Human endogenous retroviruses are the remnants of ancient retroviral infections present within our genome. These molecular fossils show similarities with present day exogenous retroviruses but act as typical Mendelian elements that are passed vertically between generations. Despite being repeatedly linked to a number of autoimmune diseases and disorders, no conclusive proof has been identified. Rheumatoid arthritis (RA) is one such disease which has been associated with an increase in HERV expression, compared to controls. In order to elucidate a clear role for HERVs in RA pathogenesis, autoantigens implicated in disease pathogenesis were scanned for sequence homology to retroviral genes. Such epitopes would induce antibodies cross reactive with host proteins, resulting in disease. Short peptides mimicking these regions were synthesised and the prevalence of anti-HERV antibodies was determined in RA patients and disease controls. Additionally, a novel real-time Polymerase Chain Reaction (PCR) assay was developed to accurately quantify levels of HERV-K (HML-2) gag expression, relative to normalised levels of housekeeping gene expression. Both serological and molecular assays showed significant increases in HERV-K (HML-2) activity in RA patients compared to disease controls with CD4+ lymphocytes harbouring the highest activity. The real-time assay was also used to determine whether factors within the synovium could modulate HERVs, resulting in their upregulation. Exogenous viral protein expression and pro-inflammatory cytokines were shown to exert a significant modulatory effect over HERV-K (HML-2) transcription. From this data, it is clear that RA patients have increased levels of HERV-K (HML-2) gag activity compared to controls. Despite this it is likely that factors within the synovium such as exogenous viral expression and pro-inflammatory cytokines also influence HERV-K (HML-2) transcription possibly contributing to a role of bystander activation, i.e. being influenced by external factors, rather than actively contributing to disease processes. The exact role of HERVs in RA pathology remains elusive; however this research proposes several mechanisms by which HERV-K (HML-2) may contribute to disease.

Breast cancer is the most common cancer in women and research efforts to unravel the underlying mechanisms that drive carcinogenesis are continuous. The emergence of high-throughput sequencing techniques and their constant advancement, in combination with large scale studies of genomic and transcriptomic data, allowed the identification of important genetic changes that take place in the breast cancer genome, including somatic mutations, copy number aberrations and genomic rearrangements.The overall aim of this thesis is to explore the presence of genetic changes that take place in the breast cancer transcriptome and their possible contribution to carcinogenesis. The aim of the first research study was the identification of expressed gene fusions in breast cancer and the study of their association with other genomic events. For achieving this, transcriptome sequencing and Single Nucleotide Polymorphism arrays data for a cohort of 55 tumors and 10 normal breast tissues were combined. Gene fusions were detected in the majority of the samples, with evident differences between breast cancer subtypes, where HER2+ samples had significantly more fusions than the other subtypes. The genome-wide analysis uncovered localization of fusion genes in specific chromosomes like 17, 8 or 20. Additionally, a positive correlation between the number of gene fusions and the number of amplifications was observed, including the association between fusions on chromosome 17 and the amplifications in HER2+ samples, which can be attributed to the highly rearranged genomes of these subtypes. Finally, the absence of highly recurrent fusions across this cohort adds to the notion that gene fusions in breast cancer are most likely private events, with the majority being “passenger” events. In the second research study, the aim was to identify a connection between viral infections and breast cancer by devising five different computational methods for the analysis of both transcriptome and exome data in a cohort of 58 breast tumors. Despite being able to detect viral sequences in our testing dataset, no significantly high numbers of viral sequences were detected in our samples. Specifically, viral sequences (~2-30 reads) were extracted belonging to viruses EBV, HHV6 and Merkel cell polyomavirus. Such low levels of viral expression direct against a viral etiology for breast cancer but one should not exclude possible cases of integrated but silent viruses.In the third research project, we analyzed in silico the transcriptional profiles of human endogenous retroviruses in breast cancer. Despite being scattered across the genome in large numbers, a number of ERVs are actively transcribed, consisting of a small percentage of the total mapped reads. Alongside protein coding genes and lncRNAs, they show distinct expression profiles across the different breast cancer subtypes with luminal and basal-like samples clear separating from each other. Additionally, distinct profiles between ER+ and ER- samples were observed. Tumor specific ERV loci show an association with the immune status of the tumors, indicating that ERVs are reactivated in tumors and could play a role in the activation of the immune response cascade.The results presented in this thesis exhibit only in a small fragment the diversity and heterogeneity of the breast cancer transcriptome. The strength of the sequencing techniques allows the in depth detection of different genomic events. Gene fusions should be considered as part of the breast cancer transcriptome but their low recurrence across samples indicates for a role as passenger events. Under the light of existing results, viral infections do not play a significant role in breast cancer. On the other hand, human endogenous retroviruses, despite originating from exogenous viruses, seems to exhibit transcriptional profiles similar to those of normal genes, indicating that they are part of the genome’s transcriptional machinery. / Doctorat en Sciences biomédicales et pharmaceutiques (Médecine) / info:eu-repo/semantics/nonPublished

