Suite à une agression inflammatoire, telle que le choc septique, des brulures graves ou un traumatisme sévère, le système immunitaire répond par une modulation massive du transcriptome dans le sang. On propose d’explorer un autre répertoire que l’expression des gènes et de s’intéresser aux éléments répétés du génome, peu étudiés dans ces contextes, et plus particulièrement aux rétrovirus endogènes humains (HERV). Ils représentent plus de 8% du génome chez l’Homme. Certains sont exprimés dans des situations similaires à l’agression inflammatoire (cancer, maladies auto-immunes) et ont un impact sur la réponse immunitaire.Dans ce travail, nous cherchons à décrire et comprendre la contribution des HERV, au sein de la réponse immunitaire de l’hôte à l’agression inflammatoire. Pour cela, nous avons développé des méthodes et outils spécifiquement dédiés à la description du HERVome, au niveau génomique et transcriptomique. Nous montrons que les HERV sont exprimés dans le sang, modulés chez les patients, et que certains pourraient jouer un rôle sur l’expression de gènes de la réponse immunitaire situés à proximité. Nous évaluons également le polymorphisme de présence des HERV dans le génome de plus de deux mille individus répartis dans les populations humaines. On met en évidence que le polymorphisme HERV est globalement important, qu’il est lié à la population d’appartenance et que certains loci sont absents dans la majorité des génomes étudiés. Finalement, par différentes approches, nous identifions des associations entre gènes de la réponse immunitaire et HERV, suggérant que ces éléments peuvent jouer un rôle important dans la réponse de l’hôte à l’agression inflammatoire / Following inflammatory injury, like a septic shock, severe burn or important trauma, the immune system responds by a massive modulation of its transcriptome in the blood. We propose to explore another repertoire than gene expression and to focus on repeated elements, especially on HERVs. They represent more than 8% of the human genome. HERVs are expressed in similar settings (cancer or auto-immune diseases) and impact immune response. In this project, we describe and aim to better understand the HERV contribution in host immune response, following inflammatory aggression. To bring elements of response, we developed specifically dedicated tools to describe the HERVome, either at genomic or transcriptomic level. We show HERVs are expressed in blood in these settings, modulated in patients and could play a role on nearby gene expression. We also evaluate the polymorphism of presence of HERV loci on more than two thousands individuals, grouped into human populations. We show an important HERV polymorphism, that it is population-specific, and that some loci are absent in the majority of the analyzed genomes.Finally, with different approaches, we identify associations between immune-response genes and HERVs, suggesting these elements can play a role in host immune response following inflammatory aggressions

High grade aggressive lymphomas have high mortality. By their nature, more than 40% of patients die from these diseases even with the improved treatment strategies currently available for oncology patients. The characteristic feature is that they are functionally heterogeneous and therefore have different biological and molecular signatures which make it difficult for all groups to respond to same line of treatment. Based on the above, I set out to look at the impact of viral and cellular gene products on these groups of diseases: In chapter 3 I developed monoclonal antibodies against HERV‐K10. I subsequently investigated their expressions in aggressive lymphomas including Diffuse Large B‐cell lymphoma, Hodgkin’s lymphoma and Primary CNS lymphomas. I showed HERV‐K10 is expressed in cell lines of aggressive lymphomas, but not in paraffin‐embedded tissues. In chapter 4 I showed that the expression of ATM using immune‐histochemistry techniques in aggressive lymphomas does offer a guide to prognosis and treatment. Nearly 30% of Diffuse Large B‐cell lymphomas express ATM, 55% of Hodgkin’s lymphomas and more than 80% of Primary CNS lymphomas. I also showed there is a correlation of ATM expression and EBV‐driven aggressive lymphomas and that this has a poor prognostic significance. Chapter 5 analysed the results obtained by generating, validating and evaluating data base of DLBCL and PCNSL from a retrospective cohort over a 17‐year period. The results confirmed that prognostic indicators including ATM, S1PR2, Autotaxin and EBV using immuno‐histochemistry techniques help with categorising aggressive lymphomas into different prognostic groups and does influence future management. In summary, my results showed there is a critical place for immuno‐histochemistry techniques in convincingly helping understand the expressions of viral and cellular gene products in aggressive lymphomas and in contributing positively to their management.