Simultaneous, single-cell measurement of messenger RNA, cell surface proteins, and intracellular proteins

Current Protocols in Cytometry

Volumn 2016, Issue , 2016, Pages 7.45.1-7.45.33

  Soh, Kah Teong ^a   Tario, Joseph D ^a   Colligan, Sean ^a   Maguire, Orla ^a   Pan, Dalin ^a   Minderman, Hans ^a   Wallace, Paul K ^a  

^a ROSWELL PARK CANCER INSTITUTE   (United States)

Author keywords

Branched DNA; Flow cytometry; In situ hybridization; Leukocytes; mRNA sequence; Target probe; Transcription factors

Indexed keywords

CELL PROTEIN; CELL SURFACE PROTEIN; FLUORESCENT DYE; MESSENGER RNA; DNA; LEUKOCYTE ANTIGEN; MEMBRANE PROTEIN;

ARTICLE; BRANCHED DNA SIGNAL AMPLIFICATION ASSAY; CONTROLLED STUDY; FLOW CYTOMETRY; HUMAN; HUMAN CELL; HUMAN TISSUE; HYBRIDIZATION; IMMUNOPHENOTYPING; IN SITU HYBRIDIZATION; NUCLEIC ACID AMPLIFICATION; NUCLEIC ACID ANALYSIS; NUCLEOTIDE SEQUENCE; PERIPHERAL BLOOD MONONUCLEAR CELL; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; RNA ANALYSIS; SIGNAL PROCESSING; SINGLE CELL ANALYSIS; APOPTOSIS; BIOLOGY; CD8+ T LYMPHOCYTE; CELL CYCLE; CELL MEMBRANE; CYTOLOGY; METABOLISM; MONONUCLEAR CELL; NUCLEIC ACID HYBRIDIZATION; PHOSPHORYLATION; PROCEDURES; TEMPERATURE;

ANTIGENS, CD; APOPTOSIS; CD8-POSITIVE T-LYMPHOCYTES; CELL CYCLE; CELL MEMBRANE; COMPUTATIONAL BIOLOGY; DNA; FLOW CYTOMETRY; HUMANS; IMMUNOPHENOTYPING; IN SITU HYBRIDIZATION; LEUKOCYTES, MONONUCLEAR; MEMBRANE PROTEINS; NUCLEIC ACID HYBRIDIZATION; PHOSPHORYLATION; POLYMERASE CHAIN REACTION; RNA, MESSENGER; TEMPERATURE;

EID: 85007546898     PISSN: 19349297     EISSN: 19349300     Source Type: Journal    
DOI: 10.1002/0471142956.cy0745s75     Document Type: Article

References (67)

