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Zhou Y, Tao L, Qiu J, Xu J, Yang X, Zhang Y, Tian X, Guan X, Cen X, Zhao Y. Tumor biomarkers for diagnosis, prognosis and targeted therapy. Signal Transduct Target Ther 2024; 9:132. [PMID: 38763973 PMCID: PMC11102923 DOI: 10.1038/s41392-024-01823-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 03/07/2024] [Accepted: 04/02/2024] [Indexed: 05/21/2024] Open
Abstract
Tumor biomarkers, the substances which are produced by tumors or the body's responses to tumors during tumorigenesis and progression, have been demonstrated to possess critical and encouraging value in screening and early diagnosis, prognosis prediction, recurrence detection, and therapeutic efficacy monitoring of cancers. Over the past decades, continuous progress has been made in exploring and discovering novel, sensitive, specific, and accurate tumor biomarkers, which has significantly promoted personalized medicine and improved the outcomes of cancer patients, especially advances in molecular biology technologies developed for the detection of tumor biomarkers. Herein, we summarize the discovery and development of tumor biomarkers, including the history of tumor biomarkers, the conventional and innovative technologies used for biomarker discovery and detection, the classification of tumor biomarkers based on tissue origins, and the application of tumor biomarkers in clinical cancer management. In particular, we highlight the recent advancements in biomarker-based anticancer-targeted therapies which are emerging as breakthroughs and promising cancer therapeutic strategies. We also discuss limitations and challenges that need to be addressed and provide insights and perspectives to turn challenges into opportunities in this field. Collectively, the discovery and application of multiple tumor biomarkers emphasized in this review may provide guidance on improved precision medicine, broaden horizons in future research directions, and expedite the clinical classification of cancer patients according to their molecular biomarkers rather than organs of origin.
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Affiliation(s)
- Yue Zhou
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Lei Tao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jiahao Qiu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jing Xu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xinyu Yang
- West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Yu Zhang
- West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
- School of Medicine, Tibet University, Lhasa, 850000, China
| | - Xinyu Tian
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xinqi Guan
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiaobo Cen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yinglan Zhao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
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Phan TTM, Phan TM, Schmit JD. Beneficial and detrimental effects of non-specific binding during DNA hybridization. Biophys J 2023; 122:835-848. [PMID: 36721368 PMCID: PMC10027450 DOI: 10.1016/j.bpj.2023.01.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 10/09/2022] [Accepted: 01/24/2023] [Indexed: 02/01/2023] Open
Abstract
DNA strands have to sample numerous states to find the alignment that maximizes Watson-Crick-Franklin base pairing. This process depends strongly on sequence, which affects the stability of the native duplex as well as the prevalence of non-native inter- and intramolecular helices. We present a theory that describes DNA hybridization as a three-stage process: diffusion, registry search, and zipping. We find that non-specific binding affects each of these stages in different ways. Mis-registered intermolecular binding in the registry search stage helps DNA strands sample different alignments and accelerates the hybridization rate. Non-native intramolecular structure affects all three stages by rendering portions of the molecule inert to intermolecular association, limiting mis-registered alignments to be sampled, and impeding the zipping process. Once in-register base pairs are formed, the stability of the native structure is important to hold the molecules together long enough for non-native contacts to break.
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Affiliation(s)
- Tam T M Phan
- Department of Physics, Kansas State University, Manhattan, Kansas
| | - Tien M Phan
- Department of Physics, Kansas State University, Manhattan, Kansas
| | - Jeremy D Schmit
- Department of Physics, Kansas State University, Manhattan, Kansas.
