1
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Ma Y, Fan Y, Xu X, Li H, Liu R, Liu C. Screening of Methyl-β-cyclodextrins as an Antifading Agent for Cyanine Dye-Labeled Streptavidin to Improve the Performance of Genotyping Chips. ACS OMEGA 2024; 9:29491-29498. [PMID: 39005797 PMCID: PMC11238297 DOI: 10.1021/acsomega.4c02099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 06/02/2024] [Accepted: 06/04/2024] [Indexed: 07/16/2024]
Abstract
As a photostabilizing agent for cyanine dye, methyl-β-cyclodextrin (MβCD) was investigated as a possible antifading agent for cyanine dye-labeled proteins. Cyanine-3 (Cy3)-labeled streptavidin (SA-Cy3) solutions containing MβCD exhibited improved resistance against photobleaching. Further research revealed that MβCD can be used as a coating material on the surface of gene chips. Chips loaded with cyanine dye (Cy3 and Cyanine-5 (Cy5))-conjugated model microbeads exhibited resistance against photobleaching with MβCD coatings. MβCD coatings improved the imaging quality of model chips and resulted in higher discrimination ratios (DR) of single base recognition by a set of control beads (NP68). In a whole genome genotyping assay for human samples, the MβCD-coated samples were found to have a better clustering performance than the noncoated ones for a group of randomly picked single nucleotide polymorphisms (SNPs).
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Affiliation(s)
- Yuhao Ma
- LASO
Biotech, Soochow 215000, P. R. China
| | - Yun Fan
- LASO
Biotech, Soochow 215000, P. R. China
| | - Xinyi Xu
- LASO
Biotech, Soochow 215000, P. R. China
| | - Hongxia Li
- LASO
Biotech, Soochow 215000, P. R. China
| | - Ruoyu Liu
- LASO
Biotech, Soochow 215000, P. R. China
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2
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Cao J, Li C, Cui Z, Deng S, Lei T, Liu W, Yang H, Chen P. Spatial Transcriptomics: A Powerful Tool in Disease Understanding and Drug Discovery. Theranostics 2024; 14:2946-2968. [PMID: 38773973 PMCID: PMC11103497 DOI: 10.7150/thno.95908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 04/25/2024] [Indexed: 05/24/2024] Open
Abstract
Recent advancements in modern science have provided robust tools for drug discovery. The rapid development of transcriptome sequencing technologies has given rise to single-cell transcriptomics and single-nucleus transcriptomics, increasing the accuracy of sequencing and accelerating the drug discovery process. With the evolution of single-cell transcriptomics, spatial transcriptomics (ST) technology has emerged as a derivative approach. Spatial transcriptomics has emerged as a hot topic in the field of omics research in recent years; it not only provides information on gene expression levels but also offers spatial information on gene expression. This technology has shown tremendous potential in research on disease understanding and drug discovery. In this article, we introduce the analytical strategies of spatial transcriptomics and review its applications in novel target discovery and drug mechanism unravelling. Moreover, we discuss the current challenges and issues in this research field that need to be addressed. In conclusion, spatial transcriptomics offers a new perspective for drug discovery.
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Affiliation(s)
- Junxian Cao
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Analysis of Complex Effects of Proprietary Chinese Medicine, Hunan Provincial Key Laboratory, Yongzhou City, Hunan Province, China
| | - Caifeng Li
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Zhao Cui
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Shiwen Deng
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Analysis of Complex Effects of Proprietary Chinese Medicine, Hunan Provincial Key Laboratory, Yongzhou City, Hunan Province, China
| | - Tong Lei
- Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Wei Liu
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Hongjun Yang
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Analysis of Complex Effects of Proprietary Chinese Medicine, Hunan Provincial Key Laboratory, Yongzhou City, Hunan Province, China
| | - Peng Chen
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Analysis of Complex Effects of Proprietary Chinese Medicine, Hunan Provincial Key Laboratory, Yongzhou City, Hunan Province, China
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3
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Kalhor K, Chen CJ, Lee HS, Cai M, Nafisi M, Que R, Palmer CR, Yuan Y, Zhang Y, Li X, Song J, Knoten A, Lake BB, Gaut JP, Keene CD, Lein E, Kharchenko PV, Chun J, Jain S, Fan JB, Zhang K. Mapping human tissues with highly multiplexed RNA in situ hybridization. Nat Commun 2024; 15:2511. [PMID: 38509069 PMCID: PMC10954689 DOI: 10.1038/s41467-024-46437-y] [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: 08/16/2023] [Accepted: 02/23/2024] [Indexed: 03/22/2024] Open
Abstract
In situ transcriptomic techniques promise a holistic view of tissue organization and cell-cell interactions. There has been a surge of multiplexed RNA in situ mapping techniques but their application to human tissues has been limited due to their large size, general lower tissue quality and high autofluorescence. Here we report DART-FISH, a padlock probe-based technology capable of profiling hundreds to thousands of genes in centimeter-sized human tissue sections. We introduce an omni-cell type cytoplasmic stain that substantially improves the segmentation of cell bodies. Our enzyme-free isothermal decoding procedure allows us to image 121 genes in large sections from the human neocortex in <10 h. We successfully recapitulated the cytoarchitecture of 20 neuronal and non-neuronal subclasses. We further performed in situ mapping of 300 genes on a diseased human kidney, profiled >20 healthy and pathological cell states, and identified diseased niches enriched in transcriptionally altered epithelial cells and myofibroblasts.
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Affiliation(s)
- Kian Kalhor
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Chien-Ju Chen
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA, USA
| | - Ho Suk Lee
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Department of Electrical Engineering, University of California San Diego, La Jolla, CA, USA
| | - Matthew Cai
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Mahsa Nafisi
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Richard Que
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Carter R Palmer
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Program in Biomedical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Yixu Yuan
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Yida Zhang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Jinghui Song
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Amanda Knoten
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Blue B Lake
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Joseph P Gaut
- Department of Pathology and Immunology, Washington University School of Medicine, St.Louis, MO, USA
| | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA, 98103, USA
| | - Peter V Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Altos Labs, San Diego, CA, USA
| | - Jerold Chun
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Sanjay Jain
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St.Louis, MO, USA
| | | | - Kun Zhang
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- Altos Labs, San Diego, CA, USA.
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4
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Fadri MTM, Lee JB, Keung AJ. Summary of ChIP-Seq Methods and Description of an Optimized ChIP-Seq Protocol. Methods Mol Biol 2024; 2842:419-447. [PMID: 39012609 DOI: 10.1007/978-1-0716-4051-7_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Chromatin immunoprecipitation (ChIP) is an invaluable method to characterize interactions between proteins and genomic DNA, such as the genomic localization of transcription factors and post-translational modification of histones. DNA and proteins are reversibly and covalently crosslinked using formaldehyde. Then the cells are lysed to release the chromatin. The chromatin is fragmented into smaller sizes either by micrococcal nuclease (MN) or sonication and then purified from other cellular components. The protein-DNA complexes are enriched by immunoprecipitation (IP) with antibodies that target the epitope of interest. The DNA is released from the proteins by heat and protease treatment, followed by degradation of contaminating RNAs with RNase. The resulting DNA is analyzed using various methods, including polymerase chain reaction (PCR), quantitative PCR (qPCR), or sequencing. This protocol outlines each of these steps for both yeast and human cells. This chapter includes a contextual discussion of the combination of ChIP with DNA analysis methods such as ChIP-on-Chip, ChIP-qPCR, and ChIP-Seq, recent updates on ChIP-Seq data analysis pipelines, complementary methods for identification of binding sites of DNA binding proteins, and additional protocol information about ChIP-qPCR and ChIP-Seq.
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Affiliation(s)
- Maria Theresa M Fadri
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
| | - Jessica B Lee
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Albert J Keung
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
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5
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Kalhor K, Chen CJ, Lee HS, Cai M, Nafisi M, Que R, Palmer C, Yuan Y, Zhang Y, Song J, Knoten A, Lake BB, Gaut JP, Keene D, Lein E, Kharchenko PV, Chun J, Jain S, Fan JB, Zhang K. Mapping Human Tissues with Highly Multiplexed RNA in situ Hybridization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.16.553610. [PMID: 37645998 PMCID: PMC10462101 DOI: 10.1101/2023.08.16.553610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
In situ transcriptomic techniques promise a holistic view of tissue organization and cell-cell interactions. Recently there has been a surge of multiplexed RNA in situ techniques but their application to human tissues and clinical biopsies has been limited due to their large size, general lower tissue quality and high background autofluorescence. Here we report DART-FISH, a versatile padlock probe-based technology capable of profiling hundreds to thousands of genes in centimeter-sized human tissue sections at cellular resolution. We introduced an omni-cell type cytoplasmic stain, dubbed RiboSoma that substantially improves the segmentation of cell bodies. We developed a computational decoding-by-deconvolution workflow to extract gene spots even in the presence of optical crowding. Our enzyme-free isothermal decoding procedure allowed us to image 121 genes in a large section from the human neocortex in less than 10 hours, where we successfully recapitulated the cytoarchitecture of 20 neuronal and non-neuronal subclasses. Additionally, we demonstrated the detection of transcripts as short as 461 nucleotides, including neuropeptides and discovered new cortical layer markers. We further performed in situ mapping of 300 genes on a diseased human kidney, profiled >20 healthy and pathological cell states, and identified diseased niches enriched in transcriptionally altered epithelial cells and myofibroblasts.
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Affiliation(s)
- Kian Kalhor
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- These authors contributed equally
| | - Chien-Ju Chen
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA, USA
- These authors contributed equally
| | - Ho Suk Lee
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Department of Electrical Engineering, University of California San Diego, La Jolla, CA, USA
| | - Matthew Cai
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Mahsa Nafisi
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Richard Que
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Carter Palmer
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
- Program in Biomedical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Yixu Yuan
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Yida Zhang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Jinghui Song
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Amanda Knoten
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Blue B. Lake
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Joseph P. Gaut
- Department of Pathology and Immunology, Washington University School of Medicine, St
| | - Dirk Keene
- University of Washington School of Medicine, Seattle, WA, USA
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA, USA Louis, MO, USA
| | - Peter V. Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Jerold Chun
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Sanjay Jain
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St
| | | | - Kun Zhang
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
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6
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Verardo D, Adelizzi B, Rodriguez-Pinzon DA, Moghaddam N, Thomée E, Loman T, Godron X, Horgan A. Multiplex enzymatic synthesis of DNA with single-base resolution. SCIENCE ADVANCES 2023; 9:eadi0263. [PMID: 37418522 PMCID: PMC10328407 DOI: 10.1126/sciadv.adi0263] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/05/2023] [Indexed: 07/09/2023]
Abstract
Enzymatic DNA synthesis (EDS) is a promising benchtop and user-friendly method of nucleic acid synthesis that, instead of solvents and phosphoramidites, uses mild aqueous conditions and enzymes. For applications such as protein engineering and spatial transcriptomics that require either oligo pools or arrays with high sequence diversity, the EDS method needs to be adapted and certain steps in the synthesis process spatially decoupled. Here, we have used a synthesis cycle comprising a first step of site-specific silicon microelectromechanical system inkjet dispensing of terminal deoxynucleotidyl transferase enzyme and 3' blocked nucleotide, and a second step of bulk slide washing to remove the 3' blocking group. By repeating the cycle on a substrate with an immobilized DNA primer, we show that microscale spatial control of nucleic acid sequence and length is possible, which, here, are assayed by hybridization and gel electrophoresis. This work is distinctive for enzymatically synthesizing DNA in a highly parallel manner with single base control.
