Meta-analyses identify 13 loci associated with age at menopause and highlight DNA repair and immune pathways

To newly identify loci for age at natural menopause, we carried out a meta-analysis of 22 genome-wide association studies (GWAS) in 38,968 women of European descent, with replication in up to 14,435 women. In addition to four known loci, we identified 13 loci newly associated with age at natural menopause (at P < 5 × 10(-8)). Candidate genes located at these newly associated loci include genes implicated in DNA repair (EXO1, HELQ, UIMC1, FAM175A, FANCI, TLK1, POLG and PRIM1) and immune function (IL11, NLRP11 and PRRC2A (also known as BAT2)). Gene-set enrichment pathway analyses using the full GWAS data set identified exoDNase, NF-κB signaling and mitochondrial dysfunction as biological processes related to timing of menopause.

Meta-analysis of genome-wide association studies in >80 000 subjects identifies multiple loci for C-reactive protein levels

BACKGROUND

C-reactive protein (CRP) is a heritable marker of chronic inflammation that is strongly associated with cardiovascular disease. We sought to identify genetic variants that are associated with CRP levels.

METHODS AND RESULTS

We performed a genome-wide association analysis of CRP in 66 185 participants from 15 population-based studies. We sought replication for the genome-wide significant and suggestive loci in a replication panel comprising 16 540 individuals from 10 independent studies. We found 18 genome-wide significant loci, and we provided evidence of replication for 8 of them. Our results confirm 7 previously known loci and introduce 11 novel loci that are implicated in pathways related to the metabolic syndrome (APOC1, HNF1A, LEPR, GCKR, HNF4A, and PTPN2) or the immune system (CRP, IL6R, NLRP3, IL1F10, and IRF1) or that reside in regions previously not known to play a role in chronic inflammation (PPP1R3B, SALL1, PABPC4, ASCL1, RORA, and BCL7B). We found a significant interaction of body mass index with LEPR (P<2.9×10(-6)). A weighted genetic risk score that was developed to summarize the effect of risk alleles was strongly associated with CRP levels and explained ≈5% of the trait variance; however, there was no evidence for these genetic variants explaining the association of CRP with coronary heart disease.

CONCLUSIONS

We identified 18 loci that were associated with CRP levels. Our study highlights immune response and metabolic regulatory pathways involved in the regulation of chronic inflammation.

Abstract 3142: Abnormal expression of the ALK protein in ovarian carcinoma is associated with low copy number amplification of the 2p23 locus

Anaplastic lymphoma kinase (ALK) is predominantly expressed in the brain and spinal cord during neonatal development and is subsequently down-regulated in the adult. In cancer, ALK is ectopically expressed as a consequence of one of several different cytogenetic translocations or inversions that lead to the expression of an oligomerized, constitutively active, intracellular tyrosine kinase. The resulting fusion protein has been identified in anaplastic large cell lymphomas, non small cell lung carcinomas and more recently breast and colorectal carcinomas. Preclinical data convincingly demonstrates that fusion transcripts can drive tumorigenesis and inhibition of ALK in vitro and in vivo leads to inhibition of cellular growth. Full length (fl) ALK is also expressed in a variety of other tumor types, and recent data suggest that at least in neuroblastoma, the flALK transcript contains activating point mutations in the tyrosine kinase domain. These data suggest that flALK may also be a therapeutic target in cancer. Here we demonstrate that a significant subset of ovarian carcinoma cell lines and biopsy specimens aberrantly express ALK. Gene expression analysis in 126 ovarian carcinoma samples demonstrated a prevalence of ALK expression of 19%. Analysis of the histological subtypes within this study, showed specific enrichment of ALK transcript in papillary ovarian carcinoma (15 of 42 samples). This subtype showed a range of ALK expression between 2 - 4 fold increase above normal ovarian tissue. We have also confirmed that in a subset of ovarian tumor cell lines and primary tumor samples that ALK transcript is converted into ALK protein. DNA sequence analysis has revealed that in these patient samples and cell lines, ALK is predominantly wild type. Single nucleotide polymorphism (SNP) analysis and fluorescent in situ hybridization (FISH) suggest that over expression may occur as a consequence of low copy number amplification. These preliminary findings suggest that ALK expression in cancer has now been observed in ovarian carcinomas by a mechanism distinct from cytogenetic translocations or inversions. Currently, we are attempting to correlate the aberrant expression of ALK with ovarian cancer prognosis as well as understand the value of inhibiting ALK expression in this cell type.

