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A critical view on autoantibodies in lupus nephritis: Concrete knowledge based on evidence. Autoimmun Rev 2024; 23:103535. [PMID: 38552995 DOI: 10.1016/j.autrev.2024.103535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/22/2024] [Accepted: 03/23/2024] [Indexed: 04/07/2024]
Abstract
Deposition of autoantibodies in glomeruli is a key factor in the development of lupus nephritis (LN). For a long time, anti-dsDNA and anti-C1q antibodies were thought to be the main cause of the kidney damage. However, recent studies have shown that the list of autoantibidies that have renal tropism and deposit in the kidney in LN is increasing and the link between anti-dsDNA and renal pathology is weak due to potential confounders. Aspecific bindings of dsDNA with cationic antibodies and of anti-dsDNA with several renal antigens such as actinin, laminin, entactin, and annexinA2 raised doubts about the specific target of these antibodies in the kidney. Moreover, the isotype of anti-dsDNA in SLE and LN has never received adequate interest until the recent observation that IgG2 are preponderant over IgG1, IgG3 and IgG4. Based on the above background, recent studies investigated the involvement of anti-dsDNA IgG2 and of other antibodies in LN. It was concluded that circulating anti-dsDNA IgG2 levels do not distinguish between LN versus non-renal SLE, and, in patients with LN, their levels do not change over time. Circulating levels of other antibodies such as anti-ENO1 and anti-H2 IgG2 were, instead, higher in LN vs non-renal SLE at the time of diagnosis and decreased following therapies. Finally, new classes of renal antibodies that potentially modify the anti-inflammatory response in the kidney are emerging as new co-actors in the pathogenetic scenario. They have been defined as 'second wave antibodies' for the link with detoxifying mechanisms limiting the oxidative stress in glomeruli that are classically stimulated in a second phase of inflammation. These findings have important clinical implications that may modify the laboratory approach to LN. Serum levels of anti-ENO1 and anti-H2 IgG2 should be measured in the follow up of patients for designing the length of therapies and identify those patients who respond to treatments. Anti-SOD2 could help to monitor and potentiate the anti-inflammatory response in the kidney.
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Comprehensive Profiling of the Rheumatoid Arthritis Antibody Repertoire. Arthritis Rheumatol 2019; 72:242-250. [DOI: 10.1002/art.41089] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 08/20/2019] [Indexed: 01/13/2023]
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Whole Genome-Derived Tiled Peptide Arrays Detect Prediagnostic Autoantibody Signatures in Non-Small-Cell Lung Cancer. Cancer Res 2019; 79:1549-1557. [PMID: 30723114 DOI: 10.1158/0008-5472.can-18-1536] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 09/26/2018] [Accepted: 01/25/2019] [Indexed: 02/07/2023]
Abstract
The majority of non-small-cell lung cancer (NSCLC) cases are diagnosed at advanced stages, primarily because earlier stages of the disease are either asymptomatic or may be attributed to other causes such as infection or long-term effects from smoking. Therefore, early detection of NSCLC would likely increase response and survival rates due to timely intervention. Here, we utilize a novel approach based on whole genome-derived tiled peptide arrays to identify epitopes associated with autoantibody reactivity in NSCLC as a potential means for early detection. Arrays consisted of 2,781,902 tiled peptides representing 20,193 proteins encoded in the human genome. Analysis of 86 prediagnostic samples and 86 matched normal controls from a high-risk cohort revealed 48 proteins with three or more reactive epitopes in NSCLC samples relative to controls. Independent mass spectrometry analysis identified 40 of the 48 proteins in prediagnostic sera from NSCLC samples, of which, 21 occurred in the immunoglobulin-bound fraction. In addition, 63 and 34 proteins encompassed three or more epitopes that were distinct for squamous cell lung cancer and lung adenocarcinoma, respectively. Collectively, these data show that tiled peptide arrays provide a means to delineate epitopes encoded across the genome that trigger an autoantibody response associated with tumor development. SIGNIFICANCE: This study provides a modality for early diagnosis of NSCLC for precision oncology that can be applied to other cancer types.
