Genetic ancestry, admixture, and population structure in rural Dominica

The Caribbean is a genetically diverse region with heterogeneous admixture compositions influenced by local island ecologies, migrations, colonial conflicts, and demographic histories. The Commonwealth of Dominica is a mountainous island in the Lesser Antilles historically known to harbor communities with unique patterns of migration, mixture, and isolation. This community-based population genetic study adds biological evidence to inform post-colonial narrative histories in a Dominican horticultural village. High density single nucleotide polymorphism data paired with a previously compiled genealogy provide the first genome-wide insights on genetic ancestry and population structure in Dominica. We assessed family-based clustering, inferred global ancestry, and dated recent admixture by implementing the fastSTRUCTURE clustering algorithm, modeling graph-based migration with TreeMix, assessing patterns of linkage disequilibrium decay with ALDER, and visualizing data from Dominica with Human Genome Diversity Panel references. These analyses distinguish family-based genetic structure from variation in African, European, and indigenous Amerindian admixture proportions, and analyses of linkage disequilibrium decay estimate admixture dates 5–6 generations (~160 years) ago. African ancestry accounts for the largest mixture components, followed by European and then indigenous components; however, our global ancestry inferences are consistent with previous mitochondrial, Y chromosome, and ancestry marker data from Dominica that show uniquely higher proportions of indigenous ancestry and lower proportions of African ancestry relative to known admixture in other French- and English-speaking Caribbean islands. Our genetic results support local narratives about the community’s history and founding, which indicate that newly emancipated people settled in the steep, dense vegetation along Dominica’s eastern coast in the mid-19^th century. Strong genetic signals of post-colonial admixture and family-based structure highlight the localized impacts of colonial forces and island ecologies in this region, and more data from other groups are needed to more broadly inform on Dominica’s complex history and present diversity.

Urethral Sphincter Mechanism Incompetence in 163 Neutered Female Dogs: Diagnosis, Treatment, and Relationship of Weight and Age at Neuter to Development of Disease

BACKGROUND

Urethral sphincter mechanism incompetence (USMI) is the most common cause of urinary incontinence in neutered bitches and is most common in dogs weighing >20 kg.

OBJECTIVES

To describe a population of neutered bitches with USMI and investigate their initial presentation, the relationship between weight and age at neuter, and treatment.

ANIMALS

One hundred and sixty-three female dogs with USMI (UI) diagnosed between January 2009 and December 2012, and 193 continent neutered control (C) bitches.

METHODS

Retrospective data were collected from neutered female dogs with USMI and healthy, continent neutered females presented between January 2009 and December 2012.

RESULTS

Urinary incontinent dogs weighed more than C dogs (P = .003), and there was no difference in age at neuter. The relationship between weight at diagnosis and age at neuter was found to impact the hazard of USMI. A decrease in the hazard of USMI was found in dogs weighing >25 kg for every month delay of neuter in the first year. The hazard did not change for dogs <15 kg. Median time from neuter to development of incontinence was 3.73 years. Phenylpropanolamine was prescribed in 75.5%, diethylstilbestrol in 21.5%, and both in 3.1% of dogs.

CONCLUSIONS AND CLINICAL IMPORTANCE

Neutering bitches expected to be >25 kg adult weight later in their first year may decrease the hazard of developing USMI, whereas age at neutering of bitches <25 kg may not impact continence. Heavier dogs have increased risk of USMI, and onset occurs within a few years of neuter.

Inferring a role for methylation of intergenic DNA in the regulation of genes aberrantly expressed in precursor B-cell acute lymphoblastic leukemia

A complete understanding of the mechanisms involved in the development of pre-B ALL is lacking. In this study, we integrated DNA methylation data and gene expression data to elucidate the impact of aberrant intergenic DNA methylation on gene expression in pre-B ALL. We found a subset of differentially methylated intergenic loci that were associated with altered gene expression in pre-B ALL patients. Notably, 84% of these regions were also bound by transcription factors (TF) known to play roles in differentiation and B-cell development in a lymphoblastoid cell line. Further, an overall downregulation of eRNA transcripts was observed in pre-B ALL patients and these transcripts were associated with the downregulation of putative target genes involved in B-cell migration, proliferation, and apoptosis. The identification of novel putative regulatory regions highlights the significance of intergenic DNA sequences and may contribute to the identification of new therapeutic targets for the treatment of pre-B ALL.

Integrated methylome and transcriptome analysis reveals novel regulatory elements in pediatric acute lymphoblastic leukemia

Acute lymphoblastic leukemia (ALL) is the most common cancer diagnosed in children under the age of 15. In addition to genetic aberrations, epigenetic modifications such as DNA methylation are altered in cancer and impact gene expression. To identify epigenetic alterations in ALL, genome-wide methylation profiles were generated using the methylated CpG island recovery assay followed by next-generation sequencing. More than 25,000 differentially methylated regions (DMR) were observed in ALL patients with ∼90% present within intronic or intergenic regions. To determine the regulatory potential of the DMR, whole-transcriptome analysis was performed and integrated with methylation data. Aberrant promoter methylation was associated with the altered expression of genes involved in transcriptional regulation, apoptosis, and proliferation. Novel enhancer-like sequences were identified within intronic and intergenic DMR. Aberrant methylation in these regions was associated with the altered expression of neighboring genes involved in cell cycle processes, lymphocyte activation and apoptosis. These genes include potential epi-driver genes, such as SYNE1, PTPRS, PAWR, HDAC9, RGCC, MCOLN2, LYN, TRAF3, FLT1, and MELK, which may provide a selective advantage to leukemic cells. In addition, the differential expression of epigenetic modifier genes, pseudogenes, and non-coding RNAs was also observed accentuating the role of erroneous epigenetic gene regulation in ALL.

Trends and Patterns in Reporting of Patient Safety Situations in Transplantation

Analysis and dissemination of transplant patient safety data are essential to understanding key issues facing the transplant community and fostering a "culture of safety." The Organ Procurement and Transplantation Network's (OPTN) Operations and Safety Committee de-identified safety situations reported through several mechanisms, including the OPTN's online patient safety portal, through which the number of reported cases has risen sharply. From 2012 to 2013, 438 events were received through either the online portal or other reporting pathways, and about half were self-reports. Communication breakdowns (22.8%) and testing issues (16.0%) were the most common types. Events included preventable errors that led to organ discard as well as near misses. Among events reported by Organ Procurement Organization (OPOs), half came from just 10 of the 58 institutions, while half of events reported by transplant centers came from just 21 of 250 institutions. Thirteen (23%) OPOs and 155 (62%) transplant centers reported no events, suggesting substantial underreporting of safety-related errors to the national database. This is the first comprehensive, published report of the OPTN's safety efforts. Our goals are to raise awareness of safety data recently reported to the OPTN, encourage additional reporting, and spur systems improvements to mitigate future risk.