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Affiliation(s)
| | | | | | | | | | - Tessa Loman
- DNA Script, 67 Avenue de Fontainebleau, 94270 Le Kremlin-Bicêtre, France
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7
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Wei X, Shang Y, Zhu Y, Gu Z, Zhang D. Encoding microcarriers for biomedicine. SMART MEDICINE 2023; 2:e20220009. [PMID: 39188559 PMCID: PMC11235794 DOI: 10.1002/smmd.20220009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/22/2022] [Indexed: 08/28/2024]
Abstract
High throughput biological analysis has become an important topic in modern biomedical research and clinical diagnosis. The flow encoding scheme based on the encoding microcarriers provides a feasible strategy for the multiplexed biological analysis. Different encoding characteristics invest the microcarriers with different encoding mechanisms. Biosensor analysis, drug screening, cell culture, and the construction and evaluation of bionic organ chips can be realized by decoding the microcarriers and quantifying the detection signal intensity. In this review, the encoding strategy of microcarriers was divided into the optical and non-optical encoding approaches according to their encoding elements, and the research progress of the microcarrier encoding strategy was elaborated. Finally, we summarized the biomedical applications and predicted their future prospects.
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Affiliation(s)
- Xiaowei Wei
- Laboratory Medicine CenterThe Second Affiliated Hospital of Nanjing Medical UniversityNanjingChina
- Department of Clinical LaboratoryInstitute of Translational MedicineThe Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjingChina
| | - Yixuan Shang
- Department of Clinical LaboratoryInstitute of Translational MedicineThe Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjingChina
| | - Yefei Zhu
- Laboratory Medicine CenterThe Second Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Zhuxiao Gu
- Department of Clinical LaboratoryInstitute of Translational MedicineThe Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjingChina
| | - Dagan Zhang
- Department of Clinical LaboratoryInstitute of Translational MedicineThe Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjingChina
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8
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Cohort profile: the Food Chain Plus (FoCus) cohort. Eur J Epidemiol 2022; 37:1087-1105. [PMID: 36245062 PMCID: PMC9630232 DOI: 10.1007/s10654-022-00924-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 09/25/2022] [Indexed: 11/16/2022]
Abstract
The Food Chain Plus (FoCus) cohort was launched in 2011 for population-based research related to metabolic inflammation. To characterize this novel pathology in a comprehensive manner, data collection included multiple omics layers such as phenomics, microbiomics, metabolomics, genomics, and metagenomics as well as nutrition profiling, taste perception phenotyping and social network analysis. The cohort was set-up to represent a Northern German population of the Kiel region. Two-step recruitment included the randomised enrolment of participants via residents’ registration offices and via the Obesity Outpatient Centre of the University Medical Center Schleswig–Holstein (UKSH). Hence, both a population- and metabolic inflammation- based cohort was created. In total, 1795 individuals were analysed at baseline. Baseline data collection took place between 2011 and 2014, including 63% females and 37% males with an age range of 18–83 years. The median age of all participants was 52.0 years [IQR: 42.5; 63.0 years] and the median baseline BMI in the study population was 27.7 kg/m2 [IQR: 23.7; 35.9 kg/m2]. In the baseline cohort, 14.1% of participants had type 2 diabetes mellitus, which was more prevalent in the subjects of the metabolic inflammation group (MIG; 31.8%). Follow-up for the assessment of disease progression, as well as the onset of new diseases with changes in subject’s phenotype, diet or lifestyle factors is planned every 5 years. The first follow-up period was finished in 2020 and included 820 subjects.
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9
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Bai X, Quek C. Unravelling Tumour Microenvironment in Melanoma at Single-Cell Level and Challenges to Checkpoint Immunotherapy. Genes (Basel) 2022; 13:genes13101757. [PMID: 36292642 PMCID: PMC9601741 DOI: 10.3390/genes13101757] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
Melanoma is known as one of the most immunogenic tumours and is often characterised by high mutation burden, neoantigen load and immune infiltrate. The application of immunotherapies has led to impressive improvements in the clinical outcomes of advanced stage melanoma patients. The standard of care immunotherapies leverage the host immunological influence on tumour cells, which entail complex interactions among the tumour, stroma, and immune cells at the tumour microenvironmental level. However, not all cancer patients can achieve a long-term durable response to immunotherapy, and a significant proportion of patients develops resistance and still die from their disease. Owing to the multi-faceted problems of tumour and microenvironmental heterogeneity, identifying the key factors underlying tumour progression and immunotherapy resistance poses a great challenge. In this review, we outline the main challenges to current cancer immunotherapy research posed by tumour heterogeneity and microenvironment complexities including genomic and transcriptomic variability, selective outgrowth of tumour subpopulations, spatial and temporal tumour heterogeneity and the dynamic state of host immunity and microenvironment orchestration. We also highlight the opportunities to dissect tumour heterogeneity using single-cell sequencing and spatial platforms. Integrative analyses of large-scale datasets will enable in-depth exploration of biological questions, which facilitates the clinical application of translational research.
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10
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Yang L, Ball A, Liu J, Jain T, Li YM, Akhter F, Zhu D, Wang J. Cyclic microchip assay for measurement of hundreds of functional proteins in single neurons. Nat Commun 2022; 13:3548. [PMID: 35729174 PMCID: PMC9213506 DOI: 10.1038/s41467-022-31336-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 06/15/2022] [Indexed: 12/02/2022] Open
Abstract
Despite the fact that proteins carry out nearly all cellular functions and mark the differences of cells, the existing single-cell tools can only analyze dozens of proteins, a scale far from full characterization of cells and tissue yet. Herein, we present a single-cell cyclic multiplex in situ tagging (CycMIST) technology that affords the comprehensive functional proteome profiling of single cells. We demonstrate the technology by detecting 182 proteins that include surface markers, neuron function proteins, neurodegeneration markers, signaling pathway proteins, and transcription factors. Further studies on cells derived from the 5XFAD mice, an Alzheimer's Disease (AD) model, validate the utility of our technology and reveal the deep heterogeneity of brain cells. Through comparison with control mouse cells, we have identified differentially expressed proteins in AD pathology. Our technology could offer new insights into cell machinery and thus may advance many fields including drug discovery, molecular diagnostics, and clinical studies.
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Affiliation(s)
- Liwei Yang
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Avery Ball
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Jesse Liu
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Tanya Jain
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Programs of Neurosciences, Weill Graduate School of Medical Sciences of Cornell University, New York, NY, USA
| | - Yue-Ming Li
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Programs of Neurosciences, Weill Graduate School of Medical Sciences of Cornell University, New York, NY, USA
- Programs of Pharmacology, Weill Graduate School of Medical Sciences of Cornell University, New York, NY, USA
| | - Firoz Akhter
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Donghui Zhu
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Jun Wang
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, 11794, USA.
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11
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Zheng B, Fang L. Spatially resolved transcriptomics provide a new method for cancer research. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:179. [PMID: 35590346 PMCID: PMC9118771 DOI: 10.1186/s13046-022-02385-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 05/06/2022] [Indexed: 12/22/2022]
Abstract
A major feature of cancer is the heterogeneity, both intratumoral and intertumoral. Traditional single-cell techniques have given us a comprehensive understanding of the biological characteristics of individual tumor cells, but the lack of spatial context of the transcriptome has limited the study of cell-to-cell interaction patterns and hindered further exploration of tumor heterogeneity. In recent years, the advent of spatially resolved transcriptomics (SRT) technology has made possible the multidimensional analysis of the tumor microenvironment in the context of intact tissues. Different SRT methods are applicable to different working ranges due to different working principles. In this paper, we review the advantages and disadvantages of various current SRT methods and the overall idea of applying these techniques to oncology studies, hoping to help researchers find breakthroughs. Finally, we discussed the future direction of SRT technology, and deeper investigation into the complex mechanisms of tumor development from different perspectives through multi-omics fusion, paving the way for precisely targeted tumor therapy.
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Affiliation(s)
- Bowen Zheng
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, People's Republic of China
| | - Lin Fang
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, People's Republic of China.
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12
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Zamani Kouhpanji MR, Stadler BJH. Magnetic Nanowires for Nanobarcoding and Beyond. SENSORS (BASEL, SWITZERLAND) 2021; 21:4573. [PMID: 34283095 PMCID: PMC8271806 DOI: 10.3390/s21134573] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 06/26/2021] [Accepted: 07/01/2021] [Indexed: 12/15/2022]
Abstract
Multifunctional magnetic nanowires (MNWs) have been studied intensively over the last decades, in diverse applications. Numerous MNW-based systems have been introduced, initially for fundamental studies and later for sensing applications such as biolabeling and nanobarcoding. Remote sensing of MNWs for authentication and/or anti-counterfeiting is not only limited to engineering their properties, but also requires reliable sensing and decoding platforms. We review the latest progress in designing MNWs that have been, and are being, introduced as nanobarcodes, along with the pros and cons of the proposed sensing and decoding methods. Based on our review, we determine fundamental challenges and suggest future directions for research that will unleash the full potential of MNWs for nanobarcoding applications.
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Affiliation(s)
- Mohammad Reza Zamani Kouhpanji
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN 55455, USA;
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Bethanie J. H. Stadler
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN 55455, USA;
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13
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Mizrak D, Bayin NS, Yuan J, Liu Z, Suciu RM, Niphakis MJ, Ngo N, Lum KM, Cravatt BF, Joyner AL, Sims PA. Single-Cell Profiling and SCOPE-Seq Reveal Lineage Dynamics of Adult Ventricular-Subventricular Zone Neurogenesis and NOTUM as a Key Regulator. Cell Rep 2021; 31:107805. [PMID: 32579931 PMCID: PMC7396151 DOI: 10.1016/j.celrep.2020.107805] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 05/13/2020] [Accepted: 06/02/2020] [Indexed: 12/14/2022] Open
Abstract
In the adult ventricular-subventricular zone (V-SVZ), neural stem cells (NSCs) generate new olfactory bulb (OB) neurons and glia throughout life. To map adult neuronal lineage progression, we profiled >56,000 V-SVZ and OB cells by single-cell RNA sequencing (scRNA-seq). Our analyses reveal the molecular diversity of OB neurons, including fate-mapped neurons, lineage progression dynamics, and an NSC intermediate enriched for Notum, which encodes a secreted WNT antagonist. SCOPE-seq technology, which links live-cell imaging with scRNA-seq, uncovers cell-size transitions during NSC differentiation and preferential NOTUM binding to proliferating neuronal precursors. Consistently, application of NOTUM protein in slice cultures and pharmacological inhibition of NOTUM in slice cultures and in vivo demonstrated that NOTUM negatively regulates V-SVZ proliferation. Timely, context-dependent neurogenesis demands adaptive signaling among neighboring progenitors. Our findings highlight a critical regulatory state during NSC activation marked by NOTUM, which attenuates WNT-stimulated proliferation in NSC progeny.
