Proteomics in Cancer: Overcoming Challenges of Solid Tumors

It has long been a challenge in biomarker research to gain solid tumor samples suitable to effectively apply proteomics in cancer. From a clinical point of view, obtaining biopsies of some tumors can be tremendously invasive, particularly in the instance of monitoring treatment success, where samples may be required repeatedly. In cancers of the blood, such as leukemia, samples can be collected with little more than a blood test to measure pharmacodynamics and predictive biomarkers. In the case of solid tumors, there are far more limited opportunities to sample the cancer itself in the case of a solid tumor. Therefore, it is important to identify biomarkers that can be monitored using relatively noninvasive methodology. One proposition for using proteomics in cancer is that we move the focus of biomarker discovery out of the tumor itself and, rather, look at cancer-associated changes in serum proteins.¹

The secretome, a name given to the biological fluid containing proteins released by cancer cells or tissues, could be a potential source for biomarkers that will aid the application of proteomics to solid tumor patients. The blood contains previously unstudied biomarkers that could reflect the ongoing physiologic state of all tissues; however, it is simultaneously a very complex biological fluid, abundant in a vast array of proteins. The secretome harbors proteins released by a cell. Essentially, the aim is to better understand which proteins are responsible for differentiation, invasion, metastasis and angiogenesis, and then have a more targeted approach to mine for these in serum samples.²

Another consideration for biomarker discovery is to interrogate biological pathways for changes. It is well recognized that proteins do not act alone but, rather, as a part of a complex system. Therefore, changes downstream of a tumor are just as viable as a source of potential biomarkers.³ This also fits in well when considered in combination with secretomes for using proteomics in cancer. Earlier research supports probing of oncogenic pathways for reliable indicators of tumor development and progress.⁴

Breast cancer accounts for approximately 28% of all cancers, with 40% of patients having metastatic disease to their lymph nodes. With the aforementioned potential sources for biomarkers, a new method for identifying biomarkers in breast cancer specifically has recently been defined by Raso et al.⁵ Here, breast tumor interstitial fluids, rich in tumour secretomes, are analyzed to determine functional pathways related specifically to breast tumor activity.

Samples were collected from three patients having surgery to remove breast lesions. Both primary cancer cells and interstitial fluids were examined using TmT-labeled samples on an LQT Orbitrap Velos (Thermo Scientific). Researchers were able to demonstrate that interstitial fluids could be more informative than primary cells in analyzing oncogenic pathways. The pathways identified in the interstitial fluids were principally connected to cell-cycle progression, adhesion and migration, and extracellular signaling related to the syndecans family of proteins. Additionally, proteins were identified that are involved in Smad and p38 MAPK pathways, which have a known relationship to tumor invasion and metastasis via TGF-β induction of cytokines.

This proposed approach represents an accurate and reliable method for identifying biomarkers for solid tumors and the signaling pathways that are deregulated in cancer. It also demonstrates that it is possible to consider interstitial fluids as a very useful and rich type of sample to study the cancer microenvironment. Most pertinent, however, is that it provides evidence for a new direction for proteomics in cancer. This particular breast cancer study describes an approach to analyzing secretomes and, hence, a potentially more applicable method to identifying translational biomarkers for solid tumors with better application in a clinical setting.

References

1. Sawyers, C.L. (2008) ‘The cancer biomarker problem‘, Nature, 452 (7187), (pp. 548-552)

2. Xue, H., Lu, B., Lai, M. (2008) ‘The cancer secretome: A reservoir of biomarkers‘, Journal of Translational Medicine, 6 (52), http://www.translational-medicine.com/content/6/1/52

3. Lawlor, K., et al. (2009) ‘Pathway-based biomarker search by high-throughput proteomics profiling of secretomes‘, Journal of Proteome Research’, 8 (3), (pp. 1489-1503)

4. Bild, A.H., et al. (2006) ‘Oncogenic pathway signatures in human cancers as a guide to targeted therapies‘, Nature, 439 (7074), (pp. 353-357)

5. Raso, C., et al. (2012) ‘Characterization of breast cancer interstitial fluids by TmT labeling, LTQ-Orbitrap velos mass spectrometry, and pathway analysis‘, Journal of Proteome Research, published online May 16, 2012. doi: 10.1021/pr2012347

For more on Breast Cancer Research:

Biomarker Research in Breast Cancer