Les syndromes démyélinisants acquis (SDA) pédiatriques sont un groupe de maladies qui affectent la substance blanche (SB) et la substance grise (SG) du système nerveux central (SNC) chez les enfants, et qui partagent certaines caractéristiques et mécanismes pathologiques. Les SDA peuvent être monophasiques ou récurrents. Les SDA comprennent des maladies telles que l'encéphalomyélite aiguë disséminée (EMDA), les troubles du spectre de la neuromyélite optique (TS-NMO), la sclérose en plaques (SEP) et le syndrome démyélinisant récurrent avec anticorps contre la glycoprotéine oligodendrocytique de myéline (anticorps anti-MOG). Ce dernier syndrome, appelé aussi maladie MOG+, a été reconnu récemment comme une entité distincte faisant partie des maladies démyélinisantes récurrentes chez les enfants. La maladie MOG+ présente des caractéristiques semblables à celles de la SEP; en effet, certains cas ont été déjà considérés comme une forme « atypique » de SEP. La maladie MOG+ et la SEP partagent des lésions dans la SB du SNC, mais la SEP est caractérisée aussi par des lésions corticales (LCs) cérébrales, insuffisamment étudiées dans la maladie MOG+. Par conséquent, le but de cette recherche a été de comparer les caractéristiques démographiques et des lésions cérébrales visibles sur des études d’imagerie par résonance magnétique (IRM) chez les enfants atteints de SEP et ceux atteints de la maladie MOG+. Pour atteindre cet objectif, nous avons utilisé des scans IRM 3T, incluant les contrastes pondérés T1, FLAIR et des images de transfert de magnétisation (ITM) de 14 enfants atteints de SEP et 13 enfants atteints de la maladie MOG+. Nous avons mesuré le nombre des LCs, le volume des lésions dans la SB et les valeurs normalisées d’ITM dans les LCs et les lésions de la SB. Nos résultats ont montré que les enfants atteints de la maladie MOG+ étaient plus jeunes au début de la maladie et que celle-ci présentait une durée plus longue que la maladie du groupe SEP. Quant aux lésions cérébrales, les LCs étaient présentes dans la maladie MOG+, mais leur nombre était significativement plus élevé dans le groupe SEP. Cependant, les valeurs normalisées d’ITM dans ces lésions (valeurs qui sont sensibles à la quantité de myéline) n'étaient pas significativement différentes entre les deux groupes. En plus, le volume des lésions de la SB était significativement plus élevé dans le groupe SEP et les valeurs normalisées d’ITM dans ces lésions, significativement inférieures comparativement à la maladie MOG+, témoignant ainsi d’une démyélinisation plus sévère et des différences potentielles dans les mécanismes de démyélinisation. / Pediatric Acquired Demyelinating Syndromes (ADS) are a group of diseases that affect the white matter (WM) and gray matter (GM) of the central nervous system (CNS) in children and that share similar pathological characteristics and mechanisms. ADS can be monophasic or recurrent. The ADS include diseases like acute disseminated encephalomyelitis (ADEM), neuromyelitis optic spectrum disorders (NMO-SD), multiple sclerosis (MS) and Relapsing Myelin Oligodendrocyte Glycoprotein (MOG) syndrome or MOG+ disease, which has been recently recognised as a distinct pathology and is part of the relapsing ADS in children. MOG+ disease shares features with MS; indeed, some MOG+ cases have been considered as an “atypical” form of MS until recently. Both MOG+ disease and MS present lesions in the WM of the CNS. MS is also characterized by focal brain cortical lesions (CL), which have not been extensively studied in MOG+ disease yet. For this reason, the aim of this research project was to compare the demographic and brain magnetic resonance imaging (MRI) characteristics of children with MS and children with MOG+ disease. To achieve our goal, we used 3T MRI including T1-weighted, FLAIR and magnetization transfer ratio (MTR) contrasts of 14 MS participants, and 13 relapsing MOG+ participants. CL counts, WM lesion volumes, normalized MTR values in CLs, and WM lesions were compared across groups. Our results show that children with MOG+ disease were younger at disease onset and had a longer disease duration compared to the MS group. CL were present in MOG+ participants, but counts were significantly higher in the MS group. However, their normalized-MTR values, which are sensitive to myelin, were not significantly different between both groups. WM lesion volumes were significantly higher in the MS group, but their normalized MTR values were significantly lower than in MOG+ WM lesions, likely reflecting more severe demyelination and potential differences in the demyelinating mechanism.