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Affiliation(s)
- Dogukan Mizrak
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - N Sumru Bayin
- Developmental Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Jinzhou Yuan
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Zhouzerui Liu
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Radu M Suciu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Micah J Niphakis
- Lundbeck La Jolla Research Center, Inc., 10835 Road to the Cure, Suite 250, San Diego, CA 92121, USA
| | - Nhi Ngo
- Lundbeck La Jolla Research Center, Inc., 10835 Road to the Cure, Suite 250, San Diego, CA 92121, USA
| | - Kenneth M Lum
- Lundbeck La Jolla Research Center, Inc., 10835 Road to the Cure, Suite 250, San Diego, CA 92121, USA
| | - Benjamin F Cravatt
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alexandra L Joyner
- Developmental Biology Program, Sloan Kettering Institute, New York, NY 10065, USA; Biochemistry, Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA.
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14
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Howard NP, Troggio M, Durel CE, Muranty H, Denancé C, Bianco L, Tillman J, van de Weg E. Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls. BMC Genomics 2021; 22:246. [PMID: 33827434 PMCID: PMC8028180 DOI: 10.1186/s12864-021-07565-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 03/30/2021] [Indexed: 11/23/2022] Open
Abstract
Background Single nucleotide polymorphism (SNP) array technology has been increasingly used to generate large quantities of SNP data for use in genetic studies. As new arrays are developed to take advantage of new technology and of improved probe design using new genome sequence and panel data, a need to integrate data from different arrays and array platforms has arisen. This study was undertaken in view of our need for an integrated high-quality dataset of Illumina Infinium® 20 K and Affymetrix Axiom® 480 K SNP array data in apple (Malus × domestica). In this study, we qualify and quantify the compatibility of SNP calling, defined as SNP calls that are both accurate and concordant, across both arrays by two approaches. First, the concordance of SNP calls was evaluated using a set of 417 duplicate individuals genotyped on both arrays starting from a set of 10,295 robust SNPs on the Infinium array. Next, the accuracy of the SNP calls was evaluated on additional germplasm (n = 3141) from both arrays using Mendelian inconsistent and consistent errors across thousands of pedigree links. While performing this work, we took the opportunity to evaluate reasons for probe failure and observed discordant SNP calls. Results Concordance among the duplicate individuals was on average of 97.1% across 10,295 SNPs. Of these SNPs, 35% had discordant call(s) that were further curated, leading to a final set of 8412 (81.7%) SNPs that were deemed compatible. Compatibility was highly influenced by the presence of alternate probe binding locations and secondary polymorphisms. The impact of the latter was highly influenced by their number and proximity to the 3′ end of the probe. Conclusions The Infinium and Axiom SNP array data were mostly compatible. However, data integration required intense data filtering and curation. This work resulted in a workflow and information that may be of use in other data integration efforts. Such an in-depth analysis of array concordance and accuracy as ours has not been previously described in the literature and will be useful in future work on SNP array data integration and interpretation, and in probe/platform development. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07565-7.
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Affiliation(s)
- Nicholas P Howard
- Institut für Biologie und Umweltwissenschaften, Carl von Ossietzky Univ., Oldenburg, Germany.,Department of Horticultural Science, Univ. of Minnesota, St Paul, USA
| | | | - Charles-Eric Durel
- Université d'Angers, Institut Agro, INRAE, IRHS, SFR 4207 QuaSaV, Beaucouzé, France
| | - Hélène Muranty
- Université d'Angers, Institut Agro, INRAE, IRHS, SFR 4207 QuaSaV, Beaucouzé, France
| | - Caroline Denancé
- Université d'Angers, Institut Agro, INRAE, IRHS, SFR 4207 QuaSaV, Beaucouzé, France
| | - Luca Bianco
- Fondazione Edmund Mach, San Michele all'Adige, TN, Italy
| | - John Tillman
- Department of Horticultural Science, Univ. of Minnesota, St Paul, USA
| | - Eric van de Weg
- Department of Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands.
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15
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16
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Liu Z, Yuan J, Lasorella A, Iavarone A, Bruce JN, Canoll P, Sims PA. Integrating single-cell RNA-seq and imaging with SCOPE-seq2. Sci Rep 2020; 10:19482. [PMID: 33173156 PMCID: PMC7655825 DOI: 10.1038/s41598-020-76599-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/26/2020] [Indexed: 12/20/2022] Open
Abstract
Live cell imaging allows direct observation and monitoring of phenotypes that are difficult to infer from transcriptomics. However, existing methods for linking microscopy and single-cell RNA-seq (scRNA-seq) have limited scalability. Here, we describe an upgraded version of Single Cell Optical Phenotyping and Expression (SCOPE-seq2) for combining single-cell imaging and expression profiling, with substantial improvements in throughput, molecular capture efficiency, linking accuracy, and compatibility with standard microscopy instrumentation. We introduce improved optically decodable mRNA capture beads and implement a more scalable and simplified optical decoding process. We demonstrate the utility of SCOPE-seq2 for fluorescence, morphological, and expression profiling of individual primary cells from a human glioblastoma (GBM) surgical sample, revealing relationships between simple imaging features and cellular identity, particularly among malignantly transformed tumor cells.
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Affiliation(s)
- Zhouzerui Liu
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Jinzhou Yuan
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Anna Lasorella
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Antonio Iavarone
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Jeffrey N Bruce
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Peter Canoll
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA.
- Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY, 10032, USA.
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17
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Abdullah MAA, Amini N, Yang L, Paluh JL, Wang J. Multiplexed analysis of neural cytokine signaling by a novel neural cell-cell interaction microchip. LAB ON A CHIP 2020; 20:3980-3995. [PMID: 32945325 PMCID: PMC7606659 DOI: 10.1039/d0lc00401d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Multipotent neural stem cells (NSCs) are widely applied in pre-clinical and clinical trials as a cell source to promote tissue regeneration in neurodegenerative diseases. Frequently delivered as dissociated cells, aggregates or self-organized rosettes, it is unknown whether disruption of the NSC rosette morphology or method of formation affect signaling profiles of these cells that may impact uniformity of outcomes in cell therapies. Here we generate a neural cell-cell interaction microchip (NCCIM) as an in vitro platform to simultaneously track an informed panel of cytokines and co-evaluate cell morphology and biomarker expression coupled to a sandwich ELISA platform. We apply multiplex in situ tagging technology (MIST) to evaluate ten cytokines (PDGF-AA, GDNF, BDNF, IGF-1, FGF-2, IL-6, BMP-4, CNTF, β-NGF, NT-3) on microchips for EB-derived rosettes, single cell dissociated rosettes and reformed rosette neurospheres. Of the cytokines evaluated, EB-derived rosettes secrete PDGF-AA, GDNF and FGF-2 prominently, whereas this profile is temporarily lost upon dissociation to single cells and in reformed neurospheres two additional cytokines, BDNF and β-NGF, are also secreted. This study on NSC rosettes demonstrates the development, versatility and utility of the NCCIM as a sensitive multiplex detector of cytokine signaling in a high throughput and controlled microenvironment. The NCCIM is expected to provide important new information to refine cell source choices in therapies as well as to support development of informative 2D or 3D in vitro models including areas of neurodegeneration or neuroplasticity.
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Affiliation(s)
- Mohammed A. A. Abdullah
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794
- Department of Chemistry, State University of New York at Albany, Albany, NY 12222
| | - Nooshin Amini
- Nanobioscience, State University of New York Polytechnic Institute, Albany, NY 12203
| | - Liwei Yang
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794
| | - Janet L. Paluh
- Nanobioscience, State University of New York Polytechnic Institute, Albany, NY 12203
- Corresponding authors. ;
| | - Jun Wang
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794
- Corresponding authors. ;
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18
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Yang L, George J, Wang J. Deep Profiling of Cellular Heterogeneity by Emerging Single-Cell Proteomic Technologies. Proteomics 2020; 20:e1900226. [PMID: 31729152 PMCID: PMC7225074 DOI: 10.1002/pmic.201900226] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 10/14/2019] [Indexed: 12/20/2022]
Abstract
The ability to comprehensively profile cellular heterogeneity in functional proteome is crucial in advancing the understanding of cell behavior, organism development, and disease mechanisms. Conventional bulk measurement by averaging the biological responses across a population often loses the information of cellular variations. Single-cell proteomic technologies are becoming increasingly important to understand and discern cellular heterogeneity. The well-established methods for single-cell protein analysis based on flow cytometry and fluorescence microscopy are limited by the low multiplexing ability owing to the spectra overlap of fluorophores for labeling antibodies. Recent advances in mass spectrometry (MS), microchip, and reiterative staining-based techniques for single-cell proteomics have enabled the evaluation of cellular heterogeneity with high throughput, increased multiplexity, and improved sensitivity. In this review, the principles, developments, advantages, and limitations of these advanced technologies in analysis of single-cell proteins, along with their biological applications to study cellular heterogeneity, are described. At last, the remaining challenges, possible strategies, and future opportunities that will facilitate the improvement and broad applications of single-cell proteomic technologies in cell biology and medical research are discussed.
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Affiliation(s)
- Liwei Yang
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, State University of New York at Stony Brook, Stony Brook, NY 11794
| | - Justin George
- Department of Chemistry, State University of New York, University at Albany, Albany, NY 12222
| | - Jun Wang
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, State University of New York at Stony Brook, Stony Brook, NY 11794
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19
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Harvey AP, Robinson E, Edgar KS, McMullan R, O’Neill KM, Alderdice M, Amirkhah R, Dunne PD, McDermott BJ, Grieve DJ. Downregulation of PPARα during Experimental Left Ventricular Hypertrophy Is Critically Dependent on Nox2 NADPH Oxidase Signalling. Int J Mol Sci 2020; 21:E4406. [PMID: 32575797 PMCID: PMC7352162 DOI: 10.3390/ijms21124406] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 12/31/2022] Open
Abstract
Pressure overload-induced left ventricular hypertrophy (LVH) is initially adaptive but ultimately promotes systolic dysfunction and chronic heart failure. Whilst underlying pathways are incompletely understood, increased reactive oxygen species generation from Nox2 NADPH oxidases, and metabolic remodelling, largely driven by PPARα downregulation, are separately implicated. Here, we investigated interaction between the two as a key regulator of LVH using in vitro, in vivo and transcriptomic approaches. Phenylephrine-induced H9c2 cardiomyoblast hypertrophy was associated with reduced PPARα expression and increased Nox2 expression and activity. Pressure overload-induced LVH and systolic dysfunction induced in wild-type mice by transverse aortic constriction (TAC) for 7 days, in association with Nox2 upregulation and PPARα downregulation, was enhanced in PPARα-/- mice and prevented in Nox2-/- mice. Detailed transcriptomic analysis revealed significantly altered expression of genes relating to PPARα, oxidative stress and hypertrophy pathways in wild-type hearts, which were unaltered in Nox2-/- hearts, whilst oxidative stress pathways remained dysregulated in PPARα-/- hearts following TAC. Network analysis indicated that Nox2 was essential for PPARα downregulation in this setting and identified preferential inflammatory pathway modulation and candidate cytokines as upstream Nox2-sensitive regulators of PPARα signalling. Together, these data suggest that Nox2 is a critical driver of PPARα downregulation leading to maladaptive LVH.
