Lecture 1a - Introduction to principles of systems biology
vrijdag 1 februari 2019 10:28
Systems biology: understand the complex of diverse biological systems
Systems biology studies:
- The interactions between the components of a biological system
- How these interactions give rise to the function and behaviour of the sytem
GOAL: predicting therapeutic interventions for metabolic dysfunction
Strategy: Create quantitative computer models to predict:
1. How disease affects energy homeostasis and cell function
2. Potential target of pharmacological intervention and/or nutritional intervention
Experimental models
- Mouse muscle cells (fibers, myoblasts, myotubes)
- Healthy and sick cells (wt and KO mouse model)
- Primary cells from mouse and human patients
Lectures Pagina 1
,Lecture 1 - Mitochondrial disease (clinical aspects)
vrijdag 1 februari 2019 10:26
Focus on clinical presentation of patients having a problem on the oxidative phosphorylation system.
Mitochondrial diseases:
- Heteregeneous multisystem disorders
○ Only does not affect the red blood cells
- Can manifest at every age
○ Most common is normal birth, in the course of their life develop signs and symptoms
Speed of signs and symptoms can differ per person
- Prevalence of 1 in 5000
- nDNA of mtDNA mutations affecting the OXPHOS system
- Any age, any organ, any mode of inheritance
- Devastating disorders often early fatal
Mitochondrial disease: from clinical presentation towards definite proof
Problem: huge dealy from presentation towards diagnosis. This is because the disease is very rare.
-> 20 to 40 new cases a year, therefore not all doctors are aware of these disorders
-> Problematic because the genetics of these type of disorders (maternal (defect in mitochondrial DNA)/mendelian
(autosomal recessive) inheritance)
Muscle biopsy: in children surgical, adults needle biopsy (classical route)
Classical route is changing by the development of the functional genomics (exome sequencing etc)
Denis Leigh -> Leigh syndrome
Patient was unique to him, next to this the patient had a brain disease.
- He wrote down the medical history
○ From the age of 6 months onwards problems started
Stopped crying, lay very still, slept for long periods, only waking when disturbed
Did not suck and had to be fed by spoon
Sweating was increased
At onset his 10 year old sister had a cold with sneezing and coughing
Admission: 7 months and 3 weeks
○ Physical examination
Pupils small with no reaction to light
Bilateral optic atrophy
Muscle stiffness
Appeared to be deaf
Upper and lower limbs markedly spastic
No reflexes
Bilateral extensor response (Babisnky's sign)
□ Normally the toes go down by checking the reflex under the foot, with the patients the toes go
up.
The upper motor neuron system is affected.
Died three days following admission
Investigate children to get impression of the brain --> Check how the pupils react to light (retina is part of the brain).
Splitlamp: you can visualize the optic nerve in the retina.
Bilateral optic atrophy: both eyes have another appearance of the optic nerve.
With this disease the optic nerve looks pale.
Reason for this is that the ganglion cells of the optic nerve are dying, those contain mitochondria.
Marjolein: after 14 months when she suffered from an infection (infection causes an increase in body temperature,
which causes the foramtion of ROS and formation of specific enzymes, but still many question marks), she started to
deteriorate. (loss of speech)
Hyperthrichosis: growing of more hair on all parts of the body
Patient had also brain abnormalities: same as the patient of Leigh.
Afterwards it was known it was due to a deficiency in the oxidative phosphorylation system.
Importance in systems biology: bits and pieces are known, more information is needed to get the bigger picture.
Lectures Pagina 2
,Importance in systems biology: bits and pieces are known, more information is needed to get the bigger picture.
Every patient born and diagnosed with Leigh syndrome have the same brain areas affected. This was investigated by a
necropsy (autopsy of the brain)
He found:
- Severe, diffuse vascular injections
- The white matter was greyer than normal
- The medulla oblongata and the pons showed red-brown discoloration
Pointing directions at subacte necrotizing encehalomyelophaty.
Microscopy behind the necropsy of a patient with subacute necrotizing encephalomyelophaty
All affected areas which showed macroscopic change were the site of a profuse proliferation of the smaller blood
vessels, capillaries, pre-capillaries, arterioles and venules.
