Protein Signature of Lung Cancer Tissues

Mehan, Michael R.; Ayers, Deborah; Thirstrup, Derek; Xiong, Wei; Ostroff, Rachel; Brody, Edward N.; Walker, Jeffrey J.; Gold, Larry; Jarvis, Thale C.; Janjić, Nebojša; Baird, Geoffrey S.; Wilcox, Sheri K.

doi:10.1371/journal.pone.0035157

Cited by 84 publications

(69 citation statements)

References 61 publications

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“…We are currently investigating the potential of this nascent technology for applications ranging from biomarker discovery and diagnostics (43,44) to histochemistry and imaging (45). With the well-established role of PDGF-BB in proliferative disorders including atherosclerosis, fibrosis, macular degeneration, and cancer (11,46,47), the SOMAmers described here also have clear potential utility as therapeutic agents.…”

Section: Discussionmentioning

confidence: 99%

Unique motifs and hydrophobic interactions shape the binding of modified DNA ligands to protein targets

Davies¹,

Gelinas

Zhang

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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215

241

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Selection of aptamers from nucleic acid libraries by in vitro evolution represents a powerful method of identifying high-affinity ligands for a broad range of molecular targets. Nevertheless, a sizeable fraction of proteins remain difficult targets due to inherently limited chemical diversity of nucleic acids. We have exploited synthetic nucleotide modifications that confer protein-like diversity on a nucleic acid scaffold, resulting in a new generation of binding reagents called SOMAmers (Slow Off-rate Modified Aptamers). Here we report a unique crystal structure of a SOMAmer bound to its target, platelet-derived growth factor B (PDGF-BB). The SOMAmer folds into a compact structure and exhibits a hydrophobic binding surface that mimics the interface between PDGF-BB and its receptor, contrasting sharply with mainly polar interactions seen in traditional proteinbinding aptamers. The modified nucleotides circumvent the intrinsic diversity constraints of natural nucleic acids, thereby greatly expanding the structural vocabulary of nucleic acid ligands and considerably broadening the range of accessible protein targets.ince the advent of SELEX (Systematic Evolution of Ligands by EXponential enrichment) 22 years ago (1, 2), aptamers have been described that bind specifically and with high affinity to many different types of targets, including proteins, peptides, and small molecules (3). Binding interactions between aptamers and their targets are characterized by shape complementarity, polar contacts, hydrogen bonding interactions, and chargecharge interactions (3-5). Other than base stacking interactions, hydrophobic contacts, which are known to make key contributions to protein-protein interactions (6-8), have been notably limited, reflecting the lack of such moieties in nucleic acid libraries typically used in SELEX.We have recently shown that augmenting the diversity of randomized libraries with functional groups absent in natural nucleic acids can dramatically improve the success rate of SELEX, especially against difficult protein targets (9, 10). We have named this unique class of binding reagents SOMAmers (Slow Off-rate Modified Aptamers), to account for their distinct composition and binding properties. Among the different types of modifications we have tested, functional groups with hydrophobic character have typically yielded SOMAmers with the highest binding affinity. Although the contribution of such functional groups to the outcome of SELEX experiments has been quite apparent (9), the structural basis for the effect of these "side chains" on folding and binding has been unclear. Here, we report two cocrystal structures of related SOMAmers bound to a protein target, platelet-derived growth factor B (PDGF-BB), solved at a resolution of 2.2 Å and 2.3 Å. The structures elucidate the striking impact of the hydrophobic aromatic functional groups in creating novel intramolecular motifs and their extensive participation in shaping the contact surface with the native protein. By combining nucleic acid secondary st...

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Section: Discussionmentioning

confidence: 99%

Unique motifs and hydrophobic interactions shape the binding of modified DNA ligands to protein targets

Davies¹,

Gelinas

Zhang

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

215

241

View full text Add to dashboard Cite

show abstract

“…This compensates for the additional proofreading steps that would be provided by a second aptamer. Multiplexed assays based on SOMAmers with a mean LOD of 300 fM (m + 3.2 × s) and a dynamic range seven orders of magnitude have been used to identify biomarkers for various medical conditions including lung cancer and chronic kidney disease [63,65].…”

Section: Improving the Specificity Of Affinity Proteomics By Adding Mmentioning

confidence: 99%

Sensitivity and specificity: twin goals of proteomics assays. Can they be combined?

Wilson¹

2013

Expert Review of Proteomics

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“…10,11 More recently, we have been able to adapt our assay protocol to analyze tissue homogenates. 12 Fresh frozen (within 5-10 min of excision) tissue can be homogenized with a mortar and pestle, including a cocktail of protease inhibitors in the homogenization buffer, and diluted to equal protein concentrations, in order to normalize the results for tissue comparison. It was important to verify that our assay buffers did not allow any potential DNase activity from the tissue proteins to degrade the SOMAmers in the assay.…”

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confidence: 99%

“…12 Analysis of proteins in NSCLC tissue was compared to protein levels in both normal tissue adjacent to the surgical margins and normal tissue distant from the extirpated cancer. Figure 9a shows no significant differences in proteins in adjacent normal tissue compared to distant normal tissue.…”

mentioning

confidence: 99%