L'ataxie spinocérébelleuse de type 7 (SCA7) est une maladie neurodégénerative due à une expansion de CAG traduit en polyQ dans la protéine ataxine-7. La SUMOylation, modification post-traductionnelle que nous avons identifiée moduler l'agrégation de la protéine mutante, est facilitée par une SUMO E3 ligase.Nous avons identifié RanBP2, une nucléoporine appartenant au complexe du pore nucléaire en tant que SUMO E3 ligase, via SUMO-1 de l'ataxine-7. En effet, le silencing de RanBP2 induit l'agrégation de l'ataxine-7 mutante, ce qui démontre l'implication de RanBP2 dans la physiopathologie de SCA7. Nous montrons également que l'ataxine-7 endogène est une cible modifiée par SUMO-1 et -2. L'ataxine-7 poly-SUMOylée, grâce à la présence de chaines SUMO2/3, est capable de recruter RNF4. Cette protéine conduit à la dégradation de l'ataxine-7 mutante par la voie du protéasome. La dégradation est abolie en présence d'un mutant de RNF4.Dans un modèle murin KI SCA7, nous avons quantifié l'expression des gènes impliqués dans la voie de la SUMOylation au niveau des régions les plus touchées du cerveau. Le niveau d'expression des ARNs messagers montre des altérations dépendantes des répétitions CAG du gène SCA7. A 6 mois (avant le début de la pathologie), les premières dérégulations sont observées; à 12 mois (à un stade avancé de la maladie), on note une diminution statistiquement significative de Sumo-1 dans le cervelet des souris Atxn7100Q/5Q. Ces résultats, alliés à l'observation de l'accumulation anormale des protéines SUMO-1 et RanBP2 dans le cervelet d'un patient SCA7, suggèrent que les voies de la SUMOylation in vivo peuvent être perturbées dans SCA7. / Spinocerebellar ataxia type 7 (SCA7) is a neurodegenerative disease caused by a CAG expansion (polyQ) in the protein ataxin-7. SUMOylation, a post-translational modification that we identified to modulate mutant protein aggregation in a SCA7 cellular model, is facilitated by a SUMO E3 ligase. Here, we identified RanBP2 (Nup358), a nucleoporin belonging to the nuclear pore complex, as the major E3 enzyme implicated in ataxin-7 modification by SUMO-1. Indeed, RanBP2 silencing renders mutant ataxin-7 more prone to aggregation, thus demonstrating the implication of RanBP2 in SCA7 pathophysiology. We also show that endogenous ataxin-7 is a target for both SUMO-1 and -2 modification. Poly-SUMOylated ataxin-7 presents a docking site composed of SUMO2/3 chains for the recruitment of RNF4: this protein is a SUMO E3 ubiquitin ligase that mediates degradation of mutant ataxin-7 by the proteasome pathway. The degradation is abolished in presence of a mutant form of RNF4. In a SCA7 knock-in mouse model we quantified expression of SUMO-pathway related genes in cerebellum and retina, the most affected regions using quantitative RT-PCR. SUMO-related genes show expanded repeat-dependent alterations in expression patterns. At 6 months (before onset), deregulations begin to occur; by 12 months (late stage of disease), there is a statistically significant impairment in Sumo-1 levels in Atxn7100Q/5Q cerebellum. These results, together with the observation that SUMO-1 and RanBP2 protein accumulate abnormally in the cerebellum of a SCA7 patient, suggest that in vivo SUMO-modifying pathways may be perturbed in SCA7.

