Cardiovascular proteomics

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Cardiovascular proteomics
Jennifer Van Eyk MD Associate Professor of
Physiology Queens University Kingston,
Ontario Eric Topol MD Provost and Chief Academic
Officer Chairman and Professor Department of
Cardiovascular Medicine The Cleveland Clinic
Foundation Cleveland, Ohio
SourceWITA Proteomics
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What is proteomics?
Cardiovascular 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 thats 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)

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Proteomics vs genomics
Cardiovascular proteomics

• 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

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How big is the proteome?
Cardiovascular proteomics
same protein, 2 different modifications
Source Incyte Genomics

• 1 gene ? 1 protein
• A protein may have 1015 posttranslational
  modifications that are disease-induced
• The proteome could be up to 10 times the size of
  the genome

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Proteomics to validate genomics
Cardiovascular proteomics

• Changes in DNA or mRNA may not correlate with
  changes in protein expression
• Whatever you see at a genomic levelyou really
  have to double-check 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

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Proteomics and genomics today
Cardiovascular proteomics

• Genomics and proteomics are currently uncoupled
• Genomic researchers report SNPs (single
  nucleotide polymorphisms) with no data on the
  protein Mikkelsson J, et al. Circulation
  2001104(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

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Proteomics and genomics in 5 years
Cardiovascular proteomics

• 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

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Cost of proteomics
Cardiovascular proteomics

• Proteomics is driven a lot by industry, capable
  of high-throughput
• Proteomics is expensive
• Cost of equipment and expertise

Source The Wistar Institute
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Academic proteomics
Cardiovascular 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

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Industry proteomics
Cardiovascular 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

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Industry proteomics
Cardiovascular proteomics

• Small biotech companies areeither driven by the
  technology that theyve made, and they are trying
  to sell technology that is very specific to
  proteomics, or they are trying to sell
  information from databases, or theyre trying to
  use that information, lets say, for
  diagnostics.
• Diagnostics are actually the first things I
  think that will be most influenced by
  proteomics. Van Eyk

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Diagnostic proteomics
Cardiovascular proteomics

• Troponin I for MI
• TnI is degraded and modified in the myocardium
  during ischemia
• TnI is released due to necrosis into the blood
  stream, either intact or with all these
  posttranslational modifications

Source Jennifer Van Eyk
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Diagnostic proteomics
Cardiovascular 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

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Diagnostic proteomics
Cardiovascular proteomics

• I believe that any disease-induced modification
  that could be specific for a disease statecan be
  used as a biomarker, as long as it is there in
  enough abundance. Van Eyk

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Therapeutic proteomics
Cardiovascular 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

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Drug discovery
Cardiovascular proteomics

• 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

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Drug discovery
Cardiovascular proteomics

• The big problem actually is that proteomics, and
  genomics also, will give us so much information.
  Its being able to pull out what information
  really means and which piece of information is
  really important, and going after those. Van Eyk

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CV applications of proteomics
Cardiovascular 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 thisis 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

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CV applications of proteomics
Cardiovascular 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

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CV applications of proteomics
Cardiovascular 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 changeand one
  you want to promote. Van Eyk

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Are we fooling ourselves?
Cardiovascular proteomics

• 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, 1213
  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

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Are we fooling ourselves?
Cardiovascular proteomics

• 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

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Are we fooling ourselves?
Cardiovascular proteomics

• Potential therapies for these diseases
• replace the missing protein
• inhibit the posttranslational changes that occur
  in acute disease (eg during CABG)

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On the horizon
Cardiovascular proteomics

• 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

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Limitations
Cardiovascular proteomics

• Rushed studies that are poorly designed will
  produce a lot of false information or information
  that doesnt 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 its not going to be a quick fixthe
  incubation phase is going to be well worth it.
• Topol

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Exciting findings
Cardiovascular proteomics

• 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 200189(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

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Recommended reading
Cardiovascular proteomics
Cardiovascular proteomicsevolution and
potential Arrell DK, Neverova I,Van Eyk JE. Circ
Res 200188(8)763-773
Source WITA Proteomics