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Overlay Tool© for aCGHViewer©: An Analysis Module Built for aCGHViewer© used to Perform Comparisons of Data Derived from Different Microarray Platforms. Cancer Inform 2017. [DOI: 10.1177/117693510700300003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The Overlay Tool© has been developed to combine high throughput data derived from various microarray platforms. This tool analyzes high-resolution correlations between gene expression changes and either copy number abnormalities (CNAs) or loss of heterozygosity events detected using array comparative genomic hybridization (aCGH). Using an overlay analysis which is designed to be performed using data from multiple microarray platforms on a single biological sample, the Overlay Tool© identifies potentially important genes whose expression profiles are changed as a result of losses, gains and amplifications in the cancer genome. In addition, the Overlay Tool© will incorporate loss of heterozygosity (LOH) probability data into this overlay procedure. To facilitate this analysis, we developed an application which computationally combines two or more high throughput datasets (e.g. aCGH/expression) into a single categorized dataset for visualization and interrogation using a gene-centric approach. As such, data from virtually any microarray platform can be incorporated without the need to remap entire datasets individually. The resultant categorized (overlay) data set can be conveniently viewed using our in-house visualization tool, aCGHViewer© (Shankar et al. 2006), which serves as a conduit to public databases such as UCSC and NCBI, to rapidly investigate genes of interest.
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Men's knowledge of their own fertility: a population-based survey examining the awareness of factors that are associated with male infertility. Hum Reprod 2016; 31:2781-2790. [PMID: 27816924 DOI: 10.1093/humrep/dew265] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 09/22/2016] [Accepted: 09/28/2016] [Indexed: 01/12/2023] Open
Abstract
STUDY QUESTION How knowledgeable are men about the medical, environmental and psychological factors that are associated with male infertility? SUMMARY ANSWER Men, across most demographic groups, have limited knowledge of the various factors that are associated with male infertility. WHAT IS KNOWN ALREADY Few surveys have focused on men's knowledge of their own fertility. Studies of both men and women have found that men are comparatively less knowledgeable about issues of fertility and reproductive health. STUDY DESIGN, SIZE, DURATION A regionally representative sample of Canadian men completed a web-based survey of male fertility and reproductive health, over a 2-month period in 2015. PARTICIPANTS/MATERIALS, SETTING, METHODS Men, aged 18-50 years, were recruited for the study. There were 701 male participants, with a mean age of 34.1 years. Each participant was asked to identify factors associated with male infertility; fertility knowledge was assessed through two open-ended questions and a comprehensive list of risk factors and attendant health issues. MAIN RESULTS AND THE ROLE OF CHANCE Men were only able to identify 51% of the risk factors and 45% of the health issues associated with male infertility. Men were most aware of the modifiable risk factors for infertility (e.g. sexually transmitted infections, smoking cigarettes), relative to their knowledge of fixed risk factors (e.g. delayed puberty, size of testicles) and the attendant health issues (e.g. cardiovascular disease, diabetes). The overall level of fertility knowledge did not vary by most demographic characteristics (e.g. age, education, employment, income), though men from ethnic minority groups displayed moderately greater awareness. Additionally, younger men, those with lower incomes and those who had no desire to have future biological children were more likely to identify themselves as unaware of associations with infertility in the open-ended questions. Self-reported knowledge was significantly associated with higher overall knowledge scores. More than half of the sample expressed an interest in obtaining information about male fertility and reproductive health, with the majority of these men indicating that medical professionals and online sources were their preferred methods for receiving information. LIMITATIONS, REASONS FOR CAUTION Participants were self-selected and required to have Internet access in order to participate. This may affect the generalizability of results. WIDER IMPLICATIONS OF THE FINDINGS Previous studies of fertility knowledge have either omitted men from their samples or when men have been included, they were asked about general fertility or women's fertility. This is the first large-scale survey that focuses solely on men's knowledge of male fertility. Insight into the areas where men's knowledge may be lacking can inform strategies for disseminating fertility-related information and improving men's fertility awareness. Public health initiatives should tailor campaigns to educate men about the lesser known associations with male infertility, particularly those that are most prevalent and preventable through lifestyle modification. STUDY FUNDING/COMPETING INTERESTS The study was funded by a grant from CIHR TE1-138296. No competing interests.
