Cardiovascular proteomics

Cardiovascular proteomics

Jennifer Van Eyk MDAssociate Professor of Physiology

Queen’s UniversityKingston, Ontario

Eric Topol MDProvost and Chief Academic Officer

Chairman and ProfessorDepartment of Cardiovascular MedicineThe Cleveland Clinic FoundationCleveland, Ohio

Source:WITA 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)

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


Proteomics vs genomics

How big is the proteome?

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


Source: Incyte Genomics

same protein, 2 different modifications

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 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


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


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


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

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


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


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


Diagnostic 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


“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



“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


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


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


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


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



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



“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


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



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



Potential therapies for these diseases

• replace the missing protein

• inhibit the posttranslational changes that occur in acute disease (eg during CABG)


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


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


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


Recommended reading


Cardiovascular proteomics:evolution and potential

Arrell DK, Neverova I,Van Eyk JE.

Circ Res 2001;88(8):763-773

Source: WITA Proteomics

Cardiovascular proteomics

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