1
|
Lubman DM. David M. Lubman-The University of Michigan-A retrospective in research. MASS SPECTROMETRY REVIEWS 2023; 42:643-651. [PMID: 34289523 PMCID: PMC8903096 DOI: 10.1002/mas.21718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 06/13/2023]
|
2
|
Liu X, Li N. New thoughts and findings on invasion and metastasis of pancreatic ductal adenocarcinoma (PDAC) from comparative proteomics: multi-target therapy. CLINICAL & TRANSLATIONAL ONCOLOGY : OFFICIAL PUBLICATION OF THE FEDERATION OF SPANISH ONCOLOGY SOCIETIES AND OF THE NATIONAL CANCER INSTITUTE OF MEXICO 2023:10.1007/s12094-023-03106-8. [PMID: 36745340 DOI: 10.1007/s12094-023-03106-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/28/2023] [Indexed: 02/07/2023]
Abstract
As one of the most aggressive malignant tumors, pancreatic ductal adenocarcinoma (PDAC) ranks as the fourth cancer-related mortality in the world. The extremely low survival rate is closely related to early invasion and distant metastasis. However, effective target therapy for weakening its malignant behavior remains limited. Over the past decades, many proteins correlating with invasion and metastasis of PDAC have been discovered using proteomics. The discovery of these proteins gives us a deeper understanding of the invasive and migratory processes of PDAC. This review is a systemic integration of these proteomics findings over the past 10 years. The discovered proteins were typically associated with the glycolytic process, hypoxic microenvironment, post-translational modification, extracellular matrix, exosomes, cancer stem cells, and immune escape. Some proteins were found to have multiple functions, and, cooperation between different proteins in the invasive and metastatic processes was found. This cooperation, and not just single protein function, may play a more significant role in the poor prognosis of PDAC. Therefore, multi-target therapy against these cooperative networks should be a primary choice in the future.
Collapse
Affiliation(s)
- Xinlu Liu
- 1st Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, 116011, China
| | - Na Li
- Department of Gastroenterology, First Affiliated Hospital of Dalian Medical University, Dalian, 116011, China.
| |
Collapse
|
3
|
Laser Capture Microdissection: A Gear for Pancreatic Cancer Research. Int J Mol Sci 2022; 23:ijms232314566. [PMID: 36498893 PMCID: PMC9741023 DOI: 10.3390/ijms232314566] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/16/2022] [Accepted: 11/19/2022] [Indexed: 11/24/2022] Open
Abstract
The advancement in molecular techniques has been attributed to the quality and significance of cancer research. Pancreatic cancer (PC) is one of the rare cancers with aggressive behavior and a high mortality rate. The asymptomatic nature of the disease until its advanced stage has resulted in late diagnosis as well as poor prognosis. The heterogeneous character of PC has complicated cancer development and progression studies. The analysis of bulk tissues of the disease was insufficient to understand the disease, hence, the introduction of the single-cell separating technique aided researchers to decipher more about the specific cell population of tumors. This review gives an overview of the Laser Capture Microdissection (LCM) technique, one of the single-cell separation methods used in PC research.
Collapse
|
4
|
Puthdee N, Sriswasdi S, Pisitkun T, Ratanasirintrawoot S, Israsena N, Tangkijvanich P. The LIN28B/TGF-β/TGFBI feedback loop promotes cell migration and tumour initiation potential in cholangiocarcinoma. Cancer Gene Ther 2022; 29:445-455. [PMID: 34548635 PMCID: PMC9113936 DOI: 10.1038/s41417-021-00387-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 07/25/2021] [Accepted: 09/03/2021] [Indexed: 02/02/2023]
Abstract
Cholangiocarcinoma (CCA), a lethal malignancy of the biliary epithelium, is the second most common primary liver cancer. The poor prognosis of CCA is due to the high rate of tumour invasion and distant metastasis. We found that the RNA-binding protein LIN28B, a known regulator of microRNA biogenesis, stem cell maintenance, and oncogenesis, is expressed in a subpopulation of CCA patients. To further investigate the potential role of LIN28B in CCA pathogenesis, we studied the effect of LIN28B overexpression in the cholangiocyte cell line MMNK-1 and cholangiocarcinoma cell lines HuCCT-1 and KKU-214. Here, we show that enhanced LIN28B expression promoted cancer stem cell-like properties in CCA, including enhanced cell migration, epithelial-to-mesenchymal transition (EMT), increased cell proliferation and spheroid formation. Proteomic analysis revealed TGF-β-induced protein (TGFBI) as a novel LIN28B target gene, and further analysis showed upregulation of other components of the TGF-β signalling pathway, including TGF-β receptor type I (TGFBRI) expression and cytokine TGFB-I, II and III secretion. Importantly, the small molecule TGF-β inhibitor SB431542 negated the effects of LIN28B on both cell migration and clonogenic potential. Overexpression of TGFBI alone promoted cholangiocarcinoma cell migration and EMT changes, but not spheroid formation, suggesting that TGFBI partially contributes to LIN28B-mediated aggressive cell behaviour. These observations are consistent with a model in which TGF-β and LIN28B work together to form a positive feedback loop during cholangiocarcinoma metastasis and provide a therapeutic intervention opportunity.
Collapse
Affiliation(s)
- Nattapong Puthdee
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sira Sriswasdi
- Department of Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Trairak Pisitkun
- Department of Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | | | - Nipan Israsena
- Center of Excellence for Stem Cell and Cell Therapy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
- Department of Pharmacology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
| | - Pisit Tangkijvanich
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Hepatitis and Liver Cancer, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| |
Collapse
|
5
|
Jo JH, Kim SA, Lee JH, Park YR, Kim C, Park SB, Jung DE, Lee HS, Chung MJ, Song SY. GLRX3, a novel cancer stem cell-related secretory biomarker of pancreatic ductal adenocarcinoma. BMC Cancer 2021; 21:1241. [PMID: 34794402 PMCID: PMC8603516 DOI: 10.1186/s12885-021-08898-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/13/2021] [Indexed: 12/02/2022] Open
Abstract
Background Cancer stem cells (CSCs) are implicated in carcinogenesis, cancer progression, and recurrence. Several biomarkers have been described for pancreatic ductal adenocarcinoma (PDAC) CSCs; however, their function and mechanism remain unclear. Method In this study, secretome analysis was performed in pancreatic CSC-enriched spheres and control adherent cells for biomarker discovery. Glutaredoxin3 (GLRX3), a novel candidate upregulated in spheres, was evaluated for its function and clinical implication. Results PDAC CSC populations, cell lines, patient tissues, and blood samples demonstrated GLRX3 overexpression. In contrast, GLRX3 silencing decreased the in vitro proliferation, migration, clonogenicity, and sphere formation of cells. GLRX3 knockdown also reduced tumor formation and growth in vivo. GLRX3 was found to regulate Met/PI3K/AKT signaling and stemness-related molecules. ELISA results indicated GLRX3 overexpression in the serum of patients with PDAC compared to that in healthy controls. The sensitivity and specificity of GLRX3 for PDAC diagnosis were 80.0 and 100%, respectively. When GLRX3 and CA19–9 were combined, sensitivity was significantly increased to 98.3% compared to that with GLRX3 or CA19–9 alone. High GLRX3 expression was also associated with poor disease-free survival in patients receiving curative surgery. Conclusion Overall, these results indicate GLRX3 as a novel diagnostic marker and therapeutic target for PDAC targeting CSCs. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08898-y.
Collapse
Affiliation(s)
- Jung Hyun Jo
- Division of Gastroenterology, Department of Internal Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea.,Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Sun A Kim
- Cowell Biodigm Co., Ltd, Seoul, South Korea
| | - Jeong Hoon Lee
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Yu Rang Park
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Chanyang Kim
- Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Soo Been Park
- Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Dawoon E Jung
- Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Hee Seung Lee
- Division of Gastroenterology, Department of Internal Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea.,Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Moon Jae Chung
- Division of Gastroenterology, Department of Internal Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea.,Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Si Young Song
- Division of Gastroenterology, Department of Internal Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea. .,Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, 03722, South Korea.
| |
Collapse
|
6
|
Integrated lipidomics and proteomics reveal cardiolipin alterations, upregulation of HADHA and long chain fatty acids in pancreatic cancer stem cells. Sci Rep 2021; 11:13297. [PMID: 34168259 PMCID: PMC8225828 DOI: 10.1038/s41598-021-92752-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 06/15/2021] [Indexed: 02/06/2023] Open
Abstract
Pancreatic cancer stem cells (PCSCs) play a key role in the aggressiveness of pancreatic ductal adenocarcinomas (PDAC); however, little is known about their signaling and metabolic pathways. Here we show that PCSCs have specific and common proteome and lipidome modulations. PCSCs displayed downregulation of lactate dehydrogenase A chain, and upregulation of trifunctional enzyme subunit alpha. The upregulated proteins of PCSCs are mainly involved in fatty acid (FA) elongation and biosynthesis of unsaturated FAs. Accordingly, lipidomics reveals an increase in long and very long-chain unsaturated FAs, which are products of fatty acid elongase-5 predicted as a key gene. Moreover, lipidomics showed the induction in PCSCs of molecular species of cardiolipin with mixed incorporation of 16:0, 18:1, and 18:2 acyl chains. Our data indicate a crucial role of FA elongation and alteration in cardiolipin acyl chain composition in PCSCs, representing attractive therapeutic targets in PDAC.