The human genome comprises 8% sequences of retroviral origin, so-called human endogenous retroviruses (HERVs). Most of these proviral sequences are defective, but some possess open reading frames. They can lead to the formation of viral transcripts, when activated by intrinsic and extrinsic factors. HERVs are thought to play a pathological role in inflammatory diseases and cancer. Since the consequences of activated proviral sequences in the human body are largely unexplored, selected envelope proteins of human endogenous retroviruses associated with inflammatory diseases, namely HERV-K18, HERV-K113, and HERV-Fc1, were investigated in the present study. A formation of glycosylated envelope proteins was demonstrated in different mammalian cell lines. Nevertheless, protein maturation seemed to be incomplete as no transport to the plasma membrane was observed. Instead, the proteins remained in the ER where they induced the expression of genes involved in unfolded protein response, such as HSPA5 and sXBP1. Furthermore, low expression levels of native envelope proteins were increased by codon optimization. Cell-free expression systems showed that both the transcriptional and translational level is affected. By generating different codon-optimized variants of HERV-K113 envelope, the influence of single rare t-RNA pools in certain cell lines was demonstrated. The mRNA secondary structure also appears to play an important role in the translation of the tested viral envelope proteins. In summary, the formation of certain HERV proteins is basically possible. However, their complete maturation and thus full biologic activity seems to depend on additional factors that might be disease-specific and await elucidation in the future.

O neuroblastoma é o tumor sólido mais comum e com maior índice de letalidade em crianças. Diversas famílias de retrovírus endógenos humanos (HERV) estão presentes no genoma humano, em diferentes níveis de integridade, e são reativadas sob diferentes circunstâncias. A atividade de HERV tem sido cada vez mais sido associada a doenças como câncer, doenças autoimunes e ainda com a infecção por vírus exógenos. O principal objetivo deste projeto foi avaliar a expressão de retrovírus endógenos das famílias H (HH), W (HW) e K (HK) em pacientes diagnosticados com neuroblastoma. Amostras tumorais e amostras controle foram submetidas a extração de RNA total, síntese de cDNA e PCR em fase única. Os produtos de HERV foram submetidos ao sequenciamento em larga escala. No total, 43 loci de HH e 14 loci de HW foram diferencialmente expressos entre os grupos e 202 loci de HK foram detectados. As análises de expressão somadas ao contexto genético e epigenético de neuroblastoma, permitiram com que várias hipóteses fossem levantadas acerca da regulação da expressão de HERV neste tumor. A hipometilação geral do tecido tumoral pode ter um papel importante na expressão gênica e na reativação de retrotransposons, podendo ser a principal razão para a expressão de HERV neste contexto. / Neuroblastoma represents the most common solid tumor as well as the most lethal form of tumor in children. Several families of human endogenous retroviruses (HERV) are present in human genome in different integrity levels, and they are reactivated under different circumstances. HERV activity has been linked to diseases such as cancer, autoimmune diseases and even with the infection by exogenous viruses. The main goal of this project was to evaluate the expression of endogenous retroviruses families H (HH), W (HW) and K (HK) in patients diagnosed with neuroblastoma. Tumor samples and control samples were subjected to RNA extraction and a single round in-house RT-PCR. HERVs amplicons were next generation sequenced to access the specific origin of transcripts. Overall, 43 HH loci and 14 HW loci were differentially expressed between groups and, 202 HK loci was detected. Taken together, HERV expression analysis and genetic and epigenetic context of neuroblastoma provided several hypotheses about regulation of HERV expression in this type of tumor. The global hypomethylation of tumoral tissue may have a role in genes expression and retrotransposons reactivation, which may be the main reason for HERV expression in this context.