Scleroderma (SSc) is an autoimmune disease characterized by dysfunctional immunity, vasculopathy, and fibrosis of the skin and internal organs. There is a poor prognosis for SSc patients and effective therapeutics have not yet been developed. Many mouse models have been developed, but most fail to recapitulate all of the symptoms seen in SSc patients. In this study we characterize a Fli1flox/flox mouse with CAG Cre under the beta-actin promoter. Based on what has been previously described in mice with deletion of Fli1 in specific cell types, we predicted that global postnatal deletion of Fli1 will result in systemic fibrosis, vasculopathy, and inflammation in these mice. The penetrance of a phenotype was highly variable; however, mice that developed a phenotype displayed disorganized vascular networks, fibrosis and proinflammatory cytokines and chemokines in the skin and lungs after 4 and 8 weeks of Fli1 deficiency. Increased macrophage and dendritic cell populations were observed in the lungs after 8 weeks. Fli1flox/flox CAG Cre mice exhibited hair loss after 5 months of Fli1 deletion. Since our experiments focus mainly on the lungs and skin, more experiments are required to characterize these mice to determine if they can be used as a novel animal model of SSc.

La huntingtine (HTT) est une protéine d’échafaudage participant à des fonctions indispensables au bon fonctionnement cellulaire. Elle est codée par le gène HTT qui présente une répétition polymorphique de triplet CAG. Une répétition excédant 35 CAG dans la HTT est à l’origine de la maladie de Huntington, une maladie neurodégénérative héréditaire sévère. Ainsi, bien que d’expression ubiquitaire, la HTT est principalement étudiée dans le système nerveux. Par exemple, ses implications dans le tissu mammaire, en condition normale et pathologique, sont inconnues. Nous avons observé que la forme mutante de la HTT accélère le développement de cancer du sein et en accentue la sévérité et que la forme sauvage est impliquée dans le développement normal de la glande mammaire. Mon projet principal de thèse était de caractériser le rôle de la HTT, de sa phosphorylation à la sérine 421 (S421-P-HTT) ainsi que du polymorphisme des répétitions CAG dans les cancers du sein.En utilisant des modèles cellulaires et murins et par des études d’expression chez des patientes atteintes d’un cancer du sein, j’ai observé que l’expression de la HTT et de la S421-P-HTT corrèlent avec le stade de différenciation tumorale. Au niveau moléculaire, la HTT régule, par sa phosphorylation à la S421, l’expression et la localisation d’une des protéines des jonctions serrées, ZO1 et module ainsi l’adhésion intercellulaire. ZO1 colocalise avec la S421-P-HTT aux jonctions intercellulaires et forme un complexe avec la HTT. La perte d’expression de HTT est pro-Métastatique chez la souris et est moindre dans les cancers du sein métastatiques. De plus, les niveaux d’expression de HTT et de ZO1 sont diminués en parallèle dans les carcinomes humains de bas grades.J’ai également montré que le polymorphisme CAG présent dans la HTT sauvage joue un « double emploi » : tandis que de longues répétitions protègent de l’apparition de cancers, elles accentuent sa sévérité lorsque la maladie se développe. Dans le sous-Type HER2 spécifiquement, la longueur de la répétition CAG est un facteur pronostic indépendant du développement de métastases.Ainsi, ces travaux ont permis de mettre en évidence un rôle clé pour la HTT au cours de la progression tumorale mammaire, et devraient conduire à une meilleure compréhension des mécanismes moléculaires impliqués dans le développement de métastases dans le cancer du sein. / Huntingtin (HTT) is a scaffold protein involved in numerous cellular mechanisms essentials for appropriate physiological functions. HTT is encoded by HTT gene which carries a polymorphic repetition of CAG triplet. When the CAG repetition exceeds 35, it leads to Huntington’s disease, a hereditary severe neurodegenerative disorder. While HTT expression is ubiquitous, it is mainly studied in nervous system. For example, HTT roles in breast physiology and cancer are unknown. We demonstrated that mutant HTT accelerates breast tumor and metastasis development and that wild-Type HTT is involved in normal mammary gland development. My main project was to characterize the roles of HTT and of its phosphorylation at S421 (S421-P-HTT) and that of the polymorphic CAG length in mammary carcinomas.First, leaning on cellular and murine models as well as on expression studies in breast cancer patients, I observed that HTT and S421-P-HTT expression correlates with tumoral differentiation stage. At the molecular level, HTT regulates through its phosphorylation at S421, the expression and localization of ZO1, a marker of intercellular junction and therefore modulates intercellular adhesion. ZO1 colocalizes with S421-P-HTT specifically at tight junctions and forms a complex with HTT. Loss of HTT is itself pro-Metastatic in mice and is decreased in metastatic human breast cancer. Moreover, HTT and ZO1 are concomitantly downregulated in low-Grade human carcinomas.On the other hand, the polymorphism of CAG repetitions in HTT has a dual-Purpose: while long repetitions protect against cancer development, it increases its severity once cancer is developed. In HER2 subtype specifically, HTT appears as an independent prognostic factor of metastasis development.Thus, these studies point out a key function of HTT outside the brain during mammary carcinoma progression and should lead to a better understanding of molecular mechanisms involved in metastasis development.