Collapse
|
7
|
Transcriptome analysis of the procession from chronic pancreatitis to pancreatic cancer and metastatic pancreatic cancer. Sci Rep 2021; 11:3409. [PMID: 33564087 PMCID: PMC7873308 DOI: 10.1038/s41598-021-83015-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 01/28/2021] [Indexed: 02/08/2023] Open
Abstract
Exploring the underlying mechanisms of cancer development is useful for cancer treatment. In this paper, we analyzed the transcriptome profiles from the human normal pancreas, pancreatitis, pancreatic cancer and metastatic pancreatic cancer to study the intricate associations among pancreatic cancer progression. We clustered the transcriptome data, and analyzed the differential expressed genes. WGCNA was applied to construct co-expression networks and detect important modules. Importantly we selected the module in a different way. As the pancreatic disease deteriorates, the number of differentially expressed genes increases. The gene networks of T cells and interferon are upregulated in stages. In conclusion, the network-based study provides gradually activated gene networks in the disease progression of pancreatitis, pancreatic cancer, and metastatic pancreatic cancer. It may contribute to the rational design of anti-cancer drugs.
Collapse
|
8
|
Mantini G, Meijer LL, Glogovitis I, In ‘t Veld SGJG, Paleckyte R, Capula M, Le Large TYS, Morelli L, Pham TV, Piersma SR, Frampton AE, Jimenez CR, Kazemier G, Koppers-Lalic D, Wurdinger T, Giovannetti E. Omics Analysis of Educated Platelets in Cancer and Benign Disease of the Pancreas. Cancers (Basel) 2020; 13:cancers13010066. [PMID: 33383671 PMCID: PMC7795159 DOI: 10.3390/cancers13010066] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/23/2020] [Accepted: 12/24/2020] [Indexed: 02/05/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is traditionally associated with thrombocytosis/hypercoagulation and novel insights on platelet-PDAC "dangerous liaisons" are warranted. Here we performed an integrative omics study investigating the biological processes of mRNAs and expressed miRNAs, as well as proteins in PDAC blood platelets, using benign disease as a reference for inflammatory noise. Gene ontology mining revealed enrichment of RNA splicing, mRNA processing and translation initiation in miRNAs and proteins but depletion in RNA transcripts. Remarkably, correlation analyses revealed a negative regulation on SPARC transcription by isomiRs involved in cancer signaling, suggesting a specific "education" in PDAC platelets. Platelets of benign patients were enriched for non-templated additions of G nucleotides (#ntaG) miRNAs, while PDAC presented length variation on 3' (lv3p) as the most frequent modification on miRNAs. Additionally, we provided an actionable repertoire of PDAC and benign platelet-ome to be exploited for future studies. In conclusion, our data show that platelets change their biological repertoire in patients with PDAC, through dysregulation of miRNAs and splicing factors, supporting the presence of de novo protein machinery that can "educate" the platelet. These novel findings could be further exploited for innovative liquid biopsies platforms as well as possible therapeutic targets.
Collapse
Affiliation(s)
- Giulia Mantini
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands; (G.M.); (L.L.M.); (R.P.); (T.Y.S.L.L.); (T.V.P.); (S.R.P.); (C.R.J.)
- Fondazione Pisana per la Scienza, 56017 Pisa, Italy;
| | - Laura L. Meijer
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands; (G.M.); (L.L.M.); (R.P.); (T.Y.S.L.L.); (T.V.P.); (S.R.P.); (C.R.J.)
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands;
| | - Ilias Glogovitis
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands; (I.G.); (S.G.J.G.I.V.); (D.K.-L.)
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 4002 Plovdiv, Bulgaria
| | - Sjors G. J. G. In ‘t Veld
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands; (I.G.); (S.G.J.G.I.V.); (D.K.-L.)
| | - Rosita Paleckyte
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands; (G.M.); (L.L.M.); (R.P.); (T.Y.S.L.L.); (T.V.P.); (S.R.P.); (C.R.J.)
| | - Mjriam Capula
- Fondazione Pisana per la Scienza, 56017 Pisa, Italy;
- Institute of Life Sciences, Sant’Anna School of Advanced Studies, 56127 Pisa, Italy
| | - Tessa Y. S. Le Large
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands; (G.M.); (L.L.M.); (R.P.); (T.Y.S.L.L.); (T.V.P.); (S.R.P.); (C.R.J.)
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands;
| | - Luca Morelli
- General Surgery Unit, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy;
| | - Thang V. Pham
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands; (G.M.); (L.L.M.); (R.P.); (T.Y.S.L.L.); (T.V.P.); (S.R.P.); (C.R.J.)
| | - Sander R. Piersma
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands; (G.M.); (L.L.M.); (R.P.); (T.Y.S.L.L.); (T.V.P.); (S.R.P.); (C.R.J.)
| | - Adam E. Frampton
- Department of Clinical and Experimental Medicine, Faculty of Health and Medical Sciences, The Leggett Building, University of Surrey, Guildford GU2 7WG, UK;
- Faculty of Health and Medical Sciences, The Leggett Building, University of Surrey, Guildford GU2 7XH, UK
| | - Connie R. Jimenez
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands; (G.M.); (L.L.M.); (R.P.); (T.Y.S.L.L.); (T.V.P.); (S.R.P.); (C.R.J.)
| | - Geert Kazemier
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands;
| | - Danijela Koppers-Lalic
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands; (I.G.); (S.G.J.G.I.V.); (D.K.-L.)
| | - Thomas Wurdinger
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands; (I.G.); (S.G.J.G.I.V.); (D.K.-L.)
- Correspondence: (T.W.); (E.G.); Tel.: +31-003-120-444-2633 (E.G.)
| | - Elisa Giovannetti
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands; (G.M.); (L.L.M.); (R.P.); (T.Y.S.L.L.); (T.V.P.); (S.R.P.); (C.R.J.)
- Fondazione Pisana per la Scienza, 56017 Pisa, Italy;
- Correspondence: (T.W.); (E.G.); Tel.: +31-003-120-444-2633 (E.G.)
| |
Collapse
|
9
|
Samonig L, Loipetzberger A, Blöchl C, Rurik M, Kohlbacher O, Aberger F, Huber CG. Proteins and Molecular Pathways Relevant for the Malignant Properties of Tumor-Initiating Pancreatic Cancer Cells. Cells 2020; 9:E1397. [PMID: 32503348 PMCID: PMC7349116 DOI: 10.3390/cells9061397] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/26/2020] [Accepted: 05/30/2020] [Indexed: 12/29/2022] Open
Abstract
Cancer stem cells (CSCs), a small subset of the tumor bulk with highly malignant properties, are deemed responsible for tumor initiation, growth, metastasis, and relapse. In order to reveal molecular markers and determinants of their tumor-initiating properties, we enriched rare stem-like pancreatic tumor-initiating cells (TICs) by harnessing their clonogenic growth capacity in three-dimensional multicellular spheroid cultures. We compared pancreatic TICs isolated from three-dimensional tumor spheroid cultures with nontumor-initiating cells (non-TICs) enriched in planar cultures. Employing differential proteomics (PTX), we identified more than 400 proteins with significantly different expression in pancreatic TICs and the non-TIC population. By combining the unbiased PTX with mRNA expression analysis and literature-based predictions of pro-malignant functions, we nominated the two calcium-binding proteins S100A8 (MRP8) and S100A9 (MRP14) as well as galactin-3-binding protein LGALS3BP (MAC-2-BP) as putative determinants of pancreatic TICs. In silico pathway analysis followed by candidate-based RNA interference mediated loss-of-function analysis revealed a critical role of S100A8, S100A9, and LGALS3BP as molecular determinants of TIC proliferation, migration, and in vivo tumor growth. Our study highlights the power of combining unbiased proteomics with focused gene expression and functional analyses for the identification of novel key regulators of TICs, an approach that warrants further application to identify proteins and pathways amenable to drug targeting.
