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Nakayama M, Yamamoto S, Hirabayashi H. Novel Cell Quantification Method Using a Single Surrogate Calibration Curve Across Various Biological Samples. AAPS J 2023; 25:26. [PMID: 36806998 DOI: 10.1208/s12248-023-00791-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/02/2023] [Indexed: 02/19/2023] Open
Abstract
Quantitative polymerase chain reaction (qPCR) is generally used to quantify transplanted cell therapy products in biological samples. As the matrix effects on PCR amplification and variability in DNA recovery from biological samples are well-known limitations that hinder the assay's performance, a calibration curve is conventionally established for each matrix. Droplet digital PCR (ddPCR) is based on the endpoint assay and advantageous in avoiding matrix effects. Moreover, the use of an external control gene may correct assay fluctuations to minimize the effects caused by inconsistent DNA recovery. In this study, we aimed to establish a novel and robust ddPCR method capable of quantifying human cells across various mouse biological samples using a single surrogate calibration curve in combination with an external control gene and DNA recovery normalization. Acceptable accuracy and precision were observed for quality control samples from different tissues, indicating the excellent quantitative and versatile potential of the developed method. Furthermore, the established method enabled the evaluation of human CD8+ T cell biodistribution in immunodeficient mice. Our findings provide new insights into the use of ddPCR-based quantification methods in biodistribution studies of cell therapy products.
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Affiliation(s)
- Miyu Nakayama
- Drug Metabolism and Pharmacokinetics Research Laboratories, Preclinical and Translational Sciences, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa, Japan.
| | - Syunsuke Yamamoto
- Drug Metabolism and Pharmacokinetics Research Laboratories, Preclinical and Translational Sciences, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa, Japan
| | - Hideki Hirabayashi
- Drug Metabolism and Pharmacokinetics Research Laboratories, Preclinical and Translational Sciences, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa, Japan
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2
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Stanley J, Hui H, Erber W, Clynick B, Fuller K. Analysis of human chromosomes by imaging flow cytometry. CYTOMETRY PART B-CLINICAL CYTOMETRY 2021; 100:541-553. [PMID: 34033226 DOI: 10.1002/cyto.b.22023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/18/2021] [Accepted: 05/14/2021] [Indexed: 12/29/2022]
Abstract
Chromosomal analysis is traditionally performed by karyotyping on metaphase spreads, or by fluorescent in situ hybridization (FISH) on interphase cells or metaphase spreads. Flow cytometry was introduced as a new method to analyze chromosomes number (ploidy) and structure (telomere length) in the 1970s with data interpretation largely based on fluorescence intensity. This technology has had little uptake for human cytogenetic applications primarily due to analytical challenges. The introduction of imaging flow cytometry, with the addition of digital images to standard multi-parametric flow cytometry quantitative tools, has added a new dimension. The ability to visualize the chromosomes and FISH signals overcomes the inherent difficulties when the data is restricted to fluorescence intensity. This field is now moving forward with methods being developed to assess chromosome number and structure in whole cells (normal and malignant) in suspension. A recent advance has been the inclusion of immunophenotyping such that antigen expression can be used to identify specific cells of interest for specific chromosomes and their abnormalities. This capability has been illustrated in blood cancers, such as chronic lymphocytic leukemia and plasma cell myeloma. The high sensitivity and specificity achievable highlights the potential imaging flow cytometry has for cytogenomic applications (i.e., diagnosis and disease monitoring). This review introduces and describes the development, current status, and applications of imaging flow cytometry for chromosomal analysis of human chromosomes.
