51
|
Laser Microdissection Workflow for Isolating Nucleic Acids from Fixed and Frozen Tissue Samples. Methods Mol Biol 2018; 1723:33-93. [PMID: 29344854 DOI: 10.1007/978-1-4939-7558-7_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Laser Capture Microdissection has earned a permanent place among modern techniques connecting histology and molecular biology. Laser Capture Microdissection has become an invaluable tool in medical research as a means for collection of specific cell populations isolated from their environment. Such genomic sample enrichment dramatically increases the sensitivity and precision of downstream molecular assays used for biomarker discovery, monitoring disease onset and progression, and in the development of personalized medicine. The diversity of research targets (cancerous and precancerous lesions in clinical and animal research, cell pellets, rodent embryos, frozen tissues, archival repository slides, etc.) and scientific objectives present a challenge in establishing standard protocols for Laser Capture Microdissection. In the present chapter, we share our experiences in design and successful execution of numerous diverse microdissection projects, and provide considerations to be taken into account in planning a microdissection study. Our workflow and protocols are standardized for a wide range of animal and human tissues and adapted to downstream analysis platforms.
Collapse
|
52
|
Wang F, Wang R, Li Q, Qu X, Hao Y, Yang J, Zhao H, Wang Q, Li G, Zhang F, Zhang H, Zhou X, Peng X, Bian Y, Xiao W. A transcriptome profile in hepatocellular carcinomas based on integrated analysis of microarray studies. Diagn Pathol 2017; 12:4. [PMID: 28086821 PMCID: PMC5237304 DOI: 10.1186/s13000-016-0596-x] [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: 08/01/2016] [Accepted: 12/30/2016] [Indexed: 02/06/2023] Open
Abstract
Background Despite new treatment options for hepatocellular carcinomas (HCC) recently, 5-year survival remains poor, ranging from 50 to 70%, which may attribute to the lack of early diagnostic biomarkers. Thus, developing new biomarkers for early diagnosis of HCC, is extremely urgent, aiming to decrease HCC-related deaths. Methods In the study, we conducted a comprehensive characterization of gene expression data of HCC based on a bioinformatics method. The results were confirmed by real time polymerase chain reaction (RT-PCR) and TCGA database to prove the credibility of this integrated analysis. Results After integrating analysis of seven HCC gene expression datasets, 1167 differential expressed genes (DEGs) were identified. These genes mainly participated in the process of cell cycle, oocyte meiosis, and oocyte maturation mediated by progesterone. The results of experiments and TCGA database validation in 10 genes was in full accordance with findings in integrated analysis, indicating the high credibility of our integrated analysis of different gene expression datasets. ASPM, CCT3, and NEK2 was showed to be significantly associated with overall survival of HCC patients in TCGA database. Conclusion This method of integrated analysis may be a useful tool to minish the heterogeneity of individual microarray, hopefully outputs more accurate HCC transcriptome profiles based on large sample size, and explores some potential biomarkers and therapy targets for HCC. Electronic supplementary material The online version of this article (doi:10.1186/s13000-016-0596-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Feifei Wang
- Department of Oncology, The First Affiliated Hospital of PLA General Hospital, Fucheng Road 51, Beijing, 100048, China
| | - Ruliang Wang
- Department of Oncology, The First Affiliated Hospital of PLA General Hospital, Fucheng Road 51, Beijing, 100048, China
| | - Qiuwen Li
- Department of Oncology, The First Affiliated Hospital of PLA General Hospital, Fucheng Road 51, Beijing, 100048, China
| | - Xueling Qu
- Department of Oncology, The First Affiliated Hospital of PLA General Hospital, Fucheng Road 51, Beijing, 100048, China
| | - Yixin Hao
- Department of Oncology, The First Affiliated Hospital of PLA General Hospital, Fucheng Road 51, Beijing, 100048, China
| | - Jingwen Yang
- Department of Oncology, The First Affiliated Hospital of PLA General Hospital, Fucheng Road 51, Beijing, 100048, China
| | - Huixia Zhao
- Department of Oncology, The First Affiliated Hospital of PLA General Hospital, Fucheng Road 51, Beijing, 100048, China
| | - Qian Wang
- Department of Oncology, The First Affiliated Hospital of PLA General Hospital, Fucheng Road 51, Beijing, 100048, China
| | - Guanghui Li
- Department of Oncology, The First Affiliated Hospital of PLA General Hospital, Fucheng Road 51, Beijing, 100048, China
| | - Fengyun Zhang
- Department of Oncology, The First Affiliated Hospital of PLA General Hospital, Fucheng Road 51, Beijing, 100048, China
| | - He Zhang
- Department of Oncology, The First Affiliated Hospital of PLA General Hospital, Fucheng Road 51, Beijing, 100048, China
| | - Xuan Zhou
- Department of Oncology, The First Affiliated Hospital of PLA General Hospital, Fucheng Road 51, Beijing, 100048, China
| | - Xioumei Peng
- Department of Oncology, The First Affiliated Hospital of PLA General Hospital, Fucheng Road 51, Beijing, 100048, China
| | - Yang Bian
- Department of Bioinformatics, Beijing Medintell Biomed Co., Ltd, Beijing, China
| | - Wenhua Xiao
- Department of Oncology, The First Affiliated Hospital of PLA General Hospital, Fucheng Road 51, Beijing, 100048, China.