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3
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Hu B, Sajid M, Lv R, Liu L, Sun C. A review of spatial profiling technologies for characterizing the tumor microenvironment in immuno-oncology. Front Immunol 2022; 13:996721. [PMID: 36389765 PMCID: PMC9659855 DOI: 10.3389/fimmu.2022.996721] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/17/2022] [Indexed: 08/13/2023] Open
Abstract
Interpreting the mechanisms and principles that govern gene activity and how these genes work according to -their cellular distribution in organisms has profound implications for cancer research. The latest technological advancements, such as imaging-based approaches and next-generation single-cell sequencing technologies, have established a platform for spatial transcriptomics to systematically quantify the expression of all or most genes in the entire tumor microenvironment and explore an array of disease milieus, particularly in tumors. Spatial profiling technologies permit the study of transcriptional activity at the spatial or single-cell level. This multidimensional classification of the transcriptomic and proteomic signatures of tumors, especially the associated immune and stromal cells, facilitates evaluation of tumor heterogeneity, details of the evolutionary trajectory of each tumor, and multifaceted interactions between each tumor cell and its microenvironment. Therefore, spatial profiling technologies may provide abundant and high-resolution information required for the description of clinical-related features in immuno-oncology. From this perspective, the present review will highlight the importance of spatial transcriptomic and spatial proteomics analysis along with the joint use of other sequencing technologies and their implications in cancers and immune-oncology. In the near future, advances in spatial profiling technologies will undoubtedly expand our understanding of tumor biology and highlight possible precision therapeutic targets for cancer patients.
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Affiliation(s)
- Bian Hu
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Transplant and Immunology Laboratory, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Muhammad Sajid
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Transplant and Immunology Laboratory, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Rong Lv
- Blood Transfusion Laboratory, Anhui Blood Center, Hefei, China
| | - Lianxin Liu
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Cheng Sun
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Transplant and Immunology Laboratory, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Chinese Academy of Sciences (CAS) Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Institute of Immunology, University of Science and Technology of China, Hefei, China
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Chang MM. Plasmid-to-plasmid Southern blot analysis validates the presence of nucleotide binding site (nbs) sequences in cloned plasmids. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 50:373-380. [PMID: 35791664 DOI: 10.1002/bmb.21642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 05/18/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
Southern blot analysis is an important molecular biology technique for identifying a specific sequence in DNA samples. Although it is no longer used extensively in recent years, the steps and underlying principles of Southern blot are applicable to modern biology. High sensitivity and limited background are keys to successful Southern blots, whereas obtaining good quality and quantity of genomic DNA as starting materials and detecting a single/low copy target sequence in the genome can be challenging. To ensure student success in performing the technique for the first time, a modified "plasmid-to-plasmid" Southern blot was implemented to confirm the presence of grape nucleotide-binding site (nbs) sequences in cloned plasmids like those described previously. The plasmid DNA and a control plasmid, pSCA7 (T1-T3-W6) containing a known grape nbs sequence, were digested with restriction enzymes, followed by agarose gel electrophoresis. The DNA band corresponding to the nbs sequence of the pSCA7 (T1-T3-W6) was extracted from the gel for PCR digoxigenin (DIG) probe synthesis. At the same time, the cloned plasmid DNA and its digested DNA fragments were blotted from the gel onto nylon membranes to be hybridized with the DIG probe followed by the detection for nbs sequences. Students successfully performed Southern blots to confirm the presence of nbs sequences in their cloned plasmids and wrote up the results following the format of scientific research papers. They learned the principles and applications of Southern blot and gained hands-on experience with associated techniques.
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Affiliation(s)
- Ming-Mei Chang
- Department of Biology, State University of New York at Geneseo, Geneseo, New York, USA
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Quek C, Bai X, Long GV, Scolyer RA, Wilmott JS. High-Dimensional Single-Cell Transcriptomics in Melanoma and Cancer Immunotherapy. Genes (Basel) 2021; 12:1629. [PMID: 34681023 PMCID: PMC8535767 DOI: 10.3390/genes12101629] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 12/19/2022] Open
Abstract
Recent advances in single-cell transcriptomics have greatly improved knowledge of complex transcriptional programs, rapidly expanding our knowledge of cellular phenotypes and functions within the tumour microenvironment and immune system. Several new single-cell technologies have been developed over recent years that have enabled expanded understanding of the mechanistic cells and biological pathways targeted by immunotherapies such as immune checkpoint inhibitors, which are now routinely used in patient management with high-risk early-stage or advanced melanoma. These technologies have method-specific strengths, weaknesses and capabilities which need to be considered when utilising them to answer translational research questions. Here, we provide guidance for the implementation of single-cell transcriptomic analysis platforms by reviewing the currently available experimental and analysis workflows. We then highlight the use of these technologies to dissect the tumour microenvironment in the context of cancer patients treated with immunotherapy. The strategic use of single-cell analytics in clinical settings are discussed and potential future opportunities are explored with a focus on their use to rationalise the design of novel immunotherapeutic drug therapies that will ultimately lead to improved cancer patient outcomes.
