Clinical Neuroscience – Summary
Inhoud
Brain development ....................................................................................................................................................................... 2
Methods: Transcriptomics ............................................................................................................................................................ 4
Leukodystrophies......................................................................................................................................................................... 7
Introduction of Concepts .......................................................................................................................................................... 7
Studying Disease Mechanisms – VWM as a case study............................................................................................................... 9
Development of Outcome Measures: Clinical Trials and Clinimetry ...........................................................................................11
Current Treatment(s) for Leukodystrophies ...............................................................................................................................14
Gene Therapy for Leukodystrophies .........................................................................................................................................17
Water Homeostasis in Leukodystrophies ..................................................................................................................................18
Multiple Sclerosis........................................................................................................................................................................21
Clinical Features of MS ............................................................................................................................................................21
Current Therapies in MS...........................................................................................................................................................23
Etiological Mechanisms and Neuropathy of MS ........................................................................................................................24
Clinical Imaging for MS ............................................................................................................................................................25
Imaging in MS..........................................................................................................................................................................26
Cognitive Dysfunction and Networks in MS ...............................................................................................................................27
Parkinson’s Disease ....................................................................................................................................................................29
Clinical Features of PD ............................................................................................................................................................29
Brain imaging and PD ..............................................................................................................................................................30
Current Therapies for PD .........................................................................................................................................................33
Disease Mechanisms in PD......................................................................................................................................................34
Neuropsychiatry..........................................................................................................................................................................37
Clinics of Obsessive Compulsive Disorder ...............................................................................................................................37
OCD Disease Models ..............................................................................................................................................................39
TMS in OCD: From Disease Model to Personalized Targeting ......................................................................................................42
Stress and Resilience in Health and Disease ............................................................................................................................45
Depression: (Novel) Strategies to Reduce its Huge Burden ........................................................................................................47
Biological Pathways of MDD ....................................................................................................................................................50
Glioma .......................................................................................................................................................................................52
Clinics of Neuro-Oncology.......................................................................................................................................................52
Methods: EEG .............................................................................................................................................................................55
,Brain development
Learning objectives
- Able to describe the landmarks in brain development
- Have knowledge of neurological disease resulting from a failure in this process
- Have basic knowledge about pediatric neurological development
Timeline
Pcd/w: post congenital days/weeks
- Neurogenesis
- Neuronal migration
Milestones in development
- Sitting without support (<0.5 y)
- Start walking alone (0.5 y)
- First words (0.5-1y)
- Social play with caregiver (<0.5 y)
- Demonstrating empathy (1 y)
- Self-awareness (1 y)
- Formation of episodic memories (3 y)
Psychiatric and neurological disorders have discrete ages of onset
Neurulation
- Neuroectodermal tissue differentiates from ectoderm → neuronal plate. Neural plate border: separation of ecto- and
neuroderm
- Neural plate bends dorsally: neural plate borders join → neural crest
- Closure of neural tube + neural crest disconnects from epidermis
o Neural crest cells: most of peripheral nervous system
- Notochord degenerate, persists as nucleus pulposus of intervertebral discs. Mesoderm cells differentiate into somites
(precursors of axial skeleton and skeletal muscle)
Spina bifida
- Incomplete closure of the neuronal tube
o Follic acid use: decrease of NTD
- Primary effects: Loss of sensation, paralysis
- Secondary effects: leakage of spinal fluid, Chiari malformation
Clue for neurological maldevelopment: neurofibromatosis:
- Spots in the skin
- Neural crest tissue is ‘left out’ when neural tube forms and migrate to form: dorsal root ganglia, enteric plexi, chromaffin
cells of medulla, melanocytes of skin
o One gene mutation in a gene, small tumors form
Regionalization
- Brain forms from tube into vesicles: prosencephalon (telencephalon, diencephalon) → mesencephalon (midbrain) →
rhombencephalon (metencephalon and myelencephalon) → spinal cord
, - Sonic hedge hoc (Shh): inferior/superior
- Hox, FGF: dorsal/ventral
- Failure in regionalization: holoprosencephaly
o Failure of separation of two hemispheres,
▪ Intellectual problems and cortical malformation leads to specific symptom (epilepsy)
Neuronal migration
- 16 weeks until birth
- Happens from the germinal matrix
o Strip of stem cells, vasculature, neurons and glial cells
o Lining the roof of lateral wall of the temporal horn
- Radial: perpendicular to the brain surface along radial glial processes
o Red neurons
- Tangential: migrate parallel to the brain surface and do not radial glial
o Green neurons
Problems in neuronal migration
C: abnormality of whole cortex. More a maldevelopment than problem in migration
F: grey matter where white matter should be
E: weird shaped cortex and grey matter
Many genes are involved in neuronal migration: making it a complex process
Gyration
- Starts in month 6-7, the fetal brain fully gyrated after 9 months (prenatally!)
