Neurogenetics
Exam
Mondeling met schriftelijke voorbereiding
Written exam with oral explanation
- 3 open questions
- Questions where you need discuss/apply the theory
- Links some things together; fill in words,…
Contents
Introduction to Neurogenetics........................................................................................................... 7
Neurological disorders are a major health problem ....................................................................... 7
Classification of neurological disorders .......................................................................................... 7
Overall ....................................................................................................................................... 7
Movement disorders ................................................................................................................. 8
Dementias ................................................................................................................................. 8
Disease of white matter ............................................................................................................. 8
Neuromuscular disorders........................................................................................................... 9
Paroxysmal disorders ................................................................................................................. 9
Neurodevelopmental disorders ................................................................................................. 9
Neurocutaneous disorders (phakomatoses) ............................................................................. 10
Cerebrovascular diseases ......................................................................................................... 10
Major adult psychiatric disorders ............................................................................................. 10
Unifying themes in neurological disorders ................................................................................... 10
Factors suggesting a neurogenetic disorder ................................................................................. 10
Inheritance patterns in neurological disorders ............................................................................. 11
Autosomal dominant ............................................................................................................... 11
Autosomal recessive ................................................................................................................ 11
X-linked dominant ................................................................................................................... 11
X-linked recessive .................................................................................................................... 11
Y-linked inheritance ................................................................................................................. 12
Examples ................................................................................................................................. 12
Most patients/families affected by neurological disorders do not have clear inheritance pattern
................................................................................................................................................ 13
From monogenic disorders to complex diseases ...................................................................... 13
Gene discovery ............................................................................................................................ 14
1
, Impact of gene discovery ......................................................................................................... 14
Classical linkage approaches in families – linkage analysis ........................................................ 14
Population genetics ................................................................................................................. 15
Example – Amyotrophic lateral sclerosis...................................................................................... 19
Most neurological diseases are genetically heterogeneous with multiple modes of inheritance –
eg ALS ...................................................................................................................................... 19
Familial ALS genes.................................................................................................................... 19
Oligogenic basis of ALS............................................................................................................. 20
Gene x environment interaction in ALS .................................................................................... 20
ALS risk genes identified through GWAS .................................................................................. 21
Polygenic risk score suggest genetic overlap between ALS and schizophrenia ........................ 21
Exome sequencing study in ALS identified TBK1 mutations ...................................................... 21
Types of disease-causing genetic variation................................................................................... 21
Classification of mutations by their effects on the DNA molecule ............................................. 21
Mutations affecting the coding sequence ................................................................................ 22
Mutations affecting the non-coding regions............................................................................. 23
Example – microtubule associated protein tau gene (MAPT) .................................................... 24
Key concepts ............................................................................................................................... 25
Genetic mechanisms ....................................................................................................................... 26
Genetic mechanisms in neurological disorders ............................................................................ 26
Loss-of-function mutations .......................................................................................................... 26
Gain-of-function mutations ......................................................................................................... 26
Examples ..................................................................................................................................... 27
Example 1: Spinal muscular atrophy (SMA) .............................................................................. 27
Example 2: CADASIL ................................................................................................................. 28
Example 3: Alexander disease .................................................................................................. 31
Example 4: NPTX1 in cerebellar ataxia ..................................................................................... 33
Example 5: TBK1 mutations in ALS ........................................................................................... 35
Mechanisms of mutations affecting non-coding regions .............................................................. 37
Introduction ............................................................................................................................ 37
ALS and FTLD-TDP share common pathology – TDP43 pathology ............................................. 37
Transcriptomic analysis of TDP43-negative neurons................................................................. 37
Identification of cryptic exons in neurons without TDP-43....................................................... 38
TDP-43 loss induces cryptic splicing of UNC13A in vitro ............................................................ 38
Most significant UNC13A risk variant is located in non- coding region located in cryptic exon . 39
Role of epigenetics in neurological disorders ............................................................................... 39
2
, Epigenetics .............................................................................................................................. 39
Example - Facioscapulohumeral muscular dystrophy (FSHD ..................................................... 40
Mosaic mutations in neurological disorders ................................................................................. 42
De novo and mosaic mutations ................................................................................................ 42