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Affiliation(s)
- Jason Stanley
- Translational Cancer Pathology Laboratory, School of Biomedical Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Henry Hui
- Translational Cancer Pathology Laboratory, School of Biomedical Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Wendy Erber
- Translational Cancer Pathology Laboratory, School of Biomedical Sciences, The University of Western Australia, Crawley, Western Australia, Australia.,PathWest Laboratory Medicine, Nedlands, Western Australia, Australia
| | - Britt Clynick
- Institute for Respiratory Health, Harry Perkins Institute of Medical Research, Nedlands, Western Australia, Australia
| | - Kathy Fuller
- Translational Cancer Pathology Laboratory, School of Biomedical Sciences, The University of Western Australia, Crawley, Western Australia, Australia
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3
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Lindrose AR, McLester-Davis LWY, Tristano RI, Kataria L, Gadalla SM, Eisenberg DTA, Verhulst S, Drury S. Method comparison studies of telomere length measurement using qPCR approaches: A critical appraisal of the literature. PLoS One 2021; 16:e0245582. [PMID: 33471860 PMCID: PMC7817045 DOI: 10.1371/journal.pone.0245582] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/05/2021] [Indexed: 12/16/2022] Open
Abstract
Use of telomere length (TL) as a biomarker for various environmental exposures and diseases has increased in recent years. Various methods have been developed to measure telomere length. Polymerase chain reaction (PCR)-based methods remain wide-spread for population-based studies due to the high-throughput capability. While several studies have evaluated the repeatability and reproducibility of different TL measurement methods, the results have been variable. We conducted a literature review of TL measurement cross-method comparison studies that included a PCR-based method published between January 1, 2002 and May 25, 2020. A total of 25 articles were found that matched the inclusion criteria. Papers were reviewed for quality of methodologic reporting of sample and DNA quality, PCR assay characteristics, sample blinding, and analytic approaches to determine final TL. Overall, methodologic reporting was low as assessed by two different reporting guidelines for qPCR-based TL measurement. There was a wide range in the reported correlation between methods (as assessed by Pearson’s r) and few studies utilized the recommended intra-class correlation coefficient (ICC) for assessment of assay repeatability and methodologic comparisons. The sample size for nearly all studies was less than 100, raising concerns about statistical power. Overall, this review found that the current literature on the relation between TL measurement methods is lacking in validity and scientific rigor. In light of these findings, we present reporting guidelines for PCR-based TL measurement methods and results of analyses of the effect of assay repeatability (ICC) on statistical power of cross-sectional and longitudinal studies. Additional cross-laboratory studies with rigorous methodologic and statistical reporting, adequate sample size, and blinding are essential to accurately determine assay repeatability and replicability as well as the relation between TL measurement methods.
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Affiliation(s)
- Alyssa R. Lindrose
- Department of Psychiatry and Behavioral Sciences, School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
- * E-mail: (ARL); (SD)
| | | | - Renee I. Tristano
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Leila Kataria
- School of Science and Engineering, Tulane University, New Orleans, Louisiana, United States of America
| | - Shahinaz M. Gadalla
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Dan T. A. Eisenberg
- Department of Anthropology, Department of Biology, Center for Studies in Demography and Ecology, University of Washington, Seattle, Washington, United States of America
| | - Simon Verhulst
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Stacy Drury
- Department of Psychiatry and Behavioral Sciences, School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
- Tulane Brain Institute, Tulane University, New Orleans, Louisiana, United States of America
- Department of Pediatrics, School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
- * E-mail: (ARL); (SD)
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4
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Contrasting seasonal patterns of telomere dynamics in response to environmental conditions in the ectothermic sand lizard, Lacerta agilis. Sci Rep 2020; 10:182. [PMID: 31932620 PMCID: PMC6957525 DOI: 10.1038/s41598-019-57084-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/17/2019] [Indexed: 01/27/2023] Open
Abstract
Telomeres, the protective, terminal parts of the chromosomes erode during cell division and as a result of oxidative damage by reactive oxygen species (ROS). Ectotherms rely on the ambient temperature for maintaining temperature-dependent metabolic rate, regulated through behavioural thermoregulation. Their temperature-dependant metabolism, hence also the ROS production, is indirectly regulated through thermoregulation. Consequently, a potential causal chain affecting telomere length and attrition is: temperature (in particular, its deviation from a species-specific optimum) – metabolism - ROS production – anti-oxidation - telomere erosion. We measured telomere length in sand lizards (Lacerta agilis) using qPCR on blood samples from 1998–2006. Effects of climatological parameters (mean temperature and average sunshine hours) in the summer and winter preceding telomere sampling were used as predictors of telomere length in mixed model analysis. During the lizards’ active period (summer), there was a largely negative effect of mean temperature and sun on telomere length, whereas a combined measure of age and size (head length) was positively related to telomere length. During the inactive period of lizards (winter), the results were largely the opposite with a positive relationship between temperature and sunshine hours and telomere length. In all four cases, thermal and age effects on telomere length appeared to be non-linear in the two sexes and seasons, with complex response surface effects on telomere length from combined age and thermal effects.
