1.Biocompatibility of rat’ s nature decellularized pancreatic biological scaffolds
Yingkuan SHAO ; Xialin YAN ; Zhiheng RAO ; Gaojian HUANG ; Jiawei LI ; Junjie HUANG ; Jin MEI ; Kezhi LIN
Acta Anatomica Sinica 2014;(4):561-568
Objective To harvest pancreatic tissues from rats , prepare decellularized bio-derived pancreatic scaffolds ( DBPS) , and to examine the integrity and biocompatibility of the scaffolds .Methods Normal pancreases were harvested from healthy adult SD rats .DBPS was prepared by perfusing SDS and Triton X-100 through bile duct and the portal vein, respectively.After decellularization, normal pancreatic tissue and DBPS were compared via HE staining , and transmission electron microscopy ( TEM ) . Abdominal wall and subcutaneous implantations were used to compare biocompatibility , and the remain quantity of residual protein and growth factors were determined via enzyme linked immunosorbent assay(ELISA).MTT assay was used to test the scaffolds’ cytotoxicity.The scaffolds were co-cultured with endotheliocyte .Results HE staining and TEM study indicated no residual cells in the DBPS as well as preservation of the complete extracellular matrix .The remain quantity of residual protein and growth factors in ECM was high .The abdominal wall and subcutaneous implantation revealed that DBPS triggered a lower immune response as compared to the control group.MTT assay showed little cytotoxicity .Endotheliocyte assembled and growed with the scaffolds together .Conclusion DBPS are completely decellularized , and exhibit a higher level of biocompatibility in vivo.Using the way of vessels can make the integrity of extracellular matrix to be fully preserves and contain more growth factors .So using vessels way is better than bile duct .
2.DPHL:A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery
Zhu TIANSHENG ; Zhu YI ; Xuan YUE ; Gao HUANHUAN ; Cai XUE ; Piersma R. SANDER ; Pham V. THANG ; Schelfhorst TIM ; Haas R.G.D. RICHARD ; Bijnsdorp V. IRENE ; Sun RUI ; Yue LIANG ; Ruan GUAN ; Zhang QIUSHI ; Hu MO ; Zhou YUE ; Winan J. Van Houdt ; Tessa Y.S. Le Large ; Cloos JACQUELINE ; Wojtuszkiewicz ANNA ; Koppers-Lalic DANIJELA ; B(o)ttger FRANZISKA ; Scheepbouwer CHANTAL ; Brakenhoff H. RUUD ; Geert J.L.H. van Leenders ; Ijzermans N.M. JAN ; Martens W.M. JOHN ; Steenbergen D.M. RENSKE ; Grieken C. NICOLE ; Selvarajan SATHIYAMOORTHY ; Mantoo SANGEETA ; Lee S. SZE ; Yeow J.Y. SERENE ; Alkaff M.F. SYED ; Xiang NAN ; Sun YAOTING ; Yi XIAO ; Dai SHAOZHENG ; Liu WEI ; Lu TIAN ; Wu ZHICHENG ; Liang XIAO ; Wang MAN ; Shao YINGKUAN ; Zheng XI ; Xu KAILUN ; Yang QIN ; Meng YIFAN ; Lu CONG ; Zhu JIANG ; Zheng JIN'E ; Wang BO ; Lou SAI ; Dai YIBEI ; Xu CHAO ; Yu CHENHUAN ; Ying HUAZHONG ; Lim K. TONY ; Wu JIANMIN ; Gao XIAOFEI ; Luan ZHONGZHI ; Teng XIAODONG ; Wu PENG ; Huang SHI'ANG ; Tao ZHIHUA ; Iyer G. NARAYANAN ; Zhou SHUIGENG ; Shao WENGUANG ; Lam HENRY ; Ma DING ; Ji JIAFU ; Kon L. OI ; Zheng SHU ; Aebersold RUEDI ; Jimenez R. CONNIE ; Guo TIANNAN
Genomics, Proteomics & Bioinformatics 2020;18(2):104-119
To address the increasing need for detecting and validating protein biomarkers in clinical specimens, mass spectrometry (MS)-based targeted proteomic techniques, including the selected reaction monitoring (SRM), parallel reaction monitoring (PRM), and massively parallel data-independent acquisition (DIA), have been developed. For optimal performance, they require the fragment ion spectra of targeted peptides as prior knowledge. In this report, we describe a MS pipe-line and spectral resource to support targeted proteomics studies for human tissue samples. To build the spectral resource, we integrated common open-source MS computational tools to assemble a freely accessible computational workflow based on Docker. We then applied the workflow to gen-erate DPHL, a comprehensive DIA pan-human library, from 1096 data-dependent acquisition (DDA) MS raw files for 16 types of cancer samples. This extensive spectral resource was then applied to a proteomic study of 17 prostate cancer (PCa) patients. Thereafter, PRM validation was applied to a larger study of 57 PCa patients and the differential expression of three proteins in prostate tumor was validated. As a second application, the DPHL spectral resource was applied to a study consisting of plasma samples from 19 diffuse large B cell lymphoma (DLBCL) patients and 18 healthy control subjects. Differentially expressed proteins between DLBCL patients and healthy control subjects were detected by DIA-MS and confirmed by PRM. These data demonstrate that the DPHL supports DIA and PRM MS pipelines for robust protein biomarker discovery. DPHL is freely accessible at https://www.iprox.org/page/project.html?id=IPX0001400000.