The development of improved sequencing technologies hasenabled the field of genomics to evolve. Handling andsequencing of large numbers of samples require an increasedlevel of automation in order to obtain high throughput andconsistent quality. Improved performance has lead to thesequencing of numerous microbial genomes and a few genomes fromhigher eukaryotes and the benefits of comparing sequences bothwithin and between species are now becoming apparent. Thisthesis describes both the development of automated purificationmethods for DNA, mainly sequencing products, and a comparativesequencing project. The initially developed purification technique is dedicatedto single stranded DNA containing vector specific sequences,exemplified by sequencing products. Specific capture probescoupled to paramagnetic beads together with stabilizing modularprobes hybridize to the single stranded target. After washing,the purified DNA can be released using water. When sequencingproducts are purified they can be directly loaded onto acapillary sequencer after elution. Since this approach isspecific it can be applied to multiplex sequencing products.Different probe sets are used for each sequencing product andthe purifications are performed iteratively. The second purification approach, which can be applied to anumber of different targets, involves biotinylated PCR productsor sequencing products that are captured using streptavidinbeads. This has been described previously, buthere theinteraction between streptavidin and biotin can be disruptedwithout denaturing the streptavidin, enabling the re-use of thebeads. The relatively mild elution conditions also enable therelease of sensitive biotinylated molecules. Another project described in this thesis is the comparativesequencing of the 40 kbcagpathogenicity island (PAI) in fourHelicobacter pyloristrains. The results included thediscovery of a novel gene, present in approximately half of theSwedish strains tested. In addition, one of the strainscontained a major rearrangement dividing thecagPAI into two parts. Further, information about thevariability of different genes could be obtained. Keywords:DNA sequencing, DNA purification, automation,solid-phase, streptavidin, biotin, modular probes,Helicobacter pylori,cagPAI. / <p>NR 20140805</p>

<p>Spinocerebellar ataxia type 7 (SCA7) is a neurodegenerative disease characterized by cerebellar ataxia and visual problems due to a progressive and selective loss of neurons within the cerebellum, brainstem and retina. The disease is caused by the expansion of a CAG repeat in the first coding exon of the SCA7 gene, resulting in an expanded polyglutamine domain in the N-terminal part of ataxin-7, a protein of unknown function.</p><p>To expand our knowledge of the ataxin-7 protein and the mechanism by which mutant ataxin-7 causes disease, we have studied the expression and function of both the normal and the mutated ataxin-7 protein. </p><p>Ataxin-7 expression was examination in brain and non-CNS tissues from SCA7 patients and age-matched controls. Expression was predominantly nuclear in neurons throughout the brain of both healthy and SCA7 individuals. We also observed aggregation of mutant ataxin-7 in the nuclei of neurons. No obvious difference in the expression level of ataxin-7 or the formation of aggregates could be observed between affected and non-affected brain regions in SCA7 patients. Based on these findings, we could conclude that the cell type specific neurodegeneration in SCA7 is not due to differences in expression levels or to the formation of ataxin-7 aggregates.