Slow Off-Rate Modified Aptamer (SOMAmer) Proteomic Analysis of Patient-Derived Malignant Glioma Identifies Distinct Cellular Proteomes

Thanasupawat, Thatchawan; Głogowska, Aleksandra; Pascoe, Chris D.; Krishnan, S; Munir, Maliha Tabassum; Begum, Farhana; Beiko, Jason; Krcek, Jerry; Bigio, Marc R. Del; Pitz, Marshall; Shen, Yaoqing; Spicer, Victor; Coombs, Kevin M.; Wilkins, John; Hombach‐Klonisch, Sabine; Klonisch, Thomas

doi:10.3390/ijms22179566

Cited by 6 publications

(2 citation statements)

References 80 publications

(84 reference statements)

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“…So far, the SOMAscan technology has been linked to the biomarker discovery of various chronic and acute diseases [ 22 , 24 , 25 , 34 , 35 , 36 , 37 , 38 , 39 , 40 ]. For cancer, the assay is prescribed feasible for hepatocellular carcinoma [ 22 ], ovarian cancer [ 41 , 42 ], non-small lung cancer [ 43 ] and malignant glioma [ 44 , 45 ].…”

Section: Discussionmentioning

confidence: 99%

High-Multiplex Aptamer-Based Serum Proteomics to Identify Candidate Serum Biomarkers of Oral Squamous Cell Carcinoma

Blatt

Kämmerer

Krüger

et al. 2023

Cancers

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Improved serological biomarkers are needed for the early detection, risk stratification and treatment surveillance of patients with oral squamous cell carcinoma (OSCC). We performed an exploratory study using advanced, highly specific, DNA-aptamer-based serum proteomics (SOMAscan, 1305-plex) to identify distinct proteomic changes in patients with OSCC pre- vs. post-resection and compared to healthy controls. A total of 63 significantly differentially expressed serum proteins (each p < 0.05) were found that could discriminate between OSCC and healthy controls with 100% accuracy. Furthermore, 121 proteins were detected that were significantly altered between pre- and post-resection sera, and 12 OSCC-associated proteins reversed to levels equivalent to healthy controls after resection. Of these, 6 were increased and 6 were decreased relative to healthy controls, highlighting the potential relevance of these proteins as OSCC tumor markers. Pathway analyses revealed potential pathophysiological mechanisms associated with OSCC. Hence, quantitative proteome analysis using SOMAscan technology is promising and may aid in the development of defined serum marker assays to predict tumor occurrence, progression and recurrence in OSCC, and to guide personalized therapies.

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Section: Discussionmentioning

confidence: 99%

High-Multiplex Aptamer-Based Serum Proteomics to Identify Candidate Serum Biomarkers of Oral Squamous Cell Carcinoma

Blatt

Kämmerer

Krüger

et al. 2023

Cancers

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show abstract

“…Tenascin C, an oligomeric glycoprotein involved in embryogenesis and oncogenesis, was identified as the target of aptamer GBI-10 [ 47 ]. SOMAScan revealed abnormal expression levels in CKM (creatine kinase, isoform M), MDK (midkine), FN1 (fibronectin 1), STAT6, STAT1, and B-cell factor CD59[ 123 ].…”

Section: The Application Of Aptamer-based Biomarker Discovery In Vari...mentioning

confidence: 99%

The application of Aptamer in biomarker discovery

Tam

et al. 2023

Biomark Res

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Biomarkers are detectable molecules that can reflect specific physiological states of cells, organs, and organisms and therefore be regarded as indicators for specific diseases. And the discovery of biomarkers plays an essential role in cancer management from the initial diagnosis to the final treatment regime. Practically, reliable clinical biomarkers are still limited, restricted by the suboptimal methods in biomarker discovery. Nucleic acid aptamers nowadays could be used as a powerful tool in the discovery of protein biomarkers. Nucleic acid aptamers are single-strand oligonucleotides that can specifically bind to various targets with high affinity. As artificial ssDNA or RNA, aptamers possess unique advantages compared to conventional antibodies. They can be flexible in design, low immunogenicity, relative chemical/thermos stability, as well as modifying convenience. Several SELEX (Systematic Evolution of Ligands by Exponential Enrichment) based methods have been generated recently to construct aptamers for discovering new biomarkers in different cell locations. Secretome SELEX-based aptamers selection can facilitate the identification of secreted protein biomarkers. The aptamers developed by cell-SELEX can be used to unveil those biomarkers presented on the cell surface. The aptamers from tissue-SELEX could target intracellular biomarkers. And as a multiplexed protein biomarker detection technology, aptamer-based SOMAScan can analyze thousands of proteins in a single run. In this review, we will introduce the principle and workflow of variations of SELEX-based methods, including secretome SELEX, ADAPT, Cell-SELEX and tissue SELEX. Another powerful proteome analyzing tool, SOMAScan, will also be covered. In the second half of this review, how these methods accelerate biomarker discovery in various diseases, including cardiovascular diseases, cancer and neurodegenerative diseases, will be discussed.

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Translation of aptamers toward clinical diagnosis and commercialization

Liu

Xin

et al. 2022

Biosensors and Bioelectronics

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Slow Off-Rate Modified Aptamer (SOMAmer) Proteomic Analysis of Patient-Derived Malignant Glioma Identifies Distinct Cellular Proteomes

Cited by 6 publications

References 80 publications

High-Multiplex Aptamer-Based Serum Proteomics to Identify Candidate Serum Biomarkers of Oral Squamous Cell Carcinoma

High-Multiplex Aptamer-Based Serum Proteomics to Identify Candidate Serum Biomarkers of Oral Squamous Cell Carcinoma

The application of Aptamer in biomarker discovery

Translation of aptamers toward clinical diagnosis and commercialization

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