Genomics to health

1
Genomics to health

• Identify genes and pathways with a role in health
  and disease, and determine how they interact with
  environmental factors
• Apply genomebased diagnostic methods for the
  prediction of susceptibility to disease, the
  prediction of drug response and the accurate
  molecular classification of disease
• Translate genomic information into therapeutic
  advances

2
DNA
RNA
PROTEIN
Ala
Thr
Glu
Leu
Arg
TRANSCRIPTION
TRANSLATION
3
The Good and Bad of Chip Technology
Sensitivity detects RNA expressed at 5
molecules per cell Quantitation Reproducibility L
arge-scale assay equivalent to over 10,000
Northern blots! Allows search for novel genes
and ESTs not previously recognized as candidate
genes Expense of chips and reagents Too much
data! (difficult to analyze)
4
PNAS 2003 1008466-8471Coordinated reduction
of genes of oxidative metabolism in humans with
insulin resistance and diabetes Potential role
of PGC1 and NRF Mary Elizabeth Patti, Atul J.
Butte, Sarah Crunkhorn, Kenneth Cusi, Rachele
Berria, Sangeeta Kashyap, Yoshinori Miyazaki,
Isaac Kohane, Maura Costello, Robert Saccone,
Edwin J. Landaker, Allison B. Goldfine, Edward
Mun, Ralph DeFronzo, Jean Finlayson, C. Ronald
Kahn and Lawrence J. Mandarino 

• Nat Genet. 2003 34267-73
• PGC-1alpha-responsive genes involved in
  oxidative phosphorylation are coordinately
  downregulated in human diabetes
• Mootha VK, Lindgren CM, Eriksson KF, Subramanian
  A, Sihag S, Lehar J, Puigserver P, Carlsson E,
  Ridderstrale M, Laurila E, Houstis N, Daly MJ,
  Patterson N, Mesirov JP, Golub TR, Tamayo P,
  Spiegelman B, Lander ES, Hirschhorn JN, Altshuler
  D, Groop LC

5
Decrased expression of genes involved in
oxidative phosphorylationMootha VK et al Nat
Genet. 2003 34267-73

• (Gene Set Enrichment Analysis (GSEA)) was used to
  test for sets of related genes (defined sets of
  genes in biological pathways)
• The maximum score was obtained for all internally
  curated sets consisting of genes involved in
  oxidative phosphorylation (OXPHOS)(106 genes)
• Although the typical decrease in expression for
  individual OXPHOS genes is very modest (20 )
  the decrease is consistent across the set. 89
  (94 of 106) of the genes showing lower expression
  in individuals with T2D relative to those with
  NGT
• A set of genes identified with the keyword
  mitochondria, a cluster of co-regulated genes
  (overlapped the OXPHOS genes OXPHOS-CR)
• There was a correlation with the difference in
  OXPHOS-CR gene expression in T2D subjects with
  the changes in total body metabolism (VO2max,
  maximum oxygen uptake)

6

• Coordinated reduction of genes of oxidative
  metabolism in humans with insulin resistance and
  diabetes Potential role of PGC1 and NRF1
• Mary Elizabeth Patti et al.
• PNAS 2003 1008466-8471

