Molecular Therapy – Exam Summary 2023 – Part 1
Week 1 - Monday
Personalized healthcare:
A bird eye’s view and future directions
There has been an exponential development in omics technologies
• Genomics = Testing 3.000.000.000 DNA bases in 1 assay
• Proteomics, glycomics, metabolomics = Testing of 10.000-50.000 proteins and metabolites in
1 assay
The combination of omics changes how people are being diagnosed
Therapy monitoring also plays a role, due to expensive treatment etc.
An example:
• 4-year-old boy with kidney stones, reoccurring infections, anaemic, blood transfusion every
4-6 weeks, shortage of red blood cells
• Skin and blood samples were sent to the lab
Diagnosis:
• Genetic screening:
o Result trio (mom+dad+child) Whole Exome Sequencing: no distinct genetic cause
(not every WES gives a diagnosis, about 50%)
o Heterozygous mutation in SEC23B, associated with dyserythropoietic anemia type II
(CSAII) in case of bi-allelic mutations (heterozygous not considered the cause)
• Metabolic screening:
o Urine organic acids and purine/pyrimidine analysis: very high orotic acid: 3404
μmol/mmol kreat – reference 0-4, without indication in serum amino acids for a urea
cycle disorder
• Diagnosis: Uridine monophosphate synthase (UMPS)
deficiency / hereditary orotic aciduria
• UMPS less active – substrate accumulates, less product
= uridine deficiency
• Personalized diagnosis: High orotic acid
, • Personalized therapy: Uridine supplementation
Treatment of Uridine monophosphate synthase (UMPS) deficiency
• 1969 Becroft et al: Hereditary orotic aciduria: long term therapy with uridine and a trial of
uracil
• 2014 Balasubramaniam et al: Inborn errors of pyrimidine metabolism, clinical update and
therapy
• 15 cases reported, in the Netherlands in meanwhile 2 newly diagnosed patients
• Uridine tri acetate (Xuriden), registered in USA, 800.000 euro/year/patient (!!)
• Not registered in NL
• Route to obtain therapeutic drug difficult (import, insurances)
Alternative:
• Food supplement@local drugstore, good for concentration, €36,95 for 50 gram
• Started on 60 mg/kg in January 2020
Effect:
• From blood transfusions every 5-7 weeks, no blood transfusions needed now for one year
• Reticulocytes and leucocytes increased
• Much more energy, eating improved, growth improved
• But orotic acid levels are still high, effect on kidney to be seen
• Relatively high dose uridine
Lessons learned:
• On personalized diagnosis:
• Technology innovation is driving impact in personalized healthcare
• Combination of genetic and metabolic screening is a strong approach towards identifying
mechanism of disease
On personalized medicine:
• Impressive effects of uridine therapy
• Increase quality of life for patient and family
• Frequent issues regarding expensive medication versus cheap supplements
Another example:
Personalized healthcare in Multiple Myeloma
• 2nd most common hematological malignancy
(rare blood cancer)
• Monoclonal plasma cells in bone marrow that
secrete a monoclonal (M) protein (one B cells
expands, creating one type of antibody instead
of a whole range)
• Diagnostic test for MM: B lood M-protein by
gel electrophoresis: Usually, a whole smear
instead of one single band can be seen. One
particular y chain can be seen
, • Treatment by chemotherapy,
• steroids and specific drugs
• ~50% of patients achieve Minimal Residual Disease (MRD)
• Need to restart therapy as soon as disease relapses, which is very common!
Current tests for MRD:
• Isolate bone marrow
• Analysis stromal cells by Flow Cytometry or Genomics (PCR, NGS)
• Problem: patchy disease, sampling a healthy disease bone can happen → invasive and
unreliable
Can we use plasma proteomics to monitor MRD in Multiple Myeloma?
• Approach: Direct measurement of
rearranged region of the M-protein by
targeted proteomics in plasma samples (=
MS MRD methode)
• Variable region needs to be targeted
(immunoglobulin)
• Higher specificity? Higher sensitivity?
