Timothy J. Aitman

Population genetics: Malaria susceptibility and CD36 mutation

A critical step in infection by Plasmodium falciparum, the microorganism that causes the most severe form of malaria, is the adhesion of parasitized red blood cells to capillary endothelium. The human protein CD36 is a major receptor for P. falciparum-infected red blood cells and may contribute to the disease by sequestering infected red blood cells and inhibiting the immune response to the parasite. We have found that African populations contain an exceptionally high frequency of mutations in CD36. Unexpectedly, these mutations that cause CD36 deficiency are associated with susceptibility to severe malaria, suggesting that the presence of distinct CD36 mutations in Africans and Asians is due to some selection pressure other than malaria.

Molecular screening of the human melanocortin-4 receptor gene: identification of a missense variant showing no association with obesity, plasma glucose, or insulin

Summary Disruption of the melanocortin-4 (MC-4) receptor gene in mice results in maturity-onset obesity, hyperinsulinaemia and hyperglycaemia. These phenotypes are characteristic of human obesity that frequently accompanies non-insulin-dependent diabetes. It is therefore possible that human MC-4 receptor gene mutations contribute to human obesity. To test this possibility, we examined by DNA sequencing the entire coding region of the human MC-4 receptor gene in 40 morbidly obese (BMI > 35 kg/m2) white British males and examined the 5′- and 3′-flanking regions in 20 out of these obese subjects. We also sequenced all these regions in 10 lean (BMI < 18 kg/m2) white British males for a reference. We identified a single nucleotide substitution that replaces valine with isoleucine at codon 103, in two obese subjects in the heterozygous state. No other nucleotide alterations were found. The prevalence of this missense variant was studied in 322 white British males (190 with BMI > 28 kg/m2 and 132 with BMI < 22 kg/m2) selected from a population-based epidemiological survey. In these subjects, no homozygotes for the isoleucine allele were found. The frequency of heterozygotes was similar (4.2 vs 4.5 %) in the two groups and there was no significant difference in BMI, total skinfold thickness, plasma insulin and glucose levels between heterozygotes and codon-103 valine homozygotes in either group. These results suggest that coding sequence mutations in the MC-4 receptor gene are unlikely to be a major cause of human obesity, at least in white British males. [Diabetologia (1997) 40: 976–979]

DNA microarrays in medical practice

The completion of the draft sequence of the human genome 1 2 has raised public awareness of “genomics” and of the ways in which the emerging technologies of the genomics “revolution” will have direct applications to patient care.3 DNA microarrays, or biochips, are prominent among these new technologies. The past five years have seen a dramatic rise in the use of DNA microarrays for biomedical research, in some cases with immediate applicability to clinical practice. The uses of microarrays for gene expression profiling, genotyping, mutation detection, and gene discovery are leading to remarkable insights into the function of thousands of genes previously known only by their gene sequence. This review discusses ways in which microarrays have started to affect clinical practice and research and how this role will develop in the next five to 10 years.nnThe data for this review reflect my personal views from 10 years of research in molecular medicine and five years on DNA microarrays. My views have developed over this period from discussions with colleagues in my own laboratory and at basic science and biotechnology meetings and from regular reading of Nature Genetics , Nature , Science , and other journals.nnFor the past 25 years, the standard techniques used to detect specific sequences of DNA or RNA in the laboratory have depended on the use of a DNA probe labelled with, for example, a radioactive isotope or a fluorescent tag. The probe is complementary in sequence to the fragment of DNA or RNA to be detected, and so it hybridises (or sticks) selectively, by Watson-Crick base pairing, to the correct fragment of DNA or RNA if that fragment is present in the test sample.nnThe principle of DNA microarrays is that technological advances have made it possible to miniaturise this DNA probe detection …

Molecular basis of the Cd36 chromosomal deletion underlying SHR defects in insulin action and fatty acid metabolism

Abstract. The human insulin resistance syndromes—type 2 diabetes, obesity, combined hyperlipidemia, and essential hypertension—are genetically complex disorders whose molecular basis is largely unknown. The spontaneously hypertensive rate (SHR) is a model of these human syndromes. In the SHR/NCrlBR strain, a chromosomal deletion event that occurred at the Cd36 locus during the evolution of this SHR strain has been proposed as a cause of defective insulin action and fatty acid metabolism. In this study, three copies of the Cd36 gene, one transcribed copy and two pseudogenes, were identified in normal rat strains, but only a single gene in SHR/NCrlBR. Analysis of SHR genomic sequence localized the chromosomal deletion event between intron 4 of the normally transcribed copy of the gene and intron 4 of the second pseudogene. The deletion led to the creation of a single chimeric Cd36 gene in SHR/NCrlBR. The boundaries of the recombination/deletion junction identified within intron 4 were surrounded by long interspersed nuclear elements (LINEs) and DNA topoisomerase I recognition sequences. An 8-bp deletion at the intron 14/exon 15 boundary of the second pseudogene abolishes the putative splice acceptor site and is the cause of an aberrant 3′ UTR previously observed in SHR/NCrlBR. We conclude that in SHR/NCrlBR, the complex trait of insulin resistance and defective fatty acid metabolism is caused by Cd36 deficiency, resulting from a chromosomal deletion caused by unequal recombination. This demonstrates that chromosomal deletions caused by unequal recombination can be a cause of quantitative or complex mammalian phenotypes.