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Affiliation(s)
- Adam P. Harvey
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast BT9 7AE, UK; (A.P.H.); (E.R.); (K.S.E.); (R.M.); (K.M.O.); (B.J.M.)
| | - Emma Robinson
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast BT9 7AE, UK; (A.P.H.); (E.R.); (K.S.E.); (R.M.); (K.M.O.); (B.J.M.)
| | - Kevin S. Edgar
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast BT9 7AE, UK; (A.P.H.); (E.R.); (K.S.E.); (R.M.); (K.M.O.); (B.J.M.)
| | - Ross McMullan
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast BT9 7AE, UK; (A.P.H.); (E.R.); (K.S.E.); (R.M.); (K.M.O.); (B.J.M.)
| | - Karla M. O’Neill
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast BT9 7AE, UK; (A.P.H.); (E.R.); (K.S.E.); (R.M.); (K.M.O.); (B.J.M.)
| | - Matthew Alderdice
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast BT7 1NN, UK; (M.A.); (R.A.); (P.D.D.)
| | - Raheleh Amirkhah
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast BT7 1NN, UK; (M.A.); (R.A.); (P.D.D.)
| | - Philip D. Dunne
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast BT7 1NN, UK; (M.A.); (R.A.); (P.D.D.)
| | - Barbara J. McDermott
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast BT9 7AE, UK; (A.P.H.); (E.R.); (K.S.E.); (R.M.); (K.M.O.); (B.J.M.)
| | - David J. Grieve
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast BT9 7AE, UK; (A.P.H.); (E.R.); (K.S.E.); (R.M.); (K.M.O.); (B.J.M.)
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20
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Liao J, Lu X, Shao X, Zhu L, Fan X. Uncovering an Organ's Molecular Architecture at Single-Cell Resolution by Spatially Resolved Transcriptomics. Trends Biotechnol 2020; 39:43-58. [PMID: 32505359 DOI: 10.1016/j.tibtech.2020.05.006] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 01/17/2023]
Abstract
Revealing fine-scale cellular heterogeneity among spatial context and the functional and structural foundations of tissue architecture is fundamental within biological research and pharmacology. Unlike traditional approaches involving single molecules or bulk omics, cutting-edge, spatially resolved transcriptomics techniques offer near-single-cell or even subcellular resolution within tissues. Massive information across higher dimensions along with position-coordinating labels can better map the whole 3D transcriptional landscape of tissues. In this review, we focus on developments and strategies in spatially resolved transcriptomics, compare the cell and gene throughput and spatial resolution in detail for existing methods, and highlight the enormous potential in biomedical research.
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Affiliation(s)
- Jie Liao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Xiaoyan Lu
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Xin Shao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Ling Zhu
- The Save Sight Institute, Faculty of Medicine and Health, the University of Sydney, Sydney, NSW 2000, Australia
| | - Xiaohui Fan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China; The Save Sight Institute, Faculty of Medicine and Health, the University of Sydney, Sydney, NSW 2000, Australia.
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21
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Giordano R, Donthu RK, Zimin AV, Julca Chavez IC, Gabaldon T, van Munster M, Hon L, Hall R, Badger JH, Nguyen M, Flores A, Potter B, Giray T, Soto-Adames FN, Weber E, Marcelino JAP, Fields CJ, Voegtlin DJ, Hill CB, Hartman GL. Soybean aphid biotype 1 genome: Insights into the invasive biology and adaptive evolution of a major agricultural pest. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 120:103334. [PMID: 32109587 DOI: 10.1016/j.ibmb.2020.103334] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/07/2020] [Accepted: 02/10/2020] [Indexed: 05/12/2023]
Abstract
The soybean aphid, Aphis glycines Matsumura (Hemiptera: Aphididae) is a serious pest of the soybean plant, Glycine max, a major world-wide agricultural crop. We assembled a de novo genome sequence of Ap. glycines Biotype 1, from a culture established shortly after this species invaded North America. 20.4% of the Ap. glycines proteome is duplicated. These in-paralogs are enriched with Gene Ontology (GO) categories mostly related to apoptosis, a possible adaptation to plant chemistry and other environmental stressors. Approximately one-third of these genes show parallel duplication in other aphids. But Ap. gossypii, its closest related species, has the lowest number of these duplicated genes. An Illumina GoldenGate assay of 2380 SNPs was used to determine the world-wide population structure of Ap. Glycines. China and South Korean aphids are the closest to those in North America. China is the likely origin of other Asian aphid populations. The most distantly related aphids to those in North America are from Australia. The diversity of Ap. glycines in North America has decreased over time since its arrival. The genetic diversity of Ap. glycines North American population sampled shortly after its first detection in 2001 up to 2012 does not appear to correlate with geography. However, aphids collected on soybean Rag experimental varieties in Minnesota (MN), Iowa (IA), and Wisconsin (WI), closer to high density Rhamnus cathartica stands, appear to have higher capacity to colonize resistant soybean plants than aphids sampled in Ohio (OH), North Dakota (ND), and South Dakota (SD). Samples from the former states have SNP alleles with high FST values and frequencies, that overlap with genes involved in iron metabolism, a crucial metabolic pathway that may be affected by the Rag-associated soybean plant response. The Ap. glycines Biotype 1 genome will provide needed information for future analyses of mechanisms of aphid virulence and pesticide resistance as well as facilitate comparative analyses between aphids with differing natural history and host plant range.
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Affiliation(s)
- Rosanna Giordano
- Puerto Rico Science, Technology and Research Trust, San Juan, PR, USA; Know Your Bee, Inc. San Juan, PR, USA.
| | - Ravi Kiran Donthu
- Puerto Rico Science, Technology and Research Trust, San Juan, PR, USA; Know Your Bee, Inc. San Juan, PR, USA.
| | - Aleksey V Zimin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Irene Consuelo Julca Chavez
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain; Institute for Research in Biomedicine, Barcelona, Spain
| | - Toni Gabaldon
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain; Institute for Research in Biomedicine, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Manuella van Munster
- CIRAD-INRA-Montpellier SupAgro, TA A54/K, Campus International de Baillarguet, Montpellier, France
| | | | | | - Jonathan H Badger
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institute of Health, DHHS, Bethesda, MD, USA
| | - Minh Nguyen
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Alejandra Flores
- College of Liberal Arts and Sciences, School of Molecular and Cellular Biology, University of Illinois, Urbana, IL, USA
| | - Bruce Potter
- University of Minnesota, Southwest Research and Outreach Center, Lamberton, MN, USA
| | - Tugrul Giray
- Department of Biology, University of Puerto Rico, San Juan, PR, USA
| | - Felipe N Soto-Adames
- Florida Department of Agriculture and Consumer Services, Division of Plant Industry, Entomology, Gainesville, FL, USA
| | | | - Jose A P Marcelino
- Puerto Rico Science, Technology and Research Trust, San Juan, PR, USA; Know Your Bee, Inc. San Juan, PR, USA; Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA
| | - Christopher J Fields
- HPCBio, Roy J. Carver Biotechnology Center, University of Illinois, Urbana, IL, USA
| | - David J Voegtlin
- Illinois Natural History Survey, University of Illinois, Urbana, IL, USA
| | | | - Glen L Hartman
- USDA-ARS and Department of Crop Sciences, University of Illinois, Urbana, IL, USA
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22
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Popov R, Shankara GK, von Bojnicic-Kninski C, Barua P, Mattes D, Breitling F, Nesterov-Mueller A. Stochastic deposition of amino acids into microcavities via microparticles. Sci Rep 2019; 9:16468. [PMID: 31712621 PMCID: PMC6848108 DOI: 10.1038/s41598-019-52994-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 10/26/2019] [Indexed: 11/10/2022] Open
Abstract
All known methods for solid-phase synthesis of molecular arrays exploit positioning techniques to deposit monomers on a substrate preferably high densely. In this paper, stochastic patterning of molecule spots (250 000 spots monomers/cm2) via random allocation of the microbeads on a microstructured glass is presented. The size and shape of the microbeads and the microcavities are selected in such a way so that only one microbead can fit into the respective microcavity. Each microbead can be loaded with a certain type of molecule e.g. amino acids and is brought in the microcavities stochastically. Applying solvent vapor and heating the substrate, the molecules are released from the microbeads and coupled to the functionalized substrate. To differentiate between the microbeads carrying different molecules, quantum dot labels are preliminary introduced into the microbeads. Fluorescence imaging and subsequent data analysis enable decoding of the molecule deposition patterns. After the coupling step is completed, the microbeads are mechanically removed from the microwells. The composition of the monomer microbeads, their deposition and the conditions of the monomer extraction are studied. The stochastic monomer patterning may be used to design novel molecular arrays.
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Affiliation(s)
- Roman Popov
- Institute of Microstructure Technology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Girish Karadka Shankara
- Institute of Microstructure Technology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Clemens von Bojnicic-Kninski
- Institute of Microstructure Technology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Pramit Barua
- Institute of Microstructure Technology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Daniela Mattes
- Institute of Microstructure Technology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Frank Breitling
- Institute of Microstructure Technology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Alexander Nesterov-Mueller
- Institute of Microstructure Technology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.
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Vickovic S, Eraslan G, Salmén F, Klughammer J, Stenbeck L, Schapiro D, Äijö T, Bonneau R, Bergenstråhle L, Navarro JF, Gould J, Griffin GK, Borg Å, Ronaghi M, Frisén J, Lundeberg J, Regev A, Ståhl PL. High-definition spatial transcriptomics for in situ tissue profiling. Nat Methods 2019; 16:987-990. [PMID: 31501547 PMCID: PMC6765407 DOI: 10.1038/s41592-019-0548-y] [Citation(s) in RCA: 595] [Impact Index Per Article: 119.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 08/02/2019] [Indexed: 12/21/2022]
Abstract
Spatial and molecular characteristics determine tissue function, yet high-resolution methods to capture both concurrently are lacking. Here, we developed high-definition spatial transcriptomics, which captures RNA from histological tissue sections on a dense, spatially barcoded bead array. Each experiment recovers several hundred thousand transcript-coupled spatial barcodes at 2-μm resolution, as demonstrated in mouse brain and primary breast cancer. This opens the way to high-resolution spatial analysis of cells and tissues.
