Download Cardiovascular proteomics

Cardiovascular proteomics
Jennifer Van Eyk MD
Associate Professor of Physiology
Queen’s University
Kingston, Ontario
Eric Topol MD
Provost and Chief Academic Officer
Source:
Chairman and Professor
WITA Proteomics
Department of Cardiovascular Medicine
The Cleveland Clinic Foundation
Cleveland, Ohio
Cardiovascular proteomics
What is proteomics?
Proteomics is the study of the proteins in a
cell at a given time
“Just right now, if we could capture the
cells that were in your heart, or in your
vasculature, or in your aorta — that’s the
proteins we are after.”
Van Eyk
Looks at
• expression of proteins by genes
• posttranslational modification of proteins
(eg phosphorylation and oxidation used
for intracellular signaling)
Cardiovascular proteomics
Proteomics vs genomics
Genomics goes after gene changes
• eg in HF — upregulation of ANF
• in hypertrophy — more myofilaments
expressed
Proteomics looks at gene changes and
posttranslational modifications
“When we study proteomics, we are
really trying to capture all of the
changes within the cell.”
Van Eyk
Cardiovascular proteomics
How big is the proteome?
same protein,
2 different
modifications
Source: Incyte Genomics
1 gene  1 protein
A protein may have 10–15 posttranslational
modifications that are disease-induced
The proteome could be up to 10 times the
size of the genome
Cardiovascular proteomics
Proteomics to validate genomics
Changes in DNA or mRNA may not
correlate with changes in protein
expression
“Whatever you see at a genomic
level…you really have to doublecheck and make sure that that is
happening also at the protein level.”
Van Eyk
Some of the disparities between the
mRNA and protein levels could just
reflect a time delay
Cardiovascular proteomics
Proteomics and genomics today
Genomics and proteomics are currently
uncoupled
Genomic researchers report SNPs (single
nucleotide polymorphisms) with no data on
the protein
Mikkelsson J, et al.
Circulation 2001;104(8):876-880
“Has to be viewed as suspect.”
“Are we going to continue to see these
isolated reports: here is a genomic
finding with no protein correlation?”
Topol
Cardiovascular proteomics
Proteomics and genomics in 5 years
Genomics is a new trend and people are just
trying to get the data out
“My guess is within 5 years you will have
to prove at the protein level as well.”
Van Eyk
Proteomics is no different. Currently, can get
away with lists of proteins without identifying
the posttranslational modifications
“That is soon going to change….
Proteomics is going to have to have the
functional verification, with time.”
Van Eyk
Cardiovascular proteomics
Cost of proteomics
Proteomics is driven a
lot by industry, capable
of high-throughput
Proteomics is expensive
Cost of equipment and
expertise
Source: The Wistar Institute
Cardiovascular proteomics
Academic proteomics
Broad-based screening
• tries to see all the proteins
• in individual labs
Focused proteomics
• looks at small group of proteins in the
proteome (subproteome)
• in core facilities
Cardiovascular proteomics
Industry proteomics
Constructing databases
• selling lists of the proteins in the heart
vs the brain
Diagnostics and therapeutics
Drug development
• compare effects of drug A vs drug B on
the proteome
Cardiovascular proteomics
Industry proteomics
“Small biotech companies are…either
driven by the technology that they’ve
made, and they are trying to sell
technology that is very specific to
proteomics, or they are trying to sell
information from databases, or they’re
trying to use that information, let’s say,
for diagnostics.”
“Diagnostics are actually the first things I
think that will be most influenced by
proteomics.”
Van Eyk
Cardiovascular proteomics
Diagnostic proteomics
Troponin I for MI
TnI is degraded and
modified in the
myocardium during
ischemia
Source: Jennifer Van Eyk
TnI is released due to
necrosis into the
blood stream, either
intact or with all these
posttranslational
modifications
Cardiovascular proteomics
Diagnostic proteomics
“If you are having a heart attack and
you have intact TnI, and I am having
a heart attack and I have the
degradation products that are linked
to more severe ischemia, then I would
predict that my heart is not going to
be doing as well as yours.”
Van Eyk
Cardiovascular proteomics
Diagnostic proteomics
“I believe that any disease-induced
modification that could be specific for
a disease state…can be used as a
biomarker, as long as it is there in
enough abundance.”