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Abstract A156: Anti-p53 auto-antibody serum profiling using high-density peptide arrays. Cancer Immunol Res 2016. [DOI: 10.1158/2326-6074.cricimteatiaacr15-a156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cancer is a result of a number of genetic alterations that disturb normal, controlled cell growth and differentiation. Mutational events leading to the activation of oncogenes or the inactivation of tumor-suppressor genes have been linked causally to the formation of tumors. p53 is one of the most important regulators of transcription, cellular cycle, DNA repair and apoptosis detected to date. Anti-p53 antibodies have been detected in the serum of cancer patients. This immune response is probably due to a self-immunization process linked to the strong immunogenicity of the p53 protein, and is associated predominantly with p53 missense mutation and p53 accumulation in the tumor. Auto-antibodies have also been proposed as potential diagnostic biomarkers for early stage diagnosis of cancers, since an increase in serum levels of certain auto-antibodies has been shown to precede the development of disease symptoms and correlate with cancer incidence for various cancers including breast and lung cancer.
Here we systematically evaluate reactivity of antibodies in p53 positive serum samples and identify reactive epitopes to normal and mutant peptides using a high-density (2.9 Million) peptide microarray. We assess the effect of linker length, peptide length, and flanking serines on antibody detection. We propose peptide array design parameters that can be applied to a whole proteome level to enable biomarker discovery and validation of novel auto-antibody epitopes associated with cancer.
Citation Format: Ken C. Lo, John C. Tan, Eric Sullivan, Ryan Bannen, Todd Richmond, Florian Grupp, Stefan Weiser, Dieter Heindl, Klaus-Peter Stengele, Albert Thomas. Anti-p53 auto-antibody serum profiling using high-density peptide arrays. [abstract]. In: Proceedings of the CRI-CIMT-EATI-AACR Inaugural International Cancer Immunotherapy Conference: Translating Science into Survival; September 16-19, 2015; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(1 Suppl):Abstract nr A156.
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Identification of somatic mutations in non-small cell lung carcinomas using whole-exome sequencing. Carcinogenesis 2012; 33:1270-6. [PMID: 22510280 DOI: 10.1093/carcin/bgs148] [Citation(s) in RCA: 162] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Lung cancer is the leading cause of cancer-related death, with non-small cell lung cancer (NSCLC) being the predominant form of the disease. Most lung cancer is caused by the accumulation of genomic alterations due to tobacco exposure. To uncover its mutational landscape, we performed whole-exome sequencing in 31 NSCLCs and their matched normal tissue samples. We identified both common and unique mutation spectra and pathway activation in lung adenocarcinomas and squamous cell carcinomas, two major histologies in NSCLC. In addition to identifying previously known lung cancer genes (TP53, KRAS, EGFR, CDKN2A and RB1), the analysis revealed many genes not previously implicated in this malignancy. Notably, a novel gene CSMD3 was identified as the second most frequently mutated gene (next to TP53) in lung cancer. We further demonstrated that loss of CSMD3 results in increased proliferation of airway epithelial cells. The study provides unprecedented insights into mutational processes, cellular pathways and gene networks associated with lung cancer. Of potential immediate clinical relevance, several highly mutated genes identified in our study are promising druggable targets in cancer therapy including ALK, CTNNA3, DCC, MLL3, PCDHIIX, PIK3C2B, PIK3CG and ROCK2.
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Abstract 164: High-throughput epigenetic analysis of susceptibility loci identified by GWAS in pancreatic cancer. Cancer Res 2010. [DOI: 10.1158/1538-7445.am10-164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Pancreatic cancer is a highly lethal cancer with few well established risk factors. A genome wide association study (GWAS) of pancreatic cancer (PanScan) is being conducted within the framework of the NCI-sponsored Cohort Consortium and the Pancreatic Cancer Case-Control Consortium (PANC4). Susceptibility loci discovered to date in PanScan are non-coding variants that lie in intronic or intergenic regions, suggesting that the underlying signals may function through regulatory mechanisms that influence gene expression or splicing. Alternatively, these may lie in unannotated transcripts and directly affect their function.
Epigenetic mechanisms, such as DNA methylation, can affect the regulation of gene expression and plays a critical role in the development of many human diseases including cancer. Powerful methods exist to analyze DNA methylation patterns in higher eukaryotes including methylated DNA immunoprecipitation (MeDIP), an affinity based approach to enrich methylated DNA regions from genomic DNA, which can be combined with microarrays to profile genomic DNA methylation patterns. We created a new semi-custom MeDIP-optimized array design based on our Human DNA Methylation 3×720K CpG Island Plus RefSeq Promoter array by tiling additional regions associated with pancreatic cancer that were identified in the PanScan study. To complement DNA methylation data a genome-wide transcriptome analysis was performed with RNA-sequencing (RNA-seq). Here we describe a comprehensive genome wide analysis of 8 pancreatic cancer cell lines to examine methylation patterns of Refseq promoters and annotated CpG islands as well as transcribed sequences.