Collapse
Affiliation(s)
- Lisa Samonig
- Department of Biosciences, Bioanalytical Research Labs, University of Salzburg, A-5020 Salzburg, Austria; (L.S.); (C.B.)
| | - Andrea Loipetzberger
- Department of Biosciences, Cancer Cluster Salzburg, Molecular Cancer and Stem Cell Research, University of Salzburg, A-5020 Salzburg, Austria;
| | - Constantin Blöchl
- Department of Biosciences, Bioanalytical Research Labs, University of Salzburg, A-5020 Salzburg, Austria; (L.S.); (C.B.)
| | - Marc Rurik
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany; (M.R.); (O.K.)
| | - Oliver Kohlbacher
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany; (M.R.); (O.K.)
- Biomolecular Interactions, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
- Institute for Translational Bioinformatics, University Hospital Tübingen, Hoppe-Seyler-Str. 9, 72076 Tübingen, Germany
- Quantitative Biology Center, University of Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Fritz Aberger
- Department of Biosciences, Cancer Cluster Salzburg, Molecular Cancer and Stem Cell Research, University of Salzburg, A-5020 Salzburg, Austria;
- Department of Biosciences, Cancer Cluster Salzburg, University of Salzburg, A-5020 Salzburg, Austria
| | - Christian G. Huber
- Department of Biosciences, Bioanalytical Research Labs, University of Salzburg, A-5020 Salzburg, Austria; (L.S.); (C.B.)
- Department of Biosciences, Cancer Cluster Salzburg, University of Salzburg, A-5020 Salzburg, Austria
| |
Collapse
|
10
|
Effects of the Bone/Bone Marrow Microenvironments on Prostate Cancer Cells and CD59 Expression. BIOMED RESEARCH INTERNATIONAL 2020; 2020:2753414. [PMID: 32337233 PMCID: PMC7165328 DOI: 10.1155/2020/2753414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 02/02/2020] [Accepted: 02/21/2020] [Indexed: 11/17/2022]
Abstract
Objective To evaluate the effects of human bone marrow mesenchymal stem cells (hBMSCs) and osteoblasts (hFOB1.19) on PC3 prostate cancer cells. Methods To simulate the in vivo interaction between the bone/bone marrow microenvironments and prostate cancer cells, we established cocultures of PC3 cells with hBMSC or hFOB1.19 cells and evaluated their effects on the proliferation, cell cycle distribution, cell migration, and invasion of PC3 cells. Quantitative reverse transcription polymerase chain reaction was used to detect CD59 mRNA expression in PC3 cells. The expression of receptor activator of nuclear factor- (NF-) κB (RANK), RANK ligand (RANKL), osteoprotegerin (OPG), CD59, NF-κB (p50 subunit), and cyclin D1 in PC3 cells was analyzed by immunofluorescence and western blotting. Results hBMSCs and hFOB1.19 cells enhanced the proliferation, migration, and invasion of PC3 cells; increased the proportion of PC3 cells in the S and G2/M phases of the cell cycle; and upregulated RANK, RANKL, OPG, CD59, cyclin D1, and NF-κB (p50 subunit) expression by PC3 cells. The RANKL inhibitor, scutellarin, inhibited these effects in PC3-hFOB1.19 cocultures. Conclusion hBMSCs and hFOB1.19 cells modulate the phenotype of PC3 prostate cancer cells and the expression of CD59 by activating the RANK/RANKL/OPG signaling pathway.
Collapse
|
11
|
Dapic I, Baljeu-Neuman L, Uwugiaren N, Kers J, Goodlett DR, Corthals GL. Proteome analysis of tissues by mass spectrometry. MASS SPECTROMETRY REVIEWS 2019; 38:403-441. [PMID: 31390493 DOI: 10.1002/mas.21598] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/17/2019] [Indexed: 06/10/2023]
Abstract
Tissues and biofluids are important sources of information used for the detection of diseases and decisions on patient therapies. There are several accepted methods for preservation of tissues, among which the most popular are fresh-frozen and formalin-fixed paraffin embedded methods. Depending on the preservation method and the amount of sample available, various specific protocols are available for tissue processing for subsequent proteomic analysis. Protocols are tailored to answer various biological questions, and as such vary in lysis and digestion conditions, as well as duration. The existence of diverse tissue-sample protocols has led to confusion in how to choose the best protocol for a given tissue and made it difficult to compare results across sample types. Here, we summarize procedures used for tissue processing for subsequent bottom-up proteomic analysis. Furthermore, we compare protocols for their variations in the composition of lysis buffers, digestion procedures, and purification steps. For example, reports have shown that lysis buffer composition plays an important role in the profile of extracted proteins: the most common are tris(hydroxymethyl)aminomethane, radioimmunoprecipitation assay, and ammonium bicarbonate buffers. Although, trypsin is the most commonly used enzyme for proteolysis, in some protocols it is supplemented with Lys-C and/or chymotrypsin, which will often lead to an increase in proteome coverage. Data show that the selection of the lysis procedure might need to be tissue-specific to produce distinct protocols for individual tissue types. Finally, selection of the procedures is also influenced by the amount of sample available, which range from biopsies or the size of a few dozen of mm2 obtained with laser capture microdissection to much larger amounts that weight several milligrams.
Collapse
Affiliation(s)
- Irena Dapic
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | | | - Naomi Uwugiaren
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Jesper Kers
- Department of Pathology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam Cardiovascular Sciences (ACS), Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - David R Goodlett
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- University of Maryland, 20N. Pine Street, Baltimore, MD 21201
| | - Garry L Corthals
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
12
|
Pettit ME, Donnarumma F, Murray KK, Solouki T. Infrared laser ablation sampling coupled with data independent high resolution UPLC-IM-MS/MS for tissue analysis. Anal Chim Acta 2018; 1034:102-109. [DOI: 10.1016/j.aca.2018.06.066] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/22/2018] [Accepted: 06/24/2018] [Indexed: 12/30/2022]
|
13
|
Sato T, Muramatsu T, Tanabe M, Inazawa J. Identification and characterization of transforming growth factor beta-induced in circulating tumor cell subline from pancreatic cancer cell line. Cancer Sci 2018; 109:3623-3633. [PMID: 30156359 PMCID: PMC6215881 DOI: 10.1111/cas.13783] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/22/2018] [Accepted: 08/23/2018] [Indexed: 01/06/2023] Open
Abstract
Distant metastasis to liver, lung, brain, or bone occurs by circulating tumor cells (CTC). We hypothesized that a subset of CTC had features that are more malignant than tumor cells at the primary site. We established a highly malignant cell line, Panc-1-CTC, derived from the human pancreatic cancer cell line Panc-1 using an in vivo selection method. Panc-1-CTC cells showed greater migratory and invasive abilities than its parent cell line in vitro. In addition, Panc-1-CTC cells had a higher tumor-forming ability than parent cells in vivo. To examine whether a difference in malignant phenotypes exists between Panc-1-CTC cells and parent cells, we carried out comprehensive gene expression array analysis. As a result, Panc-1-CTC significantly expressed transforming growth factor beta-induced (TGFBI), an extracellular matrix protein, more abundantly than did parent cells. TGFBI is considered to regulate cell adhesion, but its functions remain unclear. In the present study, knockdown of TGFBI reduced cell migration and invasion abilities, whereas overexpression of TGFBI increased both abilities. Moreover, elevated expression of TGFBI was associated with poor prognosis in patients with pancreatic cancer.
Collapse
Affiliation(s)
- Taku Sato
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.,Department of Hepatobiliary and Pancreatic Surgery, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tomoki Muramatsu
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Minoru Tanabe
- Department of Hepatobiliary and Pancreatic Surgery, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Johji Inazawa
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.,Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan
| |
Collapse
|
14
|
Zhou W, Liotta LA, Petricoin EF. The Warburg Effect and Mass Spectrometry-based Proteomic Analysis. Cancer Genomics Proteomics 2018. [PMID: 28647695 DOI: 10.21873/cgp.20032] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Compared to normal cells, cancer cells have a unique metabolism by performing lactic acid fermentation in the presence of oxygen, also known as the Warburg effect. Researchers have proposed several hypotheses to elucidate the phenomenon, but the mechanism is still an enigma. In this review, we discuss three typical models, such as "damaged mitochondria", "adaptation to hypoxia", and "cell proliferation requirement", as well as contributions from mass spectrometry analysis toward our understanding of the Warburg effect. Mass spectrometry analysis supports the "adaptation to hypoxia" model that cancer cells are using quasi-anaerobic fermentation to reduce oxygen consumption in vivo. We further propose that hypoxia is an early event and it plays a crucial role in carcinoma initiation and development.
