HLA DNA Sequence Variation among Human Populations: Molecular Signatures of Demographic and Selective Events

Molecular differences between HLA alleles vary up to 57 nucleotides within the peptide binding coding region of human Major Histocompatibility Complex (MHC) genes, but it is still unclear whether this variation results from a stochastic process or from selective constraints related to functional differences among HLA molecules. Although HLA alleles are generally treated as equidistant molecular units in population genetic studies, DNA sequence diversity among populations is also crucial to interpret the observed HLA polymorphism. In this study, we used a large dataset of 2,062 DNA sequences defined for the different HLA alleles to analyze nucleotide diversity of seven HLA genes in 23,500 individuals of about 200 populations spread worldwide. We first analyzed the HLA molecular structure and diversity of these populations in relation to geographic variation and we further investigated possible departures from selective neutrality through Tajima's tests and mismatch distributions. All results were compared to those obtained by classical approaches applied to HLA allele frequencies

Genome-Wide Analysis of Heteroduplex DNA in Mismatch Repair–Deficient Yeast Cells Reveals Novel Properties of Meiotic Recombination Pathways

Meiotic DNA double-strand breaks (DSBs) initiate crossover (CO) recombination, which is necessary for accurate chromosome segregation, but DSBs may also repair as non-crossovers (NCOs). Multiple recombination pathways with specific intermediates are expected to lead to COs and NCOs. We revisited the mechanisms of meiotic DSB repair and the regulation of CO formation, by conducting a genome-wide analysis of strand-transfer intermediates associated with recombination events. We performed this analysis in a SK1 × S288C Saccharomyces cerevisiae hybrid lacking the mismatch repair (MMR) protein Msh2, to allow efficient detection of heteroduplex DNAs (hDNAs). First, we observed that the anti-recombinogenic activity of MMR is responsible for a 20% drop in CO number, suggesting that in MMR–proficient cells some DSBs are repaired using the sister chromatid as a template when polymorphisms are present. Second, we observed that a large fraction of NCOs were associated with trans–hDNA tracts constrained to a single chromatid. This unexpected finding is compatible with dissolution of double Holliday junctions (dHJs) during repair, and it suggests the existence of a novel control point for CO formation at the level of the dHJ intermediate, in addition to the previously described control point before the dHJ formation step. Finally, we observed that COs are associated with complex hDNA patterns, confirming that the canonical double-strand break repair model is not sufficient to explain the formation of most COs. We propose that multiple factors contribute to the complexity of recombination intermediates. These factors include repair of nicks and double-stranded gaps, template switches between non-sister and sister chromatids, and HJ branch migration. Finally, the good correlation between the strand transfer properties observed in the absence of and in the presence of Msh2 suggests that the intermediates detected in the absence of Msh2 reflect normal intermediates

Telomeric Trans-Silencing in Drosophila melanogaster: Tissue Specificity, Development and Functional Interactions between Non-Homologous Telomeres

BACKGROUND: The study of P element repression in Drosophila melanogaster led to the discovery of the telomeric Trans-Silencing Effect (TSE), a homology-dependent repression mechanism by which a P-transgene inserted in subtelomeric heterochromatin (Telomeric Associated Sequences, "TAS") has the capacity to repress in trans, in the female germline, a homologous P-lacZ transgene located in euchromatin. TSE can show variegation in ovaries, displays a maternal effect as well as an epigenetic transmission through meiosis and involves heterochromatin and RNA silencing pathways. PRINCIPAL FINDINGS: Here, we analyze phenotypic and genetic properties of TSE. We report that TSE does not occur in the soma at the adult stage, but appears restricted to the female germline. It is detectable during development at the third instar larvae where it presents the same tissue specificity and maternal effect as in adults. Transgenes located in TAS at the telomeres of the main chromosomes can be silencers which in each case show the maternal effect. Silencers located at non-homologous telomeres functionally interact since they stimulate each other via the maternally-transmitted component. All germinally-expressed euchromatic transgenes tested, located on all major chromosomes, were found to be repressed by a telomeric silencer: thus we detected no TSE escaper. The presence of the euchromatic target transgene is not necessary to establish the maternal inheritance of TSE, responsible for its epigenetic behavior. A single telomeric silencer locus can simultaneously repress two P-lacZ targets located on different chromosomal arms. CONCLUSIONS AND SIGNIFICANCE: Therefore TSE appears to be a widespread phenomenon which can involve different telomeres and work across the genome. It can explain the P cytotype establishment by telomeric P elements in natural Drosophila populations

Etude du polymorphisme moléculaire des gènes HLA de classes I et II à l'échelle mondiale : analyse de la diversité nucléotidique dans les populations

L'axe principal de ce travail a consisté à analyser la diversité nucléotidique des gènes HLA de classes I et II dans une centaine de populations humaines réparties à l'échelle mondiale. Ces gènes sont les plus variables actuellement décrits chez l'Homme, et se sont révélés très informatifs pour étudier l'histoire du peuplement humain. Nos résultats moléculaires apportent une description beaucoup plus fine du polymorphisme de ce système génétique, notamment à une échelle régionale, que les approches envisagées jusqu'à aujourd'hui se limitant aux distributions de fréquences alléliques dans les populations. De plus, tenir compte des différences nucléotidiques entre allèles permet de mieux comprendre l'implication des mécanismes évolutifs (sélection et conversion génique) proposés comme les principaux moteurs de génération et de maintien du polymorphisme. Nous avons notamment mis en évidence de potentielles traces anciennes de sélection sur les allèles du gène HLA-DPB1, un locus supposé évoluer de manière neutre selon la littérature scientifique

Optimizing clinical outcome in allogeneic hematopoieticstem cell transplantation: pre-transplant and posttransplant immunogenetic markers