One of the susceptibility loci from PanScan is in the vicinity of the ABO gene on Chr9q34 where four SNPs (rs505922, rs495828, rs657152 and rs630014) are associated with a significantly increased risk of pancreatic cancer. As a pilot study, DNA methylation patterns and expressed sequences in this locus were investigated in cell lines derived from pancreatic tumors and normal pancreatic tissues. Our genome wide DNA methylation and RNA-seq analysis aims at establishing a comprehensive catalog of epigenetic patterns in pancreatic cell lines that could provide plausibility for the association signal in the ABO gene and other GWAS regions and thereby, initiate the characterization of the molecular phenotype of the susceptibility alleles for pancreatic cancer risk.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 164.
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Interpreting aCGH-defined karyotypic changes in gliomas using copy number status, loss of heterozygosity and allelic ratios. Exp Mol Pathol 2009; 88:82-9. [PMID: 19818351 DOI: 10.1016/j.yexmp.2009.09.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Accepted: 09/03/2009] [Indexed: 12/13/2022]
Abstract
We have used SNP mapping arrays to simultaneously record copy number changes, loss of heterozygosity and allele ratios (ploidy) in a series of 13 gliomas. This combined analysis has defined novel amplification events in this tumor type involving chr1:241544532-243005121 and chr18:54716681-54917277 which contain the AKT3 and ZNF532 genes, respectively. The high resolution of this analysis has also identified homozygous deletions involving chr17:25600031-26490848 and Chr19:53883612-55061878. Throughout the karyotypes of these tumors, the combined analysis revealed counter intuitive relationships between copy number and LOH that requires reinterpretation of the significance of copy number gains and losses. It was not uncommon to observe copy number gains that were associated with loss of heterozygosity as well as copy number losses that were not. These events appeared to be related to ploidy status in the tumors as determined using allelic ratio calculations. Overall, this analysis of gliomas provides evidence for the need to perform more comprehensive interpretation of the CGH data beyond copy number analysis alone to evaluate the significance of individual events in the karyotypes.
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Refractory thrombotic thrombocytopenic purpura and membranoproliferative glomerulonephritis successfully treated with rituximab: a case associated with hepatitis C virus infection. Hong Kong Med J 2009; 15:201-208. [PMID: 19494376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
Plasmapheresis remains the main treatment modality for patients with thrombotic thrombocytopenic purpura. We report a patient who had simultaneous onset of membranoproliferative glomerulonephritis and thrombotic thrombocytopenic purpura. She did not improve after 48 plasmapheresis sessions. A 6-week course of weekly intravenous doses of rituximab was then given. This achieved complete remission of her nephrotic syndrome and improvement in her renal function, so plasmapheresis was ceased. She had a low ADAMTS13 antigen level and a positive ADAMTS13 antibody, both of which reverted to normal after treatment with rituximab. This coincided with a rise in her hepatitis C virus RNA and liver transaminases. Liver biopsies did not reveal active fibrosis. Her hepatitis C virus RNA titre dropped afterwards, and she had no relapses of her thrombotic thrombocytopenic purpura and nephrotic syndrome, for more than 2 years after remission. The simultaneous onset and successful outcomes of both the membranoproliferative glomerulonephritis and thrombotic thrombocytopenic purpura illustrate the usefulness of rituximab. We discuss its use and risks, in the context of chronic hepatitis C infection.