Collapse
Affiliation(s)
- Weidong Zhou
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, U.S.A.
| | - Lance A Liotta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, U.S.A
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, U.S.A
| |
Collapse
|
15
|
Yi L, Piehowski PD, Shi T, Smith RD, Qian WJ. Advances in microscale separations towards nanoproteomics applications. J Chromatogr A 2017; 1523:40-48. [PMID: 28765000 PMCID: PMC6042839 DOI: 10.1016/j.chroma.2017.07.055] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 07/14/2017] [Accepted: 07/17/2017] [Indexed: 01/22/2023]
Abstract
Microscale separation (e.g., liquid chromatography or capillary electrophoresis) coupled with mass spectrometry (MS) has become the primary tool for advanced proteomics, an indispensable technology for gaining understanding of complex biological processes. In recent decades significant advances have been achieved in MS-based proteomics. However, the current proteomics platforms still face an analytical challenge in overall sensitivity towards nanoproteomics applications for starting materials of less than 1μg total proteins (e.g., cellular heterogeneity in tissue pathologies). Herein, we review recent advances in microscale separation techniques and integrated sample processing strategies that improve the overall sensitivity and proteome coverage of the proteomics workflow, and their contributions towards nanoproteomics applications.
Collapse
Affiliation(s)
- Lian Yi
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Paul D Piehowski
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Tujin Shi
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Richard D Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Wei-Jun Qian
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, United States.
| |
Collapse
|
16
|
Dick JM. Chemical composition and the potential for proteomic transformation in cancer, hypoxia, and hyperosmotic stress. PeerJ 2017; 5:e3421. [PMID: 28603672 PMCID: PMC5463988 DOI: 10.7717/peerj.3421] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 05/16/2017] [Indexed: 12/19/2022] Open
Abstract
The changes of protein expression that are monitored in proteomic experiments are a type of biological transformation that also involves changes in chemical composition. Accompanying the myriad molecular-level interactions that underlie any proteomic transformation, there is an overall thermodynamic potential that is sensitive to microenvironmental conditions, including local oxidation and hydration potential. Here, up- and down-expressed proteins identified in 71 comparative proteomics studies were analyzed using the average oxidation state of carbon (ZC) and water demand per residue (\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{upgreek}
\usepackage{mathrsfs}
\setlength{\oddsidemargin}{-69pt}
\begin{document}
}{}${\overline{n}}_{{\mathrm{H}}_{2}\mathrm{O}}$\end{document}n¯H2O), calculated using elemental abundances and stoichiometric reactions to form proteins from basis species. Experimental lowering of oxygen availability (hypoxia) or water activity (hyperosmotic stress) generally results in decreased ZC or \documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{upgreek}
\usepackage{mathrsfs}
\setlength{\oddsidemargin}{-69pt}
\begin{document}
}{}${\overline{n}}_{{\mathrm{H}}_{2}\mathrm{O}}$\end{document}n¯H2O of up-expressed compared to down-expressed proteins. This correspondence of chemical composition with experimental conditions provides evidence for attraction of the proteomes to a low-energy state. An opposite compositional change, toward higher average oxidation or hydration state, is found for proteomic transformations in colorectal and pancreatic cancer, and in two experiments for adipose-derived stem cells. Calculations of chemical affinity were used to estimate the thermodynamic potentials for proteomic transformations as a function of fugacity of O2 and activity of H2O, which serve as scales of oxidation and hydration potential. Diagrams summarizing the relative potential for formation of up- and down-expressed proteins have predicted equipotential lines that cluster around particular values of oxygen fugacity and water activity for similar datasets. The changes in chemical composition of proteomes are likely linked with reactions among other cellular molecules. A redox balance calculation indicates that an increase in the lipid to protein ratio in cancer cells by 20% over hypoxic cells would generate a large enough electron sink for oxidation of the cancer proteomes. The datasets and computer code used here are made available in a new R package, canprot.
Collapse
|
17
|
Laser Capture Microdissection of Pancreatic Acinar Cells to Identify Proteomic Alterations in a Murine Model of Caerulein-Induced Pancreatitis. Clin Transl Gastroenterol 2017; 8:e89. [PMID: 28406494 PMCID: PMC5415897 DOI: 10.1038/ctg.2017.15] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 01/05/2017] [Indexed: 12/13/2022] Open
Abstract
Objectives: Chronic pancreatitis (CP) is characterized by inflammation and fibrosis of the pancreas, leading to pain, parenchymal damage, and loss of exocrine and endocrine function. There are currently no curative therapies; diagnosis remains difficult and aspects of pathogenesis remain unclear. Thus, there is a need to identify novel biomarkers to improve diagnosis and understand pathophysiology. We hypothesize that pancreatic acinar regions contain proteomic signatures relevant to disease processes, including secreted proteins that could be detected in biofluids. Methods: Acini from pancreata of mice injected with or without caerulein were collected using laser capture microdissection followed by mass spectrometry analysis. This protocol enabled high-throughput analysis that captured altered protein expression throughout the stages of CP. Results: Over 2,900 proteins were identified, whereas 331 were significantly changed ≥2-fold by mass spectrometry spectral count analysis. Consistent with pathogenesis, we observed increases in proteins related to fibrosis (e.g., collagen, P<0.001), several proteases (e.g., trypsin 1, P<0.001), and altered expression of proteins associated with diminished pancreas function (e.g., lipase, amylase, P<0.05). In comparison with proteomic data from a public data set of CP patients, a significant correlation was observed between proteomic changes in tissue from both the caerulein model and CP patients (r=0.725, P<0.001). CONCLUSIONS: This study illustrates the ability to characterize proteome changes of acinar cells isolated from pancreata of caerulein-treated mice and demonstrates a relationship between signatures from murine and human CP.
Collapse
|
18
|
Annexin A10 is a candidate marker associated with the progression of pancreatic precursor lesions to adenocarcinoma. PLoS One 2017; 12:e0175039. [PMID: 28369074 PMCID: PMC5378402 DOI: 10.1371/journal.pone.0175039] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 03/20/2017] [Indexed: 12/22/2022] Open
Abstract
Annexins are a multigene family of calcium and phospholipid-binding proteins that play important roles in calcium signaling, cell motility, differentiation and proliferation. Our previous mass spectrometry-based proteomics study revealed that annexin A10 (ANXA10) was uniquely overexpressed in pancreatic CD24+ adenocarcinoma cells that were dissected from clinical PDAC tissues but was absent in CD24- adjacent normal cells. The correlation between ANXA10 expression and the progression of pancreatic cancer remains unknown. In this study, we performed an immunostaining assay to evaluate ANXA10 expression in 155 primary human tissue specimens, including normal pancreas, chronic pancreatitis (CP), pancreatic adenocarcinoma (PDAC), pancreatic intraepithelial neoplasia (PanIN, the most important precursor of PDAC), and intraductal papillary mucinous neoplasm (IPMN). The immunostaining result showed that ANXA10 was significantly overexpressed in PanINs, IPMNs, and PDACs but negative in normal pancreas and the majority of chronic pancreatitis tissues. Statistical analysis revealed that ANXA10 expression was significantly associated with PDAC and its precursor lesions (p<0.0001). Abundant ANXA10 expression was predominantly present in pancreatic ductal epithelial cells of PanINs, IPMNs, and tumor cells of PDACs. Since PDAC develops through a series of PanINs which in turn arise from pancreatic ducts, the consistent overexpression of ANXA10 in ductal epithelial cells in PanINs and PDACs but negative in normal pancreatic ducts suggests that ANXA10 could serve as a potential marker indicating the presence of PDAC at its earliest precancerous stages. Double immunostaining of ANXA10 and CD24 showed that there was a large overlap between these two markers in PDAC and high-grade neoplasia lesions. The statistical analysis showed that the coexpression of ANXA10 and CD24 was significantly correlated with the progression of pancreatic precursor lesions towards PDACs.