Cd36, a class B scavenger receptor, functions as a monomer to bind acetylated and oxidized low-density lipoproteins

Cd36 is a small‐molecular‐weight integral membrane protein expressed in a diverse, but select, range of cell types. It has an equally diverse range of ligands and physiological functions, which has implicated Cd36 in a number of diseases including insulin resistance, diabetes, and, most notably, atherosclerosis. The protein is reported to reside in detergent‐resistant microdomains within the plasma membrane and to form homo‐ and hetero‐intermolecular interactions. These data suggest that this class B scavenger receptor may gain functionality for ligand binding, and/or ligand internalization, by formation of protein complexes at the cell surface. Here, we have overexpressed Cd36 in insect cells, purified the recombinant protein to homogeneity, and analyzed its stability and solubility in a variety of nonionic and zwitterionic detergents. Octylglucoside conferred the greatest degree of stability, and by analytical ultracentrifugation we show that the protein is monomeric. A solid‐phase ligand‐binding assay demonstrated that the purified monomeric protein retains high affinity for acetylated and oxidized low‐density lipoproteins. Therefore, no accessory proteins are required for interaction with ligand, and binding is a property of the monomeric fold of the protein. Thus, the highly purified and functional Cd36 should be suitable for crystallization in octylglucoside, and the in vitro ligand‐binding assay represents a promising screen for identification of bioactive molecules targeting atherogenesis at the level of ligand binding.

Segregation of experimental autoimmune glomerulonephritis as a complex genetic trait and exclusion of Col4a3 as a candidate gene.

Experimental autoimmune glomerulonephritis (EAG), an animal model of Goodpasture’s disease, can be induced in Wistar-Kyoto (WKY) rats (RT1-l) by immunization with rat glomerular basement membrane (GBM) in adjuvant. The model in this rat strain is characterized by anti-GBM antibody production accompanied by focal necrotizing glomerulonephritis with crescent formation. The main autoantigen in humans and rats has been identified as the non-collagenous domain of the α3 chain of type IV collagen (α3(IV)NC1). By contrast, Lewis (LEW) rats with the same MHC background (RT1-l), immunized with the same antigen, develop similar levels of circulating anti-GBM antibodies, but no histological evidence of nephritis. In order to investigate the genetic basis of susceptibility to EAG, we examined the response of both F1 (WKY × LEW) and backcross (BC1; WKY × F1) rats to immunization with rat GBM. F1 animals were completely resistant to the development of EAG, while BC1 animals showed a range of responses from severe crescentic glomerulonephritis to no histological evidence of disease. The results indicate that EAG is inherited as a complex trait under the control of WKY genes unlinked to the MHC. cDNA sequence analysis of α3(IV)NC1 in the two parental strains was identical, indicating no predicted amino acid sequence variation in the α3(IV)NC1 domain between these strains. Radiation hybrid mapping, using two separate PCR amplicons from rat α3(IV)NC1, localized rat Col4a3 to a region of chromosome 9. Since Col4a3 (encoding the autoantigen) is a candidate for susceptibility to EAG, we screened the region of rat chromosome 9 where Col4a3 is localized, using polymorphic microsatellite markers in segregating BC1 progeny. No significant linkage was detected. These results exclude Col4a3 as a recessive susceptibility gene for EAG in the BC1 progeny.

Genome-wide co-expression analysis in multiple tissues

Expression quantitative trait loci (eQTLs) represent genetic control points of gene expression, and can be categorized as cis- and trans-acting, reflecting local and distant regulation of gene expression respectively. Although there is evidence of co-regulation within clusters of trans-eQTLs, the extent of co-expression patterns and their relationship with the genotypes at eQTLs are not fully understood. We have mapped thousands of cis- and trans-eQTLs in four tissues (fat, kidney, adrenal and left ventricle) in a large panel of rat recombinant inbred (RI) strains. Here we investigate the genome-wide correlation structure in expression levels of eQTL transcripts and underlying genotypes to elucidate the nature of co-regulation within cis- and trans-eQTL datasets. Across the four tissues, we consistently found statistically significant correlations of cis-regulated gene expression to be rare (<0.9% of all pairs tested). Most (>80%) of the observed significant correlations of cis-regulated gene expression are explained by correlation of the underlying genotypes. In comparison, co-expression of trans-regulated gene expression is more common, with significant correlation ranging from 2.9%–14.9% of all pairs of trans-eQTL transcripts. We observed a total of 81 trans-eQTL clusters (hot-spots), defined as consisting of ≥10 eQTLs linked to a common region, with very high levels of correlation between trans-regulated transcripts (77.2–90.2%). Moreover, functional analysis of large trans-eQTL clusters (≥30 eQTLs) revealed significant functional enrichment among genes comprising 80% of the large clusters. The results of this genome-wide co-expression study show the effects of the eQTL genotypes on the observed patterns of correlation, and suggest that functional relatedness between genes underlying trans-eQTLs is reflected in the degree of co-expression observed in trans-eQTL clusters. Our results demonstrate the power of an integrative, systematic approach to the analysis of a large gene expression dataset to uncover underlying structure, and inform future eQTL studies.

