The musculoskeletal consequences of breast reconstruction using the latissimus dorsi muscle for women following mastectomy for breast cancer: A critical review

Breast reconstruction using the latissimus dorsi (LD) flap following mastectomy is an important management option in breast cancer. However, one common, but often ignored, complication following LD flap is shoulder dysfunction. The aim of this critical review was to comprehensively assess the musculoskeletal impact of LD breast reconstruction and evaluate the functional outcome following surgery. Five electronic databases were searched including; Medline, Embase, CINAHL Plus (Cumulative Index to Nursing and Allied Health), PubMed and Web of Science. Databases were searched from 2006 to 2016, and only full text, English language articles were included. Twenty-two observational studies and two surveys were reviewed with sample sizes ranging from six to 206 participants. The majority of studies had small sample sizes and were retrospective in nature. Nevertheless, there is evidence to suggest that there is some degree of weakness and reduced mobility at the shoulder following LD muscle transfer. The literature demonstrates that there is considerable morbidity in the immediate post-operative period with functional recovery varying between studies. The majority of work tends to be limited and often gives conflicting results; therefore, further investigation is required in order to determine underlying factors that contribute to a reduction in function and activities of daily living.

DNA methylation is globally disrupted and associated with expression changes in chronic obstructive pulmonary disease small airways

DNA methylation is an epigenetic modification that is highly disrupted in response to cigarette smoke and involved in a wide spectrum of malignant and nonmalignant diseases, but surprisingly not previously assessed in small airways of patients with chronic obstructive pulmonary disease (COPD). Small airways are the primary sites of airflow obstruction in COPD. We sought to determine whether DNA methylation patterns are disrupted in small airway epithelia of patients with COPD, and evaluate whether changes in gene expression are associated with these disruptions. Genome-wide methylation and gene expression analysis were performed on small airway epithelial DNA and RNA obtained from the same patient during bronchoscopy, using Illumina's Infinium HM27 and Affymetrix's Genechip Human Gene 1.0 ST arrays. To control for known effects of cigarette smoking on DNA methylation, methylation and gene expression profiles were compared between former smokers with and without COPD matched for age, pack-years, and years of smoking cessation. Our results indicate that aberrant DNA methylation is (1) a genome-wide phenomenon in small airways of patients with COPD, and (2) associated with altered expression of genes and pathways important to COPD, such as the NF-E2-related factor 2 oxidative response pathway. DNA methylation is likely an important mechanism contributing to modulation of genes important to COPD pathology. Because these methylation events may underlie disease-specific gene expression changes, their characterization is a critical first step toward the development of epigenetic markers and an opportunity for developing novel epigenetic therapeutic interventions for COPD.

Green leaf volatiles as antiaggregants for the mountain pine beetle,Dendroctonus ponderosae Hopkins (Coleoptera: Scolytidae)

We tested the hypothesis that green leaf volatiles act as antiaggregants for the mountain pine beetle (MPB),Dendroctonus ponderosac Hopkins. In coupled gas chromatographic-electroantennographic detection (GC-EAD) analysis MPB antennae responded to 30 ng doses of all six-carbon green leaf alcohols tested [1-hexanol, (E)-2-hexen-1-ol, (Z)-2-hexen-1-ol, (E)-3-hexen-1-ol, and (Z)-3-hexen-1-ol], but not to the aldehydes, hexanal or (E)-2-hexenal, or to alcohol or aldehyde homologues with more or fewer than six carbon atoms. In field trapping experiments a blend of green leaf alcohols [1-hexanol, (Z)-2-hexen-1-ol, (E)-3-hexen-1-ol and (Z)-3-hexen-1-ol] effectively disrupted the response to attractive semiochemicals; a blend of the aldehydes hexanal and (E)-2-hexenal was inactive. The two best disruptants. (E)-2-hexen-1-ol and (Z)-3-hexen-1-ol, reduced catches of both sexes to levels not significantly different from catches in unbaited control traps. They also reduced the attack on trees baited with attractive MBP pheromones to a level not significantly different from that on unbaited control trees. Neither of the clerid predators captured,Enoclerus sphegeus (F.) norThanasimus undatulus (Say), was repelled by green leaf volatiles. Our results suggest that green leaf alcohols are promising disruptants which may be used to supplement the antiaggregation pheromone, verbenone, in protecting single high-value trees as well as carefully selected stands with low-level populations of MPBs.