1. Arroz, M., Came, N., Lin, P., Chen, W., Yuan, C., Lagoo, A., Monreal, M., de Tute, R., Vergilio, J.A., Rawstron, A.C., and Paiva, B. 2015. Consensus guidelines on plasma cell myeloma minimal residual disease analysis and reporting. Cytometry B Clin. Cytom. doi: 10.1002/cyto.b.21228. [Epub ahead of print].
2. Bauman, J.G. and Bentvelzen, P. 1988. Flow cytometric detection of ribosomal RNA in suspended cells by fluorescent in situ hybridization. Cytometry 9: 517-524. doi: 10.1002/cyto. 990090602.
3. Bayer, J.A. and Bauman, J.G. 1990. Flow cytometric detection of beta-globin mRNA in murine haemopoietic tissues using fluorescent in situ hybridization. Cytometry 11: 132-143. doi: 10.1002/cyto.990110116.
4. Bishop, J.A., Ma, X.J., Wang, H., Luo, Y., Illei, P.B., Begum, S., Taube, J.M., Koch, W.M., and Westra, W.H. 2012. Detection of transcriptionally active high-risk HPV in patients with head and neck squamous cell carcinoma as visualized by a novel E6/E7 mRNA in situ hybridization method. Am. J. Surg. Pathol. 36: 1874-1882. doi: 10.1097/PAS.0b013e318265fb2b.
5. Borzi, R.M., Piacentini, A., Monaco, M.C., Lisignoli, G., Degrassi, A., Cattini, L., Santi, S., and Facchini, A. 1996. A fluorescent in situ hybridization method in flow cytometry to detect HIV-1 specific RNA. J. Immunol. Methods 193: 167-176. doi: 10.1016/0022-1759(96)00070-1.
6. Boyum, A. 1968. Isolation of leucocytes from human blood. Further observations. Methylcellulose, dextran, and ficoll as erythrocyte aggregating agents. Scand J. Clin. Lab. Invest. Suppl. 97: 31-50.
7. Buckingham, L. and Flaws, M.L. 2007. Molecular Diagnostics: Fundamentals, Methods, and Clinical Applications. F.A. Davis, Philadelphia, Pa.
8. Buggert, M., Tauriainen, J., Yamamoto, T., Frederiksen, J., Ivarsson, M.A., Michaelsson, J., Lund, O., Hejdeman, B., Jansson, M., Sonnerborg, A., Koup, R.A., Betts, M.R., and Karlsson, A.C. 2014. T-bet and Eomes are differentially linked to the exhausted phenotype of CD8+ T cells in HIV infection. PLoS Pathog. 10: e1004251. doi: 10.1371/journal. ppat.1004251.
9. Castle, D.C. 1998. Overview of cell fractionation. Curr. Protoc. Cell Biol. 69: 3.1.1-3.1.9.
10. Chen, R.H. and Fuggle, S.V. 1993. In situ cDNA polymerase chain reaction. A novel technique for detecting mRNA expression. Am. J. Pathol. 143: 1527-1534.
11. Collins, M.L., Irvine, B., Tyner, D., Fine, E., Zayati, C., Chang, C., Horn, T., Ahle, D., Detmer, J., Shen, L.P., Kolberg, J., Bushnell, S., Urdea, M.S., and Ho, D.D. 1997. A branched DNA signal amplification assay for quantification of nucleic acid targets below 100 molecules/ml. Nucleic Acids Res. 25: 2979-2984. doi: 10.1093/nar/25.15.2979.
12. Cox, J. and Mann, M. 2007. Is proteomics the new genomics? Cell 130: 395-398. doi: 10.1016/j.cell.2007.07.032.
13. Fuss, I.J., Kanof, M.E., Smith, P.D., and Zola, H. 2009. Isolation ofwhole mononuclear cells from peripheral blood and cord blood. Curr. Protoc. Immunol. 85: 7.1.1-7.1.8.
14. Gall, J.G. and Pardue, M.L. 1969. Formation and detection of RNA-DNA hybrid molecules in cytological preparations. Proc. Natl. Acad. Sci. U.S.A. 63: 378-383. doi: 10.1073/pnas.63.2.378.
15. Garcia-Morales, R., Carreno, M., Mathew, J., Zucker, K., Cirocco, R., Ciancio, G., Burke, G., Roth, D., Temple, D., Rosen, A., Fuller, L., Esquenazi, V., Karatzas, T., Ricordi, C., Tzakis, A., and Miller, J. 1997. The effects of chimeric cells following donor bone marrow infusions as detected by PCR-flow assays in kidney transplant recipients. J. Clin. Invest. 99: 1118-1129. doi: 10.1172/JCI119240.
16. Gibbings, D.J., Marcet-Palacios, M., Sekar, Y., Ng, M.C., and Befus, A.D. 2007. CD8 alpha is expressed by human monocytes and enhances Fc gamma R-dependent responses. BMC immunol.8: 12. doi: 10.1186/1471-2172-8-12.
17. Gibellini, D.E., Re, M.C., Furlini, G., and La Placa, M. 1997. Flow cytometry analysis of an in situ PCR for the detection of human immunodeficiency virus type-1 (HIV-1) proviral DNA. Methods Mol. Biol. 71: 113-122.
18. Goolsby, C.L., Thompson, E., and Mosiman, V. 2000. Combined immunophenotyping and molecular immunophenotyping. In Immunophenotyping (C.C. Stewart and J.K.A. Nicholson, eds.) pp. 407-427. Wiley-Liss, New York.
19. Hanley, M.B., Lomas, W., Mittar, D., Maino, V., and Park, E. 2013. Detection of low abundance RNA molecules in individual cells by flow cytometry. PLoS One 8: e57002. doi: 10.1371/journal. pone.0057002.
20. Harper, M.E., Marselle, L.M., Gallo, R.C., and Wong-Staal, F. 1986. Detection of lymphocytes expressing human T-lymphotropic virus type III in lymph nodes and peripheral blood from infected individuals by in situ hybridization. Proc. Natl. Acad. Sci. U.S.A. 83: 772-776. doi: 10.1073/pnas.83.3.772.