Ziel dieser Doktorarbeit ist eine umfassende Untersuchung der Heterogenität von Mikroglia aus morphologischer, elektrophysiologischer und transkriptioneller Perspektive mit dem Schwerpunkt auf Unterschiede zwischen weißer und grauer Substanz. Im ersten Kapitel diskutiere ich die morphologische Heterogenität von Mikroglia mit dem Fokus auf Satelliten- und Parenchymale-Mikroglia. Wir führten eine eingehende Analyse mehrerer Hirnareale durch und quantifizierten die Anzahl der Satellitenmikroglia, die mit verschiedenen neuronalen Subtypen in Kontakt stehen. Wir fanden heraus, dass die Anzahl der Satellitenmikroglia stark mit der neuronalen Dichte eines bestimmten Bereichs korreliert. Im zweiten Kapitel dieser Arbeit untersuche ich die transkriptionelle Heterogenität von Mikroglia aus weißer und grauer Substanz, wobei ich die in Gliazellen neu etablierte Patch-seq-Methode anwende. Diese Methode ermöglicht es eine Kombination aus morphologischen, lektrophysiologischen und transkriptionellen Profilen einzelner Zellen zu erhalten, die es erlauben, zelluläre Unterschiede zu charakterisieren. Wir identifizieren einen zellulären Subtyp, wenn wir den Patch-seq-Datensatz mit FACS-basierter Einzelzell-RNA-seq-Datensätzen vergleichen. Dieser Subtyp gehört eindeutig zu dissoziierten Gewebeproben und ist durch die Expression von Stress-assoziierten Genen charakterisiert. Im dritten Kapitel wende ich mich der Frage zu, wie Transkripte mittels SLAM-seq nachverfolgt werden können, die während der Dissoziation des Gewebes entstehen. Das Verfahren ermöglicht es mRNA, die während der Dissoziation der Probe entsteht, metabolisch zu markieren, rechnerisch zu identifizieren und zu entfernen. Indem wir die markierten Transkripte aus dem Mikroglia “entfernen”, beobachten wir, dass ein „aktivierter Mikroglia“-Subtyp zur allgemeinen Mikroglia-Population gehört. / The aim of this doctoral work is to provide a comprehensive study and overview on the topic of the heterogeneity of microglia in the normal adult mouse brain from the morphological, electrophysiological and transcriptional perspective with the focus on differences between white and grey matters. In the first Chapter, I discuss the morphological heterogeneity of microglia in the brain with the focus on two morphologically distinct classes: satellite and parenchymal microglia. We performed an in-depth analysis of multiple brain areas and quantified the number of satellite microglia which is in contact with different neuronal subtypes. We found that satellite microglia numbers are highly correlated with neuronal densities of a certain area, while showing no preferences for any of the neuronal types. In Chapter two of this work, I study transcriptional heterogeneity of microglia from white and grey matters. For this I am employing Patch-seq, which we newly established in glial cells. This method allows a combination of morphological, electrophysiological and transcriptional profiles of single cells to assess their differences. When comparing Patch-seq dataset to the previously published FACS isolated single cell RNA-seq microglia datasets, we find a subtype of cells which uniquely belongs to FACS sample and is characterized by expression of stress-associated genes. This finding points out to the fact of dissociation-related artifacts in the single cell RNA-seq data which are not present in situ. In the third chapter, I identified transcripts which are induced during the dissociation of the tissue by employing the SLAM-seq method. This procedure allows to metabolically label newly transcribed mRNA and computationally remove transcripts from the sample. By removing the labeled transcripts from the dataset of cells isolated from the hippocampus via enzymatic dissociation, we observe that an “activated microglia” subtype merges with the general microglia population.