</p><p>To widen our studies on ataxin-7 expression, we isolated and characterized the mouse SCA7 gene homolog. Cloning of the mouse SCA7 gene revealed two SCA7 mRNA isoforms that were highly homologous to their human counterparts. Immunohistochemical analysis also revealed a conserved expression pattern of ataxin-7 in adult mouse brain. In addition, ataxin-7 expression was observed during embryonic development in brain as well as in several non-neuronal tissues such as heart, liver and lung. </p><p>Besides SCA7, eight neurodegenerative disorders are known to be caused by expanded polyglutamine repeats, including SCA 1-3, 6 and 17, DRPLA, SBMA and Huntington’s disease. The polyglutamine disorders have many features in common and a common pathological disease mechanism involving transcriptional dysregulation has been proposed. To investigate the possible involvement of transcriptional dysregulation in SCA7 pathology, we analyzed the effects of both wild-type and expanded ataxin-7 on transcription driven by the co-activator CBP, the Purkinje cell-expressed nuclear receptor RORα1 or a basic TATA promoter. As previously shown for other polyglutamine disease proteins, expansion of the polyglutamine domain in ataxin-7 leads to reduced transcription. Surprisingly, strong repression of CBP-mediated, RORα1-mediated and basal transcription was also observed with wild-type ataxin-7, suggesting that the normal ataxin-7 protein may have a role in transcriptional regulation. </p>

Spinocerebellar ataxia type 7 (SCA7) is a neurodegenerative disease characterized by cerebellar ataxia and visual problems due to a progressive and selective loss of neurons within the cerebellum, brainstem and retina. The disease is caused by the expansion of a CAG repeat in the first coding exon of the SCA7 gene, resulting in an expanded polyglutamine domain in the N-terminal part of ataxin-7, a protein of unknown function. To expand our knowledge of the ataxin-7 protein and the mechanism by which mutant ataxin-7 causes disease, we have studied the expression and function of both the normal and the mutated ataxin-7 protein. Ataxin-7 expression was examination in brain and non-CNS tissues from SCA7 patients and age-matched controls. Expression was predominantly nuclear in neurons throughout the brain of both healthy and SCA7 individuals. We also observed aggregation of mutant ataxin-7 in the nuclei of neurons. No obvious difference in the expression level of ataxin-7 or the formation of aggregates could be observed between affected and non-affected brain regions in SCA7 patients. Based on these findings, we could conclude that the cell type specific neurodegeneration in SCA7 is not due to differences in expression levels or to the formation of ataxin-7 aggregates. To widen our studies on ataxin-7 expression, we isolated and characterized the mouse SCA7 gene homolog. Cloning of the mouse SCA7 gene revealed two SCA7 mRNA isoforms that were highly homologous to their human counterparts. Immunohistochemical analysis also revealed a conserved expression pattern of ataxin-7 in adult mouse brain. In addition, ataxin-7 expression was observed during embryonic development in brain as well as in several non-neuronal tissues such as heart, liver and lung. Besides SCA7, eight neurodegenerative disorders are known to be caused by expanded polyglutamine repeats, including SCA 1-3, 6 and 17, DRPLA, SBMA and Huntington’s disease. The polyglutamine disorders have many features in common and a common pathological disease mechanism involving transcriptional dysregulation has been proposed. To investigate the possible involvement of transcriptional dysregulation in SCA7 pathology, we analyzed the effects of both wild-type and expanded ataxin-7 on transcription driven by the co-activator CBP, the Purkinje cell-expressed nuclear receptor RORα1 or a basic TATA promoter. As previously shown for other polyglutamine disease proteins, expansion of the polyglutamine domain in ataxin-7 leads to reduced transcription. Surprisingly, strong repression of CBP-mediated, RORα1-mediated and basal transcription was also observed with wild-type ataxin-7, suggesting that the normal ataxin-7 protein may have a role in transcriptional regulation.