EYA4 is inactivated biallelically at a high frequency in sporadic lung cancer and is associated with familial lung cancer risk

In an effort to identify novel biallelically inactivated tumor suppressor genes (TSG) in sporadic invasive and pre-invasive non-small cell lung cancer (NSCLC) genomes, we applied a comprehensive integrated multi-‘omics approach to investigate patient matched, paired NSCLC tumor and non-malignant parenchymal tissues. By surveying lung tumor genomes for genes concomitantly inactivated within individual tumors by multiple mechanisms, and by the frequency of disruption in tumors across multiple cohorts, we have identified a putative lung cancer TSG, Eyes Absent 4 (EYA4). EYA4 is frequently and concomitantly deleted, hypermethylated and underexpressed in multiple independent lung tumor data sets, in both major NSCLC subtypes, and in the earliest stages of lung cancer. We find not only that decreased EYA4 expression is associated with poor survival in sporadic lung cancers, but EYA4 SNPs are associated with increased familial cancer risk, consistent with EYA4’s proximity to the previously reported lung cancer susceptibility locus on 6q. Functionally, we find that EYA4 displays TSG-like properties with a role in modulating apoptosis and DNA repair. Cross examination of EYA4 expression across multiple tumor types suggests a cell type-specific tumorigenic role for EYA4, consistent with a tumor suppressor function in cancers of epithelial origin. This work shows a clear role for EYA4 as a putative TSG in NSCLC.

Divergent genomic and epigenomic landscapes of lung cancer subtypes underscore the selection of different oncogenic pathways during tumor development

For therapeutic purposes, non-small cell lung cancer (NSCLC) has traditionally been regarded as a single disease. However, recent evidence suggest that the two major subtypes of NSCLC, adenocarcinoma (AC) and squamous cell carcinoma (SqCC) respond differently to both molecular targeted and new generation chemotherapies. Therefore, identifying the molecular differences between these tumor types may impact novel treatment strategy. We performed the first large-scale analysis of 261 primary NSCLC tumors (169 AC and 92 SqCC), integrating genome-wide DNA copy number, methylation and gene expression profiles to identify subtype-specific molecular alterations relevant to new agent design and choice of therapy. Comparison of AC and SqCC genomic and epigenomic landscapes revealed 778 altered genes with corresponding expression changes that are selected during tumor development in a subtype-specific manner. Analysis of >200 additional NSCLCs confirmed that these genes are responsible for driving the differential development and resulting phenotypes of AC and SqCC. Importantly, we identified key oncogenic pathways disrupted in each subtype that likely serve as the basis for their differential tumor biology and clinical outcomes. Downregulation of HNF4α target genes was the most common pathway specific to AC, while SqCC demonstrated disruption of numerous histone modifying enzymes as well as the transcription factor E2F1. In silico screening of candidate therapeutic compounds using subtype-specific pathway components identified HDAC and PI3K inhibitors as potential treatments tailored to lung SqCC. Together, our findings suggest that AC and SqCC develop through distinct pathogenetic pathways that have significant implication in our approach to the clinical management of NSCLC.

Chromosome-wide DNA methylation analysis predicts human tissue-specific X inactivation

X-chromosome inactivation (XCI) results in the differential marking of the active and inactive X with epigenetic modifications including DNA methylation. Consistent with the previous studies showing that CpG island-containing promoters of genes subject to XCI are approximately 50% methylated in females and unmethylated in males while genes which escape XCI are unmethylated in both sexes; our chromosome-wide (Methylated DNA ImmunoPrecipitation) and promoter-targeted methylation analyses (Illumina Infinium HumanMethylation27 array) showed the largest methylation difference (D = 0.12, p < 2.2 E-16) between male and female blood at X-linked CpG islands promoters. We used the methylation differences between males and females to predict XCI statuses in blood and found that 81% had the same XCI status as previously determined using expression data. Most genes (83%) showed the same XCI status across tissues (blood, fetal: muscle, kidney and nerual); however, the methylation of a subset of genes predicted different XCI statuses in different tissues. Using previously published expression data the effect of transcription on gene-body methylation was investigated and while X-linked introns of highly expressed genes were more methylated than the introns of lowly expressed genes, exonic methylation did not differ based on expression level. We conclude that the XCI status predicted using methylation of X-linked promoters with CpG islands was usually the same as determined by expression analysis and that 12% of X-linked genes examined show tissue-specific XCI whereby a gene has a different XCI status in at least one of the four tissues examined.