Abnormalities:
- Lissencephaly: simplified gyrial pattern
- Polymicrogyria: cauliflower looking brain, because of too much gyration
CNS synaptogenesis
- Activity dependent: ‘we fire together, we hire together’
- Starts around 17-18 weeks after gestation until around adolescence
Myelination
- Starts around 28 weeks after gestation until well into adulthood
- T1 weighted MRI → white structures are the white matter (myelin)
, Methods: Transcriptomics
Learning objectives
- Explain what transcriptomics is
- Name 3 different types of transcriptomic approaches
- Explain the principles of cell cluster analysis based on gene expression: principal component analysis and community
detection
- Interpret cell cluster analysis plots
Relevance of studying the molecular make-up of tissues
- Understand cell heterogeneity and why some cell types are more affected by disease
- Study disease mechanisms
- Identify new targets for treatment
- Identify novel biomarkers
Omics
- Refers to different techniques to study the whole genome, transcriptome, proteome, metabolome or lipodome.
- Single cell (genome + transcriptome), tissue level of body fluid (proteome) level
Integrative omics strategy: combining microbiomics → metabolomics to get full picture
- Help in disease pathways, clinical classification, diagnosis and prognosis and precise intervention
- Very expensive, usually either one or maybe two omics combined
Transcriptomics: focus of RNA
- Study gene expression to
o Identify gene signature of (brain) cells
o Identify differentially expressed genes between healthy control and disease groups
Capturing heterogeneity in organs can be done with transcriptomics
Examples of transcriptomics data are:
- Bulk transcriptomics
- Single cell transcriptomics
- Spatial transcriptomics
From tissue → sequencing
- Fresh post mortem tissue/organoids or cell lines/FFPE or fresh
frozen material → cell suspension → either in FACS or MACS →
Illumina sequencing machine
o FACS: Fluorescent Activated Cell Sorting
o MACS: Magnetic Activated Cell Sorting
mRNA cannot be sequenced itself, as there are too little RNA molecules to be detected, therefore it must be rewritten into DNA,
which can be amplified:
1. Isolate single cell from tissue sample
2. Single cell lysis in a way that preserves cellular mRNA
3. mRNA molecule capture using poly-T sequence primers that bind mRNA poly-A tails
4. Convert poly T-primed mRNA into cDNA using reverse transcription
5. cDNA amplification
6. cDNA sequencing library preparation
a. insert ‘index’ nucleotide barcodes to identify each library
7. Pool cDNA sequencing libraries
8. Sequence libraries (via Next Generation Sequencing)
Illumina – Next Generation Sequencing
https://www.youtube.com/watch?v=fCd6B5HRaZ8
Terminology:
- Feature: gene
- Transcript: corresponds to one mRNA molecule
- Reads: transcript seqence
1. Sample preparation
a. Adding adapters to ends of the DNA fragments through reduced cycle amplification
b. Additional motifs introduced include indices, the sequencing binding site, regions complementary to the flow
cell oligos
Inhoud
Brain development ....................................................................................................................................................................... 2
Methods: Transcriptomics ............................................................................................................................................................ 4
Leukodystrophies......................................................................................................................................................................... 7
Introduction of Concepts .......................................................................................................................................................... 7
Studying Disease Mechanisms – VWM as a case study............................................................................................................... 9
Development of Outcome Measures: Clinical Trials and Clinimetry ...........................................................................................11
Current Treatment(s) for Leukodystrophies ...............................................................................................................................14
Gene Therapy for Leukodystrophies .........................................................................................................................................17
Water Homeostasis in Leukodystrophies ..................................................................................................................................18
Multiple Sclerosis........................................................................................................................................................................21
Clinical Features of MS ............................................................................................................................................................21
Current Therapies in MS...........................................................................................................................................................23
Etiological Mechanisms and Neuropathy of MS ........................................................................................................................24
Clinical Imaging for MS ............................................................................................................................................................25
Imaging in MS..........................................................................................................................................................................26