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Affiliation(s)
- Sanja Vickovic
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
| | - Gökcen Eraslan
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Fredrik Salmén
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Johanna Klughammer
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Linnea Stenbeck
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Denis Schapiro
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Tarmo Äijö
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
| | - Richard Bonneau
- Center for Data Science, New York University, New York, NY, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Ludvig Bergenstråhle
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - José Fernandéz Navarro
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Joshua Gould
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gabriel K Griffin
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Åke Borg
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | | | - Jonas Frisén
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute and Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Patrik L Ståhl
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
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24
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Costa JA, Dentinger PM, McGall GH, Crnogorac F, Zhou W. Fabrication of Inverted High-Density DNA Microarrays in a Hydrogel. ACS APPLIED MATERIALS & INTERFACES 2019; 11:30534-30541. [PMID: 31389236 DOI: 10.1021/acsami.9b07755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Current techniques for making high-resolution, photolithographic DNA microarrays suffer from the limitation that the 3' end of each sequence is anchored to a hard substrate and hence is unavailable for many potential enzymatic reactions. Here, we demonstrate a technique that inverts the entire microarray into a hydrogel. This method preserves the spatial fidelity of the original pattern while simultaneously removing incorrectly synthesized oligomers that are inherent to all other microarray fabrication strategies. First, a standard 5'-up microarray on a donor wafer is synthesized, in which each oligo is anchored with a cleavable linker at the 3' end and an Acrydite phosphoramidite at the 5' end. Following the synthesis of the array, an acrylamide monomer solution is applied to the donor wafer, and an acrylamide-silanized acceptor wafer is placed on top. As the polyacrylamide hydrogel forms between the two wafers, it covalently incorporates the acrydite-terminated sequences into the matrix. Finally, the oligos are released from the donor wafer upon immersing in an ammonia solution that cleaves the 3'-linkers, thus freeing the oligos at the 3' end. The array is now presented 3'-up on the surface of the gel-coated acceptor wafer. Various types of on-gel enzymatic reactions demonstrate a versatile and robust platform that can easily be constructed with far more molecular complexity than traditional photolithographic arrays by endowing the system with multiple enzymatic substrates. We produce a new generation of microarrays where highly ordered, purified oligos are inverted 3'-up, in a biocompatible soft hydrogel, and functional with respect to a wide variety of programable enzymatic reactions.
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Affiliation(s)
- Justin A Costa
- Centrillion Technologies , 2500 Faber Place , Palo Alto , California 94303 , United States
| | - Paul M Dentinger
- Centrillion Technologies , 2500 Faber Place , Palo Alto , California 94303 , United States
| | - Glenn H McGall
- Centrillion Technologies , 2500 Faber Place , Palo Alto , California 94303 , United States
| | - Filip Crnogorac
- Centrillion Technologies , 2500 Faber Place , Palo Alto , California 94303 , United States
| | - Wei Zhou
- Centrillion Technologies , 2500 Faber Place , Palo Alto , California 94303 , United States
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25
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Lim CC, Choong YS, Lim TS. Cognizance of Molecular Methods for the Generation of Mutagenic Phage Display Antibody Libraries for Affinity Maturation. Int J Mol Sci 2019; 20:E1861. [PMID: 30991723 PMCID: PMC6515083 DOI: 10.3390/ijms20081861] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/10/2019] [Accepted: 04/12/2019] [Indexed: 12/25/2022] Open
Abstract
Antibodies leverage on their unique architecture to bind with an array of antigens. The strength of interaction has a direct relation to the affinity of the antibodies towards the antigen. In vivo affinity maturation is performed through multiple rounds of somatic hypermutation and selection in the germinal centre. This unique process involves intricate sequence rearrangements at the gene level via molecular mechanisms. The emergence of in vitro display technologies, mainly phage display and recombinant DNA technology, has helped revolutionize the way antibody improvements are being carried out in the laboratory. The adaptation of molecular approaches in vitro to replicate the in vivo processes has allowed for improvements in the way recombinant antibodies are designed and tuned. Combinatorial libraries, consisting of a myriad of possible antibodies, are capable of replicating the diversity of the natural human antibody repertoire. The isolation of target-specific antibodies with specific affinity characteristics can also be accomplished through modification of stringent protocols. Despite the ability to screen and select for high-affinity binders, some 'fine tuning' may be required to enhance antibody binding in terms of its affinity. This review will provide a brief account of phage display technology used for antibody generation followed by a summary of different combinatorial library characteristics. The review will focus on available strategies, which include molecular approaches, next generation sequencing, and in silico approaches used for antibody affinity maturation in both therapeutic and diagnostic applications.
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Affiliation(s)
- Chia Chiu Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Penang 11800, Malaysia.
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26
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Rodriques SG, Stickels RR, Goeva A, Martin CA, Murray E, Vanderburg CR, Welch J, Chen LM, Chen F, Macosko EZ. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 2019; 363:1463-1467. [PMID: 30923225 PMCID: PMC6927209 DOI: 10.1126/science.aaw1219] [Citation(s) in RCA: 1169] [Impact Index Per Article: 233.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 02/28/2019] [Indexed: 12/24/2022]
Abstract
Spatial positions of cells in tissues strongly influence function, yet a high-throughput, genome-wide readout of gene expression with cellular resolution is lacking. We developed Slide-seq, a method for transferring RNA from tissue sections onto a surface covered in DNA-barcoded beads with known positions, allowing the locations of the RNA to be inferred by sequencing. Using Slide-seq, we localized cell types identified by single-cell RNA sequencing datasets within the cerebellum and hippocampus, characterized spatial gene expression patterns in the Purkinje layer of mouse cerebellum, and defined the temporal evolution of cell type-specific responses in a mouse model of traumatic brain injury. These studies highlight how Slide-seq provides a scalable method for obtaining spatially resolved gene expression data at resolutions comparable to the sizes of individual cells.
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Affiliation(s)
- Samuel G Rodriques
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Robert R Stickels
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Graduate School of Arts and Sciences, Harvard University, Cambridge, MA 02138, USA
- Division of Medical Science, Harvard Medical School, Boston, MA 02115, USA
| | | | - Carly A Martin
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Evan Murray
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Joshua Welch
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Linlin M Chen
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Fei Chen
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
| | - Evan Z Macosko
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA 02114, USA
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27
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Yuan J, Sheng J, Sims PA. SCOPE-Seq: a scalable technology for linking live cell imaging and single-cell RNA sequencing. Genome Biol 2018; 19:227. [PMID: 30583733 PMCID: PMC6305572 DOI: 10.1186/s13059-018-1607-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 12/06/2018] [Indexed: 01/09/2023] Open
Abstract
Optically decodable beads link the identity of a sample to a measurement through an optical barcode, enabling libraries of biomolecules to be captured on beads in solution and decoded by fluorescence. This approach has been foundational to microarray, sequencing, and flow-based expression profiling technologies. We combine microfluidics with optically decodable beads and show that phenotypic analysis of living cells can be linked to single-cell sequencing. As a proof-of-concept, we demonstrate the accuracy and scalability of our tool called Single Cell Optical Phenotyping and Expression sequencing (SCOPE-Seq) to combine live cell imaging with single-cell RNA sequencing.
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Affiliation(s)
- Jinzhou Yuan
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Jenny Sheng
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA. .,Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA. .,Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY, 10032, USA.
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28
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Ni S, Isa L, Wolf H. Capillary assembly as a tool for the heterogeneous integration of micro- and nanoscale objects. SOFT MATTER 2018; 14:2978-2995. [PMID: 29611588 DOI: 10.1039/c7sm02496g] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
During the past decade, capillary assembly in topographical templates has evolved into an efficient method for the heterogeneous integration of micro- and nano-scale objects on a variety of surfaces. This assembly route has been applied to a large spectrum of materials of micrometer to nanometer dimensions, supplied in the form of aqueous colloidal suspensions. Using systems produced via bulk synthesis affords a huge flexibility in the choice of materials, holding promise for the realization of novel superior devices in the fields of optics, electronics and health, if they can be integrated into surface structures in a fast, simple, and reliable way. In this review, the working principles of capillary assembly and its fundamental process parameters are first presented and discussed. We then examine the latest developments in template design and tool optimization to perform capillary assembly in more robust and efficient ways. This is followed by a focus on the broad range of functional materials that have been realized using capillary assembly, from single components to large-scale heterogeneous multi-component assemblies. We then review current applications of capillary assembly, especially in optics, electronics, and in biomaterials. We conclude with a short summary and an outlook for future developments.
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Affiliation(s)
- Songbo Ni
- IBM Research - Zurich, Säumerstrasse 4, 8803 Rüschlikon, Switzerland.
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29
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Yoon M, Min SW, Dugasani SR, Lee YU, Oh MS, Anthopoulos TD, Park SH, Im S. Charge Transport in 2D DNA Tunnel Junction Diodes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1703006. [PMID: 29105986 DOI: 10.1002/smll.201703006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Indexed: 06/07/2023]
Abstract
Recently, deoxyribonucleic acid (DNA) is studied for electronics due to its intrinsic benefits such as its natural plenitude, biodegradability, biofunctionality, and low-cost. However, its applications are limited to passive components because of inherent insulating properties. In this report, a metal-insulator-metal tunnel diode with Au/DNA/NiOx junctions is presented. Through the self-aligning process of DNA molecules, a 2D DNA nanosheet is synthesized and used as a tunneling barrier, and semitransparent conducting oxide (NiOx ) is applied as a top electrode for resolving metal penetration issues. This molecular device successfully operates as a nonresonant tunneling diode, and temperature-variable current-voltage analysis proves that Fowler-Nordheim tunneling is a dominant conduction mechanism at the junctions. DNA-based tunneling devices appear to be promising prototypes for nanoelectronics using biomolecules.
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Affiliation(s)
- Minho Yoon
- Department of Physics, Yonsei University, Seoul, 120-749, South Korea
| | - Sung-Wook Min
- Department of Physics, Yonsei University, Seoul, 120-749, South Korea
| | | | - Yong Uk Lee
- Material Research Centre, Samsung Advanced Institute of Technology, Suwon, 16678, South Korea
| | - Min Suk Oh
- Display Materials & Components Research Center, Korea Electronics Technology Institute, Seongnam, 463-816, South Korea
| | - Thomas D Anthopoulos
- Materials Science and Engineering Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Sung Ha Park
- Department of Physics, Sungkyunkwan University, Suwon, 440-746, South Korea
| | - Seongil Im
- Department of Physics, Yonsei University, Seoul, 120-749, South Korea
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30
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Decrop D, Pardon G, Brancato L, Kil D, Zandi Shafagh R, Kokalj T, Haraldsson T, Puers R, van der Wijngaart W, Lammertyn J. Single-Step Imprinting of Femtoliter Microwell Arrays Allows Digital Bioassays with Attomolar Limit of Detection. ACS APPLIED MATERIALS & INTERFACES 2017; 9:10418-10426. [PMID: 28266828 DOI: 10.1021/acsami.6b15415] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Bead-based microwell array technology is growing as an ultrasensitive analysis tool as exemplified by the successful commercial applications from Illumina and Quanterix for nucleic acid analysis and ultrasensitive protein measurements, respectively. High-efficiency seeding of magnetic beads is key for these applications and is enhanced by hydrophilic-in-hydrophobic microwell arrays, which are unfortunately often expensive or labor-intensive to manufacture. Here, we demonstrate a new single-step manufacturing approach for imprinting cheap and disposable hydrophilic-in-hydrophobic microwell arrays suitable for digital bioassays. Imprinting of arrays with hydrophilic-in-hydrophobic microwells is made possible using an innovative surface energy replication approach by means of a hydrophobic thiol-ene polymer formulation. In this polymer, hydrophobic-moiety-containing monomers self-assemble at the hydrophobic surface of the imprinting stamp, which results in a hydrophobic replica surface after polymerization. After removing the stamp, microwells with hydrophobic walls and a hydrophilic bottom are obtained. We demonstrate that the hydrophilic-in-hydrophobic imprinted microwell arrays enable successful and efficient self-assembly of individual water droplets and seeding of magnetic beads with loading efficiencies up to 96%. We also demonstrate the suitability of the microwell arrays for the isolation and digital counting of single molecules achieving a limit of detection of 17.4 aM when performing a streptavidin-biotin binding assay as model system. Since this approach is up-scalable through reaction injection molding, we expect it will contribute substantially to the translation of ultrasensitive digital microwell array technology toward diagnostic applications.