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Affiliation(s)
- Camelia Quek
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2006, Australia; (X.B.); (G.V.L.); (R.A.S.); (J.S.W.)
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Xinyu Bai
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2006, Australia; (X.B.); (G.V.L.); (R.A.S.); (J.S.W.)
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Georgina V. Long
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2006, Australia; (X.B.); (G.V.L.); (R.A.S.); (J.S.W.)
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- Royal North Shore and Mater Hospitals, Sydney, NSW 2065, Australia
| | - Richard A. Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2006, Australia; (X.B.); (G.V.L.); (R.A.S.); (J.S.W.)
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, NSW 2050, Australia
| | - James S. Wilmott
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2006, Australia; (X.B.); (G.V.L.); (R.A.S.); (J.S.W.)
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
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Shittu M, Steenwinkel T, Dion W, Ostlund N, Raja K, Werner T. RNA In Situ Hybridization for Detecting Gene Expression Patterns in the Abdomens and Wings of Drosophila Species. Methods Protoc 2021; 4:20. [PMID: 33801802 PMCID: PMC8005959 DOI: 10.3390/mps4010020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/04/2021] [Accepted: 03/05/2021] [Indexed: 01/07/2023] Open
Abstract
RNA in situ hybridization (ISH) is used to visualize spatio-temporal gene expression patterns with broad applications in biology and biomedicine. Here we provide a protocol for mRNA ISH in developing pupal wings and abdomens for model and non-model Drosophila species. We describe best practices in pupal staging, tissue preparation, probe design and synthesis, imaging of gene expression patterns, and image-editing techniques. This protocol has been successfully used to investigate the roles of genes underlying the evolution of novel color patterns in non-model Drosophila species.
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Affiliation(s)
- Mujeeb Shittu
- Department of Biological Sciences, Michigan Technological University, 740 Dow Building, Houghton, MI 49931, USA; (M.S.); (T.S.); (N.O.)
| | - Tessa Steenwinkel
- Department of Biological Sciences, Michigan Technological University, 740 Dow Building, Houghton, MI 49931, USA; (M.S.); (T.S.); (N.O.)
| | - William Dion
- Integrative Systems Biology Graduate Program, University of Pittsburgh School of Medicine, Biomedical Science, Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15213, USA;
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Bridgeside Point 1, 5th Floor, 100 Technology Drive, Pittsburgh, PA 15219, USA
| | - Nathan Ostlund
- Department of Biological Sciences, Michigan Technological University, 740 Dow Building, Houghton, MI 49931, USA; (M.S.); (T.S.); (N.O.)
| | - Komal Raja
- Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Thomas Werner
- Department of Biological Sciences, Michigan Technological University, 740 Dow Building, Houghton, MI 49931, USA; (M.S.); (T.S.); (N.O.)
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7
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Kukkar D, Kukkar P, Kumar V, Hong J, Kim KH, Deep A. Recent advances in nanoscale materials for antibody-based cancer theranostics. Biosens Bioelectron 2020; 173:112787. [PMID: 33190049 DOI: 10.1016/j.bios.2020.112787] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 10/08/2020] [Accepted: 10/30/2020] [Indexed: 02/07/2023]
Abstract
The quest for advanced management tools or options of various cancers has been on the rise to efficiently reduce their risks of mortality without the demerits of conventional treatments (e.g., undesirable side effects of the medications on non-target tissues, non-targeted distribution, slow clearance of the administered drugs, and the development of drug resistance over the duration of therapy). In this context, nanomaterials-antibody conjugates can offer numerous advantages in the development of cancer theranostics over conventional delivery systems (e.g., highly specific and enhanced biodistribution of the drug in targeted tissues, prolonged systemic circulation, low toxicity, and minimally invasive molecular imaging). This review comprehensively discusses and evaluates recent advances in the application of nanomaterial-antibody bioconjugates for cancer theranostics for the further advancement in the control of diverse cancerous diseases. Further, discussion is expanded to cover the various challenges and limitations associated with the design and development of nanomaterial-antibody conjugates applicable towards better management of cancer.