Cognitive Dysfunction and Networks in MS ...............................................................................................................................27
Parkinson’s Disease ....................................................................................................................................................................29
Clinical Features of PD ............................................................................................................................................................29
Brain imaging and PD ..............................................................................................................................................................30
Current Therapies for PD .........................................................................................................................................................33
Disease Mechanisms in PD......................................................................................................................................................34
Neuropsychiatry..........................................................................................................................................................................37
Clinics of Obsessive Compulsive Disorder ...............................................................................................................................37
OCD Disease Models ..............................................................................................................................................................39
TMS in OCD: From Disease Model to Personalized Targeting ......................................................................................................42
Stress and Resilience in Health and Disease ............................................................................................................................45
Depression: (Novel) Strategies to Reduce its Huge Burden ........................................................................................................47
Biological Pathways of MDD ....................................................................................................................................................50
Glioma .......................................................................................................................................................................................52
Clinics of Neuro-Oncology.......................................................................................................................................................52
Methods: EEG .............................................................................................................................................................................55
,Brain development
Learning objectives
- Able to describe the landmarks in brain development
- Have knowledge of neurological disease resulting from a failure in this process
- Have basic knowledge about pediatric neurological development
Timeline
Pcd/w: post congenital days/weeks
- Neurogenesis
- Neuronal migration
Milestones in development
- Sitting without support (<0.5 y)
- Start walking alone (0.5 y)
- First words (0.5-1y)
- Social play with caregiver (<0.5 y)
- Demonstrating empathy (1 y)
- Self-awareness (1 y)
- Formation of episodic memories (3 y)
Psychiatric and neurological disorders have discrete ages of onset
Neurulation
- Neuroectodermal tissue differentiates from ectoderm → neuronal plate. Neural plate border: separation of ecto- and
neuroderm
- Neural plate bends dorsally: neural plate borders join → neural crest
- Closure of neural tube + neural crest disconnects from epidermis
o Neural crest cells: most of peripheral nervous system
- Notochord degenerate, persists as nucleus pulposus of intervertebral discs. Mesoderm cells differentiate into somites
(precursors of axial skeleton and skeletal muscle)
Spina bifida
- Incomplete closure of the neuronal tube
o Follic acid use: decrease of NTD
- Primary effects: Loss of sensation, paralysis
- Secondary effects: leakage of spinal fluid, Chiari malformation
Clue for neurological maldevelopment: neurofibromatosis:
- Spots in the skin
- Neural crest tissue is ‘left out’ when neural tube forms and migrate to form: dorsal root ganglia, enteric plexi, chromaffin
cells of medulla, melanocytes of skin
o One gene mutation in a gene, small tumors form
Regionalization
- Brain forms from tube into vesicles: prosencephalon (telencephalon, diencephalon) → mesencephalon (midbrain) →
rhombencephalon (metencephalon and myelencephalon) → spinal cord
, - Sonic hedge hoc (Shh): inferior/superior
- Hox, FGF: dorsal/ventral
- Failure in regionalization: holoprosencephaly
o Failure of separation of two hemispheres,
▪ Intellectual problems and cortical malformation leads to specific symptom (epilepsy)
Neuronal migration
- 16 weeks until birth
- Happens from the germinal matrix
o Strip of stem cells, vasculature, neurons and glial cells
o Lining the roof of lateral wall of the temporal horn
- Radial: perpendicular to the brain surface along radial glial processes
o Red neurons
- Tangential: migrate parallel to the brain surface and do not radial glial
o Green neurons
Problems in neuronal migration
C: abnormality of whole cortex. More a maldevelopment than problem in migration
F: grey matter where white matter should be
E: weird shaped cortex and grey matter
Many genes are involved in neuronal migration: making it a complex process
Gyration
- Starts in month 6-7, the fetal brain fully gyrated after 9 months (prenatally!)