Collapse
|
19
|
Yokobori T, Nishiyama M. TGF-β Signaling in Gastrointestinal Cancers: Progress in Basic and Clinical Research. J Clin Med 2017; 6:jcm6010011. [PMID: 28106769 PMCID: PMC5294964 DOI: 10.3390/jcm6010011] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 12/31/2016] [Accepted: 01/16/2017] [Indexed: 12/18/2022] Open
Abstract
Transforming growth factor (TGF)-β superfamily proteins have many important biological functions, including regulation of tissue differentiation, cell proliferation, and migration in both normal and cancer cells. Many studies have reported that TGF-β signaling is associated with disease progression and therapeutic resistance in several cancers. Similarly, TGF-β-induced protein (TGFBI)—a downstream component of the TGF-β signaling pathway—has been shown to promote and/or inhibit cancer. Here, we review the state of basic and clinical research on the roles of TGF-β and TGFBI in gastrointestinal cancers.
Collapse
Affiliation(s)
- Takehiko Yokobori
- Research Program for Omics-based Medical Science, Division of Integrated Oncology Research, Gunma University Initiative for Advanced Research, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan.
| | - Masahiko Nishiyama
- Research Program for Omics-based Medical Science, Division of Integrated Oncology Research, Gunma University Initiative for Advanced Research, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan.
- Department of Molecular Pharmacology and Oncology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan.
| |
Collapse
|
20
|
Chen J, Ding P, Li L, Gu H, Zhang X, Zhang L, Wang N, Gan L, Wang Q, Zhang W, Hu W. CD59 Regulation by SOX2 Is Required for Epithelial Cancer Stem Cells to Evade Complement Surveillance. Stem Cell Reports 2016; 8:140-151. [PMID: 28017655 PMCID: PMC5233323 DOI: 10.1016/j.stemcr.2016.11.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 11/21/2016] [Accepted: 11/22/2016] [Indexed: 12/16/2022] Open
Abstract
Cancer stem cells (CSCs) are highly associated with therapy resistance and metastasis. Interplay between CSCs and various immune components is required for tumor survival. However, the response of CSCs to complement surveillance remains unknown. Herein, using stem-like sphere-forming cells prepared from a mammary tumor and a lung adenocarcinoma cell line, we found that CD59 was upregulated to protect CSCs from complement-dependent cytotoxicity. CD59 silencing significantly enhanced complement destruction and completely suppressed tumorigenesis in CSC-xenografted nude mice. Furthermore, we identified that SOX2 upregulates CD59 in epithelial CSCs. In addition, we revealed that SOX2 regulates the transcription of mCd59b, leading to selective mCD59b abundance in murine testis spermatogonial stem cells. Therefore, we demonstrated that CD59 regulation by SOX2 is required for stem cell evasion of complement surveillance. This finding highlights the importance of complement surveillance in eliminating CSCs and may suggest CD59 as a potential target for cancer therapy.
Collapse
Affiliation(s)
- Jianfeng Chen
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Collaborative Innovation Center of Cancer Medicine, Shanghai Medical College, Fudan University, 270 Dong'an Road, Shanghai 200032, China
| | - Peipei Ding
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Collaborative Innovation Center of Cancer Medicine, Shanghai Medical College, Fudan University, 270 Dong'an Road, Shanghai 200032, China
| | - Ling Li
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Collaborative Innovation Center of Cancer Medicine, Shanghai Medical College, Fudan University, 270 Dong'an Road, Shanghai 200032, China
| | - Hongyu Gu
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Collaborative Innovation Center of Cancer Medicine, Shanghai Medical College, Fudan University, 270 Dong'an Road, Shanghai 200032, China
| | - Xin Zhang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Collaborative Innovation Center of Cancer Medicine, Shanghai Medical College, Fudan University, 270 Dong'an Road, Shanghai 200032, China
| | - Long Zhang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Collaborative Innovation Center of Cancer Medicine, Shanghai Medical College, Fudan University, 270 Dong'an Road, Shanghai 200032, China
| | - Na Wang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Collaborative Innovation Center of Cancer Medicine, Shanghai Medical College, Fudan University, 270 Dong'an Road, Shanghai 200032, China
| | - Lu Gan
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Collaborative Innovation Center of Cancer Medicine, Shanghai Medical College, Fudan University, 270 Dong'an Road, Shanghai 200032, China
| | - Qi Wang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Collaborative Innovation Center of Cancer Medicine, Shanghai Medical College, Fudan University, 270 Dong'an Road, Shanghai 200032, China
| | - Wei Zhang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Collaborative Innovation Center of Cancer Medicine, Shanghai Medical College, Fudan University, 270 Dong'an Road, Shanghai 200032, China
| | - Weiguo Hu
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Collaborative Innovation Center of Cancer Medicine, Shanghai Medical College, Fudan University, 270 Dong'an Road, Shanghai 200032, China; Department of Immunology, Shanghai Medical College, Fudan University, 130 Dong'an Road, Shanghai 200032, China.
| |
Collapse
|
21
|
Yang R, Liu X, Thakolwiboon S, Zhu J, Pei X, An M, Tan Z, Lubman DM. Protein Markers Associated with an ALDH Sub-Population in Colorectal Cancer. JOURNAL OF PROTEOMICS & BIOINFORMATICS 2016; 9:238-247. [PMID: 28503055 PMCID: PMC5423664 DOI: 10.4172/jpb.1000412] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
ALDH has been shown to be a marker that denotes a sub-population of cancer stem cells in colorectal and other cancers. This sub-population of cells shows an increased risk for tumor initiation, metastasis, and resistance to chemotherapy and radiation resulting in recurrence and death. It is thus essential to identify the important signaling pathways related to ALDH1+ CSCs in colon cancer. The essential issue becomes to isolate pure sub-populations of cells from heterogeneous tissues for further analysis. To achieve this goal, tissues from colorectal cancer Stage III patients were immuno-stained with ALDH1 antibody. Target ALDH1+ and ALDH1- cells from the same tissue were micro-dissected using Laser Capture Microdissection (LCM). Captured cells were lysed and analyzed using LC-MS/MS where around 20,000 cells were available for analysis. This analysis resulted in 134 proteins which were differentially expressed between ALDH1+ and ALDH1- cells in three patient sample pairs. Based on these differentially expressed proteins an IPA pathway analysis was performed that showed two key pathways in cell to cell signaling and organismal injury and abnormalities. The IPA analysis revealed β-catenin, NFκB (p65) and TGFβ1 as important cancer-related proteins in these pathways. A TMA validation using immunofluorescence staining of tissue micro-arrays including 170 cases was used to verify that these key proteins were highly overexpressed in ALDH1+ cells in colon cancer tissues compared to ALDH1- cells.
Collapse
Affiliation(s)
- Rui Yang
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, USA
| | - Xinhua Liu
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, USA
- Experimental Center for Science and Technology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Smathorn Thakolwiboon
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, USA
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Jianhui Zhu
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, USA
| | - Xiucong Pei
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, USA
- Department of Toxicology, School of Public Health, Shenyang Medical College, Liaoning 110034, China
| | - Mingrui An
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, USA
| | - Zhijing Tan
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, USA
| | - David M Lubman
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, USA
| |
Collapse
|
22
|
Wu J, Zhu J, Yin H, Liu X, An M, Pudlo NA, Martens EC, Chen GY, Lubman DM. Development of an Integrated Pipeline for Profiling Microbial Proteins from Mouse Fecal Samples by LC-MS/MS. J Proteome Res 2016; 15:3635-3642. [PMID: 27559751 DOI: 10.1021/acs.jproteome.6b00450] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Metaproteomics is one approach to analyze the functional capacity of the gut microbiome but is limited by the ability to evenly extract proteins from diverse organisms within the gut. Herein, we have developed a pipeline to optimize sample preparation of stool obtained from germ-free (GF) mice that were gavaged a defined community of 11 bacterial strains isolated from the human gut. With 64% more proteins identified, bead-beating was confirmed to be an indispensable step for the extraction of bacterial proteins, especially for Gram-positive bacteria. Bacterial enrichment from mouse fecal samples was further optimized by evaluating three different methods: (1) a high-speed differential centrifugation (HCE) or (2) a low-speed differential centrifugation (LCE) and (3) a filter-aided method (FA). The HCE method was associated with dramatic loss of bacteria and 71% less recovery of bacterial proteins than the LCE method. Compared with LCE, the FA method also showed dramatic loss of the amount of bacteria recovered and decreased protein identifications from Gram-positive bacteria in the stool samples. Ultimately, LCE may provide an alternative and complementary method for enriching bacteria from small amounts of mouse fecal samples, which could aid in investigating bacterial function in health and disease.