Facts about mosaic mutations in brain ..................................................................................... 42
Example 1: possible somatic mutations in ALS family ............................................................... 43
Example 2: focal cortical dysplasia ........................................................................................... 43
Example question .................................................................................................................... 43
Example 3: ‘second hit’ somatic mutations produce mosaicsm ................................................ 44
Role of mitochondrial genome in neurological diseases ............................................................... 44
General.................................................................................................................................... 44
Mitochondrial mutations ......................................................................................................... 44
Mitochondrial genome analysis ............................................................................................... 45
Example questions....................................................................................................................... 45
Key Concepts ............................................................................................................................... 45
Repeat expansion disorders............................................................................................................. 46
What are tandem repeat expansions ........................................................................................... 46
General.................................................................................................................................... 46
Tandem repeat unit sizes ......................................................................................................... 46
Many tandem repeats are unstable ......................................................................................... 46
Some tandem repeats are pathogenic ..................................................................................... 47
Anticipation ............................................................................................................................. 47
Timelines of discoveries ........................................................................................................... 47
Lab methods for tandem repeats ................................................................................................. 48
Southern blotting..................................................................................................................... 48
PCR .......................................................................................................................................... 48
Repeat-primer PCR .................................................................................................................. 49
Short-read sequencing ............................................................................................................. 49
Long-read sequencing .............................................................................................................. 50
Intermezzo on human genetic variation and sequencing methods ........................................... 50
RNA-fish .................................................................................................................................. 50
Repeats and neurological diseases............................................................................................... 51
Location of pathogenic expansions matters ............................................................................. 51
Huntington’s disease ............................................................................................................... 52
Spinocerebellar ataxia ............................................................................................................. 52
Familiar adult myoclonic epilepsy (FAME) ................................................................................ 55
3
, AD risk-associated VNTR expansion in ABCA7 .......................................................................... 56
Regulatory effects.................................................................................................................... 56
key concepts................................................................................................................................ 57
Genetic disease modifiers................................................................................................................ 58
Definitions ................................................................................................................................... 58
Intro ........................................................................................................................................ 58
Illustration of the power of (genetic) modifiers ........................................................................ 58
Definitions of genetic modifier ................................................................................................. 58
Genetic modifier vs oligogenic disease ..................................................................................... 59
Approaches to identify genetic disease modifiers ........................................................................ 59
Intro ........................................................................................................................................ 59
Considerations......................................................................................................................... 59
Through human/population studies ............................................................................................. 59
Example 1: Spinal muscular atrophy......................................................................................... 59
Example 2: Huntington’s disease (HD)...................................................................................... 61
Example 3: Frontotemporal dementia (FTD) ............................................................................ 65
Example 4: Progressive supranuclear palsy (PSP) ..................................................................... 66
Through model organism genetics ............................................................................................... 67
Discussion on importance of model validity ............................................................................. 67
Multifactorial validity in animal models ................................................................................... 68
Model organisms ..................................................................................................................... 68
Choice of model system is a balance between physiological relevance against cost and
throughput .............................................................................................................................. 69
Example 1: Peripheral Neuropathy (GAL4/UAS system Drosophila) .......................................... 69
Example 2: Parkinson’s disease (Drosophila Genetic Reference Panel) ..................................... 70
Example 3: TDP-43 and ALS (Yeast, Drosophila, human) – genetic modifier screen in model
systems with relevance for human disease .............................................................................. 71
Example 4: Duchenne Muscular Dystrophy (dog) ..................................................................... 74
Example 5: Epilepsy (mice)....................................................................................................... 75
Through functional assays ........................................................................................................... 76
Functional genomics ................................................................................................................ 76
Overview methods CRISPR/cas9 .............................................................................................. 77
Example 1: Toxicity dipeptide repeat proteins in C9orf72 disease ............................................ 78
Key concepts ............................................................................................................................... 79
Therapeutic strategies ..................................................................................................................... 80
Introduction to treating genetic neurological diseases ................................................................. 80