Les rétrovirus endogènes (ERV) sont constitutifs du génome des eucaryotes et représentent environ 400000 loci dans le génome humain divisés en différentes familles. Ces HERV (Human ERV) sont pour la majorité silencieux en contexte physiologique excepté dans le placenta mais présentent une activité transcriptionnelle en contexte pathologique comme par exemple dans les cancers. Il est difficile de comprendre de façon systématique les mécanismes de régulation/dérégulation des HERV et leur implication en contexte physiopathologique car il n’existe à ce jour aucun critère permettant de distinguer qu’elles sont les longues terminaisons répétées (LTR) transcriptionnellement actives dans l’ensemble de ces éléments de régulation. Nous avons développé deux générations de puces à ADN haute densité afin d’appréhender quelles étaient les LTR réactivées dans les cancers et de comprendre les mécanismes sous-jacents à la transcription des HERV. Avec la première version de la puce HERV, nous avons notamment identifié six loci de la famille HERV-W différentiellement exprimés dans le cancer testiculaire dont le locus ERVWE1 qui code pour la syncytine-1 impliquée dans la morphogénèse placentaire. L’analyse de l’ADN des tumeurs et des tissus sains adjacents démontre que l’hypométhylation des régions U3 promotrices est un pré-requis à l’activation des HERV. La deuxième version de la puce HERV a été utilisée pour une recherche de biomarqueurs pronostiques dans le cancer du poumon non à petites cellules. Ceci a permis de mettre en évidence des réactivations de HERV dans certains échantillons cancéreux et illustre la difficulté d’une telle approche au regard des disparités inter-individus / Endogenous Retroviruses (ERVs) are inherited part of the Eukaryotic genomes, and represent about 400,000 loci in the Human genome divided in distinct families. The majority of HERVs (Human ERV) are mainly silent in most physiological contexts excepted in placenta, whereas a significant expression is observed in pathological contexts such as cancers. It is difficult to understand HERV (de)regulation mechanisms and their implication in physio-pathological contexts, as there is no criteria defining transcriptional active promoters HERV long terminal repeats (LTRs) among all these regulatory élements. We developed two versions of highdensity DNA microarray to specifically detect LTR reactivated in cancers and try to understand transcription mechanism of HERV. With the first version of HERV-microarray, we identified six HERV-W loci over-expressed in testicular cancer, including the domesticated ERVWE1 locus which produces an envelope protein dubbed Syncytin-1 associated with placenta development. The analysis of DNA from tumoral versus normal tissue reveals that hypomethylation of U3 promoters in tumors is a prerequisite of HERV activation. The second version of HERV-microarray was used to identify prognosis biomarkers in non small cell lung cancer. This study identified HERV reactivation in some samples and highlighted difficulties of such approach due to inter-individuals disparities

O neuroblastoma é o tumor sólido mais comum e com maior índice de letalidade em crianças. Diversas famílias de retrovírus endógenos humanos (HERV) estão presentes no genoma humano, em diferentes níveis de integridade, e são reativadas sob diferentes circunstâncias. A atividade de HERV tem sido cada vez mais sido associada a doenças como câncer, doenças autoimunes e ainda com a infecção por vírus exógenos. O principal objetivo deste projeto foi avaliar a expressão de retrovírus endógenos das famílias H (HH), W (HW) e K (HK) em pacientes diagnosticados com neuroblastoma. Amostras tumorais e amostras controle foram submetidas a extração de RNA total, síntese de cDNA e PCR em fase única. Os produtos de HERV foram submetidos ao sequenciamento em larga escala. No total, 43 loci de HH e 14 loci de HW foram diferencialmente expressos entre os grupos e 202 loci de HK foram detectados. As análises de expressão somadas ao contexto genético e epigenético de neuroblastoma, permitiram com que várias hipóteses fossem levantadas acerca da regulação da expressão de HERV neste tumor. A hipometilação geral do tecido tumoral pode ter um papel importante na expressão gênica e na reativação de retrotransposons, podendo ser a principal razão para a expressão de HERV neste contexto. / Neuroblastoma represents the most common solid tumor as well as the most lethal form of tumor in children. Several families of human endogenous retroviruses (HERV) are present in human genome in different integrity levels, and they are reactivated under different circumstances. HERV activity has been linked to diseases such as cancer, autoimmune diseases and even with the infection by exogenous viruses. The main goal of this project was to evaluate the expression of endogenous retroviruses families H (HH), W (HW) and K (HK) in patients diagnosed with neuroblastoma. Tumor samples and control samples were subjected to RNA extraction and a single round in-house RT-PCR. HERVs amplicons were next generation sequenced to access the specific origin of transcripts. Overall, 43 HH loci and 14 HW loci were differentially expressed between groups and, 202 HK loci was detected. Taken together, HERV expression analysis and genetic and epigenetic context of neuroblastoma provided several hypotheses about regulation of HERV expression in this type of tumor. The global hypomethylation of tumoral tissue may have a role in genes expression and retrotransposons reactivation, which may be the main reason for HERV expression in this context.