Abstract A14: DNA alterations to the Cullin-3/Ring box protein-1 E3 ubiquitin ligase complex represent a novel mechanism of NF-κB activation in lung cancer

Background: Nuclear factor kappa B (NF-κB) signaling is essential for lung cancer development, and therefore, may serve as a target for intervention. However, the genetic mechanisms responsible for its activation are not fully understood. Kelch-like ECH-associated protein 1 (KEAP1) binds protein substrates to the Cullin-3 (CUL3)/Ring box protein-1 (RBX1) E3 ubiquitin ligase complex where ubiquitination signals substrates for proteosomal degradation. Recently, inhibitor of nuclear factor kappa-B kinase subunit beta (IKKβ), an activator of NF-κB, was shown to be a substrate of KEAP1, implicating KEAP1's involvement in regulating NF-κB signaling. Loss of function of KEAP1 leads to IKKβ accumulation and NF-κB activation. We hypothesized that DNA deletions of the other E3 complex components (CUL3 and RBX1) are frequent alterations that disrupt complex function and contribute to NF-κB activation in lung cancer.

Methods: We screened DNA copy number profiles of 261 non-small cell lung cancer (NSCLC) tumors for DNA alterations at the KEAP1, CUL3, RBX1, and IKK loci. Profiles were generated by array comparative genomic hybridization on the SMRT array (sub-megabase resolution tiling) platform. We also analyzed mRNA expression of these genes and 9 well annotated NF-κB target genes, using gene expression profiles generated with Agilent gene expression microarrays for a subset (n=48) of the tumors.

Results: Our investigation of genetic disruption to the E3 ubiquitin ligase complex components revealed 54% of tumors harbored DNA copy number loss of at least one complex component (KEAP1, CUL3, or RBX1) or gain of IKKβ. Moreover, at the expression level, 81% of tumors analyzed had aberrant expression of one of these genes (underexpression of complex components or overexpression of IKKβ). Interestingly, the copy number alterations identified appeared to segregate with adenocarcinoma (AC) or squamous cell carcinoma (SCC) histology; KEAP1 loss was more prevalent in AC while CUL3 loss and IKKβ gain were more frequent in SCC. When NF-κB target gene expression was analyzed, we observed higher expression of 5/9 genes in tumors with underexpression of an E3 ubiquitin ligase complex component relative to matched non-malignant tissue from the same individual.

Conclusions: The presence and strikingly high frequency of genetic disruption and aberrant expression of the E3 ubiquitin ligase complex components (KEAP1, CUL3, and RBX1) revealed in this study provides evidence of its importance in lung cancer. These data suggest that DNA level alterations to this complex may represent a novel mechanism of NF-κB activation in lung cancer.

Citation Information: Cancer Prev Res 2010;3(12 Suppl):A14.

Abstract A16: Reversibly expressed and differentially methylated genes in airways of current and former smokers

Background: Smoking-related disease, including chronic obstructive pulmonary disease (COPD) and lung cancer, account for the third greatest cause of mortality and the number one cause of cancer-related death worldwide. Former smokers (FS) remain at an elevated risk for both diseases and are the fastest growing population of newly diagnosed lung cancer patients, emphasizing the need for greater understanding of molecular mechanisms associated with smoking and smoking cessation. Cigarette smoke induces DNA damage in airway and lung tissues at the genomic and epigenomic levels, where it is associated with changes to gene expression. Studies on current (CS), FS, and never smokers have identified reversible and irreversible changes in gene expression that occur upon smoking cessation. Since methylation is a reversible gene regulatory mark that is also aberrantly affected by cigarette smoke, we hypothesize that the reversible nature of genes differentially expressed in bronchial epithelial cells in the airways of CS and FS, may be due to changes in DNA methylation.

Methods: Bronchial epithelial cells were obtained from brushings of small airways (&lt; 2mm diameter) during bronchoscopy from 12 current smokers (CS) and 6 former smokers (FS). Methylation profiles were generated for 27,579 probes corresponding to 14,575 genes, using the Illumina Infinium Human Methylation27 platform. Methylation results were aligned to the set of reversibly expressed genes described in previous studies. Genes that become either hypermethylated and underexpressed or hypomethylated and overexpressed upon smoking cessation were selected for further study.