In the situations where this vascular proliferation was present, the nerve cells were often severely damaged, showeing a
variety of degenerative changes:
- Swelling of cell body
- Central chromotolysis
- Nuclear swelling
- General cell shrinkage
- Neuronophagia (destruction by phagocytes)
- Satellitosis (clustering of glialcells)
There is a gab between the knowledge obtained in the past, and the possibilities we have no to investigate is, but it is
rarely done anymore.
Leigh syndrome is also characterized by an increased lactic acid peak.
Mitochondrial metabolic standard screening:
- Lactate
○ Repeated blood lactic acid > 2.1mM (increased vs normal)
- Organic acids
○ CSF lactate > 1.9 mM
- Amino acids
○ Blood alanine > 450 microM
- Function tests
Lactate and Alanine are markers for a disturbed OXPHOS system. The OXPHOS system is the final biochemical pathway
in ATP production.
With mitochondrial metabolic diseases, there is also an increase in TCA cycle intermediates
Skeletal muscle mitochondrial diagnostics
- Fresh muscle homogenate
○ ATP production
○ Substrate oxidation rates
- Rest material
○ Frozen for enzyme measurements
Raggot red fibre (histological photo): is seen in certain mitochondrial diseases (is huge accumulation of mitochondria
under the sacrolemma)
Structure and function
Lectures Pagina 3
, Protein gradient is the driving force for the ATP production
KUNJI (article on how ATP is transported from the mitochondria and the cytosol)
Median age of onset of Leigh disease: most of the onset is between 0-6 months, but can also be at the age of 20.
The age of onset is a determinant for the outcome of the patient. When the age of onset is <6 months, the survival
probability is lower than patients with an age of onset >6 months.
Pathways and genes affected in patients with Leigh disease
Genes in which mutations have been identified in patients with Leigh syndrome are underlined. Nuclear DNA encoded
proteins are depicted in black, mtDNA encoded subunits in red and mitochondrial respiratory chain assembly factors in
blue.
Mitochondrial DNA
Coding for 13 mRNA's, 22 tRNA's, 2 rRNA's (circular DNA)
Heteroplasmy, Threshold and mitochondrial bottleneck
At a certain threshold a certain cell starts to increase in hetereplasm, which will cause damage.
Genetic bottleneck
Lectures Pagina 4
vrijdag 1 februari 2019 10:28
Systems biology: understand the complex of diverse biological systems
Systems biology studies:
- The interactions between the components of a biological system
- How these interactions give rise to the function and behaviour of the sytem
GOAL: predicting therapeutic interventions for metabolic dysfunction
Strategy: Create quantitative computer models to predict:
1. How disease affects energy homeostasis and cell function
2. Potential target of pharmacological intervention and/or nutritional intervention
Experimental models
- Mouse muscle cells (fibers, myoblasts, myotubes)
- Healthy and sick cells (wt and KO mouse model)
- Primary cells from mouse and human patients
Lectures Pagina 1
,Lecture 1 - Mitochondrial disease (clinical aspects)
vrijdag 1 februari 2019 10:26
Focus on clinical presentation of patients having a problem on the oxidative phosphorylation system.
Mitochondrial diseases:
- Heteregeneous multisystem disorders
○ Only does not affect the red blood cells
- Can manifest at every age
○ Most common is normal birth, in the course of their life develop signs and symptoms
Speed of signs and symptoms can differ per person
- Prevalence of 1 in 5000
- nDNA of mtDNA mutations affecting the OXPHOS system
- Any age, any organ, any mode of inheritance
- Devastating disorders often early fatal
Mitochondrial disease: from clinical presentation towards definite proof
Problem: huge dealy from presentation towards diagnosis. This is because the disease is very rare.
-> 20 to 40 new cases a year, therefore not all doctors are aware of these disorders
-> Problematic because the genetics of these type of disorders (maternal (defect in mitochondrial DNA)/mendelian
(autosomal recessive) inheritance)
Muscle biopsy: in children surgical, adults needle biopsy (classical route)
Classical route is changing by the development of the functional genomics (exome sequencing etc)
Denis Leigh -> Leigh syndrome
Patient was unique to him, next to this the patient had a brain disease.