- Gel based method has a limit of detection, but reliable
- In mass spec test – you can see that the disease is coming back – oscillating disease
Mass spectrometry strongly increases sensitivity detection M-protein
• Archived gels
• Punch out M protein bands
• Mass spec analysis
o De novo sequencing
o Semi-quantitation
• Monitor patients in time
Conclusions:
• MS MRD method is feasible for monitoring and early detection relapses
• Re-analysis of archived gels possible
, Plasma proteomic MS-MRD assay performance
• Conclusions Sequencing-MRD vs Mass Spectrometry-MRD (Comparing the mass spec test in
blood vs the bone marrow in sequencing)
• Similar sensitivity
• Perform equally well as prognostic biomarker
There is an ongoing diagnostic assay development:
• Analytical validation
ISO15189
• Internal standard and QCs
• Less PRM, more DIA
• Improved peptide prediction
and real-time identification
Lessons learned:
• Technology innovation is driving impact in personalized healthcare
• Analysis of dynamic biomarkers is key in monitoring Minimal Residual Disease to:
• Mass spectrometry has added value and good potential here
• Collaboration between clinic, lab specialists, proteomics labs + between academics and
industry is needed and works!
o Analytical development
o Clinical validation
Clinical omics data to drive personalized healthcare
• Personalized analysis: Genomics, epigenetics, transcriptomics, proteomics, gylcoproteomics,
glycomics, metabolomics, cellomics etc
• Diagnosis of (new) disease mechanisms: Deep Learning/ AI, Integrated diagnostics, System
biology
• Initiation and monitoring of (new) personalized therapies
Digital biomarkers
“Digital biomarkers are defined as objective, quantifiable physiological and behavioral data that are
collected and measured by means of digital devices such as portables, wearables, implantables, or
ingestibles. The data collected are typically used to explain, influence, and/or predict health-related
outcomes.”
Advantages:
• Continuous monitoring versus 1 snapshot observation
• Real world data versus data from clinically controlled circumstances
• More comprehensive and rich data sets
• Truely personalized
• Strong potential in molecular + clinical + digital + environmental biomarkers for optimal
insight in complex biological systems
• Better basis to drive Personalized health(care)
Week 1 - Monday
Personalized healthcare:
A bird eye’s view and future directions
There has been an exponential development in omics technologies
• Genomics = Testing 3.000.000.000 DNA bases in 1 assay
• Proteomics, glycomics, metabolomics = Testing of 10.000-50.000 proteins and metabolites in
1 assay
The combination of omics changes how people are being diagnosed
Therapy monitoring also plays a role, due to expensive treatment etc.
An example:
• 4-year-old boy with kidney stones, reoccurring infections, anaemic, blood transfusion every
4-6 weeks, shortage of red blood cells
• Skin and blood samples were sent to the lab
Diagnosis:
• Genetic screening:
o Result trio (mom+dad+child) Whole Exome Sequencing: no distinct genetic cause
(not every WES gives a diagnosis, about 50%)
o Heterozygous mutation in SEC23B, associated with dyserythropoietic anemia type II
(CSAII) in case of bi-allelic mutations (heterozygous not considered the cause)
• Metabolic screening:
o Urine organic acids and purine/pyrimidine analysis: very high orotic acid: 3404
μmol/mmol kreat – reference 0-4, without indication in serum amino acids for a urea
cycle disorder
• Diagnosis: Uridine monophosphate synthase (UMPS)
deficiency / hereditary orotic aciduria
• UMPS less active – substrate accumulates, less product
= uridine deficiency
• Personalized diagnosis: High orotic acid
, • Personalized therapy: Uridine supplementation
Treatment of Uridine monophosphate synthase (UMPS) deficiency
• 1969 Becroft et al: Hereditary orotic aciduria: long term therapy with uridine and a trial of
uracil
• 2014 Balasubramaniam et al: Inborn errors of pyrimidine metabolism, clinical update and
therapy
• 15 cases reported, in the Netherlands in meanwhile 2 newly diagnosed patients
• Uridine tri acetate (Xuriden), registered in USA, 800.000 euro/year/patient (!!)