Genome-wide DNA methylation analysis in precursor B-cells

DNA methylation is responsible for regulating gene expression and cellular differentiation and for maintaining genomic stability during normal human development. Furthermore, it plays a significant role in the regulation of hematopoiesis. In order to elucidate the influence of DNA methylation during B-cell development, genome-wide DNA methylation status of pro-B, pre-BI, pre-BII, and naïve-B-cells isolated from human umbilical cord blood was determined using the methylated CpG island recovery assay followed by next generation sequencing. On average, 182–200 million sequences were generated for each precursor B-cell subset in 10 biological replicates. An overall decrease in methylation was observed during the transition from pro-B to pre-BI, whereas no differential methylation was observed in the pre-BI to pre-BII transition or in the pre-BII to naïve B-cell transition. Most of the methylated regions were located within intergenic and intronic regions not present in a CpG island context. Putative novel enhancers were identified in these regions that were differentially methylated between pro-B and pre-BI cells. The genome-wide methylation profiles are publically available and may be used to gain a better understanding of the involvement of atypical DNA methylation in the pathogenesis of malignancies associated with precursor B-cells.

The expression of RUNDC3B is associated with promoter methylation in lymphoid malignancies

DNA methylation is an epigenetic modification that plays an important role in the regulation of gene expression. The function of RUNDC3B has yet to be determined, although its dysregulated expression has been associated with malignant potential of both breast and lung carcinoma. To elucidate the potential of using DNA methylation in RUNDC3B as a biomarker in lymphoid malignancies, the methylation status of six regions spanning the CpG island in the promoter region of RUNDC3B was determined in cancer cell lines. Lymphoid malignancies were found to have more prominent methylation and did not express RUNDC3B compared with myeloid malignancies and solid tumours, supporting the potential use of DNA methylation in this region as a biomarker for lymphoid malignancies. RUNDC3B contains a RUN domain in its N‐terminal region that mediates interaction with Rap2, an important component of the mitogen‐activated protein kinase (MAPK) cascade, which regulates cellular proliferation and differentiation. The protein sequence of RUNDC3B also contains characteristic binding sites for MAPK intermediates. Therefore, it is possible that RUNDC3B serves as a mediator between Rap2 and the MAPK signalling cascade. Three genes with MAPK‐inducible expression were downregulated in a methylated leukaemia cell line (HSPA5, Jun and Fos). Jun and Fos combine to form the activating protein 1 transcription factor, and loss of this factor is associated with the dysregulation of genes involved in differentiation and proliferation. We hypothesize that the loss of RUNDC3B secondary to aberrant hypermethylation of the early growth response 3 transcription factor binding site results in dysregulated MAPK signalling and carcinogenesis in lymphoid malignancies. © 2015 The Authors. Hematological Oncology published by John Wiley & Sons Ltd

Identification of a human papillomavirus-associated oncogenic miRNA panel in human oropharyngeal squamous cell carcinoma validated by bioinformatics analysis of the Cancer Genome Atlas

High-risk human papillomavirus (HPV) is a causative agent for an increasing subset of oropharyngeal squamous cell carcinomas (OPSCCs), and current evidence supports these tumors as having identifiable risk factors and improved response to therapy. However, the biochemical and molecular alterations underlying the pathobiology of HPV-associated OPSCC (designated HPV(+) OPSCC) remain unclear. Herein, we profile miRNA expression patterns in HPV(+) OPSCC to provide a more detailed understanding of pathologic molecular events and to identify biomarkers that may have applicability for early diagnosis, improved staging, and prognostic stratification. Differentially expressed miRNAs were identified in RNA isolated from an initial clinical cohort of HPV(+/-) OPSCC tumors by quantitative PCR-based miRNA profiling. This oncogenic miRNA panel was validated using miRNA sequencing and clinical data from The Cancer Genome Atlas and miRNA in situ hybridization. The HPV-associated oncogenic miRNA panel has potential utility in diagnosis and disease stratification and in mechanistic elucidation of molecular factors that contribute to OPSCC development, progression, and differential response to therapy.

Isolation of precursor B-cell subsets from umbilical cord blood

Umbilical cord blood is highly enriched for hematopoietic progenitor cells at different lineage commitment stages. We have developed a protocol for isolating precursor B-cells at four different stages of differentiation. Because genes are expressed and epigenetic modifications occur in a tissue specific manner, it is vital to discriminate between tissues and cell types in order to be able to identify alterations in the genome and the epigenome that may lead to the development of disease. This method can be adapted to any type of cell present in umbilical cord blood at any stage of differentiation. This method comprises 4 main steps. First, mononuclear cells are separated by density centrifugation. Second, B-cells are enriched using biotin conjugated antibodies that recognize and remove non B-cells from the mononuclear cells. Third the B-cells are fluorescently labeled with cell surface protein antibodies specific to individual stages of B-cell development. Finally, the fluorescently labeled cells are sorted and individual populations are recovered. The recovered cells are of sufficient quantity and quality to be utilized in downstream nucleic acid assays.

Abstract 5365: Genome-wide DNA methylation analysis in subsets of precursor B-cells isolated from umbilical cord blood

Tissue specific DNA methylation is accountable for regulating gene expression and cellular differentiation during normal human development. Aberrant tissue specific gene regulation may lead to the development of many disease states including cancer. Genome-wide analysis of DNA methylation (methylome) in both healthy and diseased tissue is essential to understand the functional consequence of altered DNA methylation. Acute lymphoblastic leukemia (ALL) is a malignancy associated with precursor B-cells. In order to gain a better understanding of the role of altered DNA methylation in the pathogenesis of ALL, it is essential that we characterize the DNA methylation present in healthy precursor B-cells. Umbilical cord blood is enriched for precursor B-cells and is used as a source of hematopoietic stem cells in the treatment of blood related disorders and malignancies. To study the methylome in healthy precursor B-cells, we have optimized a protocol to isolate 4 subsets of precursor B-cells from umbilical cord blood, and to then generate MBD-seq libraries from the small amount of genomic DNA (&lt; 100ng) isolated from those subsets of precursor B-cells.