Collapse
Affiliation(s)
- Jing Wu
- Department of Surgery, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Jianhui Zhu
- Department of Surgery, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Haidi Yin
- Department of Surgery, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Xinhua Liu
- Department of Surgery, University of Michigan , Ann Arbor, Michigan 48109, United States.,Experiment Center for Science and Technology, Shanghai University of Traditional Chinese Medicine , Shanghai 201203, China
| | - Mingrui An
- Department of Surgery, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Nicholas A Pudlo
- Department of Microbiology and Immunology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Grace Y Chen
- Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - David M Lubman
- Department of Surgery, University of Michigan , Ann Arbor, Michigan 48109, United States
| |
Collapse
|
23
|
Murray KK, Seneviratne CA, Ghorai S. High resolution laser mass spectrometry bioimaging. Methods 2016; 104:118-26. [PMID: 26972785 PMCID: PMC4937799 DOI: 10.1016/j.ymeth.2016.03.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 02/23/2016] [Accepted: 03/08/2016] [Indexed: 12/11/2022] Open
Abstract
Mass spectrometry imaging (MSI) was introduced more than five decades ago with secondary ion mass spectrometry (SIMS) and a decade later with laser desorption/ionization (LDI) mass spectrometry (MS). Large biomolecule imaging by matrix-assisted laser desorption/ionization (MALDI) was developed in the 1990s and ambient laser MS a decade ago. Although SIMS has been capable of imaging with a moderate mass range at sub-micrometer lateral resolution from its inception, laser MS requires additional effort to achieve a lateral resolution of 10μm or below which is required to image at the size scale of single mammalian cells. This review covers untargeted large biomolecule MSI using lasers for desorption/ionization or laser desorption and post-ionization. These methods include laser microprobe (LDI) MSI, MALDI MSI, laser ambient and atmospheric pressure MSI, and near-field laser ablation MS. Novel approaches to improving lateral resolution are discussed, including oversampling, beam shaping, transmission geometry, reflective and through-hole objectives, microscope mode, and near-field optics.
Collapse
Affiliation(s)
- Kermit K Murray
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA.
| | | | - Suman Ghorai
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
| |
Collapse
|
24
|
Pei X, Zhu J, Yang R, Tan Z, An M, Shi J, Lubman DM. CD90 and CD24 Co-Expression Is Associated with Pancreatic Intraepithelial Neoplasias. PLoS One 2016; 11:e0158021. [PMID: 27332878 PMCID: PMC4917090 DOI: 10.1371/journal.pone.0158021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 06/08/2016] [Indexed: 12/28/2022] Open
Abstract
Thy-1 (CD90) has been shown to be a potential marker for several different types of cancer. However, reports on CD90 expression in pancreatic intraepithelial neoplasia (PanIN) lesions are still limited where PanINs are the most important precursor lesion of pancreatic ductal adenocarcinoma (PDAC). Herein, we investigate candidate markers for PanIN lesions by examining the distribution and trend of CD90 and CD24 expression as well as their co-expression in various stages of PanINs. Thirty cases of PanINs, which were confirmed histopathologically and clinically, were used to evaluate protein expression of CD90 and CD24 by immunofluoresence double staining. CD90 was found to be mainly expressed in stroma around lesion ducts while not observed in acini and islets in PanINs. CD90 also showed increased expression in PanIN III compared to PanIN III. CD24 was mainly present in the cytoplasm and membrane of pancreatic ductal epithelia, especially in the apical epithelium of the duct. CD24 had higher expression in PanIN III compared with PanIN IIIIII or PanIN III. CD90 was expressed around CD24 sites, but there was little overlap between cells that expressed each of these proteins. A correlation analysis showed that these two proteins have a moderate relationship with PanIN stages respectively. These results suggest that co-expression of CD90 and CD24 may have an important role in the development and progression of PanINs, which is also conducive to early detection and treatment of PDAC.
Collapse
Affiliation(s)
- Xiucong Pei
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan, 48109, United States of America
- Department of Toxicology, School of Public Health, Shenyang Medical College, Liaoning, 110034, China
| | - Jianhui Zhu
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan, 48109, United States of America
| | - Rui Yang
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan, 48109, United States of America
| | - Zhijing Tan
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan, 48109, United States of America
| | - Mingrui An
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan, 48109, United States of America
| | - Jiaqi Shi
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, Michigan, 48109, United States of America
| | - David M. Lubman
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan, 48109, United States of America
| |
Collapse
|
25
|
Brandi J, Dalla Pozza E, Dando I, Biondani G, Robotti E, Jenkins R, Elliott V, Park K, Marengo E, Costello E, Scarpa A, Palmieri M, Cecconi D. Secretome protein signature of human pancreatic cancer stem-like cells. J Proteomics 2016; 136:1-12. [PMID: 26850699 DOI: 10.1016/j.jprot.2016.01.017] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 01/04/2016] [Accepted: 01/25/2016] [Indexed: 02/08/2023]
Abstract
UNLABELLED Emerging research has demonstrated that pancreatic ductal adenocarcinoma (PDAC) contains a sub-population of cancer stem cells (CSCs) characterized by self-renewal, anchorage-independent-growth, long-term proliferation and chemoresistance. The secretome analysis of pancreatic CSCs has not yet been performed, although it may provide insight into tumour/microenvironment interactions and intracellular processes, as well as to identify potential biomarkers. To characterize the secreted proteins of pancreatic CSCs, we performed an iTRAQ-based proteomic analysis to compare the secretomes of Panc1 cancer stem-like cells (Panc1 CSCs) and parental cell line. A total of 72 proteins were found up-/down-regulated in the conditioned medium of Panc1 CSCs. The pathway analysis revealed modulation of vital physiological pathways including glycolysis, gluconeogenesis and pentose phosphate. Through ELISA immunoassays we analysed the presence of the three proteins most highly secreted by Panc1 CSCs (ceruloplasmin, galectin-3, and MARCKS) in sera of PDAC patient. ROC curve analysis suggests ceruloplasmin as promising marker for patients negative for CA19-9. Overall, our study provides a systemic secretome analysis of pancreatic CSCs revealing a number of secreted proteins which participate in pathological conditions including cancer differentiation, invasion and metastasis. They may serve as a valuable pool of proteins from which biomarkers and therapeutic targets can be identified. BIOLOGICAL SIGNIFICANCE The secretome of CSCs is a rich reservoir of biomarkers of cancer progression and molecular therapeutic targets, and thus is a topic of great interest for cancer research. The secretome analysis of pancreatic CSCs has not yet been performed. Recently, our group has demonstrated that Panc-1 CSCs isolated from parental cell line by using the CSC selective medium, represent a model of great importance to deepen the understanding of the biology of pancreatic adenocarcinoma. To our knowledge, this is the first proteomic study of pancreatic CSC secretome. We performed an iTRAQ-based analysis to compare the secretomes of Panc1 CSCs and Panc1 parental cell line and identified a total of 43 proteins secreted at higher level by pancreatic cancer stem cells. We found modulation of different vital physiological pathways (such as glycolysis and gluconeogenesis, pentose phosphate pathway) and the involvement of CSC secreted proteins (for example 72kDa type IV collagenase, galectin-3, alpha-actinin-4, and MARCKS) in pathological conditions including cancer differentiation, invasion and metastasis. By ELISA verification we found that MARCKS and ceruloplasmin discriminate between controls and PDAC patients; in addition ROC curve analyses indicate that MARCKS does not have diagnostic accuracy, while ceruloplasmin could be a promising marker only for patients negative for CA19-9. We think that the findings reported in our manuscript advance the understanding of the pathways implicated in tumourigenesis, metastasis and chemoresistance of pancreatic cancer, and also identify a pool of proteins from which novel candidate diagnostic and therapeutic biomarkers could be discovered.