Van Eyk
Cardiovascular proteomics
Therapeutic proteomics
Go after end-effectors of the disease
process or beginning-effectors
• ie proteins that you can change with a
drug to stop the process
Requires knowledge of the proteome and
the disease process
“I believe that is the only way we are
going to get new drug targets.”
Van Eyk
Cardiovascular proteomics
Drug discovery
Past approach
• go after favorite proteins
(eg, TnI, beta-adrenergic 1 receptor)
• if one turns out to be important in disease,
create a drug against it
Proteomics approach
• provides an immense amount of
information on many, many proteins
• have 100s and 100s of potential drug
targets
Cardiovascular proteomics
Drug discovery
“The big problem actually is that
proteomics, and genomics also, will
give us so much information. It’s
being able to pull out what
information really means and which
piece of information is really
important, and going after those.”
Van Eyk
Cardiovascular proteomics
CV applications of proteomics
“Do you think that most of the processes
that are common, like HF from a dilated
cardiomyopathy, idiopathic,…or
decompensation of coronary disease,…
are going to be advanced by the whole
field over the years ahead?”
“It sounds like this…is really going to
change our approach, not just perhaps to
new diagnostics and drug discovery but to
the understanding of the disease state in
a more enhanced fashion.”
Topol
Cardiovascular proteomics
CV applications of proteomics
Dilated cardiomyopathies
• mutations in different myofilament proteins
can produce same disease phenotype
HF, stunning, systolic dysfunction
• phenotypes can be caused by myofilament
contractile defect, or calcium handling
defect, or a combination of both
Using diagnostic proteomics, hopefully you
will be able to stratify patients according to
the cause of their diseases, and you might
treat them differently
Cardiovascular proteomics
CV applications of proteomics
“With well-done proteomic studies…
you can define the protein changes
around a disease phenotype. Then all
those protein changes have to be
analyzed independently. Because a
protein change even in HF can actually
be a good change…and one you want
to promote.”
Van Eyk
Cardiovascular proteomics
Are we fooling ourselves?
Example of simple genetic diseases (such as
Marfan syndrome)
“Once you have the genetic and proteomic
side delineated, can you really see your
way through to the next step?”
“Are we fooling ourselves?… Here we are,
12–13 years since the cystic fibrosis gene,
and we have no new therapies, we have
no new ways to prevent the disease, and
we understand the gene and protein.”
Topol
Cardiovascular proteomics
Are we fooling ourselves?
These genetic diseases are more complex
than expected
• 1 gene product is mutated but many
proteins are affected, and these are not
necessarily known
• a lot of these diseases are chronic; the
body has been trying to compensate
causing further changes in proteins
Cardiovascular proteomics
Are we fooling ourselves?
Potential therapies for these diseases
• replace the missing protein
• inhibit the posttranslational changes that
occur in acute disease (eg during CABG)
Cardiovascular proteomics
On the horizon
“This is obviously very exciting. Perhaps in
the future there is probably nothing that
bubbles up to the top as having more
promise.”
Topol
“It is still a field in its infancy, even though
people have been working on proteomics on the technology - for 20 years.”
“It is going to take time to really see the
potential of it.”
Van Eyk
Cardiovascular proteomics
Limitations
Rushed studies that are poorly designed will
produce a lot of false information or
information that doesn’t help
It may be hard to get funding when the initial
excitement dies down
The studies do take a very long time, and the
public may lose interest
“Although it’s not going to be a quick
fix…the incubation phase is going to be
well worth it.”
Topol
Cardiovascular proteomics
Exciting findings
Already finding changes to proteins never
expected
For example, myosin light chain 1
• studied for 20 years and known to be
unphosphorylatable; in fact it is
phosphorylated
Arrell DK, et al.
Circ Res 2001;89(6):480-487
“We are seeing the world differently now at
the protein level. And as soon as you find
any protein that is changed, that just opens
up so many doors and possibilities.”
Van Eyk
Cardiovascular proteomics
Recommended reading
Cardiovascular proteomics:
evolution and potential
Arrell DK, Neverova I,
Van Eyk JE.
Circ Res 2001;88(8):763-773
Source: WITA Proteomics