Results: Methylation and expression analysis identified 9 genes overexpressed and hypomethylated in CS relative to FS, notably GPX2 and GSTA2 both involved in pathways previously shown to be upregulated in CS. These pathways include aryl hydrocarbon receptor signaling; a central metabolic pathway activated in response to halogenated and polycyclic aromatic hydrocarbons, and the NRF2 mediated oxidative stress response pathway, involved in the detoxification of reactive oxygen and intermediates. Additionally, 3 genes were found to be underexpressed and hypermethylated in CS relative to FS, notably SYF2 and CXCL6, involved in cell cycle regulation and inflammatory disease (including COPD) respectively.

Conclusion: Our data reveal a panel of genes whose change in gene expression upon smoking cessation may be regulated by DNA methylation, corresponding to well known genes involved in smoking metabolism and oxidative stress response. The identification of differentially methylated and expressed genes between CS and FS may provide insight into the mechanism of smoking related disease. As methylation is a reversible DNA modification, this knowledge may lead to the application of preventative epigenetic therapeutics for the growing population of FS and the immense health burden and mortality associated with cigarette smoke.

Citation Information: Cancer Prev Res 2010;3(12 Suppl):A16.

Abstract A21: Global DNA methylation analysis of bronchial epithelia of former smokers with COPD, with and without lung cancer

Introduction: Emerging evidence suggests that aberrant epigenetic regulation is involved in the development and progression of malignant and nonmalignant respiratory diseases, including chronic obstructive pulmonary disease (COPD) and lung cancer. Moreover, patients with COPD have an increased risk of developing lung cancer. Besides similar risk factors such as tobacco smoke exposure, little is known about the shared biology between COPD and lung cancer. Smoking causes aberrations in airway and lung parenchyma at both the genomic and epigenomic levels, resulting in global changes to gene expression. In this study, we hypothesize that alterations at the level of DNA methylation in airway epithelia of former smokers (FS) with COPD with and without non-small cell lung cancer (NSCLC) may be used to identify genes involved in the pathogenesis of these respiratory diseases, independent of the effects of active smoking.

Methods: Bronchial epithelial cells were obtained from brushings of small airways (&lt; 2 mm diameter) during bronchoscopy from FS with COPD (n=22), without COPD (n=22) and patients with COPD as well as previous surgical resection of Stage I NSCLC (n=6). Illumina's Infinium Methylation (HM27) assay was used to assess DNA methylation status of 27,578 CpG sites associated with 14,475 genes.

Results: COPD patients are distinguished from non-COPD patients based on airway methylation profiles. Genes differentially methylated in airways between COPD and non-COPD patients include several modulators of aryl hydrocarbon receptor and IL6 signaling, as well as genes previously implicated in COPD, including immune chemotaxis regulators (CXCL11, CCR8) and GABA receptor signaling (GABRA5). Airway epithelial DNA from COPD patients with NSCLC compared to those without NSCLC was differentially methylated at sites encoding multiple key regulators of xenobiotic metabolism, regulators of free radical savaging/detoxification and retinol metabolic pathway components including several alcohol dehydrogenase, glutathione S transferase, and UDP glucoronosyltransferase genes.

Conclusion: Our preliminary results suggest a role for DNA methylation in the deregulation of previously identified COPD-related genes, and specifically highlight differences in airways of COPD patients with/without NSCLC corresponding to well-known smoking-related metabolomic processes. Knowledge of DNA methylation disruption will further our understanding of the etiological role of COPD in the development of lung cancer, and contribute to the development of chemo-prevention strategies targeting the biology of both COPD and NSCLC. Supported by CIHR.

Citation Information: Cancer Prev Res 2010;3(12 Suppl):A21.

Integrating the multiple dimensions of genomic and epigenomic landscapes of cancer

Advances in high-throughput, genome-wide profiling technologies have allowed for an unprecedented view of the cancer genome landscape. Specifically, high-density microarrays and sequencing-based strategies have been widely utilized to identify genetic (such as gene dosage, allelic status, and mutations in gene sequence) and epigenetic (such as DNA methylation, histone modification, and microRNA) aberrations in cancer. Although the application of these profiling technologies in unidimensional analyses has been instrumental in cancer gene discovery, genes affected by low-frequency events are often overlooked. The integrative approach of analyzing parallel dimensions has enabled the identification of (a) genes that are often disrupted by multiple mechanisms but at low frequencies by any one mechanism and (b) pathways that are often disrupted at multiple components but at low frequencies at individual components. These benefits of using an integrative approach illustrate the concept that the whole is greater than the sum of its parts. As efforts have now turned toward parallel and integrative multidimensional approaches for studying the cancer genome landscape in hopes of obtaining a more insightful understanding of the key genes and pathways driving cancer cells, this review describes key findings disseminating from such high-throughput, integrative analyses, including contributions to our understanding of causative genetic events in cancer cell biology.