Les rétrovirus endogènes (ERV) sont des éléments constitutifs de la plupart des génomes eucaryotes, et représentent chez l’humain environ 400000 loci. Les HERV sont divisés en familles distinctes, composées d’éléments apparentés mais structurellement hétérogènes. Leur activité peut être néfaste, neutre, mais aussi bénéfique. La majorité des HERV semble silencieuse dans les cellules somatiques. Cependant certains présentent une forte activité en contextes physiologiques. Par ailleurs, une expression significative de HERV est fréquemment observée dans des contextes pathologiques, tels que les cancers. La mise sous silence des éléments répétés est supposée se produire principalement par la méthylation de leur ADN. Nous nous sommes donc intéressés à l’implication de la méthylation des régions régulatrices des HERV, les LTR, dans le contrôle de leur expression. D’une part cette étude nous a permis de mettre en évidence une méthylation locus- et tissu- spécifique de LTR HERV en contexte physiologique, impliquant notamment des modalités particulières de méthylation contrôlant l’expression placentaire de HERV domestiqués. D’autre part ce travail nous a permis de déterminer que six loci HERV-W, incluant un locus domestiqué, sont réactivés de manière autonome dans des tumeurs testiculaires sous l’influence d’un changement de modalité de méthylation intra-famille. Ainsi la méthylation des HERV influence leur expression, mais sous des modalités variables selon les loci et les contextes concernés / Endogenous retroviruses are constitutive elements of most eukaryotic genomes. They represent about 400,000 loci in the human genome. HERVs are divided into distinct families on the basis of phylogenetic identities but are highly heterogeneous in structures. Their activity can be detrimental, neutral, or beneficial to the host. Majority of HERVs seems silent in somatic cells. Still, some are highly expressed in physiological contexts. Besides, a significant expression of HERVs is frequently observed in pathological contexts such as cancers. Silencing of repeated elements is supposed to occur mainly through DNA methylation. We were therefore interested by the implication of HERV regulatory region (LTR) methylation in the control of their expression. First, this study identified locus and tissues –specific HERV LTR methylation in physiological context, worth noting particular methylation modalities that control domesticated HERVs placental expression. Second, we could determine a change in intra-family LTR methylation modalities in testicular tumors leading to the autonomous reactivation of six HERV-W loci, among which a domesticated one. Thus methylation clearly influences HERVs expression, but under modalities varying upon the loci and the contexts

Le génome humain contient environ 200 000 séquences d'origine rétrovirale (HERV), intégrées au fil de l'évolution et organisées aujourd'hui en familles multicopies complexes globalement réprimées par un contrôle épigénétique. L'étude du transcriptome HERV au niveau locus est compliquée par les similarités phylogénétiques au sein d'une famille et par la profusion des sites d'intégration, deux propriétés inhérentes aux éléments transposables. Dans ce travail, nous avons utilisé une méthode de conception de sondes de détection de 25 mer afin d'adresser la question de l'expression individuelle des HERV. Une puce à ADN haute densité intégrant plus de 5 500 séquences HERV et permettant une lecture fonctionnelle de l'activité de leurs LTRs a été utilisée sur un panel de tissus sains et cancéreux. Cela a permis d'identifier 1 718 séquences HERV actives, dont 326 LTRs promotrices et 209 LTRs polyA. L’étude de l’environnement génomique a mis en évidence une fenêtre d’environ 8 kb en amont des LTRs promotrices, caractérisée par une sous-représentation en gènes cellulaires en orientation sens. Nous avons également montré que le transcriptome des rétrovirus endogènes humains suit des règles de tropisme d’expression, qu’il est sensible aux états de différenciation cellulaire et qu’il ne semble pas être corrélé à l’âge des familles. Une première tentative d’exploitation de ce répertoire HERV dans un contexte clinique a visé à rechercher de nouveaux marqueurs diagnostiques du cancer de la prostate à partir de prélèvements urinaires, par la réalisation d’une étude pilote sur 45 patients / The human genome contains around 200,000 endogenous retroviral sequences (HERV) integrated during the evolution and which are nowadays organized into complex multicopy families, globally repressed by epigenetic control. The study of the HERV transcriptome at the locus level is complicated by phylogenetic similarities within one family and by the profusion of integration sites, two inherent characteristics of transposable elements. In this work, we used a method aiming to optimally characterize individual loci associated with 25 mer probes. A custom microarray dedicated to more than 5,500 HERV sequences and allowing a functional interpretation of the LTRs expression was used on a panel of normal and tumor tissues. We therefore identified 1,718 active HERV sequences, including 326 promoter LTRs and 209 polyA LTRs. The study of the genomic environment has highlighted an approximately 8 kb zone upstream of promoter LTRs characterized by a drastic reduction in sense cellular genes. We also showed that the HERV transcriptome follows tropism rules, is sensitive to the state of cell differentiation and, unexpectedly, seems not to correlate with the age of the families. In a first attempt to use the HERV repertoire in clinical, we sought to identify new markers of prostate cancer from urine samples. This goal was pursued by conducting a pilot study on 45 patients