Subsets of precursor B-cells were isolated from cord blood based on the level of expression of cell surface antigen. Initially mononuclear cells were isolated by Ficoll-plaque followed by magnetic labeling and depletion of non B-cells. B-cells were labeled with antibodies against CD19, CD34 and CD45 surface antigens and sorted by flow cytometry. Based on expression level of surface antigen, four different subsets of precursor B-cells were sorted (CD19+/CD34+; CD19+/CD34-/CD45low; CD19+/CD34-/CD45med; and CD19+/CD34-/CD45high). Immediately after cell sorting, DNA was isolated by using a commercially available kit. The entire amount of DNA from CD19+/CD34+ and CD19+/CD34-/CD45low (&lt;100ng) subsets, and 100ng of DNA from CD19+/CD34-/CD45med and CD19+/CD34-/CD45high subsets were fragmented by sonication using Diagenode Bioruptor. Sequencing libraries were generated using the Illumina Chip-seq protocol with modifications. Enrichment of methylated DNA was validated by PCR amplification of methylated (SLC25A37) and unmethylated (APC) regions. MBD-seq libraries were sequenced using Illumina next-generation sequencing technology and then sequenced data were analyzed by NextGENe® software. We found ∼45 million uniquely matched reads covering ∼700 million bases in the human genome for each precursor B-cell subset. Methylated peaks were identified using the Peak Identification tool in NextGENe. The results demonstrated a differential pattern of DNA methylation in the subsets of healthy precursor B-cells.

Citation Format: Md Almamun, Kristen H. Taylor. Genome-wide DNA methylation analysis in subsets of precursor B-cells isolated from umbilical cord blood. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5365. doi:10.1158/1538-7445.AM2013-5365

Abstract 657: Aberrant DNA methylation of RUNDC3B in lymphoid malignancies

Pathological research of epigenetic regulation provides a unique insight into disease formation. Heritable changes to DNA conformation can have significant impacts on gene expression without altering the DNA sequence. The RUN domain containing 3B gene (RUNDC3B) has been shown to be differentially expressed in caner types such as, acute lymphoblastic leukemia. This differential expression has been linked to methylation of the gene. The hypothesized function of RUNDC3B is a Rap-2 binding protein which operates regulates GTPases to create biological switches in signaling pathways, such as the Ras signaling pathway. Therefore, aberrant methylation of RUNDC3B could adversely affect Ras signaling and contribute to cancer formation.

Combined bisulfite restriction analysis and methylation specific PCR were used to determine the methylation status of RUNDC3B. This analysis was completed in cell lines from lymphoid malignancies, myeloid malignancies, various solid tumor cancers, and unaffected cell lines. We evaluated 5 regions spanning a CpG island (CGI) in the proximal promoter region of RUNDC3B. Greater than 70% of the regions analyzed in lymphoid malignancies were found to be methylated, whereas, 13.3% of myeloid malignancies, 34.3% of solid tumors, and 10.0% of healthy lymphocyte regions were found to be methylated. This suggests that RUNDC3B may be a useful biomarker for diagnosis and/or prognosis in lymphoid malignancies. Furthermore, this aberrant epigenetic modification may be a significant contributor to pathogenesis of lymphoid malignancies.

To determine the effect of aberrant DNA methylation on RUNDC3B expression, real-time PCR was utilized. Consistent with the methylation data, the lymphoid malignancies were found to be expressed at significantly lower levels than other unmethylated samples. In addition, the methylation of Region 5 of the CGI related strongly with RUNDC3B repression, suggesting a specific set of CpG dinucleotides may be responsible for RUNDC3B silencing.

The function of RUNDC3B is hypothesized based on the presence of a RUN domain. Sequence analysis of RUNDC3B was performed to expand on the hypothesized physiological role. Establishing conserved portions of the promoter region of RUNDC3B supported the conclusion that regulation of this gene is not evolutionarily novel. Analysis across a diverse set of species revealed conservation in transcription factor binding sites, CG content, and RUNDC3B-Rap2 interaction domains.

The data from our experiments has built upon the knowledge of epigenetic regulation of RUNDC3B in cancer. The aberrant methylation leading to RUNDC3B repression is more prevalent in lymphoid malignancies than in several other types of cancer. This provides a clinical role of the gene as a biomarker. As the RUNDC3B gene codes for a regulatory element of the Ras pathway, aberrant epigenetic repression may contribute to the pathogenesis of lymphoid malignancies.

Citation Format: Dane W. Burmeister, Kristen H. Taylor. Aberrant DNA methylation of RUNDC3B in lymphoid malignancies. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 657. doi:10.1158/1538-7445.AM2013-657

Large-scale analysis of DNA methylation in chronic lymphocytic leukemia

AIMS

B-cell chronic lymphocytic leukemia (CLL) is a heterogeneous malignancy that clinically ranges from indolent to rapidly progressive. CLL, like other cancers, can be affected by epigenetic alterations.

MATERIALS & METHODS

A microarray discovery-based study was initiated to determine DNA methylation in CLL cases with a range of CD38 expression (1–92%).

RESULTS

Many loci were either methylated or unmethylated across all CD38 levels, but differential methylation was also observed for some genes. Genomic sequencing of DLEU7 confirmed extensive cytosine methylation preferentially in patient samples with low CD38 expression, whereas NRP2, SFRP2 and ADAM12 were more commonly methylated in those with high CD38 expression.

CONCLUSION

This study demonstrates that CLL is affected by CpG island methylation in some genes that segregate with CD38 expression levels, while most others show similar methylation patterns across all levels. The CpG island methylation in certain functional gene groups and pathway-associated genes that are known to be deregulated in CLL provides additional insights into the CLL methylome and epigenetic contribution to cellular dysfunction. It will now be useful to investigate the effectiveness of epigenetic therapeutic reversal of these alterations to develop effective treatments for the disease.

Genome-wide DNA methylation analysis reveals novel epigenetic changes in chronic lymphocytic leukemia

We conducted a genome-wide DNA methylation analysis in CD19 (+) B-cells from chronic lymphocytic leukemia (CLL) patients and normal control samples using reduced representation bisulfite sequencing (RRBS). The methylation status of 1.8-2.3 million CpGs in the CLL genome was determined; about 45% of these CpGs were located in more than 23,000 CpG islands (CGIs). While global CpG methylation was similar between CLL and normal B-cells, 1764 gene promoters were identified as being differentially methylated in at least one CLL sample when compared with normal B-cell samples. Nineteen percent of the differentially methylated genes were involved in transcriptional regulation. Aberrant hypermethylation was found in all HOX gene clusters and a significant number of WNT signaling pathway genes. Hypomethylation occurred more frequently in the gene body including introns, exons, and 3'-UTRs in CLL. The NFATc1 P2 promoter and first intron was found to be hypomethylated and correlated with upregulation of both NFATc1 RNA and protein expression levels in CLL suggesting that an epigenetic mechanism is involved in the constitutive activation of NFAT activity in CLL cells. This comprehensive DNA methylation analysis will further our understanding of the epigenetic contribution to cellular dysfunction in CLL.