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MESH Headings
- ADAM Proteins/blood
- ADAMTS13 Protein
- Adult
- Alanine Transaminase/blood
- Antibodies, Monoclonal/administration & dosage
- Antibodies, Monoclonal/therapeutic use
- Antibodies, Monoclonal, Murine-Derived
- Arteries/pathology
- Comorbidity
- Creatinine/blood
- Female
- Glomerulonephritis, Membranoproliferative/drug therapy
- Glomerulonephritis, Membranoproliferative/epidemiology
- Glomerulonephritis, Membranoproliferative/pathology
- Hepacivirus/genetics
- Hepatitis C/epidemiology
- Humans
- Immunologic Factors/administration & dosage
- Immunologic Factors/therapeutic use
- Kidney Glomerulus/pathology
- Liver/pathology
- Plasmapheresis
- Purpura, Thrombotic Thrombocytopenic/drug therapy
- Purpura, Thrombotic Thrombocytopenic/epidemiology
- Purpura, Thrombotic Thrombocytopenic/therapy
- RNA, Viral/blood
- Rituximab
- Treatment Failure
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Application of oligonucleotides arrays for coincident comparative genomic hybridization, ploidy status and loss of heterozygosity studies in human cancers. Methods Mol Biol 2009; 556:47-65. [PMID: 19488871 DOI: 10.1007/978-1-60327-192-9_5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Many oligonucleotide arrays comprise of spotted short oligonucleotides from throughout the genome under study. Hybridization of tumor DNA samples to these arrays will provide copy number estimates at each reference point with varying degrees of accuracy. In addition to copy number changes, however, tumors often undergo loss of heterozygosity for specific regions of the genome without copy number changes and these genetic changes can only be identified using arrays that identify polymorphic alleles at each reference point. In addition, because the hybridization intensity can be measured at each of the allelic variants, allelic ratios can be established which give indications of ploidy status in the tumor which is not generally possible using most other oligonucleotide array designs. The only arrays currently available that simultaneously report copy number, ploidy, and loss of heterozygosity are the Affymetrix SNP mapping arrays. In this review, the features of the SNP mapping arrays are described and computational tools explored which allow the maximum genetic information to be extracted from the experiment. Although the methodologies to generate the SNP data are now well established, approaches to interpret the data are only just being developed. From our experience using these arrays, we provide insights into how to evaluate the SNP data to report copy number changes, loss of heterozygosity, and ploidy in the same tumor samples using a single array.
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Ploidy status and copy number aberrations in primary glioblastomas defined by integrated analysis of allelic ratios, signal ratios and loss of heterozygosity using 500K SNP Mapping Arrays. BMC Genomics 2008; 9:489. [PMID: 18928532 PMCID: PMC2576260 DOI: 10.1186/1471-2164-9-489] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2008] [Accepted: 10/17/2008] [Indexed: 12/22/2022] Open
Abstract
Background Genomic hybridization platforms, including BAC-CGH and genotyping arrays, have been used to estimate chromosome copy number (CN) in tumor samples by detecting the relative strength of genomic signal. The methods rely on the assumption that the predominant chromosomal background of the samples is diploid, an assumption that is frequently incorrect for tumor samples. In addition to generally greater resolution, an advantage of genotyping arrays over CGH arrays is the ability to detect signals from individual alleles, allowing estimation of loss-of-heterozygosity (LOH) and allelic ratios to enhance the interpretation of copy number alterations. Copy number events associated with LOH potentially have the same genetic consequences as deletions. Results We have utilized allelic ratios to detect patterns that are indicative of higher ploidy levels. An integrated analysis using allelic ratios, total signal and LOH indicates that many or most of the chromosomes from 24 glioblastoma tumors are in fact aneuploid. Some putative whole-chromosome losses actually represent trisomy, and many apparent sub-chromosomal losses are in fact relative losses against a triploid or tetraploid background. Conclusion These results suggest a re-interpretation of previous findings based only on total signal ratios. One interesting observation is that many single or multiple-copy deletions occur at common putative tumor suppressor sites subsequent to chromosomal duplication; these losses do not necessarily result in LOH, but nonetheless occur in conspicuous patterns. The 500 K Mapping array was also capable of detecting many sub-mega base losses and gains that were overlooked by CGH-BAC arrays, and was superior to CGH-BAC arrays in resolving regions of complex CN variation.
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Array comparative genome hybridization analysis of acute lymphoblastic leukaemia and acute megakaryoblastic leukaemia in patients with Down syndrome. Br J Haematol 2008; 142:934-45. [DOI: 10.1111/j.1365-2141.2008.07280.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Gain of 1q Is a Potential Univariate Negative Prognostic Marker for Survival in Medulloblastoma. Clin Cancer Res 2007; 13:7022-8. [DOI: 10.1158/1078-0432.ccr-07-1420] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Candidate glioblastoma development gene identification using concordance between copy number abnormalities and gene expression level changes. Genes Chromosomes Cancer 2007; 46:875-94. [PMID: 17620294 DOI: 10.1002/gcc.20474] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Copy number abnormalities (CNAs) in tumor cells are presumed to affect expression levels of genes located in region of abnormality. To investigate this relationship we have surveyed the losses, gains and amplifications in 30 glioblastomas using array comparative genome hybridization and compared these data with gene expression changes in the same tumors using the Affymetrix U133Plus2.0 oligonucleotide arrays. The two datasets were overlaid using our in-house overlay tool which highlights concordance between CNAs and expression level changes for the same tumors. In this survey we have highlighted genes frequently overexpressed in amplified regions on chromosomes 1, 4, 11, and 12 and have identified novel amplicons on these chromosomes. Deletions of specific regions on chromosomes 9, 10, 11, 14, and 15 have also been correlated with reduced gene expression in the regions of minimal overlap. In addition we describe a novel approach for comparing gene expression levels between tumors based on the presence or absence of chromosome CNAs. This genome wide screen provides an efficient and comprehensive survey of genes which potentially serve as the drivers for the CNAs in GBM.
