"Cancer is a disease of the genome," noted Lynda Chin, M.D., professor of dermatology, Harvard Medical School and Dana-Farber Cancer Institute. "And understanding the impact of genomic changes in the proteome is critically important for converting genomic knowledge into something that a clinician can use on their patients." Chin, a principal investigator of The Cancer Genome Atlas (TCGA) and a physician who treats patients, knows firsthand how important it is to be able to translate genomic data into clinically useful knowledge for physicians and patients. To make this happen, we first need to understand if genomic changes are detectable at the protein level and if these changes can guide protein biomarker development.
Significant advancements are being made in our understanding of the key genomic alterations involved in cancer through initiatives such as NCI's TCGA. TCGA is generating very rich multi-dimensional genomic datasets on several types of cancer. Understanding the functional changes that derive from these genomic alterations, however, is another challenge altogether, but one the CPTC initiative is prepared to take on in Phase II. In a workshop held last year, the extramural research community agreed that proteomics offers our best hope of translating genetic knowledge into effective biomarkers for cancer. As a result, NCI will provide $75 million to $120 million over five years for CPTC Phase II to focus on the integration of proteomics with genomics in what is referred to as "genomically-informed proteomics."
Building a Bridge
It is well understood that the translation from gene to protein is not a clear-cut process. For example, one gene can encode more than one protein and proteins undergo several post-translational modifications (PTM), including phosphorylation, glycosylation, lipidation, and cleavage. Splice variants, PTMs, and other protein-protein interactions are known to play a significant role in cancer processes and they cannot be ignored.
"A proteotypic bridge is needed to connect genotype with phenotype," said Henry Rodriguez, Ph.D., MBA, director, Office of Clinical Cancer Proteomics Research. CPTC will leverage the proteomic achievements of Phase I to build this much needed bridge in Phase II.
"CPTC Phase I focused on technology development and assessment. The overarching goal was to define what it takes to have reproducibility between labs for proteomic measurements because once you have that then you can start to accurately measure the biology. But if you don't know how good your measurement platform is, then it's very difficult to measure the biology," said Chris Kinsinger, Ph.D., program manager, CPTC.
"What came out of Phase I was a three-tiered strategy for protein biomarker development. The first tier is the discovery phase, where you analyze a handful of samples to try to identify proteins of interest as potential biomarker candidates. The second tier is biomarker verification, in which you look at a larger number of samples with targeted assays to the proteins that were identified to be of interest in the discovery phase. Finally, the third tier is biomarker qualification (also known as clinical validation), in which a large number of patient samples are used to test the candidate biomarkers that survived the verification phase [CPTC is not involved in clinical validation]. Using this three-tiered biomarker development strategy, we designed Phase II of CPTC with input and guidance from the scientific community," said Kinsinger.
It Takes a (Multidisciplinary) Village
An open competition Request for Applications (RFA) was issued on June 25, 2010, to begin working toward CPTC's Phase II goals. CPTC will continue its current model of a multidisciplinary, team-based scientific approach through the establishment of a network of milestone-driven Proteome Characterization Centers (PCCs).
PCCs will perform proteomic characterization (biomarker discovery) and verification (biomarker assay development and quantitation). "We anticipate supplying the network of PCCs with tissues analyzed genomically by TCGA, and these samples and datasets will be analyzed as part of the biomarker discovery phase. Proteomic investigators will work in conjunction with an investigator who specializes in genomics to inform their proteomic studies with genomics. This is what we call genomically-informed proteomics," said Kinsinger.
The goal of the discovery phase is to deliver a comprehensive inventory of the largest possible set of proteins in a biological sample, with information about its complement gene product, truncations, alternative splicing, and other genomic alterations. This inventory is then expected to provide the basis for candidate prioritization for advancement into the verification phase.
In the verification phase, the goal is to improve the success rate of moving candidate biomarkers into clinical use by testing the maximum number of candidates with the highest possible throughput and lowest possible cost to ensure optimal credentialing of biomarkers for clinical utility. The network of PCCs will use the prioritized list of biomarker candidates to develop quantitative, multiplex protein-based assays for detection in tissue and blood. Ultimately, these assays will be analytically validated by the network and verified in clinically-relevant biospecimens.
"We're interested in credentialing biomarker candidates and having strong evidence from clinical samples that say, 'Yes, these proteins really are up-regulated or down-regulated in these patient populations,' but there's still a lot of work that has to occur after that to actually turn this information into a clinical assay that's ready to be deployed in the clinic," said Kinsinger.
CPTC will also develop a Data Center and Resource Center. The CPTC Data Center will serve as the hub and central repository of all data from the PCCs. The CPTC Resource Center will function as a collection and distribution hub for common biospecimens for the PCC Network. The biospecimen core resource will be done in collaboration with caHUB.
Phase II Outputs
Ultimately, Phase II is expected to deliver the following benefits to the scientific community:
The integration of two large-scale, multidisciplinary initiatives such as CPTC (proteomics) and TCGA (genomics) will be a paradigm shift-one that hopefully will lead to a jump start in the field of molecular diagnostics.
Anna Barker, Ph.D., former deputy director, NCI, sets her sights on proteomics for identifying metastatic risk in very early stage tumors. "We [TCGA] still have to deal with a huge issue-metastasis. It's too complex but it's also what kills people. I think we are going to sort this out through the proteomics community. It's going to be a protein signature, not genomic signature, that identifies metastasis," noted Barker.