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Cell cycle-dependent and -independent telomere shortening accompanies murine brain aging. Aging (Albany NY) 2019; 10:3397-3420. [PMID: 30472697 PMCID: PMC6286833 DOI: 10.18632/aging.101655] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 11/15/2018] [Indexed: 12/16/2022]
Abstract
Replication-based telomere shortening during lifetime is species- and tissue-specific, however, its impact on healthy aging is unclear. In particular, the contribution of telomere truncation to the aging process of the CNS, where replicative senescence alone fails to explain organ aging due to low to absent mitotic activity of intrinsic populations, is undefined. Here, we assessed changes in relative telomere length in non-replicative and replicative neural brain populations and telomerase activity as a function of aging in C57BL/6 mice. Telomeres in neural cells and sub-selected neurons shortened with aging in a cell cycle-dependent and -independent manner, with preponderance in replicative moieties, implying that proliferation accelerates, but is not prerequisite for telomere shortening. Consistent with this telomere erosion, telomerase activity and nuclear TERT protein were not induced with aging. Knockdown of the Rela subunit of NF-κB, which controls both telomerase enzyme and subcellular TERT protein allocation, did also not influence telomerase activity or telomere length, in spite of its naive up-regulation selectively under aging conditions. We conclude that telomere instability is intrinsic to physiological brain aging beyond cell replication, and appears to occur independently of a functional interplay with NF-κB, but rather as a failure to induce or relocate telomerase.
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Ferreira MSV, Kirschner M, Halfmeyer I, Estrada N, Xicoy B, Isfort S, Vieri M, Zamora L, Abels A, Bouillon AS, Begemann M, Schemionek M, Maurer A, Koschmieder S, Wilop S, Panse J, Brümmendorf TH, Beier F. Comparison of flow-FISH and MM-qPCR telomere length assessment techniques for the screening of telomeropathies. Ann N Y Acad Sci 2019; 1466:93-103. [PMID: 31647584 DOI: 10.1111/nyas.14248] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 08/27/2019] [Accepted: 09/12/2019] [Indexed: 12/16/2022]
Abstract
Assessment of telomere length (TL) in peripheral blood leukocytes is part of the diagnostic algorithm applied to patients with acquired bone marrow failure syndromes (BMFSs) and dyskeratosis congenita (DKC). Monochrome multiplex-quantitative polymerase chain reaction (MM-qPCR) and fluorescence in situ hybridization (flow-FISH) are methodologies available for TL screening. Dependent on TL expressed in relation to percentiles of healthy controls, further genetic testing for inherited mutations in telomere maintenance genes is recommended. However, the correct threshold to trigger this genetic workup is still under debate. Here, we prospectively compared MM-qPCR and flow-FISH regarding their capacity for accurate identification of DKC patients. All patients (n = 105) underwent genetic testing by next-generation sequencing and in 16 patients, mutations in DKC-relevant genes were identified. Whole leukocyte TL of patients measured by MM-qPCR was found to be moderately correlated with lymphocyte TL measured by flow-FISH (r² = 0.34; P < 0.0001). The sensitivity of both methods was high, but the specificity of MM-qPCR (29%) was significantly lower compared with flow-FISH (58%). These results suggest that MM-qPCR of peripheral blood cells is inferior to flow-FISH for clinical routine screening for suspected DKC in adult patients with BMFS due to lower specificity and a higher rate of false-positive results.
