Towards the simplification of MHC typing protocols: targeting classical MHC class II genes in a passerine, the pied flycatcher Ficedula hypoleuca

<p>Abstract</p> <p>Background</p> <p>Major Histocompatibility Complex (MHC) has drawn the attention of evolutionary biologists due to its importance in crucial biological processes, such as sexual selection and immune response in jawed vertebrates. However, the characterization of classical MHC genes subjected to the effects of natural selection still remains elusive in many vertebrate groups. Here, we have tested the suitability of flanking intron sequences to guide the selective exploration of classical MHC genes driving the co-evolutionary dynamics between pathogens and their passerine (Aves, Order Passeriformes) hosts.</p> <p>Findings</p> <p>Intronic sequences flanking the usually polymorphic exon 2 were isolated from different species using primers sitting on conserved coding regions of MHC class II genes (β chain). Taking the pied flycatcher <it>Ficedula hypoleuca</it> as an example, we demonstrate that careful primer design can evade non-classical MHC gene and pseudogene amplification. At least four polymorphic and expressed loci were co-replicated using a single pair of primers in five non-related individuals (N = 28 alleles). The cross-amplification and preliminary inspection of similar MHC fragments in eight unrelated songbird taxa suggests that similar approaches can also be applied to other species.</p> <p>Conclusions</p> <p>Intron sequences flanking the usually polymorphic exon 2 may assist the specific investigation of classical MHC class II B genes in species characterized by extensive gene duplication and pseudogenization. Importantly, the evasion of non-classical MHC genes with a more specific function and non-functional pseudogenes may accelerate data collection and diminish lab costs. Comprehensive knowledge of gene structure, polymorphism and expression profiles may be useful not only for the selective examination of evolutionarily relevant genes but also to restrict chimera formation by minimizing the number of co-amplifying loci.</p

Clinical and immunological evaluation of patients with metastatic melanoma undergoing immunization with the HLA- Cw*0702-associated epitope MAGE-A12 : 170-178

Patients with metastatic melanoma who expressed HLA-Cw*0702 and whose tumors had demonstrable MAGE-A12 expression were immunized with the peptide MAGE-A12: 170-178 administered subcutaneously in incomplete Freund's adjuvant (IFA). The peptide was administered either every week or every 3 weeks for 4 cycles. Patients were evaluated for toxicity and for immunologic and clinical response to peptide immunization. Pre-treatment fine needle aspirates were obtained to document MAGE-A 12 expression for enrollment. MAGE-A12 mRNA was identified in 62% of specimens. Nine patients were selected for vaccination based on MAGE-A12 expression and the presence of HLA-Cw*0702. The immune response was monitored both by tetrameric HLA-Cw*0702/MAGE-A12:170-178 complexes and by analysis of interferon-gamma mRNA transcription using a quantitative real-time polymerase chain reaction assay after peptide-specific stimulation. The samples consisted of circulating lymphocytes analyzed ex vivo or after 10 to 14 days of in vitro sensitization. One of 9 patients sustained an ongoing partial clinical response. No convincing evidence of enhancement of the systemic immune response against MAGE-A 12: 170-178 could be documented. Because of the modest immunological and clinical results, the present protocol has been discontinued as new routes of administration are being considere

Sampling strategies for accurate computational inferences of gametic phase across highly polymorphic major histocompatibility complex loci

<p>Abstract</p> <p>Background</p> <p>Genes of the Major Histocompatibility Complex (MHC) are very popular genetic markers among evolutionary biologists because of their potential role in pathogen confrontation and sexual selection. However, MHC genotyping still remains challenging and time-consuming in spite of substantial methodological advances. Although computational haplotype inference has brought into focus interesting alternatives, high heterozygosity, extensive genetic variation and population admixture are known to cause inaccuracies. We have investigated the role of sample size, genetic polymorphism and genetic structuring on the performance of the popular Bayesian PHASE algorithm. To cover this aim, we took advantage of a large database of known genotypes (using traditional laboratory-based techniques) at single MHC class I (N = 56 individuals and 50 alleles) and MHC class II B (N = 103 individuals and 62 alleles) loci in the lesser kestrel <it>Falco naumanni</it>.</p> <p>Findings</p> <p>Analyses carried out over real MHC genotypes showed that the accuracy of gametic phase reconstruction improved with sample size as a result of the reduction in the allele to individual ratio. We then simulated different data sets introducing variations in this parameter to define an optimal ratio.</p> <p>Conclusions</p> <p>Our results demonstrate a critical influence of the allele to individual ratio on PHASE performance. We found that a minimum allele to individual ratio (1:2) yielded 100% accuracy for both MHC loci. Sampling effort is therefore a crucial step to obtain reliable MHC haplotype reconstructions and must be accomplished accordingly to the degree of MHC polymorphism. We expect our findings provide a foothold into the design of straightforward and cost-effective genotyping strategies of those MHC loci from which locus-specific primers are available.</p