| |
Collapse
|
53
|
Xie Y, Wang A, Lin J, Wu L, Zhang H, Yang X, Wan X, Miao R, Sang X, Zhao H. Mps1/TTK: a novel target and biomarker for cancer. J Drug Target 2016; 25:112-118. [PMID: 27819146 DOI: 10.1080/1061186x.2016.1258568] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Monopolar spindle1 (Mps1, also known as TTK) is the core component of the spindle assembly checkpoint, which functions to ensure proper distribution of chromosomes to daughter cells. Mps1 is hardly detectable in normal organs except the testis and placenta. However, high levels of Mps1 are found in many types of human malignancies, including glioblastoma, thyroid carcinoma, breast cancer, and other cancers. Several Mps1 inhibitors can inhibit the proliferation of cancer cells and exhibit demonstrable survival benefits. Mps1 can be utilized as a new immunogenic epitope, which is able to induce potent cytotoxic T lymphocyte activity against cancer cells while sparing normal cells. Some clinical trials have validated its safety, immunogenicity and clinical response. Thus, Mps1 may be a novel target for cancer therapy. Mps1 is differentially expressed between normal and malignant tissues, indicating its potential as a molecular biomarker for diagnosis. Meanwhile, the discovery that it clearly correlates with recurrence and survival time suggests it may serve as an independent prognostic biomarker as well.
Collapse
Affiliation(s)
- Yuan Xie
- a Department of Liver Surgery , Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
| | - Anqiang Wang
- a Department of Liver Surgery , Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
| | - Jianzhen Lin
- a Department of Liver Surgery , Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
| | - Liangcai Wu
- a Department of Liver Surgery , Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
| | - Haohai Zhang
- a Department of Liver Surgery , Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
| | - Xiaobo Yang
- a Department of Liver Surgery , Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
| | - Xueshuai Wan
- a Department of Liver Surgery , Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
| | - Ruoyu Miao
- b Liver Center and The Transplant Institute, Department of Medicine , Beth Israel Deaconess Medical Center, Harvard Medical School , Boston , MA , USA
| | - Xinting Sang
- a Department of Liver Surgery , Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
| | - Haitao Zhao
- a Department of Liver Surgery , Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
| |
Collapse
|
54
|
Thomsen MK, Nandakumar R, Stadler D, Malo A, Valls RM, Wang F, Reinert LS, Dagnaes-Hansen F, Hollensen AK, Mikkelsen JG, Protzer U, Paludan SR. Lack of immunological DNA sensing in hepatocytes facilitates hepatitis B virus infection. Hepatology 2016; 64:746-59. [PMID: 27312012 DOI: 10.1002/hep.28685] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 05/13/2016] [Accepted: 05/23/2016] [Indexed: 12/12/2022]
Abstract
UNLABELLED Hepatitis B virus (HBV) is a major human pathogen, and about one third of the global population will be exposed to the virus in their lifetime. HBV infects hepatocytes, where it replicates its DNA and infection can lead to acute and chronic hepatitis with a high risk of liver cirrhosis and hepatocellular carcinoma. Despite this, there is limited understanding of how HBV establishes chronic infections. In recent years it has emerged that foreign DNA potently stimulates the innate immune response, particularly type 1 interferon (IFN) production; and this occurs through a pathway dependent on the DNA sensor cyclic guanosine monophosphate-adenosine monophosphate synthase and the downstream adaptor protein stimulator of IFN genes (STING). In this work we describe that human and murine hepatocytes do not express STING. Consequently, hepatocytes do not produce type 1 IFN in response to foreign DNA or HBV infection and mice lacking STING or cyclic guanosine monophosphate-adenosine monophosphate synthase exhibit unaltered ability to control infection in an adenovirus-HBV model. Stimulation of IFN production in the murine liver by administration of synthetic RNA decreases virus infection, thus demonstrating that IFN possesses anti-HBV activity in the liver. Importantly, introduction of STING expression specifically in hepatocytes reconstitutes the DNA sensing pathway, which leads to improved control of HBV in vivo. CONCLUSION The lack of a functional innate DNA-sensing pathway in hepatocytes hampers efficient innate control of HBV infection; this may explain why HBV has adapted to specifically replicate in hepatocytes and could contribute to the weak capacity of this cell type to clear HBV infection. (Hepatology 2016;64:746-759).
