Copy number variation in patients with disorders of sex development due to 46,XY gonadal dysgenesis

Disorders of sex development (DSD), ranging in severity from mild genital abnormalities to complete sex reversal, represent a major concern for patients and their families. DSD are often due to disruption of the genetic programs that regulate gonad development. Although some genes have been identified in these developmental pathways, the causative mutations have not been identified in more than 50% 46,XY DSD cases. We used the Affymetrix Genome-Wide Human SNP Array 6.0 to analyse copy number variation in 23 individuals with unexplained 46,XY DSD due to gonadal dysgenesis (GD). Here we describe three discrete changes in copy number that are the likely cause of the GD. Firstly, we identified a large duplication on the X chromosome that included DAX1 (NR0B1). Secondly, we identified a rearrangement that appears to affect a novel gonad-specific regulatory region in a known testis gene, SOX9. Surprisingly this patient lacked any signs of campomelic dysplasia, suggesting that the deletion affected expression of SOX9 only in the gonad. Functional analysis of potential SRY binding sites within this deleted region identified five putative enhancers, suggesting that sequences additional to the known SRY-binding TES enhancer influence human testis-specific SOX9 expression. Thirdly, we identified a small deletion immediately downstream of GATA4, supporting a role for GATA4 in gonad development in humans. These CNV analyses give new insights into the pathways involved in human gonad development and dysfunction, and suggest that rearrangements of non-coding sequences disturbing gene regulation may account for significant proportion of DSD cases.

Conference Scene: Lessons learned from the 5th Statistical Analysis Workshop of the Pharmacogenetics Research Network

The Pharmacogenomics Research Network holds a statistical analysis workshop every other year to share novel statistical methods and study designs for pharmacogenomics research, as well as insightful analyses of substantive ongoing studies. The 5th workshop was held 15 April 2009, in Rochester (MN, USA), in conjunction with the general Pharmacogenomics Research Network meeting. This summary of the ten contributed talks highlights a variety of timely topics, including identification of functional variants, how to maximize power using various study designs, and pathway analysis approaches. We also discuss the keynote invited presentation by Terry Speed, which provided an overview of statistical issues with next-generation sequence data with an emphasis on some statistical challenges in mRNA sequence data. Novel applications of Poisson regression models demonstrated innovative, yet practical, approaches to distinguish between biological and technical sources of variation in the counts of mRNA transcript reads. Overall, the workshop emphasized the need for diverse approaches to conducting pharmacogenomics studies, as well as the evolving nature of the field.

Genomic profiling and expression studies reveal both positive and negative activities for the Drosophila Myb MuvB/dREAM complex in proliferating cells

Myb-MuvB (MMB)/dREAM is a nine-subunit complex first described in Drosophila as a repressor of transcription, dependent on E2F2 and the RBFs. Myb, an integral member of MMB, curiously plays no role in the silencing of the test genes previously analyzed. Moreover, Myb plays an activating role in DNA replication in Drosophila egg chamber follicle cells. The essential functions for Myb are executed as part of MMB. This duality of function lead to the hypothesis that MMB, which contains both known activator and repressor proteins, might function as part of a switching mechanism that is dependent on DNA sites and developmental context. Here, we used proliferating Drosophila Kc tissue culture cells to explore both the network of genes regulated by MMB (employing RNA interference and microarray expression analysis) and the genomic locations of MMB following chromatin immunoprecipitation (ChIP) and tiling array analysis. MMB occupied 3538 chromosomal sites and was promoter-proximal to 32% of Drosophila genes. MMB contains multiple DNA-binding factors, and the data highlighted the combinatorial way by which the complex was targeted and utilized for regulation. Interestingly, only a subset of chromatin-bound complexes repressed genes normally expressed in a wide range of developmental pathways. At many of these sites, E2F2 was critical for repression, whereas at other nonoverlapping sites, Myb was critical for repression. We also found sites where MMB was a positive regulator of transcript levels that included genes required for mitotic functions (G2/M), which may explain some of the chromosome instability phenotypes attributed to loss of Myb function in myb mutants.