• Not registered in NL
• Route to obtain therapeutic drug difficult (import, insurances)
Alternative:
• Food supplement@local drugstore, good for concentration, €36,95 for 50 gram
• Started on 60 mg/kg in January 2020
Effect:
• From blood transfusions every 5-7 weeks, no blood transfusions needed now for one year
• Reticulocytes and leucocytes increased
• Much more energy, eating improved, growth improved
• But orotic acid levels are still high, effect on kidney to be seen
• Relatively high dose uridine
Lessons learned:
• On personalized diagnosis:
• Technology innovation is driving impact in personalized healthcare
• Combination of genetic and metabolic screening is a strong approach towards identifying
mechanism of disease
On personalized medicine:
• Impressive effects of uridine therapy
• Increase quality of life for patient and family
• Frequent issues regarding expensive medication versus cheap supplements
Another example:
Personalized healthcare in Multiple Myeloma
• 2nd most common hematological malignancy
(rare blood cancer)
• Monoclonal plasma cells in bone marrow that
secrete a monoclonal (M) protein (one B cells
expands, creating one type of antibody instead
of a whole range)
• Diagnostic test for MM: B lood M-protein by
gel electrophoresis: Usually, a whole smear
instead of one single band can be seen. One
particular y chain can be seen
, • Treatment by chemotherapy,
• steroids and specific drugs
• ~50% of patients achieve Minimal Residual Disease (MRD)
• Need to restart therapy as soon as disease relapses, which is very common!
Current tests for MRD:
• Isolate bone marrow
• Analysis stromal cells by Flow Cytometry or Genomics (PCR, NGS)
• Problem: patchy disease, sampling a healthy disease bone can happen → invasive and
unreliable
Can we use plasma proteomics to monitor MRD in Multiple Myeloma?
• Approach: Direct measurement of
rearranged region of the M-protein by
targeted proteomics in plasma samples (=
MS MRD methode)
• Variable region needs to be targeted
(immunoglobulin)
• Higher specificity? Higher sensitivity?
- Gel based method has a limit of detection, but reliable
- In mass spec test – you can see that the disease is coming back – oscillating disease
Mass spectrometry strongly increases sensitivity detection M-protein
• Archived gels
• Punch out M protein bands
• Mass spec analysis
o De novo sequencing
o Semi-quantitation
• Monitor patients in time
Conclusions:
• MS MRD method is feasible for monitoring and early detection relapses
• Re-analysis of archived gels possible
, Plasma proteomic MS-MRD assay performance
• Conclusions Sequencing-MRD vs Mass Spectrometry-MRD (Comparing the mass spec test in
blood vs the bone marrow in sequencing)
• Similar sensitivity
• Perform equally well as prognostic biomarker
There is an ongoing diagnostic assay development:
• Analytical validation
ISO15189
• Internal standard and QCs
• Less PRM, more DIA
• Improved peptide prediction
and real-time identification
Lessons learned:
• Technology innovation is driving impact in personalized healthcare
• Analysis of dynamic biomarkers is key in monitoring Minimal Residual Disease to:
• Mass spectrometry has added value and good potential here
• Collaboration between clinic, lab specialists, proteomics labs + between academics and
industry is needed and works!
o Analytical development
o Clinical validation
Clinical omics data to drive personalized healthcare
• Personalized analysis: Genomics, epigenetics, transcriptomics, proteomics, gylcoproteomics,
glycomics, metabolomics, cellomics etc
• Diagnosis of (new) disease mechanisms: Deep Learning/ AI, Integrated diagnostics, System
biology
• Initiation and monitoring of (new) personalized therapies
Digital biomarkers
“Digital biomarkers are defined as objective, quantifiable physiological and behavioral data that are
collected and measured by means of digital devices such as portables, wearables, implantables, or
ingestibles. The data collected are typically used to explain, influence, and/or predict health-related
outcomes.”
Advantages:
• Continuous monitoring versus 1 snapshot observation
• Real world data versus data from clinically controlled circumstances
• More comprehensive and rich data sets
• Truely personalized
• Strong potential in molecular + clinical + digital + environmental biomarkers for optimal
insight in complex biological systems
• Better basis to drive Personalized health(care)