4
Exam
Mondeling met schriftelijke voorbereiding
Written exam with oral explanation
- 3 open questions
- Questions where you need discuss/apply the theory
- Links some things together; fill in words,…
Contents
Introduction to Neurogenetics........................................................................................................... 7
Neurological disorders are a major health problem ....................................................................... 7
Classification of neurological disorders .......................................................................................... 7
Overall ....................................................................................................................................... 7
Movement disorders ................................................................................................................. 8
Dementias ................................................................................................................................. 8
Disease of white matter ............................................................................................................. 8
Neuromuscular disorders........................................................................................................... 9
Paroxysmal disorders ................................................................................................................. 9
Neurodevelopmental disorders ................................................................................................. 9
Neurocutaneous disorders (phakomatoses) ............................................................................. 10
Cerebrovascular diseases ......................................................................................................... 10
Major adult psychiatric disorders ............................................................................................. 10
Unifying themes in neurological disorders ................................................................................... 10
Factors suggesting a neurogenetic disorder ................................................................................. 10
Inheritance patterns in neurological disorders ............................................................................. 11
Autosomal dominant ............................................................................................................... 11
Autosomal recessive ................................................................................................................ 11
X-linked dominant ................................................................................................................... 11
X-linked recessive .................................................................................................................... 11
Y-linked inheritance ................................................................................................................. 12
Examples ................................................................................................................................. 12
Most patients/families affected by neurological disorders do not have clear inheritance pattern
................................................................................................................................................ 13
From monogenic disorders to complex diseases ...................................................................... 13
Gene discovery ............................................................................................................................ 14
1
, Impact of gene discovery ......................................................................................................... 14
Classical linkage approaches in families – linkage analysis ........................................................ 14
Population genetics ................................................................................................................. 15
Example – Amyotrophic lateral sclerosis...................................................................................... 19
Most neurological diseases are genetically heterogeneous with multiple modes of inheritance –
eg ALS ...................................................................................................................................... 19
Familial ALS genes.................................................................................................................... 19
Oligogenic basis of ALS............................................................................................................. 20
Gene x environment interaction in ALS .................................................................................... 20
ALS risk genes identified through GWAS .................................................................................. 21
Polygenic risk score suggest genetic overlap between ALS and schizophrenia ........................ 21
Exome sequencing study in ALS identified TBK1 mutations ...................................................... 21
Types of disease-causing genetic variation................................................................................... 21
Classification of mutations by their effects on the DNA molecule ............................................. 21
Mutations affecting the coding sequence ................................................................................ 22
Mutations affecting the non-coding regions............................................................................. 23
Example – microtubule associated protein tau gene (MAPT) .................................................... 24
Key concepts ............................................................................................................................... 25
Genetic mechanisms ....................................................................................................................... 26
Genetic mechanisms in neurological disorders ............................................................................ 26
Loss-of-function mutations .......................................................................................................... 26
Gain-of-function mutations ......................................................................................................... 26
Examples ..................................................................................................................................... 27
Example 1: Spinal muscular atrophy (SMA) .............................................................................. 27
Example 2: CADASIL ................................................................................................................. 28
Example 3: Alexander disease .................................................................................................. 31
Example 4: NPTX1 in cerebellar ataxia ..................................................................................... 33
Example 5: TBK1 mutations in ALS ........................................................................................... 35
Mechanisms of mutations affecting non-coding regions .............................................................. 37
Introduction ............................................................................................................................ 37
ALS and FTLD-TDP share common pathology – TDP43 pathology ............................................. 37
Transcriptomic analysis of TDP43-negative neurons................................................................. 37
Identification of cryptic exons in neurons without TDP-43....................................................... 38
TDP-43 loss induces cryptic splicing of UNC13A in vitro ............................................................ 38
Most significant UNC13A risk variant is located in non- coding region located in cryptic exon . 39
Role of epigenetics in neurological disorders ............................................................................... 39
2
, Epigenetics .............................................................................................................................. 39
Example - Facioscapulohumeral muscular dystrophy (FSHD ..................................................... 40
Mosaic mutations in neurological disorders ................................................................................. 42
De novo and mosaic mutations ................................................................................................ 42