Abstract LB-346: A novel lung tumor suppressor implicated in somatic and familial cancers

Background: Lung cancer (LC) is the most common cause of cancer death worldwide. Previous familial linkage studies have identified a tumor suppressor locus on 6q23-25. However, no single gene has yet been implicated within this 30 Mb region. Discovering the genetic and epigenetic events that affect LC risk and development will lead to better methods for risk assessment, early detection and treatment.

Methods: Genome-wide genes disrupted by two-hit inactivation were identified by combining gene dosage, DNA methylation, and gene expression assays for a group of lung adenocarcinomas (AC) and adjacent non-malignant tissues. Gene expression, DNA hypermethylation and/or copy number aberrations were validated in data from AC, squamous cell carcinoma (SqCC), and pre-malignant lesions by querying other cohorts using gene-specific and whole-genome approaches. The role of DNA methylation in gene silencing was assessed using inhibition of DNMT by 5′-azacytidine. The association of allelic variants with LC risk was investigated in 193 familial LC cases and 213 controls collected by the Genetic Epidemiology of Lung Cancer Consortium (GELCC) using a Cochrane-Armitage trend test. The association of gene expression with prognosis was performed on public data using a Mantel-Cox log test. Stable mRNA knock-downs were generated using lentiviral delivery of a gene-specific shRNA, and apoptotic cells were counted using Annexin5/propidium iodide staining.

Results: Integration of AC gene dosage, DNA methylation and mRNA expression showed EYA4 to be frequently affected by two-hits and significantly down-regulated. Quantitative PCR techniques confirmed that EYA4 was hypermethylated (46%) and down-regulated (72%), validating our microarray results. A direct link between EYA4 methylation and expression was verified by restoration of expression after 5′-azacytidine treatment in methylated cell lines. Congruent with EYA family member function, in vitro assays revealed that EYA4 knock-down cells displayed a decrease in the number of apoptotic cells - a hallmark of cancer. Further investigations led to the discovery of frequent EYA4 disruption in SqCC and pre-neoplastic tissue. The GELCC dataset was examined to assess EYA4 allelotype association with familial risk. Doing so revealed that numerous EYA4 variants are associated with increased risk. Finally, the association of EYA4 expression with survival was investigated along with other somatically altered genes at 6q23-25. Of these genes, low EYA4 expression was found to be the most significantly associated with poor prognosis.

Conclusions: EYA4 is a frequently disrupted gene that maps to a locus previously associated with cancer risk. It is implicated in somatic as well as familial cancers, and is likely a tumor suppressor gene with apoptotic functions. The direct association of EYA4 with risk and survival underscores its relevance on a clinical level.

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 LB-346.

Transcriptome profiles of carcinoma-in-situ and invasive non-small cell lung cancer as revealed by SAGE

Background

Non-small cell lung cancer (NSCLC) presents as a progressive disease spanning precancerous, preinvasive, locally invasive, and metastatic lesions. Identification of biological pathways reflective of these progressive stages, and aberrantly expressed genes associated with these pathways, would conceivably enhance therapeutic approaches to this devastating disease.

Methodology/Principal Findings

Through the construction and analysis of SAGE libraries, we have determined transcriptome profiles for preinvasive carcinoma-in-situ (CIS) and invasive squamous cell carcinoma (SCC) of the lung, and compared these with expression profiles generated from both bronchial epithelium, and precancerous metaplastic and dysplastic lesions using Ingenuity Pathway Analysis. Expression of genes associated with epidermal development, and loss of expression of genes associated with mucociliary biology, are predominant features of CIS, largely shared with precancerous lesions. Additionally, expression of genes associated with xenobiotic metabolism/detoxification is a notable feature of CIS, and is largely maintained in invasive cancer. Genes related to tissue fibrosis and acute phase immune response are characteristic of the invasive SCC phenotype. Moreover, the data presented here suggests that tissue remodeling/fibrosis is initiated at the early stages of CIS. Additionally, this study indicates that alteration in copy-number status represents a plausible mechanism for differential gene expression in CIS and invasive SCC.