- He wrote down the medical history
○ From the age of 6 months onwards problems started
Stopped crying, lay very still, slept for long periods, only waking when disturbed
Did not suck and had to be fed by spoon
Sweating was increased
At onset his 10 year old sister had a cold with sneezing and coughing
Admission: 7 months and 3 weeks
○ Physical examination
Pupils small with no reaction to light
Bilateral optic atrophy
Muscle stiffness
Appeared to be deaf
Upper and lower limbs markedly spastic
No reflexes
Bilateral extensor response (Babisnky's sign)
□ Normally the toes go down by checking the reflex under the foot, with the patients the toes go
up.
The upper motor neuron system is affected.
Died three days following admission
Investigate children to get impression of the brain --> Check how the pupils react to light (retina is part of the brain).
Splitlamp: you can visualize the optic nerve in the retina.
Bilateral optic atrophy: both eyes have another appearance of the optic nerve.
With this disease the optic nerve looks pale.
Reason for this is that the ganglion cells of the optic nerve are dying, those contain mitochondria.
Marjolein: after 14 months when she suffered from an infection (infection causes an increase in body temperature,
which causes the foramtion of ROS and formation of specific enzymes, but still many question marks), she started to
deteriorate. (loss of speech)
Hyperthrichosis: growing of more hair on all parts of the body
Patient had also brain abnormalities: same as the patient of Leigh.
Afterwards it was known it was due to a deficiency in the oxidative phosphorylation system.
Importance in systems biology: bits and pieces are known, more information is needed to get the bigger picture.
Lectures Pagina 2
,Importance in systems biology: bits and pieces are known, more information is needed to get the bigger picture.
Every patient born and diagnosed with Leigh syndrome have the same brain areas affected. This was investigated by a
necropsy (autopsy of the brain)
He found:
- Severe, diffuse vascular injections
- The white matter was greyer than normal
- The medulla oblongata and the pons showed red-brown discoloration
Pointing directions at subacte necrotizing encehalomyelophaty.
Microscopy behind the necropsy of a patient with subacute necrotizing encephalomyelophaty
All affected areas which showed macroscopic change were the site of a profuse proliferation of the smaller blood
vessels, capillaries, pre-capillaries, arterioles and venules.
In the situations where this vascular proliferation was present, the nerve cells were often severely damaged, showeing a
variety of degenerative changes:
- Swelling of cell body
- Central chromotolysis
- Nuclear swelling
- General cell shrinkage
- Neuronophagia (destruction by phagocytes)
- Satellitosis (clustering of glialcells)
There is a gab between the knowledge obtained in the past, and the possibilities we have no to investigate is, but it is
rarely done anymore.
Leigh syndrome is also characterized by an increased lactic acid peak.
Mitochondrial metabolic standard screening:
- Lactate
○ Repeated blood lactic acid > 2.1mM (increased vs normal)
- Organic acids
○ CSF lactate > 1.9 mM
- Amino acids
○ Blood alanine > 450 microM
- Function tests
Lactate and Alanine are markers for a disturbed OXPHOS system. The OXPHOS system is the final biochemical pathway
in ATP production.
With mitochondrial metabolic diseases, there is also an increase in TCA cycle intermediates
Skeletal muscle mitochondrial diagnostics
- Fresh muscle homogenate
○ ATP production
○ Substrate oxidation rates
- Rest material
○ Frozen for enzyme measurements
Raggot red fibre (histological photo): is seen in certain mitochondrial diseases (is huge accumulation of mitochondria
under the sacrolemma)
Structure and function
Lectures Pagina 3
, Protein gradient is the driving force for the ATP production
KUNJI (article on how ATP is transported from the mitochondria and the cytosol)
Median age of onset of Leigh disease: most of the onset is between 0-6 months, but can also be at the age of 20.
The age of onset is a determinant for the outcome of the patient. When the age of onset is <6 months, the survival
probability is lower than patients with an age of onset >6 months.
Pathways and genes affected in patients with Leigh disease
Genes in which mutations have been identified in patients with Leigh syndrome are underlined. Nuclear DNA encoded
proteins are depicted in black, mtDNA encoded subunits in red and mitochondrial respiratory chain assembly factors in
blue.
Mitochondrial DNA
Coding for 13 mRNA's, 22 tRNA's, 2 rRNA's (circular DNA)
Heteroplasmy, Threshold and mitochondrial bottleneck
At a certain threshold a certain cell starts to increase in hetereplasm, which will cause damage.
Genetic bottleneck
Lectures Pagina 4
