The development of a novel zeolite-based assay for efficient and deep plasma proteomic profiling
Abstract Plasma proteins are considered the most informative source of biomarkers for disease diagnosis and monitoring. Mass spectrometry (MS)-based proteomics has been applied to identify biomarkers in plasma, but the complexity of the plasma proteome and the extremely large dynamic range of protei...
| Main Authors: | , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2024-04-01
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| Series: | Journal of Nanobiotechnology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12951-024-02404-9 |
| _version_ | 1797209042642272256 |
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| author | Nan Li Jingnan Huang Shangwen He Qiaocong Zheng Feng Ye Zhengxing Qin Dong Wang Ting Xiao Mengyuan Mao Zhenhua Zhou Tingxi Tang Longshan Zhang Xiaoqing Wang Yingqiao Wang Ying Lyu Laiyu Liu Lingyun Dai Jigang Wang Jian Guan |
| author_facet | Nan Li Jingnan Huang Shangwen He Qiaocong Zheng Feng Ye Zhengxing Qin Dong Wang Ting Xiao Mengyuan Mao Zhenhua Zhou Tingxi Tang Longshan Zhang Xiaoqing Wang Yingqiao Wang Ying Lyu Laiyu Liu Lingyun Dai Jigang Wang Jian Guan |
| author_sort | Nan Li |
| collection | DOAJ |
| description | Abstract Plasma proteins are considered the most informative source of biomarkers for disease diagnosis and monitoring. Mass spectrometry (MS)-based proteomics has been applied to identify biomarkers in plasma, but the complexity of the plasma proteome and the extremely large dynamic range of protein abundances in plasma make the clinical application of plasma proteomics highly challenging. We designed and synthesized zeolite-based nanoparticles to deplete high-abundance plasma proteins. The resulting novel plasma proteomic assay can measure approximately 3000 plasma proteins in a 45 min chromatographic gradient. Compared to those in neat and depleted plasma, the plasma proteins identified by our assay exhibited distinct biological profiles, as validated in several public datasets. A pilot investigation of the proteomic profile of a hepatocellular carcinoma (HCC) cohort identified 15 promising protein features, highlighting the diagnostic value of the plasma proteome in distinguishing individuals with and without HCC. Furthermore, this assay can be easily integrated with all current downstream protein profiling methods and potentially extended to other biofluids. In conclusion, we established a robust and efficient plasma proteomic assay with unprecedented identification depth, paving the way for the translation of plasma proteomics into clinical applications. Graphical Abstract |
| first_indexed | 2024-04-24T09:48:25Z |
| format | Article |
| id | doaj.art-22666f4f031b42e5a3fc814ca013083f |
| institution | Directory Open Access Journal |
| issn | 1477-3155 |
| language | English |
| last_indexed | 2024-04-24T09:48:25Z |
| publishDate | 2024-04-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Nanobiotechnology |
| spelling | doaj.art-22666f4f031b42e5a3fc814ca013083f2024-04-14T11:28:19ZengBMCJournal of Nanobiotechnology1477-31552024-04-0122112310.1186/s12951-024-02404-9The development of a novel zeolite-based assay for efficient and deep plasma proteomic profilingNan Li0Jingnan Huang1Shangwen He2Qiaocong Zheng3Feng Ye4Zhengxing Qin5Dong Wang6Ting Xiao7Mengyuan Mao8Zhenhua Zhou9Tingxi Tang10Longshan Zhang11Xiaoqing Wang12Yingqiao Wang13Ying Lyu14Laiyu Liu15Lingyun Dai16Jigang Wang17Jian Guan18Department of Radiation Oncology, Nanfang Hospital, Southern Medical UniversityDepartment of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, Shenzhen People’s Hospital, (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology)Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical UniversityDepartment of Radiation Oncology, Nanfang Hospital, Southern Medical UniversityDepartment of Radiation Oncology, Nanfang Hospital, Southern Medical UniversityState Key Laboratory of Heavy Oil Processing, College of Chemical Engineering, China University of Petroleum (East China)College of Chemistry and Chemical Engineering, China University of Petroleum (East China)Department of Radiation Oncology, Nanfang Hospital, Southern Medical UniversityDepartment of Radiation Oncology, Nanfang Hospital, Southern Medical UniversityDepartment of Radiation Oncology, Nanfang Hospital, Southern Medical UniversityDepartment of Radiation Oncology, Nanfang Hospital, Southern Medical UniversityDepartment of Radiation Oncology, Nanfang Hospital, Southern Medical UniversityDepartment of Radiation Oncology, Nanfang Hospital, Southern Medical UniversityDepartment of Radiation Oncology, Nanfang Hospital, Southern Medical UniversityDepartment of Traditional Chinese Medicine, Nanfang Hospital,, Southern Medical UniversityChronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical UniversityDepartment of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, Shenzhen People’s Hospital, (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology)Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, Shenzhen People’s Hospital, (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology)Department of Radiation Oncology, Nanfang Hospital, Southern Medical UniversityAbstract Plasma proteins are considered the most informative source of biomarkers for disease diagnosis and monitoring. Mass spectrometry (MS)-based proteomics has been applied to identify biomarkers in plasma, but the complexity of the plasma proteome and the extremely large dynamic range of protein abundances in plasma make the clinical application of plasma proteomics highly challenging. We designed and synthesized zeolite-based nanoparticles to deplete high-abundance plasma proteins. The resulting novel plasma proteomic assay can measure approximately 3000 plasma proteins in a 45 min chromatographic gradient. Compared to those in neat and depleted plasma, the plasma proteins identified by our assay exhibited distinct biological profiles, as validated in several public datasets. A pilot investigation of the proteomic profile of a hepatocellular carcinoma (HCC) cohort identified 15 promising protein features, highlighting the diagnostic value of the plasma proteome in distinguishing individuals with and without HCC. Furthermore, this assay can be easily integrated with all current downstream protein profiling methods and potentially extended to other biofluids. In conclusion, we established a robust and efficient plasma proteomic assay with unprecedented identification depth, paving the way for the translation of plasma proteomics into clinical applications. Graphical Abstracthttps://doi.org/10.1186/s12951-024-02404-9PlasmaProteomicsZeoliteProtein corona |
| spellingShingle | Nan Li Jingnan Huang Shangwen He Qiaocong Zheng Feng Ye Zhengxing Qin Dong Wang Ting Xiao Mengyuan Mao Zhenhua Zhou Tingxi Tang Longshan Zhang Xiaoqing Wang Yingqiao Wang Ying Lyu Laiyu Liu Lingyun Dai Jigang Wang Jian Guan The development of a novel zeolite-based assay for efficient and deep plasma proteomic profiling Journal of Nanobiotechnology Plasma Proteomics Zeolite Protein corona |
| title | The development of a novel zeolite-based assay for efficient and deep plasma proteomic profiling |
| title_full | The development of a novel zeolite-based assay for efficient and deep plasma proteomic profiling |
| title_fullStr | The development of a novel zeolite-based assay for efficient and deep plasma proteomic profiling |
| title_full_unstemmed | The development of a novel zeolite-based assay for efficient and deep plasma proteomic profiling |
| title_short | The development of a novel zeolite-based assay for efficient and deep plasma proteomic profiling |
| title_sort | development of a novel zeolite based assay for efficient and deep plasma proteomic profiling |
| topic | Plasma Proteomics Zeolite Protein corona |
| url | https://doi.org/10.1186/s12951-024-02404-9 |
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