Collapse
Affiliation(s)
- Jessica Brandi
- University of Verona, Department of Biotechnology, Proteomics and Mass Spectrometry Laboratory, Verona 37134, Italy
| | - Elisa Dalla Pozza
- University of Verona, Department of Life and Reproduction Sciences, Verona 37134, Italy
| | - Ilaria Dando
- University of Verona, Department of Life and Reproduction Sciences, Verona 37134, Italy
| | - Giulia Biondani
- University of Verona, Department of Life and Reproduction Sciences, Verona 37134, Italy
| | - Elisa Robotti
- University of Piemonte Orientale, Department of Sciences and Technological Innovation, Alessandria 15121, Italy
| | - Rosalind Jenkins
- University of Liverpool, MRC Centre for Drug Safety Science, Department of Molecular & Clinical Pharmacology, Liverpool L69 3GE, United Kingdom
| | - Victoria Elliott
- NIHR Liverpool Pancreas Biomedical Research Unit, Department of Molecular and Therapeutic Cancer Medicine, Liverpool L69 3GA, United Kingdom
| | - Kevin Park
- University of Liverpool, MRC Centre for Drug Safety Science, Department of Molecular & Clinical Pharmacology, Liverpool L69 3GE, United Kingdom
| | - Emilio Marengo
- University of Piemonte Orientale, Department of Sciences and Technological Innovation, Alessandria 15121, Italy
| | - Eithne Costello
- NIHR Liverpool Pancreas Biomedical Research Unit, Department of Molecular and Therapeutic Cancer Medicine, Liverpool L69 3GA, United Kingdom
| | - Aldo Scarpa
- University and Hospital Trust of Verona, Applied Research on Cancer Network (ARC-NET) and Department of Pathology and Diagnostics, Verona 37134, Italy
| | - Marta Palmieri
- University of Verona, Department of Life and Reproduction Sciences, Verona 37134, Italy.
| | - Daniela Cecconi
- University of Verona, Department of Biotechnology, Proteomics and Mass Spectrometry Laboratory, Verona 37134, Italy
| |
Collapse
|
26
|
Donnarumma F, Cao F, Murray KK. Laser Ablation with Vacuum Capture for MALDI Mass Spectrometry of Tissue. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:108-116. [PMID: 26374229 DOI: 10.1007/s13361-015-1249-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 08/04/2015] [Accepted: 08/08/2015] [Indexed: 06/05/2023]
Abstract
We have developed a laser ablation sampling technique for matrix-assisted laser desorption ionization (MALDI) mass spectrometry and tandem mass spectrometry (MS/MS) analyses of in-situ digested tissue proteins. Infrared laser ablation was used to remove biomolecules from tissue sections for collection by vacuum capture and analysis by MALDI. Ablation and transfer of compounds from tissue removes biomolecules from the tissue and allows further analysis of the collected material to facilitate their identification. Laser ablated material was captured in a vacuum aspirated pipette-tip packed with C18 stationary phase and the captured material was dissolved, eluted, and analyzed by MALDI. Rat brain and lung tissue sections 10 μm thick were processed by in-situ trypsin digestion after lipid and salt removal. The tryptic peptides were ablated with a focused mid-infrared laser, vacuum captured, and eluted with an acetonitrile/water mixture. Eluted components were deposited on a MALDI target and mixed with matrix for mass spectrometry analysis. Initial experiments were conducted with peptide and protein standards for evaluation of transfer efficiency: a transfer efficiency of 16% was obtained using seven different standards. Laser ablation vacuum capture was applied to freshly digested tissue sections and compared with sections processed with conventional MALDI imaging. A greater signal intensity and lower background was observed in comparison with the conventional MALDI analysis. Tandem time-of-flight MALDI mass spectrometry was used for compound identification in the tissue.
Collapse
Affiliation(s)
- Fabrizio Donnarumma
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Fan Cao
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Kermit K Murray
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA.
| |
Collapse
|
27
|
Nie S, McDermott SP, Deol Y, Tan Z, Wicha MS, Lubman DM. A quantitative proteomics analysis of MCF7 breast cancer stem and progenitor cell populations. Proteomics 2015; 15:3772-83. [PMID: 26332018 DOI: 10.1002/pmic.201500002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 07/21/2015] [Accepted: 08/26/2015] [Indexed: 12/11/2022]
Abstract
Accumulating evidence has demonstrated that breast cancers are initiated and develop from a small population of stem-like cells termed cancer stem cells (CSCs). These cells are hypothesized to mediate tumor metastasis and contribute to therapeutic resistance. However, the molecular regulatory networks responsible for maintaining CSCs in an undifferentiated state have yet to be elucidated. In this study, we used CSC markers to isolate pure breast CSCs fractions (ALDH+ and CD44+CD24- cell populations) and the mature luminal cells (CD49f-EpCAM+) from the MCF7 cell line. Proteomic analysis was performed on these samples and a total of 3304 proteins were identified. A label-free quantitative method was applied to analyze differentially expressed proteins. Using the criteria of greater than twofold changes and p value <0.05, 305, 322 and 98 proteins were identified as significantly different in three pairwise comparisons of ALDH+ versus CD44+CD24-, ALDH+ versus CD49f-EpCAM+ and CD44+CD24- versus CD49f-EpCAM+, respectively. Pathway analysis of differentially expressed proteins by Ingenuity Pathway Analysis (IPA) revealed potential molecular regulatory networks that may regulate CSCs. Selected differential proteins were validated by Western blot assay and immunohistochemical staining. The use of proteomics analysis may increase our understanding of the underlying molecular mechanisms of breast CSCs. This may be of importance in the future development of anti-CSC therapeutics.
Collapse
Affiliation(s)
- Song Nie
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Sean P McDermott
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, MI, USA.,Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Yadwinder Deol
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, MI, USA.,Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Zhijing Tan
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Max S Wicha
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, MI, USA.,Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - David M Lubman
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
28
|
Kim J, Tan Z, Lubman DM. Exosome enrichment of human serum using multiple cycles of centrifugation. Electrophoresis 2015; 36:2017-26. [PMID: 26010067 DOI: 10.1002/elps.201500131] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 03/12/2015] [Accepted: 05/06/2015] [Indexed: 12/21/2022]
Abstract
In this work, we compared the use of repeated cycles of centrifugation at conventional speeds for enrichment of exosomes from human serum compared to the use of ultracentrifugation (UC). After removal of cells and cell debris, a speed of 110 000 × g or 40 000 × g was used for the UC or centrifugation enrichment process, respectively. The enriched exosomes were analyzed using the bicinchoninic acid assay, 1D gel separation, transmission electron microscopy, Western blotting, and high-resolution LC-MS/MS analysis. It was found that a five-cycle repetition of UC or centrifugation is necessary for successful removal of nonexosomal proteins in the enrichment of exosomes from human serum. More significantly, 5× centrifugation enrichment was found to provide similar or better performance than 5× UC enrichment in terms of enriched exosome protein amount, Western blot band intensity for detection of CD-63, and numbers of identified exosome-related proteins and cluster of differentiation (CD) proteins. A total of 478 proteins were identified in the LC-MS/MS analyses of exosome proteins obtained from 5× UCs and 5× centrifugations including many important CD membrane proteins. The presence of previously reported exosome-related proteins including key exosome protein markers demonstrates the utility of this method for analysis of proteins in human serum.
Collapse
Affiliation(s)
- Jeongkwon Kim
- Department of Chemistry, Chungnam National University, Daejeon, Republic of Korea
| | - Zhijing Tan
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI, USA
| | - David M Lubman
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI, USA
| |
Collapse
|
29
|
Zeng Q, Smith DJ, Shippy SA. Proteomic analysis of individual fruit fly hemolymph. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 981-982:33-9. [DOI: 10.1016/j.jchromb.2014.11.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 11/12/2014] [Accepted: 11/25/2014] [Indexed: 11/16/2022]
|
30
|
Kato H, Lo A, Kuo S, Nie S, Marcelo CL, Lubman DM, Feinberg SE. Proteomics Characterization of Primary Human Oral Epithelial Cells Using a Novel Culture Technique for Use in Tissue Regeneration. MOJ PROTEOMICS & BIOINFORMATICS 2015; 2. [PMID: 27042699 DOI: 10.15406/mojpb.2015.02.00052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Oral mucosa keratinocytes are widely used in regenerative medicine. The unique cultured cell population "Epithelial-derived Pop-Up Keratinocytes (ePUKs)" was previously reported as undifferentiated cells. Gravity Assisted Cell Sorting (GACS) was used to isolate a small-sized population of undifferentiated cells enriched ePUKs. LC/MS/MS analysis was performed to define the cellular profile of ePUKs of primary human oral mucosa keratinocytes. Small sized ePUKs which showed increased expression of Dickkopf WNT signaling pathway inhibitor 1 (DKK1), serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1 (SERPINE1), follistatin and tenascin-C were verified by Western blots. These proteins are involved in the regulation of cellular movement, hair follicle development and the maintenance of its stem cell niche. The fabrication of a tissue-engineered oral mucosa, ex vivo produced oral mucosa equivalent (EVPOME), using ePUKs showed increased abundance of these verified proteins. These findings indicate that the specific phenotype of ePUKs and their ability to influence wound healing promotion are implicated by highly expressed cellular movement regulatory proteins. Therefore, ePUKs may be a useful cell source for use in regenerative medicine.
