Die Bildung neuen Nervenzellen im erwachsenen Gehirn—adulte Neurogenese—ist bei Säugetieren auf spezifische Regionen beschränkt. Eine der beiden bekannten ist der Hippokampus, eine Gehirnstruktur, die eine wichtige Rolle beim Lernen sowie der Gedächtnisbildung spielt. Ein Reservoir von neuralen Stammzellen befindet sich in der subgranulären Zone des hippokampalen Gyrus dentatus. Diese Zellen teilen sich fortwährend und bilden neue Nervenzellen. Die Regulation adulter hippokampaler Neurogenese wird sowohl von der Umgebung beeinflusst als auch von mehreren Genen gesteuert.
In der vorliegenden Arbeit wurden mittels Hochdurchsatz- Genexpressionsverfahren die an der Neurogenese beteiligten Gene identifiziert und ihr Zusammenspiel untersucht. Anhand von genetischen, umgebungsbedingten und zeitlichen Angaben und Variationen wurde ein vielseitiger Datensatz erstellt, der einen multidimensionalen Blick auf den proliferativen Phänotyp verschafft. Netzwerke aus Gen-Gen und Gen-Phänotyp Interaktionen wurden beschrieben und in einer mehrschichtigen Ressource zusammengefasst. Ein Kern-Netzwerk bestehend aus immerwiederkehrenden Modulen aus verschiedenen Ebenen wurde anhand von Proliferation als Keim-Phänotyp identifiziert. Aus diesem Kern-Netzwerk sind neue Gene und ihre Interaktionen hervorgegangen, die potentiell bei der Regulierung adulter Neurogenesis beteiligt sind.:Zusammenfassung i
Abstract iii
Acknowledgements vii
Contents ix
Preface xiii
General Introduction 1
Adult Neurogenesis 1
Historical setting 1
Neurogenesis exists in two regions of the adult mammalian brain 1
Implications of neurogenesis in the hippocampus 1
The Hippocampal Formation 2
Function of the hippocampus in learning and memory 2
The functional role of adult neurogenesis 2
Anatomy of the hippocampal formation 2
Neural Precursor Biology 3
The subgranular zone as a neurogenic niche 3
Neuronal maturation is a multi-step pathway 3
Regulation of Adult Neurogenesis 3
Neurogenesis is modulated by age 3
Neurogenesis is modulated by environmental factors 4
Neurogenesis is modulated by genetic background 4
Genetics of the BXD RI Cross 5
C57BL/6 and DBA/2 5
Recombinant Inbred Lines 5
The BXD panel 6
Quantitative genetics 6
Microarray Analysis 7
The concept of ‘whole genome’ expression analysis 7
Technical considerations 8
Theoretical considerations 9
Current Analytical Methods 9
Network Analysis 10
Network Description and Terminology 10
Graph Theory 10
Multiple-Network Comparison 11
Biological networks 11
Types of Biological Network 11
Sources of Network Data 12
Biological Significance of Networks 12
Aim of the current work 13
Methods and Materials 15
Animals 15
BXD panel 15
Progenitor strains 15
Animal behaviour 15
Running wheel activity 15
Enriched environment 16
Morris water maze 16
Open field test 16
Corticosterone assay 16
Histology 17
Tissue collection 17
BrdU staining 17
Statistics 17
Cell culture 18
Maintenance and differentiation 18
Immunostaining 18
RNA isolation 18
Microarray processing 18
Affymetrix arrays 18
M430v2 probe reannotation 19
Illumina arrays 19
Illumina probe reannotation 19
Bioinformatics 19
Translating the STRING network 19
QTL mapping 20
Network graph layout 20
Triplot 20
Enrichment analysis 20
Mammalian Adult Neurogenesis Gene Ontology 21
Introduction 21
Results 25
The cell stage ontology 25
The process ontology 25
Genes known to regulate hippocampal adult neurogenesis 26
Enrichment analysis 27
The MANGO gene network 27
Discussion 28
Hippocampal Coexpression Networks from the BXD Panel 31
Introduction 31
Results 32
Variation and covariation of gene expression across a panel of inbred lines 32
A hippocampal expression correlation network 32
Diverse neurogenesis phenotypes associate with discrete transcript networks 34
Discussion 34
Interactions Between Gene Expression Phenotypes and Genotype 37
Introduction 37
Results 39
QTL analysis and interval definitions 39
Pleiotropic loci and ‘trans-bands’ 39
Transcript expression proxy-QTLs can help in dissection of complex phenotypes 41
Interaction network 43
Discussion 43
Strain-Dependent Effects of Environment 47
Introduction 47
Results 48
Effects of strain and environment on precursor cell proliferation 48
Effects of strain and environment on learning behaviour 52
Transcript expression associated with different housing environments 53
Strain differences in transcript regulation 55
Distance-weighted coexpression networks 57
Discussion 58
Expression Time Course from Differentiating Cell Culture 61
Introduction 61
Results 63
Differentiation of proliferating precursors into neurons in vitro 63
Transcripts associated with stages of differentiation 63
Early events in NPC differentiation 64
A network of transcript coexpression during in vitro differentiation 66
Discussion 67
Integrated Gene Interaction Networks 71
Introduction 71
Results 72
Description of network layers 72
Merging of network layers to a multigraph 74
A network of genes controls neural precursor proliferation in the adult hippocampus 75
Novel candidate regulators of adult hippocampal neurogenesis 77
Novel pathways regulating adult hippocampal neurogenesis 77
Discussion 79
General Discussion 81
References 89
Selbständigkeitserklärung 107 / Neurogenesis, the production of new neurons, is restricted in the adult brain of mammals to only a few regions. One of these sites of adult neurogenesis is the hippocampus, a structure essential for many types of learning. A pool of stem cells is maintained in the subgranular zone of the hippocampal dentate gyrus which proliferate and can differentiate into new neurons, astrocytes and oligodendroctytes. Regulation of adult hippocampal neurogenesis occurs in response to en- vironmental stimuli and is under the control of many genes.