Abstract 4791: Genome-wide DNA methylation maps in chronic lymphocytic leukemia cells determined by next-generation sequencing

Chronic lymphocytic leukemia (CLL) is the most common leukemia of adults in the western world. The clinical course of CLL is highly variable. Some patients are able to live years with no need for treatment; whereas others progress rapidly requiring therapy within a short time after diagnosis. The identification and validation of prognostic molecular markers (including surface markers, cytogenetic abnormalities, and IGHV mutational status) have resulted in refinements in the approach to the management of these patients. Further discovery of biologically relevant factors that influence the heterogeneity and progression of CLL will not only promote our understanding of the disease process, but also allow us to identify rational therapeutic approaches. In this study, we conducted genome-wide DNA methylation analyses in purified CD19+ B-cells from 11 CLL patients with a range of CD38 expression using reduced representation bisulfite sequencing (RRBS). Using one lane of the Illumina sequencing data, we were able to consistently determine the methylation status of approximately 1.8 million CpGs; 45% of these CpGs are located in more than 23,000 CpG islands (CGIs), accounting for more than 80% of all annotated CGIs across the genome. We have identified a large number of CGIs that were differentially methylated between CLL cells and normal CD19+ B-cells. The promoter hypermethylation patterns of many genes previously reported in CLL, such as FOXD3, GRM7, DLEU7 etc, were determined in the 11 CLL samples. In addition, we have observed aberrant DNA methylation changes in all 4 HOX gene clusters in CLL. For instance, HOXD8, HOXD9, and HOXD11 were hypermethylated in 11 out of 11 CLL samples. In addition, we also identified a significant number of DNA methylation alterations in the WNT signaling pathway genes. One-way ANOVA analysis of DNA methylation profiles of 764,984 CpGs shared by all CLL samples identified 570 CpGs that were differentially methylated (p&lt;0.001) between CD38high and CD38low group (with &gt;20% CLL cells expressing CD38 as CD38high group). The cluster analysis of the 570 CpGs reveals that it is possible to separate these CLL samples into two distinct groups based on the DNA methylation profiles. The study further confirms our early findings that CLL is affected by CpG island methylation in some genes that segregate with CD38 expression levels, while most others show similar methylation patterns across all levels. The aberrant promoter hypermethylation in certain functional gene groups and pathway-associated genes that are known to be deregulated in CLL provides additional insights into the CLL methylome and epigenetic contribution to cellular dysfunction.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4791. doi:10.1158/1538-7445.AM2011-4791

Genome-wide DNA methylation maps in follicular lymphoma cells determined by methylation-enriched bisulfite sequencing

Background

Follicular lymphoma (FL) is a form of non-Hodgkin's lymphoma (NHL) that arises from germinal center (GC) B-cells. Despite the significant advances in immunotherapy, FL is still not curable. Beyond transcriptional profiling and genomics datasets, there currently is no epigenome-scale dataset or integrative biology approach that can adequately model this disease and therefore identify novel mechanisms and targets for successful prevention and treatment of FL.

Methodology/Principal Findings

We performed methylation-enriched genome-wide bisulfite sequencing of FL cells and normal CD19⁺ B-cells using 454 sequencing technology. The methylated DNA fragments were enriched with methyl-binding proteins, treated with bisulfite, and sequenced using the Roche-454 GS FLX sequencer. The total number of bases covered in the human genome was 18.2 and 49.3 million including 726,003 and 1.3 million CpGs in FL and CD19⁺ B-cells, respectively. 11,971 and 7,882 methylated regions of interest (MRIs) were identified respectively. The genome-wide distribution of these MRIs displayed significant differences between FL and normal B-cells. A reverse trend in the distribution of MRIs between the promoter and the gene body was observed in FL and CD19⁺ B-cells. The MRIs identified in FL cells also correlated well with transcriptomic data and ChIP-on-Chip analyses of genome-wide histone modifications such as tri-methyl-H3K27, and tri-methyl-H3K4, indicating a concerted epigenetic alteration in FL cells.

Conclusions/Significance

This study is the first to provide a large scale and comprehensive analysis of the DNA methylation sequence composition and distribution in the FL epigenome. These integrated approaches have led to the discovery of novel and frequent targets of aberrant epigenetic alterations. The genome-wide bisulfite sequencing approach developed here can be a useful tool for profiling DNA methylation in clinical samples.

Next generation sequencing: advances in characterizing the methylome

Epigenetic modifications play an important role in lymphoid malignancies. This has been evidenced by the large body of work published using microarray technologies to generate methylation profiles for numerous types and subtypes of lymphoma and leukemia. These studies have shown the importance of defining the epigenome so that we can better understand the biology of lymphoma. Recent advances in DNA sequencing technology have transformed the landscape of epigenomic analysis as we now have the ability to characterize the genome-wide distribution of chromatin modifications and DNA methylation using next-generation sequencing. To take full advantage of the throughput of next-generation sequencing, there are many methodologies that have been developed and many more that are currently being developed. Choosing the appropriate methodology is fundamental to the outcome of next-generation sequencing studies. In this review, published technologies and methodologies applicable to studying the methylome are presented. In addition, progress towards defining the methylome in lymphoma is discussed and prospective directions that have been made possible as a result of next-generation sequencing technology. Finally, methodologies are introduced that have not yet been published but that are being explored in the pursuit of defining the lymphoma methylome.

Abstract 168: Genome-wide survey of CpG methylation across the spectrum of B-cell lymphomas

Introduction: An international consortium was established to create comprehensive methylomes of B-cell lymphoma cell lines representing multiple stages of B-cell differentiation. One of the consortium's long-term goals is to identify genes and pathways that are perturbed by methylation in these cell lines either individually, or wholly, so that this information may be utilized to identify novel targets of aberrant methylation in patient samples.

Experimental procedures: The B-cell derived tumor cell lines included in this study represent the spectrum of B-cell development: chronic lymphocytic leukemia (Mec1); mantle cell lymphoma (Granta); diffuse large B-cell lymphoma (Val and Ly10); follicular lymphoma (RL); Burkitt's lymphoma (Raji); and multiple myeloma (U266B1).

Three methods were employed in this study: 1) Methylated CpG island amplification (MCA) and Agilent CpG island arrays; 2) HpaII tiny fragment enrichment by ligation-mediated PCR (HELP) and Agilent CpG island arrays; and 3) Bisulfite treatment in conjunction with the Illumina Infinium Methylation BeadChip.

