ORCID Profile
0000-0002-7427-2100
Current Organisation
Westlake University
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Publisher: Cold Spring Harbor Laboratory
Date: 07-04-2020
DOI: 10.1101/2020.04.07.20054585
Abstract: Severe COVID-19 patients account for most of the mortality of this disease. Early detection and effective treatment of severe patients remain major challenges. Here, we performed proteomic and metabolomic profiling of sera from 46 COVID-19 and 53 control in iduals. We then trained a machine learning model using proteomic and metabolomic measurements from a training cohort of 18 non-severe and 13 severe patients. The model correctly classified severe patients with an accuracy of 93.5%, and was further validated using ten independent patients, seven of which were correctly classified. We identified molecular changes in the sera of COVID-19 patients implicating dysregulation of macrophage, platelet degranulation and complement system pathways, and massive metabolic suppression. This study shows that it is possible to predict progression to severe COVID-19 disease using serum protein and metabolite biomarkers. Our data also uncovered molecular pathophysiology of COVID-19 with potential for developing anti-viral therapies.
Publisher: Cold Spring Harbor Laboratory
Date: 11-06-2019
DOI: 10.1101/667394
Abstract: Formalin-fixed, paraffin-embedded (FFPE), biobanked tissue s les offer an invaluable resource for clinical and biomarker research. Here we developed a pressure cycling technology (PCT)-SWATH mass spectrometry workflow to analyze FFPE tissue proteomes and applied it to the stratification of prostate cancer (PCa) and diffuse large B-cell lymphoma (DLBCL) s les. We show that the proteome patterns of FFPE PCa tissue s les and their analogous fresh frozen (FF) counterparts have a high degree of similarity and we confirmed multiple proteins consistently regulated in PCa tissues in an independent s le cohort. We further demonstrate temporal stability of proteome patterns from FFPE s les that were stored between one to 15 years in a biobank and show a high degree of the proteome pattern similarity between two types histological region of small FFPE s les, i.e. punched tissue biopsies and thin tissue sections of micrometer thickness, despite the existence of certain degree of biological variations. Applying the method to two independent DLBCL cohorts we identified myeloperoxidase (MPO), a peroxidase enzyme, as a novel prognostic marker. In summary, this study presents a robust proteomic method to analyze bulk and biopsy FFPE tissues and reports the first systematic comparison of proteome maps generated from FFPE and FF s les. Our data demonstrate the practicality and superiority of FFPE over FF s les for proteome in biomarker discovery. Promising biomarker candidates for PCa and DLBCL have been discovered.
Publisher: Cold Spring Harbor Laboratory
Date: 30-09-2019
DOI: 10.1101/787705
Abstract: An inherent bottleneck of data independent acquisition (DIA) analysis by Orbitrap-based mass spectrometers is the relatively large window width due to the relatively slow scanning rate compared to TOF. Here we present a novel gas phase separation and MS acquisition method called PulseDIA-MS, which improves the specificity and sensitivity of Orbitrap-based DIA analysis. This is achieved by iding the ordinary DIA-MS analysis covering the entire mass range into multiple injections for DIA-MS analyses with complementary windows. Using standard HeLa digests, the PulseDIA method identified 69,530 peptide precursors from 9,337 protein groups with ten MS injections of 30 min LC gradient. The PulseDIA scheme containing two complementary windows led to the highest gain of peptide and protein identifications per time unit compared to the conventional 30 min DIA method. We further applied the method to profile the proteome of 18 cholangiocarcinoma (CCA) tissue s les (benign and malignant) from nine patients. PulseDIA identified 7,796 protein groups in these CCA s les, with 14% increase of protein identifications, compared to the conventional DIA method. The missing value for protein matrix dropped by 7% with PulseDIA acquisition. 681 proteins were significantly dysregulated in tumorous CCA s les. Together, we presented and benchmarked an alternative DIA method with higher sensitivity and lower missing rate.
Publisher: Elsevier BV
Date: 04-2020
Publisher: Wiley
Date: 18-09-2019
Publisher: Wiley
Date: 14-04-2020
Publisher: Springer Science and Business Media LLC
Date: 05-08-2022
No related grants have been discovered for Xue Cai.