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Affiliation(s)
- Deborah Decrop
- Department of Biosystems, KU Leuven-University of Leuven , Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Gaspard Pardon
- Department of Micro- and Nanosystems, KTH Royal Institute of Technology , Stockholm, Sweden
| | - Luigi Brancato
- Department of Electrotechnical Engineering (ESAT-MICAS), KU Leuven-University of Leuven , Kasteelpark Arenberg 10, 3001 Leuven, Belgium
| | - Dries Kil
- Department of Electrotechnical Engineering (ESAT-MICAS), KU Leuven-University of Leuven , Kasteelpark Arenberg 10, 3001 Leuven, Belgium
| | - Reza Zandi Shafagh
- Department of Micro- and Nanosystems, KTH Royal Institute of Technology , Stockholm, Sweden
| | - Tadej Kokalj
- Department of Biosystems, KU Leuven-University of Leuven , Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Tommy Haraldsson
- Department of Micro- and Nanosystems, KTH Royal Institute of Technology , Stockholm, Sweden
| | - Robert Puers
- Department of Electrotechnical Engineering (ESAT-MICAS), KU Leuven-University of Leuven , Kasteelpark Arenberg 10, 3001 Leuven, Belgium
| | | | - Jeroen Lammertyn
- Department of Biosystems, KU Leuven-University of Leuven , Willem de Croylaan 42, 3001 Leuven, Belgium
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31
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Benito-Peña E, Valdés MG, Glahn-Martínez B, Moreno-Bondi MC. Fluorescence based fiber optic and planar waveguide biosensors. A review. Anal Chim Acta 2016; 943:17-40. [PMID: 27769374 PMCID: PMC7094704 DOI: 10.1016/j.aca.2016.08.049] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 08/25/2016] [Accepted: 08/29/2016] [Indexed: 12/21/2022]
Abstract
The application of optical biosensors, specifically those that use optical fibers and planar waveguides, has escalated throughout the years in many fields, including environmental analysis, food safety and clinical diagnosis. Fluorescence is, without doubt, the most popular transducer signal used in these devices because of its higher selectivity and sensitivity, but most of all due to its wide versatility. This paper focuses on the working principles and configurations of fluorescence-based fiber optic and planar waveguide biosensors and will review biological recognition elements, sensing schemes, as well as some major and recent applications, published in the last ten years. The main goal is to provide the reader a general overview of a field that requires the joint collaboration of researchers of many different areas, including chemistry, physics, biology, engineering, and material science.
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Affiliation(s)
- Elena Benito-Peña
- Department of Analytical Chemistry, Faculty of Chemistry, Complutense University, 28040 Madrid, Spain
| | - Mayra Granda Valdés
- Department of Analytical Chemistry, Faculty of Chemistry, University of La Habana, 10400 La Habana, Cuba
| | - Bettina Glahn-Martínez
- Department of Analytical Chemistry, Faculty of Chemistry, Complutense University, 28040 Madrid, Spain
| | - Maria C Moreno-Bondi
- Department of Analytical Chemistry, Faculty of Chemistry, Complutense University, 28040 Madrid, Spain.
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32
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Iddawela M, Rueda OM, Klarqvist M, Graf S, Earl HM, Caldas C. Reliable gene expression profiling of formalin-fixed paraffin-embedded breast cancer tissue (FFPE) using cDNA-mediated annealing, extension, selection, and ligation whole-genome (DASL WG) assay. BMC Med Genomics 2016; 9:54. [PMID: 27542606 PMCID: PMC4992321 DOI: 10.1186/s12920-016-0215-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 08/05/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The difficulties in using formalin-fixed and paraffin-embedded (FFPE) tumour specimens for molecular marker studies have hampered progress in translational cancer research. The cDNA-mediated, annealing, selection, extension, and ligation (DASL) assay is a platform for gene expression profiling from FFPE tissue and hence could allow analysis of large collections of tissue with associated clinical data from existing archives, therefore facilitating the development of novel biomarkers. METHOD RNA isolated from matched fresh frozen (FF) and FFPE cancer specimens was profiled using both the DASL whole-genome (WG) platform, and Illumina BeadArray's, and results were compared. Samples utilized were obtained from the breast cancer tumour bank held at the Cambridge University Hospitals NHS Foundation Trust. RESULTS The number of reliably detected probes was comparable between the DASL and BeadArray platforms, indicating that the source of RNA did not result in a significant difference in the detection rates (Mean probes- 17114 in FFPE & 17400 in FF). There was a significant degree of correlation between replicates within the FF and FFPE sample sets (r (2) = 0.96-0.98) as well as between the two platforms (DASL vs. BeadArray r (2) = range 0.83-0.89). Hierarchical clustering using the most informative probes showed that replicate and matched samples were grouped into the same sub-cluster, regardless of whether RNA was derived from FF or FFPE tissue. CONCLUSION Both FF and FFPE material generated reproducible gene expression profiles, although there was more noise in profiles from FFPE specimens. We have shown that the DASL WG platform is suitable for profiling formalin-fixed paraffin-embedded samples, but robust bioinformatics analysis is required.
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Affiliation(s)
- Mahesh Iddawela
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
- Department of Oncology, Addenbrooke’s Hospital, University of Cambridge, Hills Road, Cambridge, CB1 9RN UK
- Cambridge Breast Unit, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre and Cambridge Experimental Cancer Medicine Centre, Cambridge, UK
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria 3800 Australia
- School of Clinical Sciences, Monash University, Clayton, Victoria Australia
| | - Oscar M. Rueda
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
| | - Marcus Klarqvist
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
| | - Stefan Graf
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
| | - Helena M. Earl
- Department of Oncology, Addenbrooke’s Hospital, University of Cambridge, Hills Road, Cambridge, CB1 9RN UK
- Cambridge Breast Unit, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre and Cambridge Experimental Cancer Medicine Centre, Cambridge, UK
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
- Department of Oncology, Addenbrooke’s Hospital, University of Cambridge, Hills Road, Cambridge, CB1 9RN UK
- Cambridge Breast Unit, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre and Cambridge Experimental Cancer Medicine Centre, Cambridge, UK
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33
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Zhao Y, Cheng Y, Shang L, Wang J, Xie Z, Gu Z. Microfluidic synthesis of barcode particles for multiplex assays. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:151-174. [PMID: 25331055 DOI: 10.1002/smll.201401600] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 08/20/2014] [Indexed: 06/04/2023]
Abstract
The increasing use of high-throughput assays in biomedical applications, including drug discovery and clinical diagnostics, demands effective strategies for multiplexing. One promising strategy is the use of barcode particles that encode information about their specific compositions and enable simple identification. Various encoding mechanisms, including spectroscopic, graphical, electronic, and physical encoding, have been proposed for the provision of sufficient identification codes for the barcode particles. These particles are synthesized in various ways. Microfluidics is an effective approach that has created exciting avenues of scientific research in barcode particle synthesis. The resultant particles have found important application in the detection of multiple biological species as they have properties of high flexibility, fast reaction times, less reagent consumption, and good repeatability. In this paper, research progress in the microfluidic synthesis of barcode particles for multiplex assays is discussed. After introducing the general developing strategies of the barcode particles, the focus is on studies of microfluidics, including their design, fabrication, and application in the generation of barcode particles. Applications of the achieved barcode particles in multiplex assays will be described and emphasized. The prospects for future development of these barcode particles are also presented.
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Affiliation(s)
- Yuanjin Zhao
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, 210096, China; Laboratory of Environment and Biosafety Research, Institute of Southeast University in Suzhou, Suzhou, 215123, China
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34
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Chao S, Lawley C. Use of the Illumina GoldenGate assay for single nucleotide polymorphism (SNP) genotyping in cereal crops. Methods Mol Biol 2015; 1245:299-312. [PMID: 25373766 DOI: 10.1007/978-1-4939-1966-6_22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Highly parallel genotyping assays, such as the GoldenGate assay developed by Illumina, capable of interrogating up to 3,072 single nucleotide polymorphisms (SNPs) simultaneously, have greatly facilitated genome-wide studies, particularly for crops with large and complex genome structures. In this report, we provide detailed information and guidelines regarding genomic DNA preparation, SNP assay design, SNP assay protocols, and genotype calling using Illumina's GenomeStudio software.
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Affiliation(s)
- Shiaoman Chao
- USDA-ARS, Biosciences Research Lab, 1605 Albrecht Blvd N, Fargo, ND, 58102, USA,
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35
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Nesterov-Mueller A, Maerkle F, Hahn L, Foertsch T, Schillo S, Bykovskaya V, Sedlmayr M, Weber LK, Ridder B, Soehindrijo M, Muenster B, Striffler J, Bischoff FR, Breitling F, Loeffler FF. Particle-Based Microarrays of Oligonucleotides and Oligopeptides. MICROARRAYS 2014; 3:245-62. [PMID: 27600347 PMCID: PMC4979057 DOI: 10.3390/microarrays3040245] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 10/15/2014] [Accepted: 10/16/2014] [Indexed: 01/02/2023]
Abstract
In this review, we describe different methods of microarray fabrication based on the use of micro-particles/-beads and point out future tendencies in the development of particle-based arrays. First, we consider oligonucleotide bead arrays, where each bead is a carrier of one specific sequence of oligonucleotides. This bead-based array approach, appearing in the late 1990s, enabled high-throughput oligonucleotide analysis and had a large impact on genome research. Furthermore, we consider particle-based peptide array fabrication using combinatorial chemistry. In this approach, particles can directly participate in both the synthesis and the transfer of synthesized combinatorial molecules to a substrate. Subsequently, we describe in more detail the synthesis of peptide arrays with amino acid polymer particles, which imbed the amino acids inside their polymer matrix. By heating these particles, the polymer matrix is transformed into a highly viscous gel, and thereby, imbedded monomers are allowed to participate in the coupling reaction. Finally, we focus on combinatorial laser fusing of particles for the synthesis of high-density peptide arrays. This method combines the advantages of particles and combinatorial lithographic approaches.