Data summary: Comprehensive genome-wide methylation profiles were constructed for each tumor cell line using the data generated from three different methods. The number of detected differentially methylated probes, genes and gene promoters differed for each method. The number of unique methylated genes identified ranged from 25 for Granta to more than 200 for U266B1. Recurrent aberrant methylation was detected in ∼100 genes in all seven cell lines included in this study. Methylation of key miRNAs was identified in each of the cell lines.

Gene lists that included genes with promoter methylation were submitted to the database for annotation, visualization and integrated discovery (DAVID) to identify enriched functional-related gene groups. Cell differentiation, transcription factor activity and HOX were among the top three functionally enriched gene groups in all cell lines. Genes associated with the Wnt, MAPK and Hedgehog pathways were also enriched in select cell lines.

Conclusions: All approaches suffer from limitations in their ability to detect methylated sequences. The probes assayed on the Agilent CpG island array are limited to sequences that are contained within the restriction fragments produced in the MCA and HELP assays. The MCA method relies on the co-hybridization of a sample of interest to a “normal control” which may introduce biases if the “proper” control is not used. Finally, the Illumina Infinium BeadChip assays, on average, only 2 probes per gene and is the least informative of the detection assays. Despite these shortcomings, the combination of the data generated by each method has allowed the identification of novel genes and pathways that can be used to design screening assays for large numbers of patient samples.

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 168.

Epigenetic regulation of WNT signaling in chronic lymphocytic leukemia

Certain WNT and WNT network target genes are expressed at higher or lower levels in chronic lymphocytic leukemia compared with normal B-cells. This includes upregulation of nuclear complex genes, as well as genes for cytoplasmic proteins and WNT ligands and their cognate receptors. In addition, epigenetic silencing of several negative regulators of the WNT pathway have been identified. The balance between epigenetic downregulation of negative effector genes and increased expression of positive effector genes demonstrate that the epigenetic downregulation of WNT antagonists is one mechanism, perhaps the main mechanism, that is permissive to active WNT signaling in chronic lymphocytic leukemia. Moreover, constitutive activation of the WNT network and target genes is likely to impact on additional interacting signaling pathways. Based on published studies, we propose a model of WNT signaling that involves mainly permissive expression, and sometimes overexpression, of positive effectors and downregulation of negative regulators in the network. In this model, DNA methylation, histone modifications and altered expression of microRNA molecules interact to allow continuous WNT signaling.

Molecular detection of B-cell neoplasms by specific DNA methylation biomarkers

A novel, easy to perform PCR-based method employing specific DNA methylation biomarkers to detect B-cell neoplasms in a variety of B-cell lines and B lymphoblastic leukemia (B-ALL) patient specimens has been developed. This method detects as few as 5 B-ALL cells, or 1 B-ALL cell in 1,000,000 normal background blood cells using a single marker, DLC-1 gene CpG island (CGI) methylation. By adding two additional markers PCDHGA12 and RPIB9, over 80% of B-ALL cases were detected in patients' bone marrow and/or peripheral blood specimens. We have traced clinical B-ALL cases up to 10 years retrospectively and the DLC-1 methylation is correlated with patient clinical status. Thus, this epigenetic-based molecular method demonstrates its potential use in the diagnosis of B-cell neoplasia, in addition to traditional approach such as clinical features, morphology, immunophenotype, and genetic analysis.

Hypermethylation of the DLC1 CpG island does not alter gene expression in canine lymphoma

Background

This study is a comparative epigenetic evaluation of the methylation status of the DLC1 tumor suppressor gene in naturally-occurring canine lymphoma. Canine non-Hodgkin's lymphoma (NHL) has been proposed to be a relevant preclinical model that occurs spontaneously and may share causative factors with human NHL due to a shared home environment. The canine DLC1 mRNA sequence was derived from normal tissue. Using lymphoid samples from 21 dogs with NHL and 7 normal dogs, the methylation status of the promoter CpG island of the gene was defined for each sample using combined bisulfite restriction analysis (COBRA), methylation-specific PCR (MSP), and bisulfite sequencing methods. Relative gene expression was determined using real-time PCR.

Results

The mRNA sequence of canine DLC1 is highly similar to the human orthologue and contains all protein functional groups, with 97% or greater similarity in functional regions. Hypermethylation of the 5' and 3' flanking regions of the promoter was statistically significantly associated with the NHL phenotype, but was not associated with silencing of expression or differences in survival.

Conclusion

The canine DLC1 is constructed highly similarly to the human gene, which has been shown to be an important tumor suppressor in many forms of cancer. As in human NHL, the promoter CpG island of DLC1 in canine NHL samples is abnormally hypermethylated, relative to normal lymphoid tissue. This study confirms that hypermethylation occurs in canine cancers, further supporting the use of companion dogs as comparative models of disease for evaluation of carcinogenesis, biomarker diagnosis, and therapy.

DNA hypermethylation accompanied by transcriptional repression in follicular lymphoma

High-throughput microarray technologies were used to study DNA methylation accompanied by transcriptional changes in follicular lymphoma (FL). Using Methylated CpG Island Amplification with Microarrays to study CpG Island DNA methylation in FL, we discovered widespread hypermethylation of homeobox genes and previously identified targets of polycomb repressive complex 2 (PRC2) in cell lines and primary tumors, but not in benign follicular hyperplasia (BFH). DNA methylation for HOXA11, HOXD10, HOXB7, HOXC12, PAX6, LHX9, SFMBT2, EN2, and PAX7 was independently validated in the RL cell line and HOXA11, HOXD10, PAX6, and EN2 in primary tumors. Combined Bisulfite Restriction Analysis (COBRA) also established DNA methylation for the previously identified PRC2 targets DCC, DES, GAD2, AQP5, GPR61, GRIA4, GJD2, and AMPH in FL but not in BFH. Gene expression analyses revealed 411 genes that were hypermethylated and transcriptionally repressed in RL, 74% of which were reactivated by the demethylating agent 5-aza-2'-deoxycytidine (5-azaD) plus or minus the histone deacetylase inhibitor trichostatin A (TSA). Forty genes were also downregulated in primary FL. Our results suggest that extensive hypermethylation in promoters of polycomb target genes is a characteristic of FL and that loss of expression of certain SUZ12 target genes could be functionally relevant for lymphomagenesis.

Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing

We developed a novel approach for conducting multisample, multigene, ultradeep bisulfite sequencing analysis of DNA methylation patterns in clinical samples. A massively parallel sequencing-by-synthesis method (454 sequencing) was used to directly sequence >100 bisulfite PCR products in a single sequencing run without subcloning. We showed the utility, robustness, and superiority of this approach by analyzing methylation in 25 gene-related CpG rich regions from >40 cases of primary cells, including normal peripheral blood lymphocytes, acute lymphoblastic leukemia (ALL), chronic lymphocytic leukemia (CLL), follicular lymphoma (FL), and mantle cell lymphoma (MCL). A total of 294,631 sequences was generated with an average read length of 131 bp. On average, >1,600 individual sequences were generated for each PCR amplicon far beyond the few clones (<20) typically analyzed by traditional bisulfite sequencing. Comprehensive analysis of CpG methylation patterns at a single DNA molecule level using clustering algorithms revealed differential methylation patterns between diseases. A significant increase in methylation was detected in ALL and FL samples compared with CLL and MCL. Furthermore, a progressive spreading of methylation was detected from the periphery toward the center of select CpG islands in the ALL and FL samples. The ultradeep sequencing also allowed simultaneous analysis of genetic and epigenetic data and revealed an association between a single nucleotide polymorphism and the methylation present in the LRP1B promoter. This new generation of methylome sequencing will provide digital profiles of aberrant DNA methylation for individual human cancers and offers a robust method for the epigenetic classification of tumor subtypes.

Board-invited review: Applications of genomic information in livestock

The availability of whole genome sequences for individual species will change the landscape for livestock genomic research. Animal scientists will have access to whole-genome sequence-based technologies such as high-throughput SNP genotyping assays, gene expression profiling, methylation profiling, RNA interference, and genome resequencing that will revolutionize the scale upon which research will be conducted. These technologies will also alter the ways we think about addressing industry and scientific problems. In this review, we discuss the scientific bases for these emerging technologies and present recent highlights of their application in human, model species, and livestock as well as their potential for future applications in livestock. Additionally, we discuss strategies for their use in the genetic improvement and management of livestock. In particular, we present a strategy for the simultaneous identification of causal mutations underlying phenotypic traits in livestock and discuss issues that will arise in the application of whole genome selection for the prediction of genetic merit in livestock. We also point out that the statistical analysis that underlies the whole genome selection methodology is a sophisticated enhancement of single marker association mapping analysis to allow the entire genome to be simultaneously analyzed.

Relational analysis of CpG islands methylation and gene expression in human lymphomas using possibilistic C-means clustering and modified cluster fuzzy density

Heterogeneous genetic and epigenetic alterations are commonly found in human non-Hodgkin's lymphomas (NHL). One such epigenetic alteration is aberrant methylation of gene promoter-related CpG islands, where hypermethylation frequently results in transcriptional inactivation of target genes, while a decrease or loss of promoter methylation (hypomethylation) is frequently associated with transcriptional activation. Discovering genes with these relationships in NHL or other types of cancers could lead to a better understanding of the pathobiology of these diseases. The simultaneous analysis of promoter methylation using Differential Methylation Hybridization (DMH) and its associated gene expression using Expressed CpG Island Sequence Tag (ECIST) microarrays generates a large volume of methylation-expression relational data. To analyze this data, we propose a set of algorithms based on fuzzy sets theory, in particular Possibilistic c-Means (PCM) and cluster fuzzy density. For each gene, these algorithms calculate measures of confidence of various methylation-expression relationships in each NHL subclass. Thus, these tools can be used as a means of high volume data exploration to better guide biological confirmation using independent molecular biology methods.

Large-Scale CpG Methylation Analysis Identifies Novel Candidate Genes and Reveals Methylation Hotspots in Acute Lymphoblastic Leukemia

This study examined DNA methylation associated with acute lymphoblastic leukemia (ALL) and showed that selected molecular targets can be pharmacologically modulated to reverse gene silencing. A CpG island (CGI) microarray containing more than 3,400 unique clones that span all human chromosomes was used for large-scale discovery experiments and led to 262 unique CGI loci being statistically identified as methylated in ALL lymphoblasts. The methylation status of 10 clones encompassing 11 genes (DCC, DLC-1, DDX51, KCNK2, LRP1B, NKX6-1, NOPE, PCDHGA12, RPIB9, ABCB1, and SLC2A14) identified as differentially methylated between ALL patients and controls was independently verified. Consequently, the methylation status of DDX51 was found to differentiate patients with B- and T-ALL subtypes (P = 0.011, Fisher's exact test). Next, the relationship between methylation and expression of these genes was examined in ALL cell lines (NALM-6 and Jurkat) before and after treatments with 5-aza-2-deoxycytidine and trichostatin A. More than a 10-fold increase in mRNA expression was observed for two previously identified tumor suppressor genes (DLC-1 and DCC) and also for RPIB9 and PCDHGA12. Although the mechanisms that lead to the CGI methylation of these genes are unknown, bisulfite sequencing of the promoter of RPIB9 suggests that expression is inhibited by methylation within SP1 and AP2 transcription factor binding motifs. Finally, specific chromosomal methylation hotspots were found to be associated with ALL. This study sets the stage for acquiring a better biological understanding of ALL and for the identification of epigenetic biomarkers useful for differential diagnosis, therapeutic monitoring, and the detection of leukemic relapse.

Differential DNA methylation patterns of small B-cell lymphoma subclasses with different clinical behavior

Non-Hodgkin's lymphoma (NHL) is a group of malignancies of the immune system with variable clinical behaviors and diverse molecular features. Despite the progress made in classification of NHLs based on classical methods, molecular classifications are a work in progress. Toward this goal, we used an array-based technique called differential methylation hybridization (DMH) to study small B-cell lymphoma (SBCL) subtypes. A total of 43 genomic DMH experiments were performed. From these results, several statistical methods were used to generate a set of differentially methylated genes for further validation. Methylation of LHX2, POU3F3, HOXC10, NRP2, PRKCE, RAMP, MLLT2, NKX6.1, LRP1B and ARF4 was validated in cell lines and patient samples and demonstrated subtype-related preferential methylation patterns. For LHX2 and LRP1B, bisulfite sequencing, real-time reverse transcriptase-polymerase chain reaction and induction of gene expression following treatment with the demethylating agent, 5'-aza-2'-deoxycytidine, were confirmed. This new epigenetic information is helping to define molecular portraits of distinct subtypes of SBCL that are not recognized by current classification systems and provides valuable potential insights into the biology of these tumors.