Collapse
Affiliation(s)
- Martin K Thomsen
- Department of Biomedicine and, University of Aarhus, Aarhus, Denmark.,Aarhus Research Center for Innate Immunology, University of Aarhus, Aarhus, Denmark
| | - Ramya Nandakumar
- Department of Biomedicine and, University of Aarhus, Aarhus, Denmark.,Aarhus Research Center for Innate Immunology, University of Aarhus, Aarhus, Denmark
| | - Daniela Stadler
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, Munich, Germany
| | - Antje Malo
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, Munich, Germany
| | - Roser Marin Valls
- Department of Biomedicine and, University of Aarhus, Aarhus, Denmark
| | - Fan Wang
- Department of Biomedicine and, University of Aarhus, Aarhus, Denmark
| | - Line S Reinert
- Department of Biomedicine and, University of Aarhus, Aarhus, Denmark.,Aarhus Research Center for Innate Immunology, University of Aarhus, Aarhus, Denmark
| | | | | | - Jacob Giehm Mikkelsen
- Department of Biomedicine and, University of Aarhus, Aarhus, Denmark.,Aarhus Research Center for Innate Immunology, University of Aarhus, Aarhus, Denmark
| | - Ulrike Protzer
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, Munich, Germany
| | - Søren R Paludan
- Department of Biomedicine and, University of Aarhus, Aarhus, Denmark.,Aarhus Research Center for Innate Immunology, University of Aarhus, Aarhus, Denmark
| |
Collapse
|
55
|
Castro NP, Merchant AS, Saylor KL, Anver MR, Salomon DS, Golubeva YG. Adaptation of Laser Microdissection Technique for the Study of a Spontaneous Metastatic Mammary Carcinoma Mouse Model by NanoString Technologies. PLoS One 2016; 11:e0153270. [PMID: 27077656 PMCID: PMC4831786 DOI: 10.1371/journal.pone.0153270] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 03/25/2016] [Indexed: 02/07/2023] Open
Abstract
Laser capture microdissection (LCM) of tissue is an established tool in medical research for collection of distinguished cell populations under direct microscopic visualization for molecular analysis. LCM samples have been successfully analyzed in a number of genomic and proteomic downstream molecular applications. However, LCM sample collection and preparation procedure has to be adapted to each downstream analysis platform. In this present manuscript we describe in detail the adaptation of LCM methodology for the collection and preparation of fresh frozen samples for NanoString analysis based on a study of a model of mouse mammary gland carcinoma and its lung metastasis. Our adaptation of LCM sample preparation and workflow to the requirements of the NanoString platform allowed acquiring samples with high RNA quality. The NanoString analysis of such samples provided sensitive detection of genes of interest and their associated molecular pathways. NanoString is a reliable gene expression analysis platform that can be effectively coupled with LCM.
Collapse
Affiliation(s)
- Nadia P. Castro
- Tumor Growth Factor Section, Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD, 21702, United States of America
| | - Anand S. Merchant
- CCRIFX Bioinformatics Core, National Cancer Institute, Bethesda, MD, 20892, United States of America
| | - Karen L. Saylor
- Tumor Growth Factor Section, Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD, 21702, United States of America
| | - Miriam R. Anver
- Pathology-Histotechnology Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, United States of America
| | - David S. Salomon
- Tumor Growth Factor Section, Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD, 21702, United States of America
| | - Yelena G. Golubeva
- Pathology-Histotechnology Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, United States of America
| |
Collapse
|