Investigating tamoxifen resistance in the luminal B estrogen receptor positive breast cancer subtype: Tailoring treatment in hormone responsive breast cancer

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Background: We recently reported that the two estrogen receptor (ER) positive breast cancer (BC) molecular subtypes can be defined by their expression of proliferation genes using a gene expression index (GGI): the luminal A and B subtypes have low and high levels respectively (J Clin Onc, in press). When treated with adjuvant tamoxifen, luminal A tumors have a good prognosis, however the clinical outcome of the luminal B subtype was poor. This study aimed to explain the biological basis for these observations using global gene expression profiling and an in vitro model of ER+ BC. Methods: 246 ER+ BC samples from women treated with adjuvant tamoxifen monotherapy were analyzed with affymetrix gene expression arrays and evaluated using gene set enrichment analysis (GSEA). ER+ MCF-7 BC cells (control) treated with tamoxifen (TAM) and heregulin (HRG) were used to investigate molecular pathways identified using GSEA. Results: We found that a gene set suggesting ERBB2 pathway activation was significantly enriched in the luminal B subtype (p=0.02). Only 10% of samples overexpressed HER2 by immunohistochemistry, suggesting that activation of HER2 signaling pathways is independent of HER2 overexpression and may contribute to TAM resistance in this subtype. To validate this hypothesis, MCF-7 cell-lines were treated with HRG (HRG-MCF7) to create a model of ERBB2 pathway activation. HRG-MCF7 cells displayed phosphorylation of HER2/3 without HER2 overexpression. Treatment with HRG overcame TAM induced cell cycle arrest with higher S-phase fraction (p<0.01) and increased anchorage- independent colony formation (p<0.01). Gene expression profiling confirmed significant enrichment of the ERBB2 gene set (p<0.01) and higher GGI levels (p=0.02) in HRG-MCF7 cells compared with control. Conclusions: HRG-MCF7 cells may be useful as an in vitro model of the TAM resistant luminal B subtype. In this group, targeting activated HER2 signaling may be a helpful treatment strategy despite the lack of HER2 overexpression. Our data suggests that agents like lapatinib may be effective only in the luminal B and not the luminal A tumors, demonstrating the importance of stratifying by subtype in future clinical trials of ER+ disease.

No significant financial relationships to disclose.

A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes

Recent studies suggest that thousands of genes may contribute to breast cancer pathophysiologies when deregulated by genomic or epigenomic events. Here, we describe a model "system" to appraise the functional contributions of these genes to breast cancer subsets. In general, the recurrent genomic and transcriptional characteristics of 51 breast cancer cell lines mirror those of 145 primary breast tumors, although some significant differences are documented. The cell lines that comprise the system also exhibit the substantial genomic, transcriptional, and biological heterogeneity found in primary tumors. We show, using Trastuzumab (Herceptin) monotherapy as an example, that the system can be used to identify molecular features that predict or indicate response to targeted therapies or other physiological perturbations.

Mitochondrial-related gene expression changes are sensitive to agonal-pH state: implications for brain disorders

Mitochondrial defects in gene expression have been implicated in the pathophysiology of bipolar disorder and schizophrenia. We have now contrasted control brains with low pH versus high pH and showed that 28% of genes in mitochondrial-related pathways meet criteria for differential expression. A majority of genes in the mitochondrial, chaperone and proteasome pathways of nuclear DNA-encoded gene expression were decreased with decreased brain pH, whereas a majority of genes in the apoptotic and reactive oxygen stress pathways showed an increased gene expression with a decreased brain pH. There was a significant increase in mitochondrial DNA copy number and mitochondrial DNA gene expression with increased agonal duration. To minimize effects of agonal-pH state on mood disorder comparisons, two classic approaches were used, removing all subjects with low pH and agonal factors from analysis, or grouping low and high pH as a separate variable. Three groups of potential candidate genes emerged that may be mood disorder related: (a) genes that showed no sensitivity to pH but were differentially expressed in bipolar disorder or major depressive disorder; (b) genes that were altered by agonal-pH in one direction but altered in mood disorder in the opposite direction to agonal-pH and (c) genes with agonal-pH sensitivity that displayed the same direction of changes in mood disorder. Genes from these categories such as NR4A1 and HSPA2 were confirmed with Q-PCR. The interpretation of postmortem brain studies involving broad mitochondrial gene expression and related pathway alterations must be monitored against the strong effect of agonal-pH state. Genes with the least sensitivity to agonal-pH could present a starting point for candidate gene search in neuropsychiatric disorders.