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Overlay tool for aCGHViewer: an analysis module built for aCGHViewer used to perform comparisons of data derived from different microarray platforms. Cancer Inform 2007; 3:307-19. [PMID: 19455250 PMCID: PMC2675835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Overlay Tool has been developed to combine high throughput data derived from various microarray platforms. This tool analyzes high-resolution correlations between gene expression changes and either copy number abnormalities (CNAs) or loss of heterozygosity events detected using array comparative genomic hybridization (aCGH). Using an overlay analysis which is designed to be performed using data from multiple microarray platforms on a single biological sample, the Overlay Tool identifies potentially important genes whose expression profiles are changed as a result of losses, gains and amplifications in the cancer genome. In addition, the Overlay Tool will incorporate loss of heterozygosity (LOH) probability data into this overlay procedure. To facilitate this analysis, we developed an application which computationally combines two or more high throughput datasets (e.g. aCGH/expression) into a single categorized dataset for visualization and interrogation using a gene-centric approach. As such, data from virtually any microarray platform can be incorporated without the need to remap entire datasets individually. The resultant categorized (overlay) data set can be conveniently viewed using our in-house visualization tool, aCGHViewer (Shankar et al. 2006), which serves as a conduit to public databases such as UCSC and NCBI, to rapidly investigate genes of interest.
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Genome wide copy number abnormalities in pediatric medulloblastomas as assessed by array comparative genome hybridization. Brain Pathol 2007; 17:282-96. [PMID: 17465989 PMCID: PMC8095649 DOI: 10.1111/j.1750-3639.2007.00072.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Array-based comparative genomic hybridization was used to characterize 22 medulloblastomas in order to precisely define genetic alterations in these malignant childhood brain tumors. The 17p(-)/17q(+) copy number abnormality (CNA), consistent with the formation of isochromosome 17q, was the most common event (8/22). Amplifications in this series included MYCL, MYCN and MYC previously implicated in medulloblastoma pathogenesis, as well as novel amplicons on chromosomes 2, 4, 11 and 12. Losses involving chromosomes 1, 2, 8, 10, 11, 16 and 19 and gains of chromosomes 4, 7, 8, 9 and 18 were seen in greater than 20% of tumors in this series. A homozygous deletion in 11p15 defines the minimal region of loss on this chromosome arm. In order to map the minimal regions involved in losses, gains and amplifications, we combined aCGH data from this series with that of two others obtained using the same RPCI BAC arrays. As a result of this combined analysis of 72 samples, we have defined specific regions on chromosomes 1, 8p, 10q, 11p and 16q which are frequently involved in CNAs in medulloblastomas. Using high density oligonucleotide expression arrays, candidate genes were identified within these consistently involved regions in a subset of the tumors.
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Overlay analysis of the oligonucleotide array gene expression profiles and copy number abnormalities as determined by array comparative genomic hybridization in medulloblastomas. Genes Chromosomes Cancer 2007; 46:53-66. [PMID: 17044047 DOI: 10.1002/gcc.20388] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Combined analysis of gene expression array data and array-based comparative genomic hybridization data have been used in a series of 26 pediatric brain tumors to define up- and downregulated genes that coincide with losses, gains, and amplifications involving specific chromosome regions. Frequent losses were defined in chromosome arms 3q, 6q, 8p, 10q, 16q, 17p, and gains were identified in chromosome 7, and chromosome arms 9p and 17q. Amplification of a 2p region was seen in only one tumor, which corresponded to increased expression of the MYCN and DDX1 genes. To facilitate the analysis of the two data sets, we have developed a custom overlay tool that defines genes that are underexpressed in regions of deletions and overexpressed in regions of gain, across the genome and specifically within regions showing recurrent involvement in medulloblastomas.