<p>The development of improved sequencing technologies hasenabled the field of genomics to evolve. Handling andsequencing of large numbers of samples require an increasedlevel of automation in order to obtain high throughput andconsistent quality. Improved performance has lead to thesequencing of numerous microbial genomes and a few genomes fromhigher eukaryotes and the benefits of comparing sequences bothwithin and between species are now becoming apparent. Thisthesis describes both the development of automated purificationmethods for DNA, mainly sequencing products, and a comparativesequencing project.</p><p>The initially developed purification technique is dedicatedto single stranded DNA containing vector specific sequences,exemplified by sequencing products. Specific capture probescoupled to paramagnetic beads together with stabilizing modularprobes hybridize to the single stranded target. After washing,the purified DNA can be released using water. When sequencingproducts are purified they can be directly loaded onto acapillary sequencer after elution. Since this approach isspecific it can be applied to multiplex sequencing products.Different probe sets are used for each sequencing product andthe purifications are performed iteratively.</p><p>The second purification approach, which can be applied to anumber of different targets, involves biotinylated PCR productsor sequencing products that are captured using streptavidinbeads. This has been described previously, buthere theinteraction between streptavidin and biotin can be disruptedwithout denaturing the streptavidin, enabling the re-use of thebeads. The relatively mild elution conditions also enable therelease of sensitive biotinylated molecules.</p><p>Another project described in this thesis is the comparativesequencing of the 40 kb<i>cag</i>pathogenicity island (PAI) in four<i>Helicobacter pylori</i>strains. The results included thediscovery of a novel gene, present in approximately half of theSwedish strains tested. In addition, one of the strainscontained a major rearrangement dividing the<i>cag</i>PAI into two parts. Further, information about thevariability of different genes could be obtained.</p><p><b>Keywords:</b>DNA sequencing, DNA purification, automation,solid-phase, streptavidin, biotin, modular probes,<i>Helicobacter pylori</i>,<i>cag</i>PAI.</p>

Androgen receptor (AR) gene CAG polymorphisms may be associated with body shape, and are associated with certain breast and prostate cancers. In addition, body shape is associated with risk for a variety of diseases, including heart disease, diabetes, and certain forms of cancer. The CAG repeat in exon l of the AR gene was quantified using Perkin Elmer Applied Biosystems GeneScan analysis software in 96 and 59 healthy Caucasian men and women, respectively, who were over the age of 50 years. All participants had body measurements taken and donated a blood sample. Waist measurements included circumferences at the 1) umbilicus (wstumb), 2) top of the iliac crest (wstili), and 3) midpoint between the lowest rib and the iliac crest (wstwst). Waist-hip ratio (Wl-IR) was calculated using each corresponding waist measurement, respectively (WHRUMB, WHRILI, WHRWST). Mean repeat length was significantly different (p < 0.01) between men (22 ± 0.3 repeats) and women (23 ± 0.3 repeats). There was a significant relationship (p < 0.05) between mean individual CAG repeat number and tertile of WHRUMB in women based on the mean number of CAG repeats for each woman. Waist measurements in women were significantly different for all pairwise comparisons (p < 0.05). In addition, the three measurements of WHR in women, WHRUMB, WHRILI, and WHRWST, were significantly different from each other (p < 0.05). Thus, lesser numbers of CAG repeats may indicate a more androgenic phenotype in women.

Abstract: The purpose of this study was to determine if a correlation exists between suicide and CAG repeat length in Huntington’s disease. Methodology: A case-control study using the COHORT Study de-identified database was conducted. Responses were collected from 163 participants. Depression, substance abuse history and use of benzodiazepines were covariates. Responses to the UHDRS behavioral section pertaining to the frequency and severity of suicidal ideation (“feels life is not worth living”, “has suicidal thoughts”) were analyzed. Results: Despite taking depression, benzodiazepine use, and history of substance abuse into account, there was a predictive relationship between CAG repeat length and frequency of suicidal ideation (p = .010). When the effect of depression was taken into account, there was no significant relationship between CAG repeat length and the severity of suicidal ideation. Recommendations: The findings from this quantitative analysis supported using CAG length in a clinician’s risk factor assessment to determine the frequency of suicidality.

