Functional Gene-Expression Analysis Shows Involvement of Schizophrenia-Relevant Pathways in Patients with 22q11 Deletion Syndrome

22q11 Deletion Syndrome (22q11DS) is associated with dysmorphology and a high prevalence of schizophrenia-like symptoms. Several genes located on chromosome 22q11 have been linked to schizophrenia. The deletion is thought to disrupt the expression of multiple genes involved in maturation and development of neurons and neuronal circuits, and neurotransmission. We investigated whole-genome gene expression of Peripheral Blood Mononuclear Cells (PBMC's) of 8 22q11DS patients and 8 age- and gender-matched controls, to (1) investigate the expression levels of 22q11 genes and (2) to investigate whether 22q11 genes participate in functional genetic networks relevant to schizophrenia. Functional relationships between genes differentially expressed in patients (as identified by Locally Adaptive Statistical procedure (LAP) or satisfying p<0.05 and fold-change >1.5) were investigated with the Ingenuity Pathways Analysis (IPA). 14 samples (7 patients, 7 controls) passed quality controls. LAP identified 29 deregulated genes. Pathway analysis showed 262 transcripts differentially expressed between patients and controls. Functional pathways most disturbed were cell death, cell morphology, cellular assembly and organization, and cell-to-cell signaling. In addition, 10 canonical pathways were identified, among which the signal pathways for Natural Killer-cells, neurotrophin/Trk, neuregulin, axonal guidance, and Huntington's disease. Our findings support the use of 22q11DS as a research model for schizophrenia. We identified decreased expression of several genes (among which COMT, Ufd1L, PCQAP, and GNB1L) previously linked to schizophrenia as well as involvement of signaling pathways relevant to schizophrenia, of which Neurotrophin/Trk and neuregulin signaling seems to be especially notable

Multi-site genetic analysis of diffusion images and voxelwise heritability analysis : a pilot project of the ENIGMA–DTI working group

The ENIGMA (Enhancing NeuroImaging Genetics through Meta-Analysis) Consortium was set up to analyze brain measures and genotypes from multiple sites across the world to improve the power to detect genetic variants that influence the brain. Diffusion tensor imaging (DTI) yields quantitative measures sensitive to brain development and degeneration, and some common genetic variants may be associated with white matter integrity or connectivity. DTI measures, such as the fractional anisotropy (FA) of water diffusion, may be useful for identifying genetic variants that influence brain microstructure. However, genome-wide association studies (GWAS) require large populations to obtain sufficient power to detect and replicate significant effects, motivating a multi-site consortium effort. As part of an ENIGMA–DTI working group, we analyzed high-resolution FA images from multiple imaging sites across North America, Australia, and Europe, to address the challenge of harmonizing imaging data collected at multiple sites. Four hundred images of healthy adults aged 18–85 from four sites were used to create a template and corresponding skeletonized FA image as a common reference space. Using twin and pedigree samples of different ethnicities, we used our common template to evaluate the heritability of tract-derived FA measures. We show that our template is reliable for integrating multiple datasets by combining results through meta-analysis and unifying the data through exploratory mega-analyses. Our results may help prioritize regions of the FA map that are consistently influenced by additive genetic factors for future genetic discovery studies. Protocols and templates are publicly available at (http://enigma.loni.ucla.edu/ongoing/dti-working-group/)

Geenid ja alkoholitarvitamine: levinud geenipolümorfismide mõju rahvastikus

Väitekirja elektrooniline versioon ei sisalda publikatsioone.Alkoholi kuritarvitamine on üks peamistest ennetatavate surmade ja terviserikete põhjustajatest. Lähtuvalt sellest, kui palju probleeme tekib tarvitajale endale ja teda ümbritsevatele, on alkohol loetud kõige kahjulikumaks uimastiks1. Kuigi olukord on tasapisi paranemas, paistab Eesti rahvusvahelisel tasandil veel jätkuvalt silma ohtra alkoholitarbimisega2. Mehed tarvitavad alkoholi ning kogevad alkoholiga seotud probleeme enamasti rohkem kui naised. Nii ka meie rahvastikupõhises pikaajalises sünnikohortide uuringus – poisid alustasid alkoholi tarvitamisega varem ning tegelesid sellega sagedamini kui tüdrukud. Nooreks täiskasvanueaks oli selle tulemusena meeste seas tunduvalt rohkem neid, kes alkoholi kuritarvitamisega hädas. Alkoholiprobleemide kogemise tõenäosust tõstsid ka stressirikkad elusündmused ning halvad suhted pereliikmete ja õpetajatega. Kuna alkoholism on krooniline ja ravile raskesti alluv, on selle haiguse tekkimist ennustavate bioloogiliste näitajate uurimine äärmiselt päevakajaline. Analüüsides geenide mõju alkoholitarbimisele, leidsime, et probleemset alkoholitarbimist ennustasid just sellised geneetilised eripärad, mis olid seotud madalama stressitaluvuse ja suurema avatusega keskkondlike mõjude suhtes. Seosed ei olnud aga üleüldised ja sõltusid suures osas sünnikohordist – perioodist, mil inimene sündinud oli. Sotsiaalsed normid ja hoiakud alkoholi tarbimisse koonduvad sünnikohortide kaupa ning mõjutavad otseselt uimastite tarvitamist. 1990. aastatel alguse saanud kiired ühiskondlikud muutused mõjutavad meie siirdeühiskonnas väärtushinnanguid, vaba aja tegevusi, suhteid ja igapäevast toimetulekut. Kultuurilised ja ühiskondlikud muutused vormivad pidevalt inimeste identiteeti ja elustiili ning võivad vahendada ka geeniefekte alkoholitarbimisele. [1 Nutt DJ, King LA, Phillips LD (2010) Drug harms in the UK: a multicriteria decision analysis. Lancet 376:1558-1565. 2 OECD (2015) Tackling harmful alcohol use: Economics and public health policy. OECD Publishing.]Problematic use of alcohol is one of the leading causes of preventable deaths and disability. Based on the harm to the user and others, alcohol has been considered to be the most harmful drug1. Men generally drink more alcohol and have more alcohol-related problems than women. Also in our population-representative longitudinal birth cohort study in Estonia, the boys started consuming alcohol earlier and were more frequent alcohol consumers than girls. By young adulthood, there were significantly more men than women diagnosed with alcohol use disorder. The more frequent was the alcohol consumption during the teenage years, the more problable was the occurrence of alcohol problems by young adulthood. In addition, the more stressful life events, the worse relationships with family members and with teachers the children experienced, the higher was the likelihood of developing alcohol use problems later on in life. The chronic nature of alcoholism is the reason why the search for predictive biomarkers is so urgent. When we analyzed the effects of common genetic variances on alcohol use and abuse, the genotypes associated with higher levels of stress reactivity and openness to environmental influences were the ones also linked to problematic alcohol use. However, the relations were not universal and strongly depended on birth cohort – the time period when one was born. Social norms and attitudes regarding alcohol use cluster in birth cohorts, and this clustering has a direct effect on drug use. The rapid socioeconomic changes that have taken place in Estonia since the beginning of 1990s and are still ongoing affect the values, activities, relationships, leisure time choices and everyday functioning of the people living in this transition society. Cultural transformation processes continuously shape the identities and lifestyles of individuals, and can also moderate the genetic effects on alcohol consumption. [1 Nutt DJ, King LA, Phillips LD (2010) Drug harms in the UK: a multicriteria decision analysis. Lancet 376:1558-1565.