Conclusions/Significance

This study is the first report of large-scale expression profiling of CIS of the lung. Unbiased expression profiling of these preinvasive and invasive lesions provides a platform for further investigations into the molecular genetic events relevant to early stages of squamous NSCLC development. Additionally, up-regulated genes detected at extreme differences between CIS and invasive cancer may have potential to serve as biomarkers for early detection.

Methylated DNA immunoprecipitation

The identification of DNA methylation patterns is a common procedure in the study of epigenetics, as methylation is known to have significant effects on gene expression, and is involved with normal development as well as disease. Thus, the ability to discriminate between methylated DNA and non-methylated DNA is essential for generating methylation profiles for such studies. Methylated DNA immunoprecipitation (MeDIP) is an efficient technique for the extraction of methylated DNA from a sample of interest. A sample of as little as 200 ng of DNA is sufficient for the antibody, or immunoprecipitation (IP), reaction. DNA is sonicated into fragments ranging in size from 300-1000 bp, and is divided into immunoprecipitated (IP) and input (IN) portions. IP DNA is subsequently heat denatured and then incubated with anti-5'mC, allowing the monoclonal antibody to bind methylated DNA. After this, magnetic beads containing a secondary antibody with affinity for the primary antibody are added, and incubated. These bead-linked antibodies will bind the monoclonal antibody used in the first step. DNA bound to the antibody complex (methylated DNA) is separated from the rest of the DNA by using a magnet to pull the complexes out of solution. Several washes using IP buffer are then performed to remove the unbound, non-methylated DNA. The methylated DNA/antibody complexes are then digested with Proteinase K to digest the antibodies leaving only the methylated DNA intact. The enriched DNA is purified by phenol:chloroform extraction to remove the protein matter and then precipitated and resuspended in water for later use. PCR techniques can be used to validate the efficiency of the MeDIP procedure by analyzing the amplification products of IP and IN DNA for regions known to lack and known to contain methylated sequences. The purified methylated DNA can then be used for locus-specific (PCR) or genome-wide (microarray and sequencing) methylation studies, and is particularly useful when applied in conjunction with other research tools such as gene expression profiling and array comparative genome hybridization (CGH). Further investigation into DNA methylation will lead to the discovery of new epigenetic targets, which in turn, may be useful in developing new therapeutic or prognostic research tools for diseases such as cancer that are characterized by aberrantly methylated DNA.

Methylation analysis by DNA immunoprecipitation (MeDIP)

Alteration in epigenetic regulation of gene expression is a common event in human cancer and developmental disease. CpG island hypermethylation and consequent gene silencing is observed for many genes involved in a diverse range of functions and pathways that become deregulated in the disease state. Comparative profiling of the methylome is therefore useful in disease gene discovery. The ability to identify epigenetic alterations on a global scale is imperative to understanding the patterns of gene silencing that parallel disease progression. Methylated DNA immunoprecipitation (MeDIP) is a technique that isolates methylated DNA fragments by immunoprecipitating with 5'-methylcytosine-specific antibodies. The enriched methylated DNA can then be analyzed in a locus-specific manner using PCR assay or in a genome-wide fashion by comparative genomic hybridization against a sample without MeDIP enrichment. This article describes the detailed protocol for MeDIP and hybridization of MeDIP DNA to a whole-genome tiling path BAC array.

SIGMA2: a system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes

Background

High throughput microarray technologies have afforded the investigation of genomes, epigenomes, and transcriptomes at unprecedented resolution. However, software packages to handle, analyze, and visualize data from these multiple 'omics disciplines have not been adequately developed.

Results

Here, we present SIGMA², a system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes. Multi-dimensional datasets can be simultaneously visualized and analyzed with respect to each dimension, allowing combinatorial integration of the different assays belonging to the different 'omics.

Conclusion

The identification of genes altered at multiple levels such as copy number, loss of heterozygosity (LOH), DNA methylation and the detection of consequential changes in gene expression can be concertedly performed, establishing SIGMA² as a novel tool to facilitate the high throughput systems biology analysis of cancer.