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Affiliation(s)
- Alexander Nesterov-Mueller
- Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Frieder Maerkle
- Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Lothar Hahn
- Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Tobias Foertsch
- Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Sebastian Schillo
- Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Valentina Bykovskaya
- Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Martyna Sedlmayr
- Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Laura K Weber
- Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Barbara Ridder
- Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Miriam Soehindrijo
- Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Bastian Muenster
- Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Jakob Striffler
- Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - F Ralf Bischoff
- German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
| | - Frank Breitling
- Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Felix F Loeffler
- Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
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Yuan J, Zhao X, Wang X, Gu Z. Image decoding of photonic crystal beads array in the microfluidic chip for multiplex assays. Sci Rep 2014; 4:6755. [PMID: 25341876 PMCID: PMC4208063 DOI: 10.1038/srep06755] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 10/03/2014] [Indexed: 12/15/2022] Open
Abstract
Along with the miniaturization and intellectualization of biomedical instruments, the increasing demand of health monitoring at anywhere and anytime elevates the need for the development of point of care testing (POCT). Photonic crystal beads (PCBs) as one kind of good encoded microcarriers can be integrated with microfluidic chips in order to realize cost-effective and high sensitive multiplex bioassays. However, there are difficulties in analyzing them towards automated analysis due to the characters of the PCBs and the unique detection manner. In this paper, we propose a strategy to take advantage of automated image processing for the color decoding of the PCBs array in the microfluidic chip for multiplex assays. By processing and alignment of two modal images of epi-fluorescence and epi-white light, every intact bead in the image is accurately extracted and decoded by PC colors, which stand for the target species. This method, which shows high robustness and accuracy under various configurations, eliminates the high hardware requirement of spectroscopy analysis and user-interaction software, and provides adequate supports for the general automated analysis of POCT based on PCBs array.
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Affiliation(s)
- Junjie Yuan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
- Laboratory of Environment and Biosafety Research Institute of Southeast University in Suzhou, Suzhou 215123, China
| | - Xiangwei Zhao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
- Laboratory of Environment and Biosafety Research Institute of Southeast University in Suzhou, Suzhou 215123, China
| | - Xiaoxia Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
- Laboratory of Environment and Biosafety Research Institute of Southeast University in Suzhou, Suzhou 215123, China
| | - Zhongze Gu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
- Laboratory of Environment and Biosafety Research Institute of Southeast University in Suzhou, Suzhou 215123, China
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Zhou H, Steffenson BJ, Muehlbauer G, Wanyera R, Njau P, Ndeda S. Association mapping of stem rust race TTKSK resistance in US barley breeding germplasm. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1293-304. [PMID: 24710821 PMCID: PMC4035542 DOI: 10.1007/s00122-014-2297-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 03/12/2014] [Indexed: 05/18/2023]
Abstract
Loci conferring resistance to the highly virulent African stem rust race TTKSK were identified in advanced barley breeding germplasm and positioned to chromosomes 5H and 7H using an association mapping approach. African races of the stem rust pathogen (Puccinia graminis f. sp. tritici) are a serious threat to barley production worldwide because of their wide virulence. To discover and characterize resistance to African stem rust race TTKSK in US barley breeding germplasm, over 3,000 lines/cultivars were assessed for resistance at the seedling stage in the greenhouse and also the adult plant stage in the field in Kenya. Only 12 (0.3 %) and 64 (2.1 %) lines exhibited a resistance level comparable to the resistant control at the seedling and adult plant stage, respectively. To map quantitative trait loci (QTL) for resistance to race TTKSK, an association mapping approach was conducted, utilizing 3,072 single nucleotide polymorphism (SNP) markers. At the seedling stage, two neighboring SNP markers (0.8 cM apart) on chromosome 7H (11_21491 and 12_30528) were found significantly associated with resistance. The most significant one found was 12_30528; thus, the resistance QTL was named Rpg-qtl-7H-12_30528. At the adult plant stage, two SNP markers on chromosome 5H (11_11355 and 12_31427) were found significantly associated with resistance. This resistance QTL was named Rpg-qtl-5H-11_11355 for the most significant marker identified. Adult plant resistance is of paramount importance for stem rust. The marker associated with Rpg-qtl-5H-11_11355 for adult plant resistance explained only a small portion of the phenotypic variation (0.02); however, this QTL reduced disease severity up to 55.0 % under low disease pressure and up to 21.1 % under heavy disease pressure. SNP marker 11_11355 will be valuable for marker-assisted selection of adult plant stem rust resistance in barley breeding.
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Affiliation(s)
- H. Zhou
- Department of Plant Pathology, University of Minnesota, St. Paul, MN USA
| | - B. J. Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN USA
| | - Gary Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN USA
- Department of Plant Biology, University of Minnesota, St. Paul, MN USA
| | - Ruth Wanyera
- Kenya Agricultural Research Institute, Njoro, Kenya
| | - Peter Njau
- Kenya Agricultural Research Institute, Njoro, Kenya
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Rödiger S, Liebsch C, Schmidt C, Lehmann W, Resch-Genger U, Schedler U, Schierack P. Nucleic acid detection based on the use of microbeads: a review. Mikrochim Acta 2014. [DOI: 10.1007/s00604-014-1243-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
Over the last few years, several initiatives have described efforts to combine previously invented techniques in molecular biology with parallel detection principles to sequence or genotype DNA signatures. The Infinium system from Illumina and the Affymetrix GeneChips are two systems suitable for whole-genome scoring of variable positions. However, directed candidate-gene approaches are more cost effective and several academic groups and the private sector provide techniques with moderate typing throughput combined with large sample capacity suiting these needs. Recently, whole-genome sequencing platforms based on the sequencing-by-synthesis principle were presented by 454 Life Sciences and Solexa, showing great potential as alternatives to conventional genotyping approaches. In addition to these sequencing initiatives, many efforts are pursuing novel ideas to facilitate fast and cost-effective whole genome sequencing, such as ligation-based sequencing. Reliable methods for routine re-sequencing of human genomes as a tool for personalized medicine, however, remain to be developed.
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Affiliation(s)
- Max Käller
- AlbaNova University Center, School of Biotechnology, Department of Gene Technology, Royal Institute of Technology, Roslagstullsbacken 21, SE-106 91 Stockholm, Sweden.
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Hadd AG, Brown JT, Andruss BF, Ye F, WalkerPeach CR. Adoption of array technologies into the clinical laboratory. Expert Rev Mol Diagn 2014; 5:409-20. [PMID: 15934817 DOI: 10.1586/14737159.5.3.409] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Array-based methods are making substantial contributions to the discovery of disease biomarkers and are fueling the growth of multianalyte testing for disease diagnosis and treatment. The distillation of high-density array results into sets of signature markers promises to improve disease staging, risk stratification and treatment decisions. To accommodate the growing requirement for multiplex testing, clinical laboratories are converting several single-analyte tests into array-based formats. However, adoption of array technologies provides several challenges to the laboratory, which must evaluate these new formats, train laboratory personnel, market the new services and obtain reimbursement for new analytes. Liquid-bead arrays are an attractive format for routine clinical diagnostics due to a combination of appropriate analyte density, simultaneous array decoding and detection, and flexibility for rapid customization. In this review, the suitability of several array platforms to diagnostic testing and applications of liquid-bead arrays for cystic fibrosis testing, multidisease carrier status assays and leukemia subtyping are discussed. As our understanding of the clinical utility of new or established biomarkers and recommendations for testing change, flexibility and adaptability of array platforms will be imperative. Future development of novel assay formats and improved quantitation will expand the number of diseases tested and lead to further integration into the diagnostic laboratory.
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Affiliation(s)
- Andrew G Hadd
- Ambion Diagnostics, 2130 Woodward Street, Austin, TX 78744, USA.
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Ahmed FE. Microarray RNA transcriptional profiling: Part I. Platforms, experimental design and standardization. Expert Rev Mol Diagn 2014; 6:535-50. [PMID: 16824028 DOI: 10.1586/14737159.6.4.535] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This review summarizes, in a balanced and comprehensive manner, the various components of microarrays and their types, substrate architecture, platforms for microarray probe implementation, standardizations and confounders. The review is intended to familiarize the beginner with the principles of experimental design and the selection of an appropriate microarray platform. This parallel technology has revolutionized transcriptomic approaches to data profiling and has a major role in the identification of expressed genes, classification and diagnosis studies. The technology is still evolving and guidelines for standardization and reporting have been developed and are being improved.
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Affiliation(s)
- Farid E Ahmed
- Leo W Jenkins Cancer Center, Department of Radiation Oncology, LSB 014, The Brody School of Medicine at East Carolina University, Greenville, NC 27858, USA.
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Klein R, Li X, Kuo JZ, Klein BEK, Cotch MF, Wong TY, Taylor KD, Rotter JI. Associations of candidate genes to age-related macular degeneration among racial/ethnic groups in the multi-ethnic study of atherosclerosis. Am J Ophthalmol 2013; 156:1010-1020.e1. [PMID: 23938121 DOI: 10.1016/j.ajo.2013.06.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 06/03/2013] [Accepted: 06/04/2013] [Indexed: 10/26/2022]
Abstract
PURPOSE To describe the relationships of selected candidate genes to the prevalence of early age-related macular degeneration (AMD) in a cohort of whites, blacks, Hispanics, and Chinese Americans. DESIGN Cross-sectional study. METHODS setting: Multicenter study. study population: A total of 2456 persons aged 45-84 years with genotype information and fundus photographs. procedures: Twelve of 2862 single nucleotide polymorphisms (SNPs) from 11 of 233 candidate genes for cardiovascular disease were selected for analysis based on screening with marginal unadjusted P value <.001 within 1 or more racial/ethnic groups. Logistic regression models tested for association in case-control samples. main outcome measure: Prevalence of early AMD. RESULTS Early AMD was present in 4.0% of the cohort and varied from 2.4% in blacks to 6.0% in whites. The odds ratio increased from 2.3 for 1 to 10.0 for 4 risk alleles in a joint effect analysis of Age-Related Maculopathy Susceptibility 2 rs10490924 and Complement Factor H Y402H (P for trend = 4.2×10(-7)). Frequencies of each SNP varied among the racial/ethnic groups. Adjusting for age and other factors, few statistically significant associations of the 12 SNPs with AMD were consistent across all groups. In a multivariate model, most candidate genes did not attenuate the comparatively higher odds of AMD in whites. The higher frequency of risk alleles for several SNPs in Chinese Americans may partially explain their AMD frequency's approaching that of whites. CONCLUSIONS The relationships of 11 candidate genes to early AMD varied among 4 racial/ethnic groups, and partially explained the observed variations in early AMD prevalence among them.
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Affiliation(s)
- Ronald Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin.
