow access to valuable tools for rabies control. When combined with programs using new developments in oral rabies vaccine that can immunize whole populations of wildlife reservoirs, that technology offers encouragement in our effort to control one of the diseases of antiquity.

Animals↗