Silencing Bcl-2 in models of mantle cell lymphoma is associated with decreases in cyclin D1, nuclear factor-kappaB, p53, bax, and p27 levels

Molecular mechanisms responsible for lymphoma resistance to apoptosis often involve the bcl-2 pathway. In this study, we investigated the cell signaling pathways activated in bcl-2-overexpressing human mantle cell lymphoma cell lines (JVM-2 and Z-138) that have been treated with oblimersen, a molecular gene silencing strategy that effectively suppresses bcl-2 in vitro and in vivo. Z-138 cells expressed higher levels of bcl-2 and were more sensitive to the effects of bcl-2 silencing, mediated by oblimersen or bcl-2 small interfering RNA, in vitro. Tumors derived following injection of Z-138 cells were sensitive to oblimersen as judged by decreases in tumor growth rate and decreases in cell proliferation (as measured by Ki-67). Immunohistochemistry and Western blot analysis of oblimersen-treated Z-138 tumors revealed a dose-dependent decrease in bcl-2 levels and an associated increase in the proapoptotic proteins caspase-3 and caspase-9. Silencing bcl-2 in Z-138 xenografts revealed an associated dose-dependent suppression of bax, a decrease in nuclear factor-kappaB and phospho-nuclear factor-kappaB, and transient loss of p53 levels. Coimmunoprecipitation studies suggest that the latter observation is mediated by an association between bcl-2 and phospho-mdm2. Bcl-2 silencing also led to p27 down-regulation and coimmunoprecipitation studies point to a role for bcl-2 in regulation of p27 localization/degradation. Bcl-2 silencing was also correlated with loss of cyclin D1a protein levels but not cyclin D1b levels. Coimmunoprecipitation studies indicate that bcl-2 may mediate its effects on cyclin D1a via interaction with p38 mitogen-activated protein kinase as well as a previously unreported interaction between bcl-2 and cyclin D1a.

Low back pain in people with a stoma: patients' views

PURPOSE

Low back pain (LBP) is a major health problem in western society. Stoma surgery, which involves creating a permanent opening in the abdominal wall, may interfere with the function of the abdominal muscles. Therefore people with a stoma may be at greater risk of developing LBP. A literature review revealed no research exploring a possible link between stoma formation and LBP, nor any study involving patients' perceptions. Therefore, the aims of this study were to determine (1) whether people with a stoma have LBP, (2) whether people with LBP and a stoma perceive that the conditions are linked, and (3) what issues regarding LBP should be included in a large survey of persons with a stoma.

METHODS

Members of the Ileostomy Association of Northern Ireland volunteered to participate in a focus group study. Events from this group were recorded, transcribed, and validated. Thematic analysis was performed.

RESULTS

Three themes were identified: (1) the presence of LBP, (2) a perceived link between LBP and a stoma, and (3) relevant issues for LBP. Ten of the 11 participants had experienced at least one episode of LBP, however 5 (50%) emphasized that they did not have a back problem. Six participants had no LBP prior to their surgery, but have experienced episodes of LBP since. The majority thought that the stoma and their LBP experience were linked. Suggested reasons for this link were changes in muscle strength, posture, and activities. Others included having an epidural or a pouching system that did not optimally suit their needs.

CONCLUSIONS

The results suggest that LBP is a problem for some people with an abdominal stoma and support the need for further study in this population. Two possible areas of future study are an investigation of what the term low back pain means to this population, and further study of the mechanisms that may link stoma surgery to an increased risk of LBP.

Epigenomics: mapping the methylome

DNA methylation is integral to normal development and disease processes. However, the genomic distribution of methylated sequences--the methylome--is poorly understood. We have recently developed a platform technology for rapid assessment of methylation status throughout the human genome in a high-resolution, high-throughput manner. This is achieved by coupling a methylated DNA immunoprecipitation (MeDIP) method for isolating methyl cytosine rich fragments with array-based comparative genomic hybridization (array CGH). Using a combination of whole genome tiling path BAC arrays and CpG island microarrays, DNA methylation profiles are obtained simultaneously at both genome-wide and locus-specific levels. A comparison between male and female DNA using MeDIP-array CGH revealed unexpected hypomethylation of the inactive x-chromosome in gene-poor regions. Furthermore, comparisons between cancer and noncancer cell types yielded differential methylation patterns that link genetic and epigenetic instability offering a new approach to decipher misregulation in cancer. Finally, we provide new data showing epigenomic instability in lung cancer cells with concurrent regions of genetic and epigenetic alterations harboring known oncogenes.