Recent research demonstrated that besides a role in sex determination and male fertility, the Y chromosome is involved in additional functions including prostate cancer, sex-specific effects on the brain and behaviour, graft-versus-host disease, nociception, aggression and autoimmune diseases. The results presented in this thesis include an analysis of sex-biased genes encoded on the X and Y chromosomes of rodents. Expression data from six different somatic tissues was analyzed and we found that the X chromosome is enriched in female biased genes and depleted of male biased ones. The second study described copy number variation (CNV) patterns in a world-wide collection of human Y chromosome samples. Contrary to expectations, duplications and not deletions were the most frequent variations. We also discovered novel CNV patterns of which some were significantly overrepresented in specific haplogroups. A substantial part of the thesis focuses on analysis of spatial expression of two Y-encoded brain-specific genes, namely PCDH11Y and NLGN4Y. The perhaps most surprising discovery was the observation that X and Y transcripts of both gene pairs are mostly expressed in different cells in human spinal cord and medulla oblongata. Also, we detected spatial expression differences for the PCDH11X gene in spinal cord. The main focus of the spatial investigations was to uncover genetically coded sexual differences in expression during early development of human central nervous system (CNS). Also, investigations of the expression profiles for 13 X and Y homolog gene pairs in human CNS, adult brain, testes and still-born chimpanzee brain samples were included. Contrary to previous studies, we found only three X-encoded genes from the 13 X/Y homologous gene pairs studied that exhibit female-bias. We also describe six novel non-coding RNAs encoded in the human MSY, some of which are polyadenylated and with conserved expression in chimpanzee brain. The description of dimorphic cellular expression patterns of X- and Y-linked genes should boost the interest in the human specific gene PCDH11Y, and draw attention to other Y-encoded genes expressed in the brain during development. This may help to elucidate the role of the Y chromosome in sex differences during early CNS development in humans. / <p>chinese, finnish, norwegian, schizophrenia, bipolar, bipolar disorder, msy, male specific region Y, PAR1, PAR2, pseudoautosomal, male-biased, female-biased, male biased, female biased, ashkenazi population, structure, variants, YHRD, Elena Jazin, Björn Reinius, Per Ahlberg, brain, hjärna, CNS, central nervous system, IR2, inverted repeat 2, isodicentric, genetics, genetik, padlock, rolling circle, amplification, PCR, sY1191, sY1291, STS, DDX3Y, DAZ, AZFa, AZFb, AZFc, AZF, Repping, haplogroup J, rearrangements, DE-M145, I-M170, E-M96, Q-M242, R-M207, O-M175, G-M201, D-M174, C-M130, NO-M214, N-M231, poland</p>

Traumatic brain injury (TBI) is a leading cause of disability worldwide. Annually, 150 to 200/1,000,000 people become disabled as a result of brain trauma. Axonal degeneration is a critical, early event following TBI of all severities but whether axon degeneration is a driver of TBI remains unclear. Molecular pathways underlying the pathology of TBI have not been defined and there is no efficacious treatment for TBI. Despite this significant societal impact, surprisingly little is known about the molecular mechanisms that actively drive axon degeneration in any context and particularly following TBI. Although severe brain injury may cause immediate disruption of axons (primary axotomy), it is now recognized that the most frequent form of traumatic axonal injury (TAI) is mediated by a cascade of events that ultimately result in secondary axonal disconnection (secondary axotomy) within hours to days. Proposed mechanisms include immediate post-traumatic cytoskeletal destabilization as a direct result of mechanical breakage of microtubules, as well as catastrophic local calcium dysregulation resulting in microtubule depolymerization, impaired axonal transport, unmitigated accumulation of cargoes, local axonal swelling, and finally disconnection. The portion of the axon that is distal to the axotomy site remains initially morphologically intact. However, it undergoes sudden rapid fragmentation along its full distal length ~72 h after the original axotomy, a process termed Wallerian degeneration. Remarkably, mice mutant for the Wallerian degeneration slow (Wlds) protein exhibit ~tenfold (for 2–3 weeks) suppressed Wallerian degeneration. Yet, pharmacological replication of the Wlds mechanism has proven difficult. Further, no one has studied whether Wlds protects from TAI. Lastly, owing to Wlds presumed gain-of-function and its absence in wild-type animals, direct evidence in support of a putative endogenous axon death