Slow Off-Rate Modified Aptamer (SOMAmer) Proteomic Analysis of Patient-Derived Malignant Glioma Identifies Distinct Cellular Proteomes
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Malignant gliomas derive from brain glial cells and represent >75% of primary brain tumors. This includes anaplastic astrocytoma (grade III; AS), the most common and fatal glioblastoma multiforme (grade IV; GBM), and oligodendroglioma (ODG). We have generated patient-derived AS, GBM, and ODG cell models to study disease mechanisms and test patient-centered therapeutic strategies. We have used an aptamer-based high-throughput SOMAscan® 1.3K assay to determine the proteomic profiles of 1307 different analytes. SOMAscan® proteomes of AS and GBM self-organized into closely adjacent proteomes which were clearly distinct from ODG proteomes. GBM self-organized into four proteomic clusters of which SOMAscan® cluster 4 proteome predicted a highly inter-connected proteomic network. Several up- and down-regulated proteins relevant to glioma were successfully validated in GBM cell isolates across different SOMAscan® clusters and in corresponding GBM tissues. Slow off-rate modified aptamer proteomics is an attractive analytical tool for rapid proteomic stratification of different malignant gliomas and identified cluster-specific SOMAscan® signatures and functionalities in patient GBM cells.
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The SomaLogic aptamer-based platform can reliably quantify over 7,000 proteins in a variety of biofluids and cellular extracts.
“Although the SomaLogic aptamer-based platform is especially powerful and can reliably quantify over 7,000 proteins in a variety of biofluids and cellular extracts103–106, it is not yet possible to reliably quantify the entire proteome.”
From Measuring biological age using omics data (2022) · cites this paper as [105]
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Measuring biological age using omics data
Rutledge, J., Oh, H., & Wyss-Coray, T. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-022-00511-7 · Cited by 570 · see citing works
Translation of aptamers toward clinical diagnosis and commercialization
Liu, S., Xu, Y., Xin, J., Tan, H., & Ying, B. (2022) · Biosensors and Bioelectronics · doi:10.1016/j.bios.2022.114168 · Cited by 100 · see citing works
The application of Aptamer in biomarker discovery
Li, Y., Tam, W. W. L., Yu, Y., Zhuo, Z., Xue, Z., Tsang, C., Qiao, X., Wang, W., Wang, W., Li, Y., et al. (2023) · Biomarker Research · doi:10.1186/s40364-023-00510-8 · Cited by 82 · see citing works
Highly Sensitive Protein Detection by Aptamer-Based Single-MoleculePreprint
Chatterjee, T., Johnson-Buck, A. E., & Walter, N. G. (2022) · SSRN Electronic Journal · doi:10.1016/j.bios.2022.114639 · Cited by 24 · see citing works
Blatt, S., Kämmerer, P. W., Krüger, M., Surabattula, R., Thiem, D. G. E., Dillon, S. T., Al‐Nawas, B., Libermann, T. A., & Schuppan, D. (2023) · Cancers · doi:10.3390/cancers15072071 · Cited by 9 · see citing works
Lacinski, R. A., Dziadowicz, S. A., Roth, C., Ma, L., Melemai, V. K., Fitzpatrick, B., Chaharbakhshi, E. O., Heim, T. E., Lohse, I., Schoedel, K. E., et al. (2024) · Frontiers in Oncology · doi:10.3389/fonc.2024.1417459 · Cited by 3 · see citing works
Russo, T. D. B., Gristina, V., Pepe, F., Scimone, C., Busuito, G., Cozzolino, D., Sarracino, C., Ratto, G., Incorvaia, L., Barraco, N., et al. (2026) · Cancers · doi:10.3390/cancers18193240
- Authors
- Thanasupawat, T., Glogowska, A., Pascoe, C., Krishnan, S. N., Munir, M., Begum, F., Beiko, J., Krcek, J., Del Bigio, M. R., Pitz, M., Shen, Y., Spicer, V., Coombs, K. M., Wilkins, J., Hombach-Klonisch, S., & Klonisch, T.
- Affiliations
- University of Manitoba (CA)
- Department of Human Anatomy and Cell Science, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Children's Hospital Research Institute of Manitoba (CA)
- CancerCare Manitoba (CA)
- BC Cancer Agency (CA)
- Manitoba Centre for Proteomics and Systems Biology, Winnipeg, MB R3E 3P4, Canada
- Corresponding author
- Klonisch, Thomas
- ORCID
- Venue
- International Journal of Molecular Sciences
- Publisher
- MDPI AG
- Published
- 2021-09-03
- Volume
- 22
- Issue
- 17
- Pages
- 9566
- ISSN
- 1422-0067 (ISSN-L)
- PMC
- PMC8431317
- OpenAlex
- W3196732079
- Cited by
- 8
- References
- 86
- Citations by year
- 2026: 1 · 2024: 1 · 2023: 2 · 2022: 4
- FWCI
- 0.98
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- International Journal of Molecular Sciences (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Brain Tumor Funders' Collaborative
- Research Manitoba
- Cancer Research Society
- Department of Surgery, University of Manitoba
- Canadian Institutes of Health Research
- Natural Sciences and Engineering Research Council of Canada
- Topics
- Health Sciences › Medicine › Genetics › Glioma Diagnosis and Treatment
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced Biosensing Techniques and Applications
- Keywords
- high-grade glioma, glioblastoma, anaplastic astrocytoma, oligodendroglioma, proteomic networks, brain tumors
- MeSH terms
- Brain Neoplasms, Glioma, Humans, Neoplasm Proteins, Tumor Cells, Cultured, Proteome, Proteomics, Aptamers, Nucleotide
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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