DNA Aptamers for the Characterization of Histological Structure of Lung Adenocarcinoma

Abstract

Nucleic acid aptamers are becoming popular as molecular probes for identification and imaging pathology and, at the same time, as a convenient platform for targeted therapy. Recent studies have shown that aptamers may be effectively used for tumor characterization and as commercially available monoclonal antibodies. Here we present three DNA aptamers binding to whole transformed lung cancer tissues, including tumor cells, connective tissues, and blood vessels. Protein targets have been revealed using affinity purification followed by mass spectrometry analyses, and they have been validated using a panel of correspondent antibodies and 3D imaging of tumor tissues. Each of the proteins targeted by the aptamers is involved in cancer progression and most of them are crucial for lung adenocarcinoma. We propose the use of these aptamers in aptahistochemistry for the characterization of the histological structure of lung adenocarcinoma. The value of the presented aptamers is their application together or separately for indicating the spread of neoplastic transformation, for complex differential diagnostics, and for targeted therapy of the tumor itself as well as all transformed structures of the adjacent tissues. Moreover, it has been demonstrated that these aptamers could be used for intraoperative tumor visualization and margin assessment.

Molecular Epitope Determination of Aptamer Complexes of the Multidomain Protein C‐Met by Proteolytic Affinity‐Mass Spectrometry

“…The molecular identification of specific aptamer epitopes to C‐Met, determined here for the first time by mass spectrometry, should be of considerable interest for future drug development studies with aptamers. Although C‐Met antibodies have been admitted to first clinical trials, recent studies indicate considerable difficulties in the development of inhibiting antibodies with high stability and specificity . Except for the monoclonal antibody Onortuzumab that inhibits binding to HBF, no antibody has been described inhibiting the C‐Met interaction with HGF.…”

“…Although C-Met antibodies have been admitted to first clinical trials, recent studies indicate considerable difficulties in the development of inhibiting antibodies with high stability and specificity. [21,22] Except for the monoclonal antibody Onortuzumab that inhibits binding to HBF, no antibody has been described inhibiting the C-Met interaction with HGF. Major problems for the development of antibodies may be encountered by difficulties in antibody delivery, and by the possible formation of immunogenic anti-drug antibodies.…”

“…Here, we report the identification of the interaction epitopes of C‐Met with two DNA aptamers (CLN0003 and CLN0004) that bind to C‐Met with high affinity and specificity (Figure ; s. Table ). Corresponding aptamers (CLN0003 and CLN0004 and analogous oligonucleotide sequences) have shown high affinity binding to C‐Met and have recently gained high interest in their development for cancer therapy . For the identification of aptamer epitopes of C‐Met and determination of binding affinities, selective proteolytic extraction of C‐Met‐aptamer complexes in combination with electrospray (ESI) and MALDI mass spectrometry, and SPR (surface plasmon resonance) biosensor analysis were used as principal tools (PROTEX‐SPR‐MS) (Supplementary Figure S1).…”

“…Corresponding aptamers (CLN0003 and CLN0004 and analogous oligonucleotide sequences) have shown high affinity binding to C-Met and have recently gained high interest in their development for cancer therapy. [20][21][22][23][24] For the identification of aptamer epitopes of C-Met and determination of binding affinities, selective proteolytic extraction of C-Met-aptamer complexes in combination with electrospray (ESI) and MALDI mass spectrometry, and SPR (surface plasmon resonance) biosensor analysis were used as principal tools (PROTEX-SPR-MS) [25,26] ( Supplementary Figure S1). The PROTEX-SPR-MS method has been successfully applied in a number of recent studies for epitope identifications of protein-antibody complexes, protein-peptide interactions, and carbohydrate-protein complexes.…”

Emerging cancer-specific therapeutic aptamers

“…For the advanced application of biomarker discovery using aptamers, previously isolated DNA aptamers have been used in immunohistochemistry assays (aptahistochemistry) in postoperative human lung adenocarcinoma tissues (44). The relatively new concept of aptahistochemisty uses cancer-specific aptamers instead of antibodies.…”