7
Effects of insulin and age on skeletal muscle
PGC-1? and PGC-1? mRNA expression Skeletal
muscle specimens were taken from young (n86) and
elderly (n68) twins before and after a
hyperinsulinemic clamp
preclamp
postclamp
Ling et al, J Clin Invest, 2004
8
Association between skeletal muscle PGC-1? mRNA
expression and the Gly482Ser genotype
Ling et al, J Clin Invest, 2004
9
Decreased oxidative phosphorylation
Primary sequence polymorphism in PGC-1a/b
Glucose
Decreased transcription of metabolic
and mitochondrial genes
Decreased lipid oxidation
Increased FFA levels
Decreased transcription of metabolic
and mitochondrial genes
NRF PPAR
Decreased activity of PGC-1
Other transcription factors
Accumulation of lipid in skeletal muscle
Impaired insulin release
Obesity and nutrient excess
Inactivity
Insulin resistance, obesity and diabetes
Modified from Patti ME et al. PNAS 2003
10
(No Transcript)
11
Why spend time on molecular genetics of diabetes?
Gene identification
Pharmacogenetics Medicine response profiles
Disease genetics rational nosological
classification
Utility
Rare mendelian diseases causal genes
Common complex diseases susceptibility genes
Genes for drug metabolism and/or action
SNP profiles for drug efficacy
What is tested
New etiology insights Novel drug development Gene
therapy Disease prevention
Personalized medicine with high efficacy and less
adverse effects
Benefits
12
SNPs and pharmacogenetics
What is a SNP?
Different people have a different nucleotide at
a given location on a chromosome
What is a SNP map?
Location of SNPs on human DNA
Human DNA
How can a SNP map be used to predict medicine
response?
Section of SNP genotype profile
Patients with efficacy in clinical trials
Patients without efficacy in clinical trials
Predictive of efficacy
Predictive of no efficacy
13
Development of a pharmacogenetic medicine
response profile
Abbreviated SNP linkage disequilibrium profile
for efficacy and common adverse events
Used to select patients for phase III clinical
trials
Abbreviated SNP linkage disequilibrium profile
for serious, rare adverse events
Comprehensive medicine response profile to
predict efficacy and adverse events
14
Effect of sulphonylurea and metformin in
diabetic patients with type 2 diabetes and
MODY3 Trial Profile
Pearson ER et al Lancet 2003 3621275-1281
15
Effect of sulphonylurea and metformin in
diabetic patients with type 2 diabetes and
MODY3 Response Profile
Type 2 diabetes
HNF-1a
Pearson ER et al Lancet 2003 3621275-1281
16
Effect of sulphonylurea and metformin in
diabetic patients with type 2 diabetes and
MODY3 IVGTT data
Pearson ER et al Lancet 2003 3621275-1281
17
Glucose Glucose
Glut 2
Insulin
Nucleus
L-PK
Mitochondria
Ca2
K
B
-
ATP
-
Pearson ER et al Lancet 2003 3621275-1281
SU
18
Neonatal diabetes
Definition Insulin requiring hyperglycemia that
is diagnosed within the first 3 months of
life Prevalence 1 in 400,000 neonates Transient
(TNDM) resolving within a median of 3
months Majority of cases being attributable to
an abnormality in an imprinted region of
chromosome 6 Permanent (PNDM) insulin treatment
is required for life rare cases caused by
homozygous or compound heterozygous mutations in
the GCK gene. Or in raresyndromes New England
Journal of Medicine 3501838-1849,
2004 Activating Mutations in the Gene Encoding
the ATP-Sensitive Potassium-Channel Subunit
Kir6.2 and Permanent Neonatal Diabetes
19
(No Transcript)
20
Marek (I)

• A full-term boy born 03.03.2001
• Birth weight 3100g, birth length 51cm
• At age 18 days of life was investigated by GP for
  prolonged neonatal jaundice was found to be
  mildly hyperglycaemic (8.7 mmol/l).
• At re-investigation in 2.5 months, his BG was
  13.6 mmol/l and he was referred to our department

21
Marek (II)

• At admission
• Age 77 days (2.5 months)
• Weight 5660 g, length 59 cm
• Permanent glycosuria BG 22.6 mmol/L
• No signs of diabetic ketoacidosis
• C-peptide 183 pmol/L
• Autoantibodies (antiGAD) negative
• HbA1c 7.4 (DCCT)

22
Clinical diagnosis Permanent neonatal diabetes
mellitus
Marek (III)

• Treatment
• Initially continuous i.v. insulin infusion
• Afterwards, NPH insulin in 3 daily doses he was
  normoglycaemic at 3.25 IU/day
• (0.4 IU/kg/day)
• By September 2004 (age 3.5 years), he was given
  insulin 0.22 IU/kg/day and his metabolic control
  was excellent (HbA1c 7.0 DCCT)

23
Marek (IV)

• Recently, we provided molecular genetic analysis
  of the Kir6.2 gene using PCR and direct
  sequencing and found a heterozygous mutation
  R201H
• parents and older brother are healthy and do not
  carry the Kir6.2 mutation

24
Marek treatment (I)

• September 2004
• Insulin demand 0.22 IU/kg/day (3 injections)
• C-peptide lt166 pmol/l
• Glucagon stimulation test negative
• HBA1c 7.0 DCCT
• Beginning of the Glibenclamide treatment 0.05
  mg/kg x 2
• One week later, insulin therapy could be
  terminated

25
Marek treatment (II)

• November 2004
• Glibenclamide 1.875mg/D
• C-peptide 527pmol/l
• Glucagon stimulation test positive
• Meal stimulation test - positive
• HBA1c 5.5 (DCCT)
• Optimal glycaemic profile

26
Stimulated C-peptide
Stimulation by standard meal
Stimulation by glucagon
27
(No Transcript)
28
(No Transcript)