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Affiliation(s)
- Deepak Kukkar
- Department of Nanotechnology, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, 140406, India
| | - Preeti Kukkar
- Department of Chemistry, Mata Gujri College, Fatehgarh Sahib, Punjab, 140406, India
| | - Vanish Kumar
- National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar, Punjab, 140306, India
| | - Jongki Hong
- College of Pharmacy, Kyung Hee University, 26 Kyungheedae-ro, Seoul, 02447, Republic of Korea
| | - Ki-Hyun Kim
- Department of Civil and Environmental Engineering, Hanyang University, Seoul, 04763 Republic of Korea.
| | - Akash Deep
- Central Scientific Instruments Organization (CSIR-CSIO), Sector 30 C, Chandigarh, 160030, India.
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8
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Nerurkar SN, Goh D, Cheung CCL, Nga PQY, Lim JCT, Yeong JPS. Transcriptional Spatial Profiling of Cancer Tissues in the Era of Immunotherapy: The Potential and Promise. Cancers (Basel) 2020; 12:E2572. [PMID: 32917035 PMCID: PMC7563386 DOI: 10.3390/cancers12092572] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/05/2020] [Accepted: 09/06/2020] [Indexed: 12/18/2022] Open
Abstract
Intratumoral heterogeneity poses a major challenge to making an accurate diagnosis and establishing personalized treatment strategies for cancer patients. Moreover, this heterogeneity might underlie treatment resistance, disease progression, and cancer relapse. For example, while immunotherapies can confer a high success rate, selective pressures coupled with dynamic evolution within a tumour can drive the emergence of drug-resistant clones that allow tumours to persist in certain patients. To improve immunotherapy efficacy, researchers have used transcriptional spatial profiling techniques to identify and subsequently block the source of tumour heterogeneity. In this review, we describe and assess the different technologies available for such profiling within a cancer tissue. We first outline two well-known approaches, in situ hybridization and digital spatial profiling. Then, we highlight the features of an emerging technology known as Visium Spatial Gene Expression Solution. Visium generates quantitative gene expression data and maps them to the tissue architecture. By retaining spatial information, we are well positioned to identify novel biomarkers and perform computational analyses that might inform on novel combinatorial immunotherapies.
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Affiliation(s)
- Sanjna Nilesh Nerurkar
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore;
| | - Denise Goh
- Institute of Molecular and Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR), Singapore 169856, Singapore; (D.G.); (P.Q.Y.N.); (J.C.T.L.)
| | | | - Pei Qi Yvonne Nga
- Institute of Molecular and Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR), Singapore 169856, Singapore; (D.G.); (P.Q.Y.N.); (J.C.T.L.)
| | - Jeffrey Chun Tatt Lim
- Institute of Molecular and Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR), Singapore 169856, Singapore; (D.G.); (P.Q.Y.N.); (J.C.T.L.)
| | - Joe Poh Sheng Yeong
- Institute of Molecular and Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR), Singapore 169856, Singapore; (D.G.); (P.Q.Y.N.); (J.C.T.L.)
- Department of Anatomical Pathology, Singapore General Hospital, Singapore 169856, Singapore
- Singapore Immunology Network (SIgN), Agency of Science, Technology and Research (A*STAR), Singapore 138648, Singapore
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9
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Diagnosis of uncommon renal epithelial neoplasms: performances of fluorescence in situ hybridization. Hum Pathol 2019; 92:81-90. [DOI: 10.1016/j.humpath.2019.08.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 08/08/2019] [Accepted: 08/09/2019] [Indexed: 11/21/2022]
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10
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Ballester M, Rodríguez F. In situ hybridization with labeled probes: assessment of african Swine Fever virus in formalin-fixed paraffin-embedded tissues. Methods Mol Biol 2015; 1247:209-18. [PMID: 25399099 DOI: 10.1007/978-1-4939-2004-4_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
In situ hybridization (ISH) has become a very valuable molecular diagnostic tool to detect specific DNA or RNA sequences in biological samples through the use of complementary DNA- or RNA-labeled probes. Here, we describe an optimized in situ hybridization protocol to detect African swine fever virus (ASFV) DNA in formalin-fixed, paraffin-embedded tissues using digoxigenin-labeled probes.