Colon cancer prognosis prediction by gene expression profiling

This study assessed the possibility to build a prognosis predictor, based on microarray gene expression measures, in stage II and III colon cancer patients. Tumour (T) and non-neoplastic mucosa (NM) mRNA samples from 18 patients (nine with a recurrence, nine with no recurrence) were profiled using the Affymetrix HGU133A GeneChip. The k-nearest neighbour method was used for prognosis prediction using T and NM gene expression measures. Six-fold cross-validation was applied to select the number of neighbours and the number of informative genes to include in the predictors. Based on this information, one T-based and one NM-based predictor were proposed and their accuracies were estimated by double cross-validation. In six-fold cross-validation, the lowest numbers of informative genes giving the lowest numbers of false predictions (two out of 18) were 30 and 70 with the T and NM gene expression measures, respectively. A 30-gene T-based predictor and a 70-gene NM-based predictor were then built, with estimated accuracies of 78 and 83%, respectively. This study suggests that one can build an accurate prognosis predictor for stage II and III colon cancer patients, based on gene expression measures, and one can use either tumour or non-neoplastic mucosa for this purpose.

Rooting a phylogenetic tree with nonreversible substitution models

BACKGROUND

We compared two methods of rooting a phylogenetic tree: the stationary and the nonstationary substitution processes. These methods do not require an outgroup.

METHODS

Given a multiple alignment and an unrooted tree, the maximum likelihood estimates of branch lengths and substitution parameters for each associated rooted tree are found; rooted trees are compared using their likelihood values. Site variation in substitution rates is handled by assigning sites into several classes before the analysis.

RESULTS

In three test datasets where the trees are small and the roots are assumed known, the nonstationary process gets the correct estimate significantly more often, and fits data much better, than the stationary process. Both processes give biologically plausible root placements in a set of nine primate mitochondrial DNA sequences.

CONCLUSIONS

The nonstationary process is simple to use and is much better than the stationary process at inferring the root. It could be useful for situations where an outgroup is unavailable.

Normalization of cDNA microarray data

Normalization means to adjust microarray data for effects which arise from variation in the technology rather than from biological differences between the RNA samples or between the printed probes. This paper describes normalization methods based on the fact that dye balance typically varies with spot intensity and with spatial position on the array. Print-tip loess normalization provides a well-tested general purpose normalization method which has given good results on a wide range of arrays. The method may be refined by using quality weights for individual spots. The method is best combined with diagnostic plots of the data which display the spatial and intensity trends. When diagnostic plots show that biases still remain in the data after normalization, further normalization steps such as plate-order normalization or scale-normalization between the arrays may be undertaken. Composite normalization may be used when control spots are available which are known to be not differentially expressed. Variations on loess normalization include global loess normalization and two-dimensional normalization. Detailed commands are given to implement the normalization techniques using freely available software.

Genes for glycosylphosphatidylinositol toxin biosynthesis in Plasmodium falciparum

About 2.5 million people die of Plasmodium falciparum malaria every year. Fatalities are associated with systemic and organ-specific inflammation initiated by a parasite toxin. Recent studies show that glycosylphosphatidylinositol (GPI) functions as the dominant parasite toxin in the context of infection. GPIs also serve as membrane anchors for several of the most important surface antigens of parasite invasive stages. GPI anchoring is a complex posttranslational modification produced through the coordinated action of a multicomponent biosynthetic pathway. Here we present eight new genes of P. falciparum selected for encoding homologs of proteins essential for GPI synthesis: PIG-A, PIG-B, PIG-M, PIG-O, GPI1, GPI8, GAA-1, and DPM1. We describe the experimentally verified mRNA and predicted amino acid sequences and in situ localization of the gene products to the parasite endoplasmic reticulum. Moreover, we show preliminary evidence for the PIG-L and PIG-C genes. The biosynthetic pathway of the malaria parasite GPI offers potential targets for drug development and may be useful for studying parasite cell biology and the molecular basis for the pathophysiology of parasitic diseases.