MiMiR – an integrated platform for microarray data sharing, mining and analysis

BackgroundDespite considerable efforts within the microarray community for standardising data format, content and description, microarray technologies present major challenges in managing, sharing, analysing and re-using the large amount of data generated locally or internationally. Additionally, it is recognised that inconsistent and low quality experimental annotation in public data repositories significantly compromises the re-use of microarray data for meta-analysis. MiMiR, the Mi croarray data Mi ning R esource was designed to tackle some of these limitations and challenges. Here we present new software components and enhancements to the original infrastructure that increase accessibility, utility and opportunities for large scale mining of experimental and clinical data.ResultsA user friendly Online Annotation Tool allows researchers to submit detailed experimental information via the web at the time of data generation rather than at the time of publication. This ensures the easy access and high accuracy of meta-data collected. Experiments are programmatically built in the MiMiR database from the submitted information and details are systematically curated and further annotated by a team of trained annotators using a new Curation and Annotation Tool. Clinical information can be annotated and coded with a clinical Data Mapping Tool within an appropriate ethical framework. Users can visualise experimental annotation, assess data quality, download and share data via a web-based experiment browser called MiMiR Online. All requests to access data in MiMiR are routed through a sophisticated middleware security layer thereby allowing secure data access and sharing amongst MiMiR registered users prior to publication. Data in MiMiR can be mined and analysed using the integrated EMAAS open source analysis web portal or via export of data and meta-data into Rosetta Resolver data analysis package.ConclusionThe new MiMiR suite of software enables systematic and effective capture of extensive experimental and clinical information with the highest MIAME score, and secure data sharing prior to publication. MiMiR currently contains more than 150 experiments corresponding to over 3000 hybridisations and supports the Microarray Centres large microarray user community and two international consortia. The MiMiR flexible and scalable hardware and software architecture enables secure warehousing of thousands of datasets, including clinical studies, from microarray and potentially other -omics technologies.

EMAAS: An extensible grid-based Rich Internet Application for microarray data analysis and management

BackgroundMicroarray experimentation requires the application of complex analysis methods as well as the use of non-trivial computer technologies to manage the resultant large data sets. This, together with the proliferation of tools and techniques for microarray data analysis, makes it very challenging for a laboratory scientist to keep up-to-date with the latest developments in this field. Our aim was to develop a distributed e-support system for microarray data analysis and management.ResultsEMAAS (Extensible MicroArray Analysis System) is a multi-user rich internet application (RIA) providing simple, robust access to up-to-date resources for microarray data storage and analysis, combined with integrated tools to optimise real time user support and training. The system leverages the power of distributed computing to perform microarray analyses, and provides seamless access to resources located at various remote facilities. The EMAAS framework allows users to import microarray data from several sources to an underlying database, to pre-process, quality assess and analyse the data, to perform functional analyses, and to track data analysis steps, all through a single easy to use web portal. This interface offers distance support to users both in the form of video tutorials and via live screen feeds using the web conferencing tool EVO. A number of analysis packages, including R-Bioconductor and Affymetrix Power Tools have been integrated on the server side and are available programmatically through the Postgres-PLR library or on grid compute clusters. Integrated distributed resources include the functional annotation tool DAVID, GeneCards and the microarray data repositories GEO, CELSIUS and MiMiR. EMAAS currently supports analysis of Affymetrix 3 and Exon expression arrays, and the system is extensible to cater for other microarray and transcriptomic platforms.ConclusionEMAAS enables users to track and perform microarray data management and analysis tasks through a single easy-to-use web application. The system architecture is flexible and scalable to allow new array types, analysis algorithms and tools to be added with relative ease and to cope with large increases in data volume.

A high-resolution radiation hybrid map of the proximal region of rat Chromosome 4

Abstract. Radiation hybrid (RH) mapping has been used to produce genome maps in the human and mouse, but as yet the technique has been applied little to other species. We describe the use of RH mapping in the rat, using a newly available rat/hamster RH panel, to construct an RH map of the proximal part of rat Chromosome (Chr) 4. This region is of interest because quantitative trait loci (QTLs) for defective insulin and catecholamine action, hypertension, and dyslipidemia map to this region. The RH map includes 23 rat genes or microsatellites previously mapped to this part of Chr 4, one rat gene not previously mapped in the rat, and markers for four new genes, homologs of which map to the syntenic region of the mouse genome. The RH map integrates genetic markers previously mapped on several rat crosses, increases the resolution of existing maps, and may provide a suitable basis for physical map construction and gene identification in this chromosomal region. Our results demonstrate the utility of RH mapping in the rat genome and show that RH mapping can be used to localize, in the rat genome, the homologs of genes from other species such as the mouse. This will facilitate identification of candidate genes underlying QTLs on this chromosomal segment.