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Affiliation(s)
- Monica S Ventura Ferreira
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, University Hospital Aachen, Aachen, Germany
| | - Martin Kirschner
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, University Hospital Aachen, Aachen, Germany
| | - Insa Halfmeyer
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, University Hospital Aachen, Aachen, Germany
| | - Natalia Estrada
- Hematology Service, Institut Català d'Oncologia (ICO)-Hospital Germans Trias i Pujol, Institut de Recerca Contra la Leucèmia Josep Carreras, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Blanca Xicoy
- Hematology Service, Institut Català d'Oncologia (ICO)-Hospital Germans Trias i Pujol, Institut de Recerca Contra la Leucèmia Josep Carreras, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Susanne Isfort
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, University Hospital Aachen, Aachen, Germany
| | - Margherita Vieri
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, University Hospital Aachen, Aachen, Germany
| | - Lurdes Zamora
- Hematology Service, Institut Català d'Oncologia (ICO)-Hospital Germans Trias i Pujol, Institut de Recerca Contra la Leucèmia Josep Carreras, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Anne Abels
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, University Hospital Aachen, Aachen, Germany
| | - Anne-Sophie Bouillon
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, University Hospital Aachen, Aachen, Germany
| | - Matthias Begemann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Mirle Schemionek
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, University Hospital Aachen, Aachen, Germany
| | - Angela Maurer
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, University Hospital Aachen, Aachen, Germany
| | - Steffen Koschmieder
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, University Hospital Aachen, Aachen, Germany
| | - Stefan Wilop
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, University Hospital Aachen, Aachen, Germany
| | - Jens Panse
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, University Hospital Aachen, Aachen, Germany
| | - Tim H Brümmendorf
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, University Hospital Aachen, Aachen, Germany
| | - Fabian Beier
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, University Hospital Aachen, Aachen, Germany
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Vasilishina A, Kropotov A, Spivak I, Bernadotte A. Relative Human Telomere Length Quantification by Real-Time PCR. Methods Mol Biol 2019; 1896:39-44. [PMID: 30474838 DOI: 10.1007/978-1-4939-8931-7_5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Telomere measurement by quantitative PCR amplification is a well-known simple method to detect telomere length that involves large numbers of samples. The method has been developed by Cawthon in 2002 (Cawthon, Nucleic Acids Res 30:47e-47, 2002) and remains the most frequently used technique either in original or modified version. Telomere length is estimated by comparing the amount of telomere repeat amplification product (T) to a single copy gene (S) product. The T/S ratio correlates with the average telomere length. Cawthon suggested and recommended the use of 36B4 (RPLP0) as a single copy gene. However, Cawthon's suggestion was no longer considered a single copy gene and the gene was not suitable and appropriate for normalization.We thereby introduced a simple method for relative measurement of average human telomere length using quantitative real-time PCR. Our protocol was based on Cawthon's initial technique (Cawthon, Nucleic Acids Res 30:47e-47, 2002), modified by single-copy gene (SCG) primers and optimized.This technique is rapid, low cost, not demanding on DNA amount (or live cells), and can be used for a high-throughput screening and time monitoring.
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Affiliation(s)
- A Vasilishina
- Institute of Cytology, Russian Academy of Sciences, Saint-Petersburg, Russian Federation
| | - A Kropotov
- Institute of Cytology, Russian Academy of Sciences, Saint-Petersburg, Russian Federation
| | - I Spivak
- Institute of Cytology, Russian Academy of Sciences, Saint-Petersburg, Russian Federation
| | - A Bernadotte
- Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russian Federation. .,Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Laboratory of Simple Systems, Moscow, Russian Federation.
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Teubel I, Elchinova E, Roura S, Fernández MA, Gálvez-Montón C, Moliner P, de Antonio M, Lupón J, Bayés-Genís A. Telomere attrition in heart failure: a flow-FISH longitudinal analysis of circulating monocytes. J Transl Med 2018; 16:35. [PMID: 29463269 PMCID: PMC5819711 DOI: 10.1186/s12967-018-1412-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 02/15/2018] [Indexed: 11/11/2022] Open
Abstract