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Identifying candidate colon cancer tumor suppressor genes using inhibition of nonsense-mediated mRNA decay in colon cancer cells. Oncogene 2006; 26:2873-84. [PMID: 17086209 DOI: 10.1038/sj.onc.1210098] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Inhibition of the nonsense-mediated decay (NMD) mechanism in cells results in stabilization of transcripts carrying premature translation termination codons. A strategy referred to as gene identification by NMD inhibition (GINI) has been proposed to identify genes carrying nonsense mutations. Genes containing frameshift mutations in colon cancer cell line have been identified using a modified version of GINI. To increase the efficiency of identifying mutant genes using GINI, we have now further improved the strategy. In this approach, inhibition of NMD with emetine is complemented with inhibiting NMD by blocking the phosphorylation of the hUpf1 protein with caffeine. In addition, to enhance the GINI strategy, comparing mRNA level alterations produced by inhibiting transcription alone or inhibiting transcription together with NMD following caffeine pretreatment were used for the efficient identification of false positives produced as a result of stress response to NMD inhibition. To demonstrate the improved efficiency of this approach, we analysed colon cancer cell lines showing microsatellite instability. Bi-allelic inactivating mutations were found in the FXR1, SEC31L1, NCOR1, BAT3, PHF14, ZNF294, C19ORF5 genes as well as genes coding for proteins with yet unknown functions.
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Lack of detection of influenza genes in archived formalin-fixed, paraffin wax-embedded brain samples of encephalitis lethargica patients from 1916 to 1920. Virchows Arch 2003; 442:591-6. [PMID: 12695912 DOI: 10.1007/s00428-003-0795-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2002] [Accepted: 02/03/2003] [Indexed: 11/28/2022]
Abstract
A method was developed for detection of influenza genes in formalin-fixed brains of mice that had been experimentally infected with influenza A/NWS/33 (H1N1) virus. Using this technique, messenger ribonucleic acid (mRNA) of the beta-actin gene was detected in eight clinical brain samples from the 1916-1920 outbreak of encephalitis lethargica, showing preservation of particular mRNAs. However, we did not detect influenza nucleotide sequences of M, NP, and NS genes from these same samples. We conclude either that influenza was not the causative agent of encephalitis lethargica or, possibly, that the virus had a hit-and-run mechanism and was no longer present in the brain at the time of death of the patients.
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Scrotal orchiectomy for a large testicular seminoma. THE CANADIAN JOURNAL OF UROLOGY 2001; 8:1234-6. [PMID: 11375787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
Our patient had neglected a growing left testicular mass over a 5-year period. Due to the large size of the tumor a scrotal delivery was necessary. Pathology showed a 1.6 kg pure classic seminoma. Metastatic work up revealed stage IIC disease and he was treated with primary cisplatin-based chemotherapy and remains free of recurrence after 24 months. The potential risk of scrotal violation is discussed.
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Transient outward current contributes to Wenckebach-like rhythms in isolated rabbit ventricular cells. THE AMERICAN JOURNAL OF PHYSIOLOGY 1997; 273:H1-11. [PMID: 9249468 DOI: 10.1152/ajpheart.1997.273.1.h1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Wenckebach-like rhythms in isolated rabbit ventricular cells are characterized by beat-to-beat increments in action potential duration (APD) and latency, giving rise to a beat-to-beat decrease in the recovery interval and culminating in a skipped beat. These systematic APD changes are associated with a beat-to-beat decrease in the slope of the early repolarizing phase (phase 1) of the action potential, which is partially controlled by the transient outward potassium current (Ito). When Ito is blocked with 4-aminopyridine, periodic Wenckebach rhythms are replaced by aperiodic Wenckebach rhythms, in which the beat-to-beat changes in the slope of phase 1 and in APD disappear but the beat-to-beat increase in latency remains. A beat-to-beat decrease in Ito, paralleling the beat-to-beat changes in the slope of phase 1 and in APD, is seen in action-potential clamp experiments with Wenckebach rhythms previously recorded in the same cell. Simulations with an ionic model of Ito show cyclical changes in Ito consistent with the experimental data. These results demonstrate a key role for Ito in the generation of maintained periodic Wenckebach rhythms in isolated rabbit ventricular cells.
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