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Affiliation(s)
- Maria Ballester
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193, Bellaterra, Spain,
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11
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Rohde A, Hammerl JA, Appel B, Dieckmann R, Al Dahouk S. FISHing for bacteria in food – A promising tool for the reliable detection of pathogenic bacteria? Food Microbiol 2015; 46:395-407. [DOI: 10.1016/j.fm.2014.09.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 08/15/2014] [Accepted: 09/05/2014] [Indexed: 12/28/2022]
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12
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Carvajal-Hausdorf D, Schalper KA, Neumeister V, Rimm DL. Quantitative measurement of cancer tissue biomarkers in the lab and in the clinic. J Transl Med 2015; 95:385-96. [PMID: 25502176 PMCID: PMC4383674 DOI: 10.1038/labinvest.2014.157] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 11/18/2014] [Indexed: 02/06/2023] Open
Abstract
Detection of biomolecules in tissues provides contextual information and the possibility to assess the interaction of different cell types and markers. Routine qualitative assessment of immune- and oligonucleotide-based methods in research and the clinic has been associated with assay variability because of lack of stringent validation and subjective interpretation of results. As a result, the vast majority of in situ assays in clinical usage are nonquantitative and, although useful, often of questionable scientific validity. Here, we revisit the reporters and methods used for single- and multiplexed in situ visualization of protein and RNA. Then we examine methods for the use of quantitative platforms for in situ measurement of protein and mRNA levels. Finally, we discuss the challenges of the transition of these methods to the clinic and their potential role as tools for development of companion diagnostic tests.
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Affiliation(s)
| | - Kurt A. Schalper
- Department of Pathology, Yale University School of Medicine, New Haven, CT
| | | | - David L. Rimm
- Department of Pathology, Yale University School of Medicine, New Haven, CT
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13
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Schwartz S. Preparation of Amniocytes for Interphase Fluorescence In Situ Hybridization (FISH). ACTA ACUST UNITED AC 2015; 85:8.9.1-8.9.16. [DOI: 10.1002/0471142905.hg0809s85] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Stuart Schwartz
- Cytogenetics Laboratory, Laboratory Corporation of America® Holdings Research Triangle Park North Carolina
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14
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Yangquanwei Z, Neethirajan S, Karunakaran C. Cytogenetic analysis of quinoa chromosomes using nanoscale imaging and spectroscopy techniques. NANOSCALE RESEARCH LETTERS 2013; 8:463. [PMID: 24191931 PMCID: PMC4228249 DOI: 10.1186/1556-276x-8-463] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 10/26/2013] [Indexed: 05/02/2023]
Abstract
Here we present a high-resolution chromosomal spectral map derived from synchrotron-based soft X-ray spectromicroscopy applied to quinoa species. The label-free characterization of quinoa metaphase chromosomes shows that it consists of organized substructures of DNA-protein complex. The analysis of spectra of chromosomes using the scanning transmission X-ray microscope (STXM) and its superposition of the pattern with the atomic force microscopy (AFM) and scanning electron microscopy (SEM) images proves that it is possible to precisely locate the gene loci and the DNA packaging inside the chromosomes. STXM has been successfully used to distinguish and quantify the DNA and protein components inside the quinoa chromosomes by visualizing the interphase at up to 30-nm spatial resolution. Our study represents the successful attempt of non-intrusive interrogation and integrating imaging techniques of chromosomes using synchrotron STXM and AFM techniques. The methodology developed for 3-D imaging of chromosomes with chemical specificity and temporal resolution will allow the nanoscale imaging tools to emerge from scientific research and development into broad practical applications such as gene loci tools and biomarker libraries.
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Affiliation(s)
- Zhong Yangquanwei
- BioNano Laboratory, Biological Engineering, University of Guelph, Guelph, Ontario, N1G 2 W1, Canada
| | - Suresh Neethirajan
- BioNano Laboratory, Biological Engineering, University of Guelph, Guelph, Ontario, N1G 2 W1, Canada
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15
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Pan Z, Zhao Y, Yang Q, Song X, Wang X. Novel Magnetic Gold Electrode Applied for Direct Capture and Sensitive Detection of DNA Targets. CHEM LETT 2012. [DOI: 10.1246/cl.2012.1718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Zhengqi Pan
- Emergency Department, Zhongnan Hospital of Wuhan University
| | - Yan Zhao
- Emergency Department, Zhongnan Hospital of Wuhan University
| | - Qisheng Yang
- Emergency Department, Zhongnan Hospital of Wuhan University
| | - Xiaobing Song
- Emergency Department, Zhongnan Hospital of Wuhan University
| | - Xiang Wang
- Emergency Department, Zhongnan Hospital of Wuhan University
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