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 3142.

Abstract 2153: Copy number variants in histologically normal breast epithelium from reduction mammoplasty controls and breast cancer cases

Whole genome arrays have been used to study DNA aberrations in a wide variety of samples. The genetics of breast cancer has been intensely studied using multiple techniques including whole genome SNP genotyping. Research using genotyping data to study copy number variants (CNVs) has been limited by suboptimal algorithms for segmentation. Recently, a new algorithm has been developed that is easy to use and highly adaptive to individual data sets. Since genomic changes are now appreciated prior to the appearance of malignancy - even in histologically normal epithelium - it was our aim to apply this algorithm and test whether CNVs differ between histologically normal ducts from reduction mammoplasty controls (RM) and histologically normal ducts from breast cancer cases (HN).

Using data imported from Illumina's Human 610-quad beadchip, CNV segmentation and copy number status was calculated using the OmicSoft algorithm. This algorithm utilizes three types of information, the Log2Ratio, B-Allele Frequency and the genotype calls. Segmentation criteria were optimized and then validated on 4 well-characterized breast cancer cell lines (MCF7, MDA-MB-231, T47D, BT474) and these data were compared to publically available Affymetrix SNP6 chip data. The validated segmentation method was then applied to data obtained with the Illumina beadchip from 19 snap-frozen human breast epithelial samples. Ducts from 8 RM (mean age 47y) and 11 HN (mean age 54y) samples from untreated ER+ cancers were identified by a pathologist and captured via laser microdissection. Samples were anonymous and obtained through an IRB approved protocol.

Data from the cell lines were analyzed using OmicSoft's Array Studio. There was good concordance with the publically available data, although the Illumina-generated data had fewer segments. This may be because there are more SNP/CNV markers on the Affy SNP6.0 chip and thus higher resolution. Using the optimized segmentation criteria, small CNVs were detected in all RM and HN samples. In the 8 RM cases, there was an average of 39 segments and 5-12 CNVs per case. The 11 HN cases had an average of 37 segments and 4-12 CNVs per case. The CNVs were small sized (35-400KB) and were more often losses than gains, with approximately 75% and 85% of the CNVs representing losses in RMs and HNs respectively. The gains were low level amplifications with copy number of 3N. The most common loss was on chromosome 3q (97KB), found in 2/8 (25%) RMs and 6/11 (55%) HNs (p=0.18) and had no association with self-identified ethnicity.

OmicSoft's algorithm for segmentation was easy to use and is ideal for CNV analysis because it can be modified to provide optimal segmentation for specific data sets. Small CNVs are detected commonly in histologically normal breast epithelium, but substantial differences in CNVs are not present between RM and HN samples. These changes must occur later in tumor development.

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 2153.