Array CGH technologies and their applications to cancer genomes

Cancer is a disease characterized by genomic instability. Comparative genomic hybridization (CGH) is a technique designed for detecting segmental genomic alterations. Recent advances in array-based CGH technology have enabled examination of chromosomal regions in unprecedented detail, revolutionizing our understanding of tumour genomes. A number of array-based technologies have been developed, aiming to improve the resolution of CGH, enabling researchers to refine and define regions in the genome that may be causal to cancer, and facilitating gene discovery at a rapid rate. This article reviews the various array CGH platforms and their use in the study of cancer genomes. In addition, the need for high-resolution analysis is discussed as well as the importance of studying early-stage disease to discover genetic alterations that may be causal to cancer progression and aetiology.

The need for inpatient palliative care facilities for noncancer patients in the Thames Valley

Inpatient facilities in palliative care units are generally considered to be mainly for cancer patients. We present and discuss the results of a survey that attempted to estimate the number of noncancer patients requiring inpatient palliative care. Questionnaires sent to all general practices in the Thames Valley area asked about the diagnosis and the number of bed-days that would have been required for each noncancer patient in the practice dying in the last year or still in their care. The replies suggest that about 11 noncancer patients per practice per year were in need of respite or continuing care. For the Thames Valley area this would amount to at least 66,000 bed-days per year for noncancer patients, compared with the current provision, mainly for cancer patients, of about 40,000 bed-days per year. The diagnoses involved and the reasons why our figures may overestimate need, are discussed. There can be no doubt that, if the need is to be met, current facilities will be inadequate and additional beds and services will be required.

The relation of mothers' controlling vocalizations to children's intrinsic motivation

Twenty-six mother-child dyads played together in a laboratory setting. Play sessions were surreptitiously videotaped (with mothers' permission), and each maternal vocalization was transcribed and coded, first into 1 of 24 categories and then ipso facto into one of three supercategories--namely, controlling, autonomy supportive, and neutral. The degree of mothers' controllingness was calculated as the percentage of vocalizations coded as controlling. This index was correlated with the intrinsic motivation of their 6- or 7-year-old children, as assessed primarily by the free-choice behavioral measure and secondarily by a child self-report measure of interest and liking for the task. Both correlations were significantly negative, thereby suggesting that the robust laboratory findings of a negative relation between controlling contexts and individuals' intrinsic motivation are directly generalizable to the domain of parenting. Results are discussed in terms of the processes that undermine intrinsic motivation and the means through which parental controllingness is communicated.

Pure tone audiograms from hearing-impaired children. II. Predicting speech-hearing from the audiogram

Pure tone audiograms and speech audiograms using sentence lists were obtained from 150 8-16-year-old children with pure tone hearing losses ranging from mild to severe. Most of the hearing impairments were cochlear in origin. Three 'speech-hearing' measures were selected from the speech audiograms, and it was shown that the correlation coefficients between two of these and the pure tone hearing thresholds were roughly in agreement with figures from previous studies of adults = 0.882 for Speech Reception Threshold and 0.533 for Discrimination Score. In addition, a correlation of 0.329 was found between the slope of the speech audiogram and pure tone thresholds. The strength of different summaries of the pure tone audiogram for predicting the various speech-hearing measures were compared. It was found that although the traditional summaries did quite well, their relative strengths varied according to the speech-hearing measure under consideration. The best summary predictors for all the speech-hearing measures were, either alone or in combination, two indices which have been proposed recently by the present authors, and which measure both the degree of pure tone hearing loss and the slope of the pure tone audiogram. However, the gains in predictive strength achieved with these indices were small.

Pure tone audiograms from hearing-impaired children. I. A statistical approach to summarizing audiogram information

Principal component analyses of the better-ear pure-tone audiograms from 201 hearing-impaired children are reported. The analyses show that two components, one measuring degree of hearing loss, the other the slope of the audiogram, account for 86% of the total variability. Two indices are proposed which correspond to the two components, but which have numerically simple coefficients and which, unlike the raw components, are perfectly "clean" measures of the two variables. Since these indices, 11 and 12, still account for 84% of the total audiogram variability, it is suggested that they may provide a quantitative basis for summarizing pure tone audiograms for general use.