Comprehensive oligonucleotide array-comparative genomic hybridization analysis: new insights into the molecular pathology of the DMD gene

We report on the effectiveness of a custom-designed oligonucleotide-based comparative genomic hybridization microarray (array-CGH) to interrogate copy number across the entire 2.2-Mb genomic region of the DMD gene and its applicability in diagnosis. The high-resolution array-CGH, we developed, successfully detected a series of 42 previously characterized large rearrangements of various size, localization and type (simple or complex deletions, duplications, triplications) and known intronic CNVs/Indels. Moreover, the technique succeeded in identifying a small duplication of only 191 bp in one patient previously negative for DMD mutation. Accurate intronic breakpoints localization by the technique enabled subsequent junction fragments identification by sequencing in 86% of cases (all deletion cases and 62.5% of duplication cases). Sequence examination of the junctions supports a role of microhomology-mediated processes in the occurrence of DMD large rearrangements. In addition, the precise knowledge of the sequence context at the breakpoints and analysis of the resulting consequences on maturation of pre-mRNA contribute to elucidating the cause of discrepancies in phenotype/genotype correlations in some patients. Thereby, the array-CGH proved to be a highly efficient and reliable diagnostic tool, and the new data it provides will have many potential implications in both, clinics and research.     

Investigating the genetic diversity of Echinococcus granulosus sensu stricto with new microsatellites

Parasitology Research - Cystic echinococcosis is a zoonotic disease with worldwide distribution caused by the larval stage of the Cestode parasite Echinococcus granulosus sensu lato. Due to the...     

Integrated molecular landscape of amyotrophic lateral sclerosis provides insights into disease etiology

Amyotrophic lateral sclerosis (ALS) is a severe, progressive and ultimately fatal motor neuron disease caused by a combination of genetic and environmental factors, but its underlying mechanisms are largely unknown. To gain insight into the etiology of ALS, we here conducted genetic network and literature analyses of the top‐ranked findings from six genome‐wide association studies of sporadic ALS (involving 3589 cases and 8577 controls) as well as genes implicated in ALS etiology through other evidence, including familial ALS candidate gene association studies. We integrated these findings into a molecular landscape of ALS that allowed the identification of three main processes that interact with each other and are crucial to maintain axonal functionality, especially of the long axons of motor neurons, i.e. (1) Rho‐GTPase signaling; (2) signaling involving the three regulatory molecules estradiol, folate, and methionine; and (3) ribonucleoprotein granule functioning and axonal transport. Interestingly, estradiol signaling is functionally involved in all three cascades and as such an important mediator of the molecular ALS landscape. Furthermore, epidemiological findings together with an analysis of possible gender effects in our own cohort of sporadic ALS patients indicated that estradiol may be a protective factor, especially for bulbar‐onset ALS. Taken together, our molecular landscape of ALS suggests that abnormalities within three interconnected molecular processes involved in the functioning and maintenance of motor neuron axons are important in the etiology of ALS. Moreover, estradiol appears to be an important modulator of the ALS landscape, providing important clues for the development of novel disease‐modifying treatments.     

Comparative genomic hybridization: a new tool for reproductive pathology

OBJECTIVE: To demonstrate the effectiveness of comparative genomic hybridization (CGH) for analysis of reproductive pathology specimens in clinical cytogenetics laboratories. DESIGN: A total of 856 CGH analyses were performed on various placental and fetal tissues derived from 368 specimens of spontaneous abortions and on placentas from 219 pregnancies with live-born infants. The live-born infants were clinically evaluated as normally developed, with either a normal birth weight or with intrauterine growth restriction; some live-born infants had an abnormal prenatal triple screen with normal cytogenetic results on amniotic fluid cell cultures. RESULTS: Comparative genomic hybridization analysis was successfully performed on 856 samples from spontaneously aborted specimens and term placentas. Failure of analysis occurred in 1.6% of samples and was due to an insufficient amount of tissue for DNA extraction. Comparative genomic hybridization identified aneuploidy in 53% of spontaneous abortion samples and 3.1% of term placentas. CONCLUSIONS: Comparative genomic hybridization analysis is a useful clinical tool for detection of aneuploidy in placental and fetal tissues. It provides a genome-wide screen while eliminating tissue culture failures, culture artifacts, and maternal cell contamination. We present practical guidelines for interpreting CGH profiles derived from human reproductive specimens.     