Investigating the Roles of Poly (ADP-ribose) Polymerase 1 in Cortical Development

Poly (ADP-ribose) polymerase 1 (PARP1) is a ubiquitously expressed enzyme that post-translationally modifies proteins via poly (ADP-ribosylation) (PARylation). PARP1 serves various functions, including DNA damage repair, regulation of cell death pathways, chromatin modification, RNA processing, and transcriptional regulation. Accordingly, mutations in Parp1 or Adprhl2 (encoding the protein ADP-ribosylhydrolase 3, which removes PAR polymers) cause intellectual disability, ataxia, episodic psychosis, neurodegeneration, and developmental delay. Altered PARP1 expression is also associated with numerous neurodegenerative and neuroimmune disorders, including Alzheimer's disease, Parkinson's disease, multiple sclerosis, rheumatoid arthritis, major depressive disorder, and epilepsy. Despite ubiquitous expression and an apparent connection with brain disorders, PARP1's role in neurodevelopment has not been widely studied. Our lab has recently uncovered a novel interaction between PARP1 and the receptor tyrosine kinase ErbB4, which binds its ligand NRG1 to mediate numerous functions during neurodevelopment, including radial migration of excitatory neurons, tangential migration of inhibitory neurons, synaptogenesis, and differentiation. Additionally, ErbB4 has multiple splice forms that confer different signaling modalities. Specifically, the ErbB4-juxtamembrane (JM)-a isoform is cleavable via the enzymes tumor necrosis factor-alpha (TACE) and presenilin/gamma-secretase. Upon NRG1 binding and ErbB4-JMa cleavage, the ErbB4 intracellular domain (E4ICD) is released, which regulates transcription through direct promoter binding. Previous findings have shown that E4ICD complexes with co-factors to repress gliogenesis during early development. Due to PARP1's prominent roles in chromatin modification and transcriptional control, this begs the question as to whether PARP1 is likewise regulating glial gene expression via E4ICD. The aims of this dissertation are two-fold: 1) investigate the role of PARP1 in regulating astrocytic gene expression via E4ICD and 2) further characterize the effect of PARP1 loss on brain development. To explore the role of PARP1-E4ICD in the regulation of astrogenesis, I utilized mouse primary embryonic neural precursor cell (NPC) cultures and transgenic mice with a germline knockout of PARP1, ErbB4, or ErbB4-JMa. I found that NRG1-mediated repression of GFAP expression upon FGF removal from NPC cultures was dependent upon the presence of PARP1, ErbB4, and ErbB4-JMa. Additionally, I showed that PARP1 KO and ErbB4 KO mice overexpress GFAP at birth, indicating the importance of both proteins in vivo. To investigate the effect of PARP1 loss on neurodevelopment more broadly, I analyzed the brain and cortical size of PARP1 KO mice at birth, finding a reduction in brain weight relative to body size, which is associated with a thinner cortex and a reduced cortical surface area. Furthermore, I discovered that PARP1 loss alters early-born neuron migration and increases the density of deeper-layer neurons. To investigate changes in gene expression associated with these findings, I performed RNA-sequencing of the embryonic PARP1 KO cortex. I found that PARP1 loss increases the expression of genes involved in neuronal migration and adhesion, including Reln, which encodes the glycoprotein Reelin. Accordingly, my findings indicate that PARP1 loss increases the abundance of Reelin-expressing cells in the developing (E15.5) and adolescent (P5) mouse brain. I further demonstrated that PARP1 loss, inhibition, or acute knockdown increases Cajal-Retzius cell abundance in vitro, suggesting PARP1 regulates Cajal-Retzius cell development via a cell-autonomous mechanism. Finally, atomic force microscopy showed that NPCs isolated from the PARP1 KO cortex adhere more strongly to the cell adhesion molecule N-cadherin, likely due to excess Reelin. Overall, these findings demonstrate that PARP1 regulates astrogenesis, Cajal-Retzius cell development, and cell adhesion in the developing brain.PHDNeuroscienceUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/169918/1/mmnels_1.pd