Contribution of Genome-Wide Association Studies to Scientific Research: A Pragmatic Approach to Evaluate Their Impact

The factual value of genome-wide association studies (GWAS) for the understanding of multifactorial diseases is a matter of intense debate. Practical consequences for the development of more effective therapies do not seem to be around the corner. Here we propose a pragmatic and objective evaluation of how much new biology is arising from these studies, with particular attention to the information that can help prioritize therapeutic targets. We chose multiple sclerosis (MS) as a paradigm disease and assumed that, in pre-GWAS candidate-gene studies, the knowledge behind the choice of each gene reflected the understanding of the disease prior to the advent of GWAS. Importantly, this knowledge was based mainly on non-genetic, phenotypic grounds. We performed single-gene and pathway-oriented comparisons of old and new knowledge in MS by confronting an unbiased list of candidate genes in pre-GWAS association studies with those genes exceeding the genome-wide significance threshold in GWAS published from 2007 on. At the single gene level, the majority (94 out of 125) of GWAS-discovered variants had never been contemplated as plausible candidates in pre-GWAS association studies. The 31 genes that were present in both pre- and post-GWAS lists may be of particular interest in that they represent disease-associated variants whose pathogenetic relevance is supported at the phenotypic level (i.e. the phenotypic information that steered their selection as candidate genes in pre-GWAS association studies). As such they represent attractive therapeutic targets. Interestingly, our analysis shows that some of these variants are targets of pharmacologically active compounds, including drugs that are already registered for human use. Compared with the above single-gene analysis, at the pathway level GWAS results appear more coherent with previous knowledge, reinforcing some of the current views on MS pathogenesis and related therapeutic research. This study presents a pragmatic approach that helps interpret and exploit GWAS knowledge.     

Human BF*F-subtypes: segregation analysis with inclusion of MHC haplotypes

Summary The segregation of factor B(BF)F subtypes was analyzed in conjunction with other MHC markers in 15 families with 89 offspring. Informative data for BF F subtypes were obtained from 11 families, 6 of them with known recombinant individuals for the HLA-B/DR/GLO region. The subtypes did not contribute further to the localization of the cross-overs, but followed the known segregation of conventional BF allotypes. In 2 families of one kinship, the recognition of heterozygous BF^*FAFB individuals could be established following the inclusion of three generations. The rarer of the two BF F subtype alleles, BF^*FA, is positively associated with the HLA haplotypes BW62, CW3, C4A^*3 and A29, CWX, B44, C4A^*3, B^*1, DR7. BF F subtypes are regarded as a very useful additional tool for studies of MHC organization and disease association.     

Antioxidants and antioxidative enzymes in wild-type and transgenic Lycopersicon genotypes of different chilling tolerance

The Mehler–Ascorbate–Peroxidase cycle is a protection system against reactive oxygen species (ROS) occurring during over-excitation of the photosynthetic apparatus. In the cultivated tomato, Lycopersicon esculentum, long-term chilling under moderate light leads to oxidation of the Calvin cycle key enzyme, ribulose-1,5-bisphosphate carboxylase (rubisco), presumably by generation of ROS. In contrast, high-altitude lines of the wild tomato species L. peruvianum were tolerant against the same chilling stress. In the present study, we analysed leaf contents of antioxidants (ascorbate, glutathione) and activities of enzymes of the Mehler–Ascorbate–Peroxidase cycle in the two Lycopersicon species. While antioxidant levels and activities of chloroplast superoxide dismutase (SOD) and ascorbate peroxidase (APX), both inducible by chilling stress, were similar in chilling-tolerant and chilling-sensitive genotypes, chilled L. esculentum showed lower glutathione reductase (GR) activities than high-altitude L. peruvianum. We constructed transgenic plants overexpressing an Escherichia coli GR in the chloroplast (approximately 60-fold of the wild-type (WT) activity). However, these plants resembled identical chilling sensitivity of the photosynthetic apparatus as WT plants as measured after a photoinhibition treatment and by the effect of long-term chilling on rubisco activity. We conclude that the Mehler–Ascorbate–Peroxidase cycle is not the limiting factor for the sensitivity of the photosynthetic apparatus of L. esculentum towards long-term chilling under moderate light. We suggest that a possible cause for the higher chilling tolerance of L. peruvianum is prevention of ROS formation by better conversion of light energy to photochemistry at suboptimal temperatures.     

Clytostoma callistegioides (Bignoniaceae) wax extract with activity on aphid settling

A bioassay-guided fractionation of leaf extracts from Clytostoma callistegioides (Cham.) Bureau ex Griseb. (Bignoniaceae) led to isolation of a natural mixture of four fatty acids with anti-insect activity against aphids. The compounds were identified by GC–MS as palmitic, stearic, linoleic and linolenic acids and quantified as their methyl esters. The anti-aphid activity of the natural mixture was traced to linolenic and linoleic acids, as shown by the settling inhibition activity of synthetic samples. Interestingly, the saturated acids (palmitic and stearic) tested alone stimulated settling on one of the tested aphids (Myzus persicae), but not on the other tested species (Rhopalosiphum padi). Although ubiquitous, none of these free acids have been previously reported in this Bignoniaceae species. The leaf surface chemistry, which is likely involved in modulating aphid settling behavior, was further investigated for the occurrence of lipophilic substances by histochemical staining. Short, stalked glandular trichomes, previously undescribed for this species, stained with osmium tetroxide and Sudan III, suggesting that the secretion of the defensive acids is related to these surface trichomes.