Identification of genetic variation and putative regulatory regions in bovine CARD15

Mutations in caspase recruitment domain 15 (CARD15) are associated with susceptibility to Crohn's disease and Blau Syndrome. We performed comparative analyses of the bovine, murine, and human CARD15 transcripts to elucidate functionality of bovine CARD15 and examine its potential role in bovine disease resistance. Comparative analyses of intronic sequence across seven divergent species were performed to identify putative regulatory element binding motifs. High levels of interspecies conservation in sequence, genomic structure, and protein domains were detected indicating common functionality for CARD15 in cattle, human, and mouse. We identified species-specific regulatory elements in the 5' and 3' untranslated regions, suggesting that modes of regulation may have diverged across species. Thirty-one conserved putative regulatory element binding motifs were identified in the CARD15 intronic sequence of seven species. To assess the extent of genetic diversity within bovine CARD15, 41 individuals from two subspecies were sequenced and screened for polymorphisms. Thirty-six single nucleotide polymorphisms (SNPs) were identified. Finally, 20 subspecies-specific haplotypes were predicted with 7 and 13 unique haplotypes explaining the diversity within B. taurus taurus and B. taurus indicus animals, respectively. Strong evidence for a simple causal relationship between these SNP loci and their haplotypes with Johne's disease was not detected.

Discovery of novel epigenetic markers in non-Hodgkin's lymphoma

Non-Hodgkin's lymphoma (NHL) is a group of malignancies with heterogeneous genetic and epigenetic alterations. Discovery of molecular markers that better define NHL should improve diagnosis, prognosis and understanding of the biology. We developed a CpG island DNA microarray for discovery of aberrant methylation targets in cancer, and now apply this method to examine NHL cell lines and primary tumors. This methylation profiling revealed differential patterns in six cell lines originating from different subtypes of NHL. We identified 30 hypermethylated genes in these cell lines and independently confirmed 10 of them. Methylation of 6 of these genes was then further examined in 75 primary NHL specimens composed of four subtypes representing different stages of maturation. Each gene (DLC-1, PCDHGB7, CYP27B1, EFNA5, CCND1 and RARbeta2) was frequently hypermethylated in these NHLs (87, 78, 61, 53, 40 and 38%, respectively), but not in benign follicular hyperplasia. Although some genes such as DLC-1 and PCDHGB7 were methylated in the vast majority of NHLs, others were differentially methylated in specific subtypes. The methylation of the candidate tumor suppressor gene DLC-1 was detected in a high proportion of primary tumor and plasma DNA samples by using quantitative methylation-specific PCR analysis. This promoter hypermethylation inversely correlated with DLC-1 gene expression in primary NHL samples. Thus, this CpG island microarray is a powerful discovery tool to identify novel methylated genes for further studies of their relevant molecular pathways in NHLs and identification of potential epigenetic biomarkers of disease.

Analysis of a biomarker for Wegener's granulomatosis

Summary This molecular epidemiology study integrated questionnaire and genotype information to examine a disease susceptibility hypothesis. The study was based on a previously reported association demonstrated between a single nucleotide polymorphism (SNP) identified as A-564G within the promoter of the proteinase-3 gene (PRTN3) and the autoimmune disease Wegener's granulomatosis (WG). To further examine the strength of this association, we employed a family-based design in which the inheritance of alternate alleles could be ascertained from the parents of affected and unaffected progeny. Genotype information for the study participants was derived from DNA samples from participants who collected buccal cells using a harvesting method that was non-invasive and self-administered. A brief questionnaire captured demographic data on the participants, the family relationships between participants, and the prevalence of autoimmune disease among family members. Samples were obtained on 132 individuals representing 43 WG cases and 89 unaffected controls. Thirty-four nuclear families containing at least one unaffected sibling or parent of a WG case were represented in this sample. We found no evidence for an association between A-564G and the likelihood of a WG diagnosis. We examined five additional SNPs and a sixth SNP haplotype within the PRTN3 promoter region in a family-based association analysis and found no evidence that mutations within PRTN3 are associated with WG diagnosis.

Haplotype variation in bovine Toll-like receptor 4 and computational prediction of a positively selected ligand-binding domain

Toll-like receptor 4 (TLR4) is a cell-surface receptor that activates innate and adaptive immune responses. Because it recognizes a broad class of pathogen-associated molecular patterns presented by lipopolysaccharides and lipoteichoic acid, TLR4 is a candidate gene for resistance to a large number of diseases. In particular, mouse models suggest TLR4 as a candidate gene for resistance to major agents in bovine respiratory disease and Johne's disease. The coding sequence of bovine TLR4 is divided into three exons, with intron/exon boundaries and intron sizes similar to those of human TLR4 transcript variant 1. We amplified each exon in 40 individuals from 11 breeds and screened the sequence for single-nucleotide polymorphisms (SNPs). We identified 32 SNPs, 28 of which are in the coding sequence, for an average of one SNP per 90 bp of coding sequence. Eight SNPs were nonsynonymous and potentially alter specificity of pathogen recognition or efficiency of signaling. To evaluate the functional importance of these SNPs, we used codon-substitution models to detect diversifying selection in an extracellular region that may physically interact with ligands. One nonsynonymous SNP is located within this region, and other substitutions are in adjacent regions that may interact with coreceptor molecules. The 32 SNPs were found in 20 haplotypes that can be assigned to geographic ranges of origin. Haplotype-tagging SNP analysis indicated that 12 SNPs need to be genotyped to distinguish these 20 haplotypes. These data provide a basic understanding of bovine TLR4 sequence variation and supply haplotype markers for disease association studies.

A randomised, double-blind, placebo-controlled, comparative study of topical skin analgesics and the anxiety and discomfort associated with venous cannulation

OBJECTIVES

To compare the effect of topical skin anaesthetic agents on the discomfort and anxiety associated with venous cannulation.

DESIGN

Randomised, double-blind, placebo-controlled, within subject, volunteer trial.

METHODS

20 healthy volunteers underwent venous cannulation on three separate occasions having received topical skin application of either 4% amethocaine gel (Ametop), 5% eutectic mixture of lidocaine and prilocaine (EMLA) or E45 cream (placebo). Visual analogue and verbal rating scales were used to assess pain and anxiety associated with the venous cannulation, and anticipated anxiety for future cannulation, under each drug condition.

RESULTS

Subjects were aged 22-53 years (mean 32.8 years). The mean visual analogue scores (VAS) for discomfort were found to be significantly lower (p< 0.001) with Ametop (VAS = 18mm) and EMLA (VAS = 29mm) compared with the control (VAS = 38mm). There was a positive correlation (R2 = 72%, p<0.001) between discomfort and the predicted anxiety if cannulation was to be repeated with the same cream. With the placebo a positive correlation (R2 = 19.8%, p = 0.05) was found between the level of anxiety before cannulation and the level of discomfort recorded.