This work employs high-throughput gene expression technologies to identify these genes and their interactions with each other and the neurogenesis phenotype. Harnessing variation from genetic, environmental and temporal sources, a multi-faceted dataset has been generated which offers a multidimensional view of the neural precursor proliferation phenotype. Networks of gene-gene and gene-phenotype interac- tions have been described and merged into a multilayer resource. A core subnetwork derived from modules recurring in the different layers has been identified using the proliferation phenotype as a seed. This subnetwork has suggested novel genes and interactions potentially involved in the regulation of adult hippocampal neurogenesis.:Zusammenfassung i
Abstract iii
Acknowledgements vii
Contents ix
Preface xiii
General Introduction 1
Adult Neurogenesis 1
Historical setting 1
Neurogenesis exists in two regions of the adult mammalian brain 1
Implications of neurogenesis in the hippocampus 1
The Hippocampal Formation 2
Function of the hippocampus in learning and memory 2
The functional role of adult neurogenesis 2
Anatomy of the hippocampal formation 2
Neural Precursor Biology 3
The subgranular zone as a neurogenic niche 3
Neuronal maturation is a multi-step pathway 3
Regulation of Adult Neurogenesis 3
Neurogenesis is modulated by age 3
Neurogenesis is modulated by environmental factors 4
Neurogenesis is modulated by genetic background 4
Genetics of the BXD RI Cross 5
C57BL/6 and DBA/2 5
Recombinant Inbred Lines 5
The BXD panel 6
Quantitative genetics 6
Microarray Analysis 7
The concept of ‘whole genome’ expression analysis 7
Technical considerations 8
Theoretical considerations 9
Current Analytical Methods 9
Network Analysis 10
Network Description and Terminology 10
Graph Theory 10
Multiple-Network Comparison 11
Biological networks 11
Types of Biological Network 11
Sources of Network Data 12
Biological Significance of Networks 12
Aim of the current work 13
Methods and Materials 15
Animals 15
BXD panel 15
Progenitor strains 15
Animal behaviour 15
Running wheel activity 15
Enriched environment 16
Morris water maze 16
Open field test 16
Corticosterone assay 16
Histology 17
Tissue collection 17
BrdU staining 17
Statistics 17
Cell culture 18
Maintenance and differentiation 18
Immunostaining 18
RNA isolation 18
Microarray processing 18
Affymetrix arrays 18
M430v2 probe reannotation 19
Illumina arrays 19
Illumina probe reannotation 19
Bioinformatics 19
Translating the STRING network 19
QTL mapping 20
Network graph layout 20
Triplot 20
Enrichment analysis 20
Mammalian Adult Neurogenesis Gene Ontology 21
Introduction 21
Results 25
The cell stage ontology 25
The process ontology 25
Genes known to regulate hippocampal adult neurogenesis 26
Enrichment analysis 27
The MANGO gene network 27
Discussion 28
Hippocampal Coexpression Networks from the BXD Panel 31
Introduction 31
Results 32
Variation and covariation of gene expression across a panel of inbred lines 32
A hippocampal expression correlation network 32
Diverse neurogenesis phenotypes associate with discrete transcript networks 34
Discussion 34
Interactions Between Gene Expression Phenotypes and Genotype 37
Introduction 37
Results 39
QTL analysis and interval definitions 39
Pleiotropic loci and ‘trans-bands’ 39
Transcript expression proxy-QTLs can help in dissection of complex phenotypes 41
Interaction network 43
Discussion 43
Strain-Dependent Effects of Environment 47
Introduction 47
Results 48
Effects of strain and environment on precursor cell proliferation 48
Effects of strain and environment on learning behaviour 52
Transcript expression associated with different housing environments 53
Strain differences in transcript regulation 55
Distance-weighted coexpression networks 57
Discussion 58
Expression Time Course from Differentiating Cell Culture 61
Introduction 61
Results 63
Differentiation of proliferating precursors into neurons in vitro 63
Transcripts associated with stages of differentiation 63
Early events in NPC differentiation 64
A network of transcript coexpression during in vitro differentiation 66
Discussion 67
Integrated Gene Interaction Networks 71
Introduction 71
Results 72
Description of network layers 72
Merging of network layers to a multigraph 74
A network of genes controls neural precursor proliferation in the adult hippocampus 75
Novel candidate regulators of adult hippocampal neurogenesis 77
Novel pathways regulating adult hippocampal neurogenesis 77
Discussion 79
General Discussion 81
References 89
Selbständigkeitserklärung 107
| Identifer | oai:union.ndltd.org:DRESDEN/oai:qucosa:de:qucosa:28652 |
| Date | 30 January 2015 |
| Creators | Overall, Rupert |
| Contributors | Kempermann, Gerd, Brand, Michael, Williams, Robert, Technische Universität Dresden |
| Source Sets | Hochschulschriftenserver (HSSS) der SLUB Dresden |
| Language | English |
| Detected Language | English |
| Type | doc-type:doctoralThesis, info:eu-repo/semantics/doctoralThesis, doc-type:Text |
| Rights | info:eu-repo/semantics/openAccess |
Page generated in 0.0027 seconds