Abstract B45: Epigenetic signature of human breast cancer subtypes

Gene expression profiling has been used to extend classification of human breast cancers into five main sub-types having distinct clinical outcomes. The established prognostic markers ER, PR and HER-2 remain prominent components of this refined scheme that delineates luminal (luminal A, luminal B and HER-2) from non-luminal (basal/BRCA1 mutant and normal-like) breast cancers. Gene expression combined with immunohistochemical localization of various tumor markers in the normal mammary gland support the hypothesis that luminal and non-luminal breast tumors originate from different cell types. In the current study we explore epigenetic determinants of the different breast cancer sub-types using the genome-wide DNA methylation patterns (Illumina Infinium) of fifty human breast cancer cell lines. Principal component analysis of baseline gene expression profiles (Agilent) showed a clear separation between the luminal and non-luminal sub-types in agreement with previously published studies using a largely overlapping panel of breast cell lines. Comparative marker selection analysis using the GenePattern analysis package was then performed independently on the DNA methylation and gene expression datasets. When the results of these two analyses were compared, a statistically significant reciprocal overlap of the selected markers was observed. These results strongly suggest that a large fraction of the most robust luminal gene expression classifiers are silenced by promoter methylation in non-luminal cells, and conversely that many of the best non-luminal classifiers are silenced in luminal cells. The classifier genes indentified in the breast cancer cell line panel include the most highly referenced luminal (KRT8, ESR1, AR, TFF1, TFF3, TOB1 and XBP-1) and non-luminal markers (DSC3, VIM, SFRP1, KRT5, KRT16, KRT17, and RUNX3 that have been used to classify primary breast cancers. These striking differences in DNA methylation patterns strengthen the hypotheses that luminal and non-luminal sub-types arise from different precursor cells and that their transcriptional programs may be largely established during the process of cell specification in the mammary epithelial bi-layer. Since CpG island methylation is stable and robustly preserved in archival tissues, it is likely that a methylation signature comprised of a few key genes could be used to, for example, identify poor-prognosis, basal-type breast cancers. It is also possible that such a test would be more quantitative, accurate and reproducible than the “triple-negative” diagnosis currently based on the absence of immumohistochemical staining for ER, PR and HER-2.

Citation Information: Cancer Res 2009;69(23 Suppl):B45.

Microelectromechanical system assembled ion optics: An advance to miniaturization and assembly of electron and ion optics

Deep-reactive ion etching of n-doped silicon-on-insulator is utilized to make ion optical components to aid in the miniaturization of mass analyzers. The microelectromechanical system components are bound to aluminum nitride substrates and employed three-dimensional assembly. The assembly methods are tested for breakdown (V(b)), durability, and alignment. Demonstration of ion manipulation is shown with a 1 mm Bradbury-Nielsen gate, 500 mum Einzel lens, 500 mum coaxial ring ion trap, and reflectron optics. Data are presented showing the resolution, attenuation, and performance of each of these devices. We demonstrate advantages and disadvantages of this technology and its applications to mass analysis.

Liver histology of Asian patients with chronic hepatitis B on prolonged lamivudine therapy

BACKGROUND

Long-term effect of YMDD mutations on liver histology in Chinese hepatitis B patients is unknown.

AIM

To examine the effect of prolonged lamivudine treatment on liver histology in Chinese patients with and without YMDD mutations.

METHODS

Liver histology was assessed in 85 patients on long-term lamivudine at baseline and year 1, and at year 3 for 25 patients.

RESULTS

Comparing patients with and without YMDD mutations at year 1, the former had higher baseline median necroinflammatory (11 vs. six respectively, P = 0.014) and fibrosis scores (three vs. one respectively, P = 0.001). The proportion of patients with improvement in necroinflammation and worsening of fibrosis was comparable for patients with and without YMDD mutations at year 1 (57.1%, 14.3% vs. 55%, 15% respectively) and year 3 (57.9%, 26.3% vs. 50%, 16.7% respectively). Comparing the histology at year 1 and 3, more patients with YMDD mutations developing after year 1 had worsening of necroinflammation than patients with persistent YMDD wild type (53.8% vs. 25% respectively).

CONCLUSIONS

Patients who developed YMDD mutations had higher baseline histological scores. With YMDD mutations, the liver histology became less favourable after 3 years than at the first year, although there was still improvement when compared with that at baseline.