CONCLUSIONS

Ametop and EMLA topical anaesthetic agents produce effective skin analgesia for venous cannulation. The use of topical analgesia can reduce perceived anxiety about future cannulation procedures. This has application in the management of anxious patients undergoing intravenous sedation, suggesting that topical analgesia prior to venous cannulation may significantly aid anxiolysis.

Primary fallopian tube carcinoma: the Queensland experience

The purpose of this study was to review the experience with fallopian tube carcinoma in Queensland and to compare it with previously published data. Thirty-six patients with primary fallopian tube carcinoma treated at the Queensland Gynaecological Cancer Center from 1988 to 1999 were reviewed in a retrospective clinicopathologic study. All patients had primary surgery and 31/36 received chemotherapy postoperatively. Abnormal vaginal bleeding (15/36) and abdominal pain (14/36) were the most common presenting symptoms at the time of diagnosis. Median follow-up was 70.3 months and the median overall survival was 68.1 months. Surgical stage I disease (P = 0.02) and the absence of residual tumor after operation (P = 0.03) were the only factors associated with improved survival. Twenty of the 36 patients (55%) presented with stage I disease and survival was 62.7% at 5 years. No patient with postoperative residual tumor survived. The majority of the patients with fallopian tube carcinoma present with stage I disease at diagnosis, but their survival probability is low compared with that of other early stage gynecological malignancies. If primary surgical debulking cannot achieve macroscopic tumor clearence, the chance of survival is extremely low.

Treatment of Wegener's granulomatosis with immune globulin: CNS involvement in an adolescent female

OBJECTIVE

To describe the use of intravenous immune globulin (IVIG) to treat Wegener's granulomatosis (WG) in an adolescent female with an abnormal magnetic resonance imaging (MRI) scan and electroencephalogram (EEG), as well as central nervous system involvement manifesting as generalized seizures.

CASE SUMMARY

A 15-year-old white girl diagnosed with WG and receiving prednisone and cyclophosphamide was admitted with new-onset tonic-clonic seizures. The patient received phenobarbital and phenytoin to control seizures and was receiving cyclophosphamide and corticosteroids for WG. She developed cyclophosphamide-induced cystitis and was started on a four-day therapeutic course of IVIG following the discontinuation of cyclophosphamide. After 16 days of hospitalization, repeat EEG and MRI were within normal limits, and laboratory and clinical improvement was evident in at least nine of the affected organ systems including pulmonary, hematologic, renal, ocular, cutaneous, musculoskeletal, central nervous system, gastrointestinal, and genitourinary. The patient was discharged with clinical involvement of WG documented in two organ systems, hematologic and renal.

DISCUSSION

WG is a form of vasculitis believed to develop due to an autoimmune disorder. The diagnosis is based on radiographic and histopathologic findings, as well as the presence of elevated antineutrophil cytoplasmic antibodies and a suggestive clinical presentation. The presentation is widely variable and is most commonly associated with upper-airway involvement such as sinusitis, cough, pulmonary infiltrates, and cavitary nodules. Renal involvement signifies generalized disease. Conventional treatment for WG includes cyclophosphamide and prednisone. Little information is available describing therapeutic alternatives. Cytotoxicity related to immunosuppressant regimens limits continuous treatment and may necessitate the use of alternative agents.

CONCLUSIONS

This case describes the use of IVIG in an adolescent patient presenting with WG as a generalized, active disease with neurologic complications. IVIG may be useful in generalized, active WG complicated by intolerance to cyclophosphamide and seizures, but further study is necessary to define its role.

Blockade of cytochrome P-450 epoxygenase pathway attenuates the natriuresis of N(G)-monomethyl-L-arginine infusion in the spontaneously hypertensive rat

Previous studies demonstrated that there is increased renal synthesis of cytochrome P-450-dependent arachidonic acid metabolites in the vasculature and tubules of the Okamoto spontaneously hypertensive rat (SHR). It has also been shown that the natriuretic response of the SHR to NG-monomethyl-L-arginine (L-NMMA) infusion is exaggerated compared with that of the normotensive Wistar-Kyoto rat. The purpose of this study was to determine the roles of cytochrome P-450 epoxygenase and cyclooxygenase pathways in the natriuresis that is observed with the systemic infusion of a high dose of L-NMMA to inhibit nitric oxide synthesis in the SHR and the Wistar-Kyoto rats. After a control clearance period of 20 minutes groups of adult SHR (n = 14) were given L-NMMA (15 mg/kg bolus followed by 500 microg/kg/min continuous infusion). In other groups of SHR either ketoconazole (0.5 mg/kg, n = 9) to inhibit the renal activity of cytochrome P-450 epoxygenase pathway or indomethacin (3 mg/kg, n = 7) to inhibit cyclooxygenase activity was administered intravenously 20 minutes before the control clearance period. After the control clearance period L-NMMA was infused as previously described. Infusion of L-NMMA in the control group of SHR resulted in a significant increase in fractional excretion of sodium (FE Na from 1.78% +/- 0.24% to 6.90% +/- 0.61%). In the ketoconazole-treated group of SHR, L-NMMA infusion resulted in a significant natriuresis (from 2.22% +/- 0.58% to 4.70% +/- 0.93%); however, the natriuretic response was significantly attenuated compared with that of the control group of SHR that received only L-NMMA (delta FE Na, 2.47% +/- 0.40% vs 5.24% +/- 0.55%). Indomethacin administration did not affect the natriuretic response to L-NMMA infusion in the SHR. In conclusion, the natriuretic response to L-NMMA infusion in the SHR is significantly attenuated by administration of ketoconazole but not indomethacin. This result suggests that the natriuretic effect of L-NMMA infusion in the SHR is mediated at least partly by cytochrome P-450 metabolites of the epoxygenase pathway.

Age as a variable in an exercise program for the treatment of simple urinary stress incontinence

This study compared the effectiveness of biofeedback on pubococcygeal muscle strengthening and simple urinary stress incontinence in older and younger women. Women aged 55 years and older and women younger than 55 years of age were taught Kegel exercises, using biofeedback, for the treatment of simple urinary stress incontinence. Eighty percent of the younger group and 67% of the older group eliminated stress incontinence. Also, the younger women required less pubococcygeal strength than the older women to control incontinence.

A light-guidance system to be used for CT-guided biopsy

We describe a light-guidance system that uses intersecting helium-neon laser beams to provide precise guidance for biopsy approaches from any direction (including compound angles) during CT-guided biopsy of the chest and abdomen. Interactive software provides visualization of the proposed path, indicates the segment of that path that will pass through each section, and displays the settings for the apparatus.