Facts about mosaic mutations in brain ..................................................................................... 42
Example 1: possible somatic mutations in ALS family ............................................................... 43
Example 2: focal cortical dysplasia ........................................................................................... 43
Example question .................................................................................................................... 43
Example 3: ‘second hit’ somatic mutations produce mosaicsm ................................................ 44
Role of mitochondrial genome in neurological diseases ............................................................... 44
General.................................................................................................................................... 44
Mitochondrial mutations ......................................................................................................... 44
Mitochondrial genome analysis ............................................................................................... 45
Example questions....................................................................................................................... 45
Key Concepts ............................................................................................................................... 45
Repeat expansion disorders............................................................................................................. 46
What are tandem repeat expansions ........................................................................................... 46
General.................................................................................................................................... 46
Tandem repeat unit sizes ......................................................................................................... 46
Many tandem repeats are unstable ......................................................................................... 46
Some tandem repeats are pathogenic ..................................................................................... 47
Anticipation ............................................................................................................................. 47
Timelines of discoveries ........................................................................................................... 47
Lab methods for tandem repeats ................................................................................................. 48
Southern blotting..................................................................................................................... 48
PCR .......................................................................................................................................... 48
Repeat-primer PCR .................................................................................................................. 49
Short-read sequencing ............................................................................................................. 49
Long-read sequencing .............................................................................................................. 50
Intermezzo on human genetic variation and sequencing methods ........................................... 50
RNA-fish .................................................................................................................................. 50
Repeats and neurological diseases............................................................................................... 51
Location of pathogenic expansions matters ............................................................................. 51
Huntington’s disease ............................................................................................................... 52
Spinocerebellar ataxia ............................................................................................................. 52
Familiar adult myoclonic epilepsy (FAME) ................................................................................ 55
3
, AD risk-associated VNTR expansion in ABCA7 .......................................................................... 56
Regulatory effects.................................................................................................................... 56
key concepts................................................................................................................................ 57
Genetic disease modifiers................................................................................................................ 58
Definitions ................................................................................................................................... 58
Intro ........................................................................................................................................ 58
Illustration of the power of (genetic) modifiers ........................................................................ 58
Definitions of genetic modifier ................................................................................................. 58
Genetic modifier vs oligogenic disease ..................................................................................... 59
Approaches to identify genetic disease modifiers ........................................................................ 59
Intro ........................................................................................................................................ 59
Considerations......................................................................................................................... 59
Through human/population studies ............................................................................................. 59
Example 1: Spinal muscular atrophy......................................................................................... 59
Example 2: Huntington’s disease (HD)...................................................................................... 61
Example 3: Frontotemporal dementia (FTD) ............................................................................ 65
Example 4: Progressive supranuclear palsy (PSP) ..................................................................... 66
Through model organism genetics ............................................................................................... 67
Discussion on importance of model validity ............................................................................. 67
Multifactorial validity in animal models ................................................................................... 68
Model organisms ..................................................................................................................... 68
Choice of model system is a balance between physiological relevance against cost and
throughput .............................................................................................................................. 69
Example 1: Peripheral Neuropathy (GAL4/UAS system Drosophila) .......................................... 69
Example 2: Parkinson’s disease (Drosophila Genetic Reference Panel) ..................................... 70
Example 3: TDP-43 and ALS (Yeast, Drosophila, human) – genetic modifier screen in model
systems with relevance for human disease .............................................................................. 71
Example 4: Duchenne Muscular Dystrophy (dog) ..................................................................... 74
Example 5: Epilepsy (mice)....................................................................................................... 75
Through functional assays ........................................................................................................... 76
Functional genomics ................................................................................................................ 76
Overview methods CRISPR/cas9 .............................................................................................. 77
Example 1: Toxicity dipeptide repeat proteins in C9orf72 disease ............................................ 78
Key concepts ............................................................................................................................... 79
Therapeutic strategies ..................................................................................................................... 80
Introduction to treating genetic neurological diseases ................................................................. 80
4