Allogeneic hematopoietic stem cell transplantation (alloHSCT) is a standard treatment for hematological disorders like acute leukemia and primary immune deficiencies. Various parameters at the pre, peri and post-transplant stages have been shown to significantly influence clinical outcome and patient’s prognosis. In this thesis submitted to the University of Geneva for the degree of Privat-Docent, several of the latest advances in transplantation immunology, histocompatibility and immunogenetics are examined by integrating five of my recent studies to a review of the scientific literature on this thematic. Two main aspects are discussed more specifically. At the pre-transplant stage, the importance of optimal genetic compatibility between donor and patient and the development of integrative donor selection algorithms that allow to better predict post-transplant risks are discussed through the lens of the HLA-DPB1 paradigm. Different contributions and models to adjust and fine-tune the degree of HLA matching, such as the concept of permissive mismatches, are presented, including a perspective on the availability of new therapeutic protocols and alloHSCT platforms. Indeed, the increasing choice among different types of donors means that almost every patient can now benefit from a suitable donor. However, several questions remain open and are revisited regularly with the publication of new data and results. For instance, what is the best option to consider when several potential donors are available within and outside the patient’s family? If the current gold standards for matching are not achievable, which mismatch constellation(s) should be favored? Because the therapy is highly personalized, different approaches are not mutually exclusive and can be tailored to the patient’s needs. At the post-transplant stage, immune recovery of the patient is central to the success of this cellular therapy. Notably, the reconstitution of a broad and tolerant T-cell repertoire is required to alleviate the burden of post-transplant complications such as graft-versus-host disease and infections. The development of high throughput sequencing approaches has enabled the indepth characterization of the repertoire and has uncovered the complexity of the adaptive immune response to foreign (and self) antigens. In this context, the interest of alloHSCT as a unique model in humans to explore the dynamics and architecture of the T-cell receptor (TCR) repertoire is presented. In addition, the hurdles at characterizing and predicting the alloimmune response and the promises of translating these results to an optimized and personalized posttransplant monitoring of patients are discussed. </p

Etude moléculaire du polymorphisme HLA-Cw en Iran : Contributions à l'analyse de la variabilité génétique humaine

L'axe principal de ce travail a consisté à analyser la diversité moléculaire du gène HLA-C de classe I, dans un échantillon de 120 Iraniens non-apparentés, puis de comparer les résultats obtenus avec des données collectées dans la littérature. Les gènes HLA font partie des plus variables actuellement décrits chez l'Homme, et de nombreuses études ont révélé leur grande informativité pour l'histoire du peuplement humain. Néanmoins, le gène HLA-C a longtemps constitué une exception dans ces investigations, par le fait que la sérologie, la technique qui était habituellement employée pour détecter le polymorphisme, s'appliquait mal pour ce locus. Dans ce travail, une méthode de typage au niveau de l'ADN a été adaptée pour être appliquée à large échelle, afin de caractériser avec précision le polymorphisme de ce gène dans une population originaire d'Iran. La provenance géographique de l'échantillon a également tenu une place prépondérante dans l'orientation de cette étude. En effet, l'Iran est situé à un carrefour géographique entre l'Europe, l'Asie, et l'Afrique, dans un cadre historique propice aux migrations et aux échanges culturels, et dans une région proposée comme l'un des possibles lieux d'origine de l'émergence de l'Homme moderne (Homo sapiens sapiens)

De l'Europe à l'Inde: structure génétique et diversité des populations de part et d'autre de leurs frontières géographiques et culturelles

In this study, we compared HLA-C molecular polymorphism in 39 human populations located from Europe to the Indian subcontinent. This geographic area encompasses more or less the spoken area of the Indo-European linguistic phylum, but some Afro-asiatic and Dravidian speakers were also considered in the comparisons. Our results indicate that geography is one of the main factors acting on population differentiations in Europe. Moreover, we detect a genetic boundary following a north-east / south-west axis cutting through the Alps and the Pyrenees and which separates the western European populations from those located around the Mediterranean basin. On the other hand, we do not find any significant correlation between geography and genetics in the Middle East and the Indian subcontinent. Although geography does not play a major role in these two regions, the factors that could explain the observed genetic diversity are not the same. Indeed, the Middle Eastern populations constitute a genetically homogeneous group, which could reflect a high level of gene flow due to the numerous migrations that took place in that region throughout history. Conversely, the Indian-Pakistani populations are very heterogeneous genetically, particularly the Dravidian speakers. The differentiation of these populations seems to result from rapid genetic drift under the complex influence of social, cultural, linguistic and religious boundaries.Nos résultats nous indiquent que la géographie est l'un des facteurs déterminant les différenciations des populations situées en Europe. De plus, une frontière génétique est repérée le long d'un axe nord-est / sud-ouest à hauteur des Alpes et à travers les Pyrénées, qui met grosso modo en évidence une séparation entre les populations du pourtour méditerranéen et celle d'Europe de l'ouest. En revanche, on ne retrouve pas de corrélation entre géographie et génétique au Proche-Orient ni dans le sous-continent indien. Si la géographie ne semble pas jouer de rôle prépondérant au sein de ces deux groupes, les différenciations génétiques s'expliquent de manière très différente dans ces deux cas. En effet, les populations proche-orientales constituent un groupe génétiquement homogène, ce qui s'expliquerait par un taux élevé de flux génique dû aux migrations dont cette région, située à un carrefour continental, a été le théâtre à travers l'histoire. Au contraire, les populations du groupe indo-pakistanais sont très hétérogènes. La différenciation de ces dernières, dont plusieurs parlent une langue dravidienne, semble avoir été gouvernée par une dérive génétique rapide sous l'influence complexe de barrières culturelles, sociales, linguistiques et/ou religieuses