Comparative genomic hybridization and molecular cytogenetic characterization of two prostate cancer xenografts

Conventional cytogenetic analysis of two prostate tumor xenografts, LuCaP 23.1 and RP22090, was unsatisfactory for comprehensive genetic evaluation of the cell lines. Fluorescence in situ hybridization (FISH) for chromosome enumeration and comparative genomic hybridization (CGH) for numerical imbalance detection were performed and resulted in a more complete molecular cytogenetic characterization of these lines. Both xenografts were hypertriploid and had significant numerical imbalances. For example, LuCaP 23.1 had gain of all or part of chromosomes 3, 5, 6, 7, 8, 11, and 12 and the X chromosome and loss of all or part of chromosomes 2, 3 6, 8, 9, 10, 17, and 18. In RP22090, gain of all or part of chromosomes 5, 7, 8, 9, 10, 12, 14, and 15 was seen, whereas loss was seen for all or part of chromosomes 4, 6, 8, 15, 16, 17, 19, 20, and 22. Both xenografts reflect the high frequency of chromosomal changes seen in some late-stage prostate cancers, including many novel changes and some changes such as the loss of 8p and gain of 8q, which have been reported previously in primary and metastatic prostate cancers. Consistent changes in both lines, such as loss of chromosomes 6 and chromosome arm 8p and gain of chromosome 7 and chromosome arm 8q, may represent genetic events specific for prostate cancer development, but imbalances on other chromosomes such as 3, 9, 19, and 20, not frequently reported in prostate cancers, may reflect potentially important changes that should also be examined. Genes Chromosom. Cancer 18:299–304, 1997. © 1997 Wiley-Liss, Inc.     

Marginal-zone B-cell lymphoma of extranodal mucosa-associated lymphoid tissue type: molecular genetics provides new insights into pathogenesis.

Marginal zone B-cell lymphoma of extranodal mucosa-associated lymphoid tissue (MALT) type is recognized as a distinct clinicopathologic entity in the revised European-American lymphoma (REAL) and recently published World Health Organization (WHO) classifications. These neoplasms are thought to arise from the extranodal equivalent of the lymph node marginal zone. Two recurrent chromosomal translocations, to date, have been implicated in the pathogenesis of these neoplasms. The t(11;18)(q21;q21), which is far more common, disrupts the api2 gene on chromosome 11q21 and the malt1 (mlt) gene on chromosome 18q21, resulting in the synthesis of a novel fusion gene and protein, API2-MALT1. The t(1;14)(p22;q32), which is uncommon, juxtaposes the bcl-10 gene on chromosome 1p22 adjacent to the immunoglobulin heavy chain (IgH) gene on chromosome 14, wherein BCL10 is overexpressed via the influence of the IgH enhancer. BCL-10 may then form a complex with MALT1 in the cell. Both translocations result in increased inhibition of apoptosis, conferring a survival advantage. Recent work suggests that API2-MALT1 and BCL-10-MALT1 may activate NF-kB and a common downstream signaling pathway.     

Comparative genomic hybridization analysis of hepatoblastomas

Prior cytogenetic analyses of hepatoblastomas have shown the most common recurring abnormalities to be trisomy for chromosomes 2 and 20, and a recurrent translocation involving chromosomes 1 and 4 identified in a minority of cases. Four cases have shown double minute chromosomes, which provide cytogenetic evidence for gene amplification, although no particular genes or genetic regions have been shown to be amplified. To further investigate the cytogenetic changes involved in the pathogenesis and progression of hepatoblastoma, this study analyzes 10 tumors by comparative genomic hybridization. Regions of relative gain or loss were found in nine tumors. The most common recurrent abnormalities were gain of the long arm of chromosome 1 (six tumors), gain of chromosomes 2 (seven tumors), 17 (four tumors), and 20 (three tumors), and loss of chromosomes 4 and 11 (two tumors each). Four cases showed restricted regions of high-level gain at 1q32 or 2q24, regions that have previously been reported to be amplified in other tumors, but not in hepatoblastomas. A specific amplified gene has yet to be identified at these loci, although candidate genes have been proposed and may offer targets for future studies. Genes Chromosomes Cancer 27:196-201, 2000.     

Burkitt's lymphoma: new insights into molecular pathogenesis

The World Health Organisation classification reports three subcategories of Burkitt's lymphoma (BL)--endemic, non-endemic, and immunodeficiency associated--proposed to reflect the major clinical and genetic subtypes of this disease. These different types of BL have been reviewed and studied by immunohistochemistry and molecular methods. The results point out the heterogeneity of BL and suggest that AIDS related BL may have a different pathogenesis from that of classic BL.     