EcoP15I ist ein Vertreter der multifunktionalen, heterooligomeren Typ III Restriktionsendonukleasen. Typ III Restriktionsendonukleasen sind wegen der Lage ihres Spaltortes, ca. 25 bp vom Erkennungsort entfernt, von besonderem Interesse für Anwendungen in der Medizin und funktionellen Genomanalyse. EcoP15I erkennt die DNA-Sequenz 5''-CAGCAG und benötigt für eine effektive DNA-Spaltung zwei invers orientierte Erkennungsorte auf einem DNA-Molekül. Nach dem bisherigen DNA-Translokations-Modell bindet je ein EcoP15I-Protein an je einen Erkennungsort und startet dann durch ATP-Hydrolyse vermittelte DNA-Translokation. Die Kollision der beiden EcoP15I-DNA-Komplexe initiiert die DNA-Doppelstrang-Spaltung. Experimente zur Erkennungsort-Suche von EcoP15I zeigen, dass über längere Distanzen offenbar nicht das "Sliding", sondern ein dreidimensionaler Prozess die bevorzugte Bewegung von EcoP15I an der DNA ist. Eine erhöhte Anzahl von Wiederholungen von CAG-Trinukleotiden (CAG-Repeats) im Exon 1 des Gens für Chorea Huntington (Huntington Disease - HD) führt zur Manifestation dieser neurodegenerativen Erkrankung. Für die Diagnostik der Erkrankung ist die exakte Bestimmung der Anzahl der CAG-Repeats von Bedeutung. Diese Arbeit zeigt die Spaltung von HD Gen Exon 1 DNA durch EcoP15I. Die halbautomatische, hoch-sensitive Analyse dieses Spaltmusters ermöglicht die exakte Bestimmung der Anzahl der CAG-Repeats. Diese Arbeit liefert den ersten Nachweis für die DNA-Translokation durch eine Typ III-Restriktionsendonuklease. Die postulierten EcoP15I-DNA-Schlaufen wurden mit Hilfe der Rasterkraftmikroskopie (SFM) abgebildet. Dadurch wird das DNA-Translokations-Modell der DNA-Spaltung durch EcoP15I bestätigt. Es werden Gemeinsamkeiten und Unterschiede des gesamten DNA-Spaltvorganges der Typ III Restriktionsendonuklease EcoP15I in bezug auf andere Restriktionsendonukleasen diskutiert. / EcoP15I is a multifunctional, hetero-oligomeric Type III restriction enzyme. Type III restriction enzymes are of general interest in medicine and functional genome analysis because they cut DNA 25 bp downstream of their recognition site. EcoP15I recognises the DNA sequence 5`-CAGCAG and needs two inverse oriented recognition sites for effective DNA cleavage. According to the present translocation collision model DNA cleavage was proposed to result from ATP dependent DNA translocation, which is expected to induce DNA loop formation, and collision of two enzyme-DNA complexes. Experiments show that EcoP15 moves rather in a three-dimensional than in a "sliding" process in search for its recognition site. Huntington''s disease (HD) is a progressive neurodegenerative disorder with autosomal-dominant inheritance. The disease is caused by a CAG trinucleotide repeat expansion located in the first exon of the HD gene. To diagnose the illness the exact determination of the number of CAG repeats is necessary. This study shows that the number of CAG repeats in the HD gene can be determined by restriction of the DNA with the endonuclease EcoP15I and subsequent high-resolution analysis of the restriction fragment pattern using the ALFexpress DNA Analysis System. Here, for the first time DNA translocation by the Type III restriction enzyme EcoP15I is demonstrated. The postulated EcoP15-DNA loops are visualised using scanning force microscopy. This confirms the translocation-collision model for DNA cleavage by EcoP15. Similarities and differences between the DNA cleavage processes of the Type III restriction enzyme EcoP15I and other restriction enzymes are discussed.