<p>Human endogenous retroviruses (HERVs) represent approximately 7% of the human genome. This investigation was focused on one particular HERV, ERV3, with the main purpose of characterising its gene expression patterns and genomic distribution of ERV3-like sequences. Furthermore, this careful expression study should provide insights into the biological role of HERVs. The impact of HERVs in health and disease is not yet clarified. ERV3 is expressed as three envelope (<i>env</i>) transcripts, of which two also contain a cellular gene, <i>H-plk</i> (human proviral linked <i>Krüppel</i>). ERV3 <i>env</i> expression was mainly investigated at the RNA level. The gene expression of two other HERVs, HERV-K and HERV-E was analysed and compared with ERV3 activity.</p><p>Real-time PCRs were developed and in combination with in situ hybridisation, it was found that ERV3 is expressed in a tissue- and cell-specific way. High levels of ERV3 mRNA (up to six times over Histone3.3) were demonstrated in placenta, sebaceous glands, foetal and adult adrenal glands, brown adipose tissue, corpus luteum, pituitary gland, thymus and testis. In monocytic cells including both normal monocytes and malignant U-937 cells, elevated mRNA levels were observed after retinoic acid (RA)-induced differentiation. ERV3-encoded Env protein was detected in selected cases, one following RA-treatment. In addition, several new ERV3-like sequences were discovered in the human genome. </p><p>ERV3 was found to have conserved open reading frames in contrast to other ERV3-like sequences in the human genome. This suggests that ERV3 may be involved in important cellular processes such as differentiation, cell fusion, immunomodulation and protection against infectious retroviruses. The developed techniques and obtained results will allow further studies of HERV expression to better correlate HERV activity to both normal development and disease. </p>

Human endogenous retroviruses (HERVs) represent approximately 7% of the human genome. This investigation was focused on one particular HERV, ERV3, with the main purpose of characterising its gene expression patterns and genomic distribution of ERV3-like sequences. Furthermore, this careful expression study should provide insights into the biological role of HERVs. The impact of HERVs in health and disease is not yet clarified. ERV3 is expressed as three envelope (env) transcripts, of which two also contain a cellular gene, H-plk (human proviral linked Krüppel). ERV3 env expression was mainly investigated at the RNA level. The gene expression of two other HERVs, HERV-K and HERV-E was analysed and compared with ERV3 activity. Real-time PCRs were developed and in combination with in situ hybridisation, it was found that ERV3 is expressed in a tissue- and cell-specific way. High levels of ERV3 mRNA (up to six times over Histone3.3) were demonstrated in placenta, sebaceous glands, foetal and adult adrenal glands, brown adipose tissue, corpus luteum, pituitary gland, thymus and testis. In monocytic cells including both normal monocytes and malignant U-937 cells, elevated mRNA levels were observed after retinoic acid (RA)-induced differentiation. ERV3-encoded Env protein was detected in selected cases, one following RA-treatment. In addition, several new ERV3-like sequences were discovered in the human genome. ERV3 was found to have conserved open reading frames in contrast to other ERV3-like sequences in the human genome. This suggests that ERV3 may be involved in important cellular processes such as differentiation, cell fusion, immunomodulation and protection against infectious retroviruses. The developed techniques and obtained results will allow further studies of HERV expression to better correlate HERV activity to both normal development and disease.