Serial analysis of gene expression provides new insights into regulatory T cells

It is now possible to induce donor-specific transplantation tolerance in adult rodents using a number of therapeutic strategies. Such peripheral tolerance is maintained by regulatory CD4+ T cells, not only in transplantation models, but also in autoimmunity. Differential gene expression analyses have been used to identify potential new markers for regulatory T cells, aiming to reveal new insights into their mechanisms of action, and to find novel targets for therapeutic manipulation of the immune system.     

Virome analysis provides new insights into the association between viruses and Parkinson's disease

Parkinson's disease (PD) is a kind of neurodegenerative disease that causes a huge burden to society. Previous studies have suggested the association between PD and multiple viruses. However, there is still a lack of a virome study about PD. This study systematically identified viruses from the public RNA-sequencing data of more than 700 samples from both PD patients and the control group (most were healthy people). Only nine viruses such as human betaherpesvirus 5 and Merkel cell polyomavirus have been detected in several human brain tissues of the central nervous system, the appendix, and blood of PD patients, and all of these viruses were also detected in the control group. Most viruses were observed to have low abundance in no more than three tissues. No statistically significant differences were observed between the virus abundance in the PD patients and the control group for all viruses. The positive rates of most viruses in PD patients were higher or similar to that in the control group, although those were less than 5% for most viruses. Overall, this is the first study to systematically investigate the virome in PD patients, and provides new insights into the association between viruses and PD.     

鼻咽癌的比较基因组杂交研究

目的：研究鼻咽癌的遗传变异特性。方法：采用激光微切割技术分离鼻咽癌细胞DNA，用比较基因组杂交检测6例鼻咽癌组织。结果：6q12-22、8q染色体区域的扩增，染色体11q23-24、13q基因缺失。结论：鼻咽癌具有染色体变异，其中6q12-22、8q、11q23-24和13q区域可能存在一些与鼻咽癌相关的未知基因。     

Cardiac memory … new insights into molecular mechanisms

'Cardiac memory' describes an electrocardiographic T wave vector change, recorded during normal sinus rhythm that reflects the QRS complex vector during prior periods of ventricular pacing or arrhythmia. In this brief review we consider the mechanisms responsible for cardiac memory, which offer a unique window for relating molecular determinants of repolarization to their expression in the function of ion channels and in the electrophysiology of the heart. Understanding the steps that translate the molecular mechanisms for memory into clinical expression in this relatively straightforward model facilitates our comprehension of the complex pathways that order normal cardiac repolarization and repolarization changes.     

Comparative genomic hybridization in the investigation of myeloid leukemias

Comparative genomic hybridization (CGH) was used for the examination of ten cases of myeloid leukemia (eight acute myeloid leukemias and two myelodysplastic syndromes). In five cases, genomic gains or losses were identified, which mapped to chromosomal regions known to be involved in this group of malignancies. In comparison to the results obtained by banding analysis, discrepancies were found in three of the ten cases; in two cases, chromosomal imbalances were not identified by CGH because they were present only in small subclones. In the other case, there were no evaluable metaphase cells for banding analysis; CGH revealed an overrepresentation of chromosome 8, which was confirmed by interphase cytogenetics with a chromosome 8-specific alphoid probe. All abnormalities revealed by CGH were confirmed by G-banding or subsequent interphase cytogenetic analysis, which demonstrates the high specificity of the method. Furthermore, in all cases, CGH identified the chromosomal imbalances present in the major clone as detected by banding analysis. The good correlation between CGH and chromosome banding results in myeloid leukemias makes this tumor a good model for the assessment of tools that are developed for automated and quantitative CGH analysis.     

Immunocytochemical analysis of synaptic proteins provides new insights into diabetes-mediated plasticity in the rat hippocampus

The hippocampus, an important integration center for learning and memory in the mammalian brain, undergoes neurological changes in response to a variety of stimuli that are suggestive of ongoing synaptic reorganization. Accordingly, the aim of this study was to identify markers of synaptic plasticity using rapid and reliable techniques such as radioimmunocytochemistry and confocal microscopy, thereby providing a "birds-eye view" of the whole hippocampus under hypercorticosteronemic conditions. The regulation of microtubule-associated protein 2, synaptophysin and postsynaptic density-95 was examined in two different animal models of hypercorticosteronemia: corticosterone administration and streptozotocin-induced diabetes using both a short-term (1 week) and long-term (5 weeks) treatment. Glucocorticoids and/or hyperglycemia increased synaptophysin expression in CA1, CA3 and the dentate gyrus, regions that exhibit synaptic plasticity in response to glucocorticoid exposure. In these models, postsynaptic density-95 expression increased in the CA3 region, particularly in the diabetic rats, while microtubule-associated protein 2 exhibited more selective changes. Fluoro-Jade histochemistry did not detect neuronal damage, suggesting that glucocorticoids and/or hyperglycemia induce plastic and not irreversible neuronal changes at these time points. Collectively, these results demonstrate that changes in the expression and distribution of synaptic proteins provide another measure of synaptic plasticity in the rat hippocampus in response to glucocorticoid exposure, changes that may accompany or contribute to neuroanatomical, neurochemical, and behavioral changes observed in experimental models of type 1 diabetes.     