signaling pathway is lacking, which is critical to identify original treatment targets and the development of viable therapeutic approaches. Novel insight into the pathophysiology of Wallerian degeneration was gained by the discovery that mutant Drosophila flies lacking dSarm (sterile a/Armadillo/Toll-Interleukin receptor homology domain protein) cell-autonomously recapitulated the Wlds phenotype. The pro-degenerative function of the dSarm gene (and its mouse homolog Sarm1) is widespread in mammals as shown by in vitro protection of superior cervical ganglion, dorsal root ganglion, and cortical neuron axons, as well as remarkable in-vivo long-term survival (>2 weeks) of transected sciatic mouse Sarm1 null axons. Although the molecular mechanism of function remains to be clarified, its discovery provides direct evidence that Sarm1 is the first endogenous gene required for Wallerian degeneration, driving a highly conserved genetic axon death program. The central goals of this thesis were to determine (1) whether post-traumatic axonal integrity is preserved in mice lacking Sarm1, and (2) whether loss of Sarm1 is associated with improved functional outcome after TBI. I show that mice lacking the mouse Toll receptor adaptor Sarm1 gene demonstrate multiple improved TBI-associated phenotypes after injury in a closed-head mild TBI model. Sarm1-/- mice developed fewer beta amyloid precursor protein (βAPP) aggregates in axons of the corpus callosum after TBI as compared to Sarm1+/+ mice. Furthermore, mice lacking Sarm1 had reduced plasma concentrations of the phosphorylated axonal neurofilament subunit H, indicating that axonal integrity is maintained after TBI. Strikingly, whereas wild type mice exhibited a number of behavioral deficits after TBI, I observed a strong, early preservation of neurological function in Sarm1-/- animals. Finally, using in vivo proton magnetic resonance spectroscopy, I found tissue signatures consistent with substantially preserved neuronal energy metabolism in Sarm1-/- mice compared to controls immediately following TBI. My results indicate that the Sarm1-mediated prodegenerative pathway promotes pathogenesis in TBI and suggest that anti-Sarm1 therapeutics are a viable approach for preserving neurological function after TBI.

Indiana University-Purdue University Indianapolis (IUPUI) / Magnetic resonance (MR) spectroscopy is a neuroimaging technique. It is widely used to quantify the concentration of important metabolites in a brain tissue. Imbalance in concentration of brain metabolites has been found to be associated with development of neurological impairment. There has been increasing trend of using MR spectroscopy as a diagnosis tool for neurological disorders. We established statistical methodology to analyze data obtained from the MR spectroscopy in the context of the HIV associated neurological disorder. First, we have developed novel methodology to study the association of marker of neurological disorder with MR spectrum from brain and how this association evolves with time. The entire problem fits into the framework of scalar-on-function regression model with individual spectrum being the functional predictor. We have extended one of the existing cross-sectional scalar-on-function regression techniques to longitudinal set-up. Advantage of proposed method includes: 1) ability to model flexible time-varying association between response and functional predictor and (2) ability to incorporate prior information. Second part of research attempts to study the influence of the clinical and demographic factors on the progression of brain metabolites over time. In order to understand the influence of these factors in fully non-parametric way, we proposed LongCART algorithm to construct regression tree with longitudinal data. Such a regression tree helps to identify smaller subpopulations (characterized by baseline factors) with differential longitudinal profile and hence helps us to identify influence of baseline factors. Advantage of LongCART algorithm includes: (1) it maintains of type-I error in determining best split, (2) substantially reduces computation time and (2) applicable even observations are taken at subject-specific time-points. Finally, we carried out an in-depth analysis of longitudinal changes in the brain metabolite concentrations in three brain regions, namely, white matter, gray matter and basal ganglia in chronically infected HIV patients enrolled in HIV Neuroimaging Consortium study. We studied the influence of important baseline factors (clinical and demographic) on these longitudinal profiles of brain metabolites using LongCART algorithm in order to identify subgroup of patients at higher risk of neurological impairment. / Partial research support was provided by the National Institutes of Health grants U01-MH083545, R01-CA126205 and U01-CA086368