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Ostendorff HP, Awad A, Braunschweiger KI, Liu Z, Wan Z, Rothschild KJ, Lim MJ. Multiplexed VeraCode bead-based serological immunoassay for colorectal cancer. J Immunol Methods 2013; 400-401:58-69. [PMID: 24161315 DOI: 10.1016/j.jim.2013.09.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 09/13/2013] [Accepted: 09/17/2013] [Indexed: 02/06/2023]
Abstract
Colorectal cancer (CRC) is the second leading cause of cancer deaths in the US and Western world. Despite increased screening and advances in treatment, the mortality rate (ca. 50,000/year) and high national health-care burden for CRC are likely to remain high unless an effective non-invasive screening test for CRC is instituted for a large segment of the population. Blood-based protein biomarkers hold great promise for early disease diagnosis and personalized medicine; yet robust and reproducible multiplexing platforms and methodologies have lagged behind their genomic counterparts. Here, we report the development of a novel, multiplexed, hybrid immunoassay for CRC that is formatted on barcoded VeraCode™ micro-beads, which have until now only been used for genomic assays. The method combines a sandwich immunoassay format for detection of serum protein biomarkers with an antigen assay for autoantibody detection. The serum protein biomarkers CEA and GDF15 as well as autoantibodies to the p53 tumor associated antigen (TAA) were used to exemplify the method. This multiplex biomarker panel was configured to run on Illumina's holographically barcoded VeraCode™ micro-bead platform, which is capable of measuring hundreds of analytes simultaneously in a single well from small volumes of blood (<50 μL) using a 96-well industry standard microtiter plate. This novel use of the VeraCode™ micro-bead platform translates into a potentially low volume, high throughput, multiplexed assay for CRC, for the purposes of biomarker validation, as well as patient screening, diagnostics and prognostics. In an evaluation of a 186 patient sera training set (CRC and normal), we obtained a diagnostic sensitivity of 54% and a specificity of 98%. We anticipate that by expanding and refining the biomarkers in this initial panel, and performing more extensive clinical validations, such an assay could ultimately provide a basis for CRC population screening to complement the more invasive, expensive and low throughput (but highly sensitive and specific) colonoscopy.
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Shah SA, Herrington DM, Howard TD, Divers J, Arnett DK, Burke GL, Kao WH, Guo X, Siscovick DS, Chakravarti A, Lima JA, Psaty BM, Tomaselli GF, Rich SS, Bowden DW, Post W. Associations between NOS1AP single nucleotide polymorphisms (SNPs) and QT interval duration in four racial/ethnic groups in the Multi-Ethnic Study of Atherosclerosis (MESA). Ann Noninvasive Electrocardiol 2013; 18:29-40. [PMID: 23347024 DOI: 10.1111/anec.12028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
BACKGROUNDS QT is a risk factor for sudden cardiac death (SCD). A genome-wide association study identified NOS1AP variants associated with QT, which have been replicated in predominantly Caucasian (CAU) populations. We used the Multi-Ethnic Study of Atherosclerosis to examine association of QT with NOS1AP variants in an ethnically diverse cohort. METHODS Twenty-eight tagging SNPs spanning NOS1AP were genotyped in 2847 MESA participants (approximately equal numbers of CAU, African Americans (AFA), Hispanics (HIS), and Chinese (CHN)), age 45-84 years, without cardiovascular disease. QT was measured using 12-lead ECG. Associations between QT and NOS1AP variants were evaluated using linear regression, adjusted for heart rate, age, gender, and field center stratified by ancestry, using an additive inheritance model. Ancestry informative markers (AIMs) and principal components using AIMs were used as additional covariates. RESULTS More NOS1AP SNPs were associated with QT in CAU than the other races. In CAU, each copy of rs1932933 risk allele was associated with an increase in QT (4.9 msec, P = 7.20 × 10-7). Significant associations in CAU and HIS were located at the 5' end, while associations in CHN were located at the 3' end. CONCLUSIONS NOS1AP variants were associated with QT in CAU, with weaker evidence for selected variants in HIS and CHN. Location of significant SNPs varied across ancestry. We identified possible novel associations at the 3' end of NOS1AP, where we observed significant association with QT in CHN only. Genotyping within these regions may determine functional variants affecting QT and SCD risk. In addition, investigations are needed across ethnically diverse population cohorts.
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Affiliation(s)
- Sidharth A Shah
- Section on Cardiology, Wake Forest School of Medicine, Winston-Salem, NC, USA.
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Fuchs TC, Mally A, Wool A, Beiman M, Hewitt P. An Exploratory Evaluation of the Utility of Transcriptional and Urinary Kidney Injury Biomarkers for the Prediction of Aristolochic Acid–Induced Renal Injury in Male Rats. Vet Pathol 2013; 51:680-94. [DOI: 10.1177/0300985813498779] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The predictive value of different urinary and transcriptional biomarkers was evaluated in a proof-of-principle toxicology study in rats using aristolochic acid (AA), a known nephrotoxic agent. Male Wistar rats were orally dosed with 0.1, 1, or 10 mg/kg for 12 days. Urine was collected on days 1, 5, and 12 over 24 hours. Gene expression analysis was also conducted using quantitative real-time polymerase chain reaction and Illumina whole-genome chips. Protein biomarkers (Kim-1, Timp-1, vascular endothelial growth factor, osteopontin, clusterin, cystatin C, calbindin D-28K, β2-microglobulin, α–glutathione S-transferase, GSTY1b, RPA-1, and neutrophil gelatinase-associated lipocalin) were measured in these urine samples. Treatment with AA resulted in a slight dose- and/or time-dependent increase in urinary β2-microglobulin, lipocalin 2, and osteopontin before an increase in serum creatinine or serum urea nitrogen was observed. A strong decrease in urinary calbindin D-28K was also detected. The Compugen Ltd. prediction model scored both the 1- and 10-mg/kg AA dose groups as positive for nephrotoxicity despite the absence of renal histopathological changes. In addition, several previously described transcriptional biomarkers were identified as early predictors of renal toxicity as they were detected before morphological alterations had occurred. Altogether, these findings demonstrated the predictive values of renal biomarkers approved by the Food and Drug Administration, European Medicines Agency, and Pharmaceuticals & Medical Devices Agency in AA-induced renal injury in rats and confirmed the utility of renal transcriptional biomarkers for detecting progression of compound-induced renal injury in rats. In addition, several transcriptional biomarkers identified in this exploratory study could present early predictors of renal tubular epithelium injury in rats.
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Affiliation(s)
- T. C. Fuchs
- Merck Serono, Non-Clinical Safety, Darmstadt, Germany
| | - A. Mally
- Department of Toxicology, University of Wuerzburg, Wuerzburg, Germany
| | - A. Wool
- Compugen Ltd., Tel Aviv, Israel
| | | | - P. Hewitt
- Merck Serono, Non-Clinical Safety, Darmstadt, Germany
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Manesse M, Phillips AF, LaFratta CN, Palacios MA, Hayman RB, Walt DR. Dynamic microbead arrays for biosensing applications. LAB ON A CHIP 2013; 13:2153-2160. [PMID: 23615790 DOI: 10.1039/c3lc00044c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In this paper we present the development of an optical tweezers platform capable of creating on-demand dynamic microbead arrays for the multiplexed detection of biomolecules. We demonstrate the use of time-shared optical tweezers to dynamically assemble arrays of sensing microspheres, while simultaneously recording fluorescence signals in real time. The detection system is able to achieve multiplexing by using quantum dot nanocrystals as both signaling probes and encoding labels on the surface of the trapped microbeads. The encoding can be further extended by using a range of bead sizes. Finally, the platform is used to detect and identify three genes expressed by pathogenic strains of Escherichia coli O157:H7. The in situ actuation enabled by the optical tweezers, combined with multiplexed fluorescence detection offers a new tool, readily adaptable to biosensing applications in microfluidic devices, and could potentially enable the development of on-demand diagnostics platforms.
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Affiliation(s)
- Mael Manesse
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts, USA
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Zhou H, Steffenson BJ. Association mapping of Septoria speckled leaf blotch resistance in U.S. barley breeding germplasm. PHYTOPATHOLOGY 2013; 103:600-609. [PMID: 23342987 DOI: 10.1094/phyto-10-12-0271-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Septoria speckled leaf blotch (SSLB) is a sporadic but important disease of barley (Hordeum vulgare) in the Upper Midwest region of the United States and Prairie Provinces of Canada that is caused primarily by Septoria passerinii. Most of the widely grown cultivars in the region are susceptible to the disease. To identify and map SSLB resistance loci in U.S. barley breeding germplasm, we employed an association mapping approach using 3,840 breeding lines and cultivars and nearly 3,000 single-nucleotide polymorphism markers previously mapped to the seven barley chromosomes. SSLB infection responses (IRs) were assayed on seedling plants in the greenhouse using a 0-to-5 scale. From the analysis of four yearly panels consisting of 960 lines each, four quantitative trait loci (QTL) for SSLB resistance were identified: one on chromosome 1H (Rsp-qtl-H_12_31144), one on chromosome 3H (Rsp-qtl-3H_12_31488), and two on chromosome 6H (Rsp-qtl-6H_11_21032 and Rsp-qtl-6H_11_10064). Individual resistance QTL reduced the mean IR from 9 to 38% compared with lines lacking any resistance alleles. However, the combination of all four resistance QTL together reduced the mean IR by 83%. The markers found associated with these QTL will be valuable for programs utilizing marker-assisted selection for SSLB resistance.
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Affiliation(s)
- Hao Zhou
- Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, USA
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Bumgarner R. Overview of DNA microarrays: types, applications, and their future. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2013; Chapter 22:Unit 22.1.. [PMID: 23288464 DOI: 10.1002/0471142727.mb2201s101] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
This unit provides an overview of DNA microarrays. Microarrays are a technology in which thousands of nucleic acids are bound to a surface and are used to measure the relative concentration of nucleic acid sequences in a mixture via hybridization and subsequent detection of the hybridization events. This overview first discusses the history of microarrays and the antecedent technologies that led to their development. This is followed by discussion of the methods of manufacture of microarrays and the most common biological applications. The unit ends with a brief description of the limitations of microarrays and discusses how microarrays are being rapidly replaced by DNA sequencing technologies.
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Affiliation(s)
- Roger Bumgarner
- Department of Microbiology, University of Washington, Seattle, Washington, USA
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Evaluation of Different Normalization and Analysis Procedures for Illumina Gene Expression Microarray Data Involving Small Changes. MICROARRAYS 2013; 2:131-52. [PMID: 27605185 PMCID: PMC5003482 DOI: 10.3390/microarrays2020131] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 05/08/2013] [Accepted: 05/10/2013] [Indexed: 12/28/2022]
Abstract
While Illumina microarrays can be used successfully for detecting small gene expression changes due to their high degree of technical replicability, there is little information on how different normalization and differential expression analysis strategies affect outcomes. To evaluate this, we assessed concordance across gene lists generated by applying different combinations of normalization strategy and analytical approach to two Illumina datasets with modest expression changes. In addition to using traditional statistical approaches, we also tested an approach based on combinatorial optimization. We found that the choice of both normalization strategy and analytical approach considerably affected outcomes, in some cases leading to substantial differences in gene lists and subsequent pathway analysis results. Our findings suggest that important biological phenomena may be overlooked when there is a routine practice of using only one approach to investigate all microarray datasets. Analytical artefacts of this kind are likely to be especially relevant for datasets involving small fold changes, where inherent technical variation-if not adequately minimized by effective normalization-may overshadow true biological variation. This report provides some basic guidelines for optimizing outcomes when working with Illumina datasets involving small expression changes.
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