Comparative genomic hybridization analysis of a pleuropulmonary blastoma

Pleuropulmonary blastoma (PPB) is a rare, aggressive dysontogenetic tumor of childhood. We report the comparative genomic hybridization (CGH) study performed on a case of PPB in a 3-year-old-boy. The tumor was characterized by several chromosomal imbalances. Gains observed affected regions: 1q12-q23, 3q23-qter, 8pter-q24.1, 9p13-q21, 17p12-p11, 17q11-q22, 17q23-q25, 19pter-p11, and 19q11-q13.3. Whole chromosome gains were detected at 2 and 7. Loss of genetic material was found at regions: 6q13-qter, 10pter-p13, 10q22-qter, and 20p13. To our knowledge, there have been no CGH reports on PPB, but it is interesting to note that 1) the alterations found confirm previous cytogenetic reports describing gains of chromosomes 2 and 8 as recurrent abnormalities in this type of tumor, suggesting that a gene or genes of putative relevance in PPB pathogenesis are mapped at 8p11-p12, and 2) the CGH profile of this case is very similar to those observed in embryonal rhabdomyosarcomas, in which gains of 2 or 2q, 7 or 7q, and 8 or 8p and loss of 10q22-qter are consistently found. This finding supports the hypothesis that PPB may be tumorigenetically related with embryonal rhabdomyosarcoma.     

原发性胃癌的比较基因组杂交研究

目的　研究胃癌发生和发展过程中是否涉及其它未知的癌基因和抑癌基因。方法　采用比较基因组杂交法(com parative genom ic hybridization,CGH)分析了43 例原发性胃癌。结果　3p(8/43)、8q(8/43)、20 号染色体[20(9/43),20p(7/43)、20q(4/43)]、12q(16/43)、13q(12/43)的扩增,19 号染色体[19(15/43),19p(13/43)]、17 号染色体[17(8/43),17p(10/43)]、16 号染色体(10/43)和1p(11/43)区域的缺失为胃癌的特征性变化。结论　提示3p、8q、12q、13q、20 号染色体、17 号染色体、16 号染色体和1p 区域可能存在一些与胃癌形成相关的未知基因。     

Comparative genomic hybridization study of primary neuroblastoma tumors

Neuroblastoma tumors show a complex interaction of genetic abnormalities, among which some are of significant prognostic importance; however, analysis of chromosome changes in this tumor is often unsuccessful. Twenty primary tumors were studied by comparative genomic hybridization (CGH), and abnormalities were found in 19. While these changes included deletions of chromosome arm lp (45%) and MYCN oncogene amplification (30%), gains of chromosome 17 material were much more frequent (75%). We also found evidence in two cases of a new amplification site at band 2p23. Genes Chromosom. Cancer 18:162–169, 1997. © 1997 Wiley-Liss, Inc.     

A new genome of Acidithiobacillus thiooxidans provides insights into adaptation to a bioleaching environment

Acidithiobacillus thiooxidans is a sulfur oxidizing acidophilic bacterium found in many sulfur-rich environments. It is particularly interesting due to its role in bioleaching of sulphide minerals. In this work, we report the genome sequence of At. thiooxidans Licanantay, the first strain from a copper mine to be sequenced and currently used in bioleaching industrial processes. Through comparative genomic analysis with two other At. thiooxidans non-metal mining strains (ATCC 19377 and A01) we determined that these strains share a large core genome of 2109 coding sequences and a high average nucleotide identity over 98%. Nevertheless, the presence of 841 strain-specific genes (absent in other At. thiooxidans strains) suggests a particular adaptation of Licanantay to its specific biomining environment. Among this group, we highlight genes encoding for proteins involved in heavy metal tolerance, mineral cell attachment and cysteine biosynthesis. Several of these genes were located near genetic motility genes (e.g. transposases and integrases) in genomic regions of over 10 kbp absent in the other strains, suggesting the presence of genomic islands in the Licanantay genome probably produced by horizontal gene transfer in mining environments.