Collapse
Affiliation(s)
- Hiroko Kato
- Department of Oral and Maxillofacial Surgery, University of Michigan, USA; Department of Biomimetics, Niigata University Postgraduate School of Medical and Dental Sciences, Japan
| | - Andy Lo
- Department of Surgery, University of Michigan Medical Center, USA
| | - Shiuhyang Kuo
- Department of Oral and Maxillofacial Surgery, University of Michigan, USA
| | - Song Nie
- Department of Surgery, University of Michigan Medical Center, USA
| | - Cynthia L Marcelo
- Department of Oral and Maxillofacial Surgery, University of Michigan, USA
| | - David M Lubman
- Department of Surgery, University of Michigan Medical Center, USA
| | - Stephen E Feinberg
- Department of Oral and Maxillofacial Surgery, University of Michigan, USA
| |
Collapse
|
31
|
Zhu J, Thakolwiboon S, Liu X, Zhang M, Lubman DM. Overexpression of CD90 (Thy-1) in pancreatic adenocarcinoma present in the tumor microenvironment. PLoS One 2014; 9:e115507. [PMID: 25536077 PMCID: PMC4275230 DOI: 10.1371/journal.pone.0115507] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 11/24/2014] [Indexed: 01/15/2023] Open
Abstract
CD90 (Thy-1) plays important roles in oncogenesis and shows potential as a candidate marker for cancer stem cells (CSCs) in various malignancies. Herein, we investigated the expression of CD90 in pancreatic adenocarcinoma (PDAC), with a comparison to normal pancreas and non-malignant pancreatic disease, by immunohistochemical (IHC) analysis of tissue microarrays containing 183 clinical tissue specimens. Statistical analysis was performed to evaluate the correlation between CD90 expression and the major clinicopathological factors after adjustment of age and gender. The IHC data showed that CD90 was significantly overexpressed in PDAC and its metastatic cancers as compared to chronic pancreatitis and benign islet tumors, while it was negative in normal pancreas and 82.7% of adjacent normal pancreas tissues. The abundant CD90 expression was predominantly present in PDAC stroma, such as fibroblasts and vascular endothelial cells, which could serve as a promising marker to distinguish pancreatic adenocarcinoma from normal pancreas and non-malignant pancreatic diseases. Double immunostaining of CD90 with CD24, a CSC marker for PDAC, showed that there was little overlap between these two markers. However, CD90+ fibroblast cells were clustered around CD24+ malignant ducts, suggesting that CD90 may be involved in the tumor-stroma interactions and promote pancreatic cancer development. Furthermore, CD90 mostly overlapped with α-smooth muscle actin (αSMA, a marker of activated pancreatic stellate cells (PSCs)) in PDAC stroma, which demonstrated that CD90+ stromal cells consist largely of activated PSCs. Double immunostaining of CD90 and a vascular endothelial cell marker CD31 demonstrated that CD90 expression on vascular endothelial cells was significantly increased in PDACs as compared to normal pancreas and non-malignant pancreatic diseases. Our findings suggest that CD90 could serve as a promising marker for pancreatic adenocarcinoma where desmoplastic stroma plays an important role in tumor growth and angiogenesis.
Collapse
Affiliation(s)
- Jianhui Zhu
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States of America
| | - Smathorn Thakolwiboon
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States of America
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Xinhua Liu
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States of America
- Experiment Center for Science and Technology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Min Zhang
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan 48109, United States of America
| | - David M. Lubman
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States of America
| |
Collapse
|
32
|
Longuespée R, Fléron M, Pottier C, Quesada-Calvo F, Meuwis MA, Baiwir D, Smargiasso N, Mazzucchelli G, De Pauw-Gillet MC, Delvenne P, De Pauw E. Tissue Proteomics for the Next Decade? Towards a Molecular Dimension in Histology. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2014; 18:539-52. [DOI: 10.1089/omi.2014.0033] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Rémi Longuespée
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
| | - Maximilien Fléron
- Mammalian Cell Culture Laboratory, GIGA-Research, Department of Biomedical and Preclinical Sciences, University of Liège, Liège, Belgium
| | - Charles Pottier
- Laboratory of Experimental Pathology, GIGA-Cancer, Department of Pathology, University of Liège, Liège, Belgium
| | - Florence Quesada-Calvo
- Hepato-Gastroenterology and Digestive Oncology Department, Liège University Hospital, University of Liège, Liège, Belgium
| | - Marie-Alice Meuwis
- Hepato-Gastroenterology and Digestive Oncology Department, Liège University Hospital, University of Liège, Liège, Belgium
| | - Dominique Baiwir
- GIGA-R, GIGA Proteomic Facilities, University of Liège, Liège, Belgium
| | - Nicolas Smargiasso
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
| | - Marie-Claire De Pauw-Gillet
- Mammalian Cell Culture Laboratory, GIGA-Research, Department of Biomedical and Preclinical Sciences, University of Liège, Liège, Belgium
| | - Philippe Delvenne
- Laboratory of Experimental Pathology, GIGA-Cancer, Department of Pathology, University of Liège, Liège, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
| |
Collapse
|
33
|
Bandyopadhyay U, Fenton WA, Horwich AL, Nagy M. Production of RNA for transcriptomic analysis from mouse spinal cord motor neuron cell bodies by laser capture microdissection. J Vis Exp 2014:e51168. [PMID: 24457537 PMCID: PMC4089401 DOI: 10.3791/51168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Preparation of high-quality RNA from cells of interest is critical to precise and meaningful analysis of transcriptional differences among cell types or between the same cell type in health and disease or following pharmacologic treatments. In the spinal cord, such preparation from motor neurons, the target of interest in many neurologic and neurodegenerative diseases, is complicated by the fact that motor neurons represent <10% of the total cell population. Laser capture microdissection (LMD) has been developed to address this problem. Here, we describe a protocol to quickly recover, freeze, and section mouse spinal cord to avoid RNA damage by endogenous and exogenous RNases, followed by staining with Azure B in 70% ethanol to identify the motor neurons while keeping endogenous RNase inhibited. LMD is then used to capture the stained neurons directly into guanidine thiocyanate lysis buffer, maintaining RNA integrity. Standard techniques are used to recover the total RNA and measure its integrity. This material can then be used for downstream analysis of the transcripts by RNA-seq and qRT-PCR.
Collapse
|
34
|
Du Y, Teng X, Wang N, Zhang X, Chen J, Ding P, Qiao Q, Wang Q, Zhang L, Yang C, Yang Z, Chu Y, Du X, Zhou X, Hu W. NF-κB and enhancer-binding CREB protein scaffolded by CREB-binding protein (CBP)/p300 proteins regulate CD59 protein expression to protect cells from complement attack. J Biol Chem 2013; 289:2711-24. [PMID: 24338025 DOI: 10.1074/jbc.m113.525501] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The complement system can be activated spontaneously for immune surveillance or induced to clear invading pathogens, in which the membrane attack complex (MAC, C5b-9) plays a critical role. CD59 is the sole membrane complement regulatory protein (mCRP) that restricts MAC assembly. CD59, therefore, protects innocent host cells from attacks by the complement system, and host cells require the constitutive and inducible expression of CD59 to protect themselves from deleterious destruction by complement. However, the mechanisms that underlie CD59 regulation remain largely unknown. In this study we demonstrate that the widely expressed transcription factor Sp1 may regulate the constitutive expression of CD59, whereas CREB-binding protein (CBP)/p300 bridge NF-κB and CREB, which surprisingly functions as an enhancer-binding protein to induce the up-regulation of CD59 during in lipopolysaccharide (LPS)-triggered complement activation, thus conferring host defense against further MAC-mediated destruction. Moreover, individual treatment with LPS, TNF-α, and the complement activation products (sublytic MAC (SC5b-9) and C5a) could increase the expression of CD59 mainly by activating NF-κB and CREB signaling pathways. Together, our findings identify a novel gene regulation mechanism involving CBP/p300, NF-κB, and CREB; this mechanism suggests potential drug targets for controlling various complement-related human diseases.
Collapse
Affiliation(s)
- Yiqun Du
- From the Cancer Institute, Collaborative Innovation Center of Cancer Medicine, Fudan University Shanghai Cancer Center and Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|