Background Cross-sectional investigations report shorter telomeres in patients with heart failure (HF); however, no studies describe telomere length (TL) trajectory and its relationship with HF progression. Here we aimed to investigate telomere shortening over time and its relationship to outcomes. Methods Our study cohort included 101 ambulatory patients with HF. Blood samples were collected at baseline (n = 101) and at the 1-year follow-up (n = 54). Using flow-FISH analysis of circulating monocytes, we simultaneously measured three monocyte subsets—classical (CD14++CD16−), intermediate (CD14++CD16+), and nonclassical (CD14+CD16++)—and their respective TLs based on FITC-labeled PNA probe hybridization. The primary endpoints were all-cause death and the composite of all-cause death or HF-related hospitalization, assessed at 2.3 ± 0.6 years. All statistical analyses were executed by using the SPSS 15.0 software, and included Student’s t test and ANOVA with post hoc Scheffe analysis, Pearson or Spearman rho correlation and univariate Cox regression when applicable. Results We found high correlations between TL values of different monocyte subsets: CD14++CD16+ vs. CD14++CD16−, R = 0.95, p < 0.001; CD14++CD16+ vs. CD14+CD16++, R = 0.90, p < 0.001; and CD14++CD16− vs. CD14+CD16++, R = 0.89, p < 0.001. Mean monocyte TL exhibited significant attrition from baseline to the 1-year follow-up (11.1 ± 3.3 vs. 8.3 ± 2.1, p < 0.001). TL did not significantly differ between monocyte subsets at either sampling time-point (all p values > 0.1). Cox regression analyses did not indicate that TL or ΔTL was associated with all-cause death or the composite endpoint. Conclusions Overall, this longitudinal study demonstrated a ~ 22% reduction of TL in monocytes from ambulatory patients with HF within 1 year. TL and ΔTL were not related to outcomes over long-term follow-up. Electronic supplementary material The online version of this article (10.1186/s12967-018-1412-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Iris Teubel
- Flow Cytometry Facility, Germans Trias i Pujol Health Science Research Institute, Badalona, Spain
| | - Elena Elchinova
- Cardiology Service, Germans Trias i Pujol University Hospital, Carretera del Canyet s/n, 08916, Badalona, Spain.,Department of Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Santiago Roura
- ICREC Research Program, Germans Trias i Pujol Health Science Research Institute, Badalona, Spain.,Center of Regenerative Medicinein Barcelona, Barcelona, Spain.,CIBERCV, Instituto de Salud Carlos III, Madrid, Spain
| | - Marco A Fernández
- Flow Cytometry Facility, Germans Trias i Pujol Health Science Research Institute, Badalona, Spain
| | - Carolina Gálvez-Montón
- ICREC Research Program, Germans Trias i Pujol Health Science Research Institute, Badalona, Spain.,CIBERCV, Instituto de Salud Carlos III, Madrid, Spain
| | - Pedro Moliner
- Cardiology Service, Germans Trias i Pujol University Hospital, Carretera del Canyet s/n, 08916, Badalona, Spain
| | - Marta de Antonio
- Cardiology Service, Germans Trias i Pujol University Hospital, Carretera del Canyet s/n, 08916, Badalona, Spain.,CIBERCV, Instituto de Salud Carlos III, Madrid, Spain
| | - Josep Lupón
- Cardiology Service, Germans Trias i Pujol University Hospital, Carretera del Canyet s/n, 08916, Badalona, Spain.,Department of Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain.,CIBERCV, Instituto de Salud Carlos III, Madrid, Spain
| | - Antoni Bayés-Genís
- Cardiology Service, Germans Trias i Pujol University Hospital, Carretera del Canyet s/n, 08916, Badalona, Spain. .,Department of Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain. .,CIBERCV, Instituto de Salud Carlos III, Madrid, Spain.
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Lai C, Stepniak D, Sias L, Funatake C. A sensitive flow cytometric method for multi-parametric analysis of microRNA, messenger RNA and protein in single cells. Methods 2017; 134-135:136-148. [PMID: 29277634 DOI: 10.1016/j.ymeth.2017.12.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 11/17/2017] [Accepted: 12/15/2017] [Indexed: 12/31/2022] Open
Abstract
Analysis of RNA expression in mixed cell populations often requires laborious and costly cell sorting. Here we describe a flow cytometric assay that combines antibody staining and in situ hybridization for multi-parametric analysis of single cells. This method, referred to as the PrimeFlow™ RNA Assay, enables simultaneous detection of protein markers and RNA targets in mixed cell populations. Both coding and non-coding RNA sequences can be measured with a limit of detection of approximately 10 copies of mRNA and 20 copies of microRNA per cell. In this study, we used mouse bone marrow-derived macrophages to demonstrate that our method allows for analysis of the activation and polarization status of cells using expression patterns of protein and RNA. We then performed analysis of four cell subsets of mouse resident peritoneal cells and showed that the two macrophage populations present in this compartment are relatively heterogeneous in terms of expression of two M2 markers: Arg1, Retnla, and a B-cell attractant chemokine Cxcl13. In addition, we profiled the expression of a panel of microRNA in the four peritoneal cell subsets, showing that the assay can be readily adapted to parallel, high-throughput screening of multiple cell populations. This new method allows for single cell analysis of multiple RNA targets without the need for cell sorting, enables direct correlation between RNA and protein expression, and promises to accelerate biomarker and drug discovery.
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Affiliation(s)
- Chunfai Lai
- Thermo Fisher Scientific, 3380 Central Expressway, Santa Clara, CA 95051, United States.
| | - Dariusz Stepniak
- Thermo Fisher Scientific, 5781 Van Allen Way, Carlsbad, CA 92008, United States
| | - Leslie Sias
- Thermo Fisher Scientific, 3380 Central Expressway, Santa Clara, CA 95051, United States
| | - Castle Funatake
- Thermo Fisher Scientific, 5781 Van Allen Way, Carlsbad, CA 92008, United States
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