An HMM model for coiled-coil domains and a comparison with PSSM-based predictions

MOTIVATION

Large-scale sequence data require methods for the automated annotation of protein domains. Many of the predictive methods are based either on a Position Specific Scoring Matrix (PSSM) of fixed length or on a window-less Hidden Markov Model (HMM). The performance of the two approaches is tested for Coiled-Coil Domains (CCDs). The prediction of CCDs is used frequently, and its optimization seems worthwhile.

RESULTS

We have conceived MARCOIL, an HMM for the recognition of proteins with a CCD on a genomic scale. A cross-validated study suggests that MARCOIL improves predictions compared to the traditional PSSM algorithm, especially for some protein families and for short CCDs. The study was designed to reveal differences inherent in the two methods. Potential confounding factors such as differences in the dimension of parameter space and in the parameter values were avoided by using the same amino acid propensities and by keeping the transition probabilities of the HMM constant during cross-validation.

AVAILABILTY

The prediction program and the databases are available at http://www.wehi.edu.au/bioweb/Mauro/Marcoil

Identification of proteins from Plasmodium falciparum that are homologous to reticulocyte binding proteins in Plasmodium vivax

Plasmodium falciparum infections can be fatal, while P. vivax infections usually are not. A possible factor involved in the greater virulence of P. falciparum is that this parasite grows in red blood cells (RBCs) of all maturities whereas P. vivax is restricted to growth in reticulocytes, which represent only approximately 1% of total RBCs in the periphery. Two proteins, expressed at the apical end of the invasive merozoite stage from P. vivax, have been implicated in the targeting of reticulocytes for invasion by this parasite. A search of the P. falciparum genome databases has identified genes that are homologous to the P. vivax rbp-1 and -2 genes. Two of these genes are virtually identical over a large region of the 5' end but are highly divergent at the 3' end. They encode high-molecular-mass proteins of >300 kDa that are expressed in late schizonts and localized to the apical end of the merozoite. To test a potential role in merozoite invasion of RBCs, we analyzed the ability of these proteins to bind to mature RBCs and reticulocytes. No binding to mature RBCs or cell preparations enriched for reticulocytes was detected. We identified a parasite clone that lacks the gene for one of these proteins, showing that the gene is not required for normal in vitro growth. Antibodies to these proteins can inhibit merozoite invasion of RBCs.

Estimation of antigen-responsive T cell frequencies in PBMC from human subjects

A new method for estimating the frequency of antigen-responsive T cells, using a cell proliferation assay, is described. In this assay, the uptake of tritiated thymidine by peripheral blood mononuclear cells which have been exposed to antigen, is measured for each well on a microtiter plate. Whereas this assay is generally used as part of a limiting dilution assay, here we estimate the frequency of responding cells using a single, carefully chosen cell density. The traditional analysis of such data uses a cut-off to separate wells which contain no responding cells and wells which contain at least one responding cell. The new method uses the scintillation count to estimate the number of responding cells for each well on the plate. We do this by fitting a two-stage model, the first stage being a Poisson model with antigen-specific frequency parameters, and the second stage a linear model with plate-specific parameters.

Comparison of nitroprusside, nitroglycerin, and deep isoflurane anesthesia for induced hypotension

Three methods of inducing hypotension were studied for their effects on the cardiovascular system and intrapulmonary shunting. Thirty patients were anesthetized with isoflurane in 70% N2O to a total of 1.25 to 1.3 MAC. Patients were divided into three groups of 10 each on the basis of the drug used to induce hypotension; sodium nitroprusside (SNP), nitroglycerin (NTG), or deep isoflurane anesthesia (ISF). Cardiac index was significantly decreased by NTG and ISF at a mean arterial blood pressure of 40 mm Hg compared to SNP (P less than 0.05). Systemic vascular resistance was decreased in all groups. Mixed venous oxygen content was significantly decreased from control in the NTG and ISF groups. There was no difference between the groups in arterial and mixed venous O2 content. Intrapulmonary shunting decreased with induction and, in the NTG and SNP groups, increased slightly but not significantly with induction of hypotension. Our data do not show a clear superiority of any agent over the other to induce hypotension, although SNP and perhaps ISF appear to be better than NTG to induce hypotension.