Progression into the first meiotic division is sensitive to histone H2A-H2B dimer concentration in Saccharomyces cerevisiae

The yeast Saccharomyces cerevisiae contains two genes for histone H2A and two for histone H2B located in two divergently transcribed gene pairs: HTA1-HTB1 and HTA2-HTB2. Diploid strains lacking HTA1-HTB1 (hta1-htb1 delta/hta1-htb1 delta, HTA2-HTB2/HTA2-HTB2) grow vegetatively, but will not sporulate. This sporulation phenotype results from a partial depletion of H2A-H2B dimers. Since the expression patterns of HTA1-HTB1 and HTA2-HTB2 are similar in mitosis and meiosis, the sporulation pathway is therefore more sensitive than the mitotic cycle to depletion of H2A-H2B dimers. After completing premeiotic DNA replication, commitment to meiotic recombination, and chiasma resolution, the hta1-htb1 delta/hta1-htb1 delta, HTA2-HTB2/HTA2-HTB2 mutant arrests before the first meiotic division. The arrest is not due to any obvious disruptions in spindle pole bodies or microtubules. The meiotic block is not bypassed in backgrounds homozygous for spo13, rad50 delta, or rad9 delta mutations, but is bypassed in the presence of hydroxyurea, a drug known to inhibit DNA chain elongation. We hypothesize that the deposition of H2A-H2B dimers in the mutant is unable to keep pace with the replication fork, thereby leading to a disruption in chromosome structure that interferes with the meiotic divisions.

Accommodation of time delay variations in automatic infusion of sodium nitroprusside

A new self-tuning regulator for control of mean arterial blood pressure using sodium nitroprusside is presented. In addition to adapting to various patient response gains and time constants, the controller can accommodate variations in pure time delays, a problem that has not been addressed fully in previously proposed controllers. The control algorithm derivation is based on incorporating a self-tuning controller with an adaptive discrete time delay compensator. The derivation, however, is general and can potentially be applied to other pharmacological agents in addition to sodium nitroprusside. The a priori information required for implementation of the controller is the estimate of the order of the patient response transfer function and the range of the pure time delay. An attractive feature of the controller is its capability to optimize the level of the infused drug during the transient phase of the control without creating an output offset. This feature tends to reduce the overall level of the infused drug. Hence, it may be useful when the cost of a drug or its long-term administration side effects is of concern, such as in the case of sodium nitroprusside.

Two- and three-dimensional image reconstructions from stained and autoradiographed histological sections

A complete system has been developed to utilize histological serial sections for two- and three-dimensional image reconstructions. Eighty to 120 sections are digitized using a personal computing system augmented with a imaging board and CCD camera. The image files are transmitted to a VAX computer for processing and image reconstruction, and the processed images are transmitted back to the personal computer for display and recording using a film recorder or PostScript printer. The software developed for the system allows serial sections to be placed into proper registration in a 256(3) array, 256 grey levels. Autoradiographs of the sections are obtained in the presence of appropriate standards which are used to recalibrate grey levels to represent linearly the radioactivity of each pixel in the sections and scale the values to allow maximum use of the grey scale. Starting from coronally sectioned material the system has been used to analyse and reconstruct rat nasal turbinates. In two dimensions horizontal and sagittal sections have been obtained while in three dimensions back-to-front and surface-rendered images have been constructed. Useful rendering of differential metabolic activity within an organ of complex geometry has been obtained, and there appears to be no reason why the system cannot be used for any material for which serial sectioning is appropriate.

Venous admixture effect during one-lung anaesthesia

The venous admixture was measured before, during, and after deflation of one lung during anaesthesia for thoracotomy in 10 subjects ventilated with 50% oxygen. The mean oxygen saturation fell from 99% before deflation of the lung to 89% after 30 minutes’ atelectasis. The pH and carbon dioxide tension did not change significantly. The shunt was 38% of cardiac output five minutes after and 41% 30 minutes after deflation. The reciprocal of the arterial venous oxygen content difference correlated positively with the shunt, suggesting that increased venous admixture is accompanied by increased cardiac output.