Abnormalities:
- Lissencephaly: simplified gyrial pattern
- Polymicrogyria: cauliflower looking brain, because of too much gyration
CNS synaptogenesis
- Activity dependent: ‘we fire together, we hire together’
- Starts around 17-18 weeks after gestation until around adolescence
Myelination
- Starts around 28 weeks after gestation until well into adulthood
- T1 weighted MRI → white structures are the white matter (myelin)
, Methods: Transcriptomics
Learning objectives
- Explain what transcriptomics is
- Name 3 different types of transcriptomic approaches
- Explain the principles of cell cluster analysis based on gene expression: principal component analysis and community
detection
- Interpret cell cluster analysis plots
Relevance of studying the molecular make-up of tissues
- Understand cell heterogeneity and why some cell types are more affected by disease
- Study disease mechanisms
- Identify new targets for treatment
- Identify novel biomarkers
Omics
- Refers to different techniques to study the whole genome, transcriptome, proteome, metabolome or lipodome.
- Single cell (genome + transcriptome), tissue level of body fluid (proteome) level
Integrative omics strategy: combining microbiomics → metabolomics to get full picture
- Help in disease pathways, clinical classification, diagnosis and prognosis and precise intervention
- Very expensive, usually either one or maybe two omics combined
Transcriptomics: focus of RNA
- Study gene expression to
o Identify gene signature of (brain) cells
o Identify differentially expressed genes between healthy control and disease groups
Capturing heterogeneity in organs can be done with transcriptomics
Examples of transcriptomics data are:
- Bulk transcriptomics
- Single cell transcriptomics
- Spatial transcriptomics
From tissue → sequencing
- Fresh post mortem tissue/organoids or cell lines/FFPE or fresh
frozen material → cell suspension → either in FACS or MACS →
Illumina sequencing machine
o FACS: Fluorescent Activated Cell Sorting
o MACS: Magnetic Activated Cell Sorting
mRNA cannot be sequenced itself, as there are too little RNA molecules to be detected, therefore it must be rewritten into DNA,
which can be amplified:
1. Isolate single cell from tissue sample
2. Single cell lysis in a way that preserves cellular mRNA
3. mRNA molecule capture using poly-T sequence primers that bind mRNA poly-A tails
4. Convert poly T-primed mRNA into cDNA using reverse transcription
5. cDNA amplification
6. cDNA sequencing library preparation
a. insert ‘index’ nucleotide barcodes to identify each library
7. Pool cDNA sequencing libraries
8. Sequence libraries (via Next Generation Sequencing)
Illumina – Next Generation Sequencing
https://www.youtube.com/watch?v=fCd6B5HRaZ8
Terminology:
- Feature: gene
- Transcript: corresponds to one mRNA molecule
- Reads: transcript seqence
1. Sample preparation
a. Adding adapters to ends of the DNA fragments through reduced cycle amplification
b. Additional motifs introduced include indices, the sequencing binding site, regions complementary to the flow
cell oligos
