| Autor: |
Ashkarran AA; Department of Radiology and Precision Health Program, Michigan State University, East Lansing, MI 48824, USA., Gharibi H; Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden., Sadeghi SA; Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, MI 48824, United States., Modaresi SM; Biozentrum, University of Basel, 4056 Basel, Switzerland., Wang Q; Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, MI 48824, United States., Lin TJ; Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA., Yerima G; Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, CA 94720, USA., Tamadon A; Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, CA 94720, USA., Sayadi M; Department of Biomedical Engineering, Michigan State University, East Lansing, MI 48824, USA., Jafari M; Division of ENT Diseases, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden., Lin Z; Department of Radiology and Precision Health Program, Michigan State University, East Lansing, MI 48824, USA., Ritz D; Proteomics Core Facility, Biozentrum, University of Basel, 4056 Basel, Switzerland., Kakhniashvili D; Proteomics and Metabolomics Core Facility, University of Tennessee Health Science Center, Memphis, TN, USA., Guha A; Cardio-Oncology Program, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA., Mofrad MRK; Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, CA 94720, USA., Sun L; Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, MI 48824, United States., Landry MP; Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA.; Department of Neuroscience, University of California, Berkeley, Berkeley, CA 94720, USA.; Chan Zuckerberg Biohub, San Francisco, CA 94063, USA., Saei AA; Biozentrum, University of Basel, 4056 Basel, Switzerland.; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 17165, Sweden., Mahmoudi M; Department of Radiology and Precision Health Program, Michigan State University, East Lansing, MI 48824, USA. |
| Abstrakt: |
The protein corona, a dynamic biomolecular layer that forms on nanoparticle (NP) surfaces upon exposure to biological fluids is emerging as a valuable diagnostic tool for improving plasma proteome coverage analyzed by liquid chromatography-mass spectrometry (LC-MS/MS). Here, we show that spiking small molecules, including metabolites, lipids, vitamins, and nutrients (namely, glucose, triglyceride, diglycerol, phosphatidylcholine, phosphatidylethanolamine, L-α-phosphatidylinositol, inosine 5'-monophosphate, and B complex), into plasma can induce diverse protein corona patterns on otherwise identical NPs, significantly enhancing the depth of plasma proteome profiling. The protein coronas on polystyrene NPs when exposed to plasma treated with an array of small molecules (n=10) allowed for detection of 1793 proteins marking an 8.25-fold increase in the number of quantified proteins compared to plasma alone (218 proteins) and a 2.63-fold increase relative to the untreated protein corona (681 proteins). Furthermore, we discovered that adding 1000 μg/ml phosphatidylcholine could singularly enable the detection of 897 proteins. At this specific concentration, phosphatidylcholine selectively depleted the four most abundant plasma proteins, including albumin, thus reducing the dynamic range of plasma proteome and enabling the detection of proteins with lower abundance. By employing an optimized data-independent acquisition (DIA) approach, the inclusion of phosphatidylcholine led to the detection of 1436 proteins in a single plasma sample. Our molecular dynamic results revealed that phosphatidylcholine interacts with albumin via hydrophobic interactions, h-bonds, and water-bridges. Addition of phosphatidylcholine also enabled the detection of 337 additional proteoforms compared to untreated protein corona using a top-down proteomics approach. These significant achievements are made utilizing only a single NP type and one small molecule to analyze a single plasma sample, setting a new standard in plasma proteome profiling. Given the critical role of plasma proteomics in biomarker discovery and disease monitoring, we anticipate widespread adoption of this methodology for identification and clinical translation of proteomic biomarkers into FDA approved diagnostics. |