21. Holtke, H.J. and Kessler, C. 1990. Non-radioactive labeling of RNA transcripts in vitro with the hapten digoxigenin (DIG); hybridization and ELISA-based detection. Nucleic Acids Res. 18: 5843-5851. doi: 10.1093/nar/18.19.5843.
22. Intlekofer, A.M., Banerjee, A., Takemoto, N., Gordon, S.M., Dejong, C.S., Shin, H., Hunter, C.A., Wherry, E.J., Lindsten, T., and Reiner, S.L. 2008. Anomalous type 17 response to viral infection by CD8+ T cells lacking T-bet and eomesodermin. Science 321: 408-411. doi: 10.1126/science.1159806.
23. Kapke, G.E., Watson, G., Sheffler, S., Hunt, D., and Frederick, C. 1997. Comparison of the chiron quantiplex branched DNA (bDNA) assay and the Abbott Genostics solution hybridization assay for quantification of hepatitis B viral DNA. J. Viral. Hepat. 4: 67-75. doi: 10.1046/j.1365-2893.1997.00127.x.
24. Klemm, S., Semrau, S., Wiebrands, K., Mooijman, D., Faddah, D.A., Jaenisch, R., and van Oudenaarden, A. 2014. Transcriptional profiling of cells sorted by RNA abundance. Nat. Methods 11: 549-551. doi: 10.1038/nmeth.2910.
25. Knox, J.J., Cosma, G.L., Betts, M.R., and McLane, L.M. 2014. Characterization of T-bet and eomes in peripheral human immune cells. Front Immunol. 5: 217. doi: 10.3389/fimmu.2014.00217.
26. Koopman, P. 2001. In situ hybridization to mRNA: From black art to guiding light. Int. J. Dev. Biol. 45: 619-622.
27. Levsky, J.M. and Singer, R.H. 2003. Fluorescence in situ hybridization: Past, present and future. J Cell Sci 116: 2833-2838. doi: 10.1242/jcs.00633.
28. Li, B.D., Timm, E.A., Jr., Riedy, M.C., Harlow, S.P., and Stewart, C.C. 1994. Molecular phenotyping by flow cytometry. Methods Cell Biol. 42(Pt B): 95-130. doi: 10.1016/ S0091-679X(08)61070-5.
29. Liang, Y.J., Lao, X.M., Liang, L.Z., and Liao, G.Q. 2015. Genome-wide analysis of cancer cellderived Foxp3 target genes in human tongue squamous cell carcinoma cells. Int. J. Oncol. 46: 1935-1943.
30. McLane, L.M., Banerjee, P.P., Cosma, G.L., Makedonas, G.,Wherry, E.J., Orange, J.S., and Betts, M.R. 2013. Differential localization of T-bet and Eomes in CD8 T cell memory populations. J. Immunol. 190: 3207-3215. doi: 10.4049/ jimmunol.1201556.
31. Minderman, H., Humphrey, K., Arcadi, J.K., Wierzbicki, A., Maguire, O.,Wang, E.S., Block, A.W., Sait, S.N., George, T.C., andWallace, P.K. 2012. Image cytometry-based detection of aneuploidy by fluorescence in situ hybridization in suspension. Cytometry A 81: 776-784. doi: 10.1002/cyto.a.22101. Epub 2012 Jul 26.
32. Mutty, C.E., Timm, E.A., Jr., and Stewart, C.C. 1999. Effects of thermal exposure on immunophenotyping combined with in situ PCR, measured by flow cytometry. Cytometry 36: 303-311. doi: 10.1002/(SICI)1097-0320(19990801) 36: 4%3c303:: AID-CYTO4%3e3.0.CO;2-.
33. Neale, G.A., Coustan-Smith, E., Stow, P., Pan, Q., Chen, X., Pui, C.H., and Campana, D. 2004. Comparative analysis of flow cytometry and polymerase chain reaction for the detection of minimal residual disease in childhood acute lymphoblastic leukemia. Leukemia 18: 934-938. doi: 10.1038/sj.leu.2403348.
34. Patterson, B.K., Goolsby, C., Hodara, V., Lohman, K.L., and Wolinsky, S.M. 1995. Detection of CD4+ T cells harboring human immunodeficiency virus type 1 DNA by flow cytometry using simultaneous immunophenotyping and PCR-driven in situ hybridization: Evidence of epitope masking of the CD4 cell surface molecule in vivo. J. Virol. 69: 4316-4322.
35. Patterson, B.K.,Mosiman, V.L., Cantarero, L., Furtado, M., Bhattacharya, M., and Goolsby, C. 1998. Detection of HIV-RNA-positive monocytes in peripheral blood of HIV-positive patients by simultaneous flow cytometric analysis of intracellular HIV RNA and cellular immunophenotype. Cytometry 31: 265-274. doi: 10.1002/(SICI)1097-0320(19980401)31: 4%3c265:: AID-CYTO6%3e3.0.CO;2-I.
36. Patterson, B.K., Till, M., Otto, P., Goolsby, C., Furtado, M.R., McBride, L.J., and Wolinsky, S.M. 1993. Detection of HIV-1 DNA and messenger RNA in individual cells by PCRdriven in situ hybridization and flow cytometry. Science 260: 976-979. doi: 10.1126/science .8493534.
37. Phelan, M.C. and Lawler, G. 1997. Cell counting. Curr. Protoc. Cytom. 00: A.3A.1-A.3A.4.
38. Player,A.N., Shen, L.P.,Kenny, D.,Antao,V.P., and Kolberg, J.A. 2001. Single-copy gene detection using branched DNA (bDNA) in situ hybridization. J. Histochem. Cytochem. 49: 603-612. doi: 10.1177/002215540104900507.
39. Porichis, F., Hart, M.G., Griesbeck, M., Everett, H.L., Hassan, M., Baxter, A.E., Lindqvist, M., Miller, S.M., Soghoian, D.Z., Kavanagh, D.G., Reynolds, S., Norris, B., Mordecai, S.K., Nguyen, Q., Lai, C., and Kaufmann, D.E. 2014. High-throughput detection of miRNAs and gene-specific mRNA at the single-cell level by flow cytometry. Nat. Commun. 5: 5641. doi: 10.1038/ncomms6641.
40. Roederer, M. 2001. Spectral compensation for flow cytometry: Visualization artifacts, limitations, and caveats. Cytometry 45: 194-205. doi: 10.1002/1097-0320(20011101)45: 3%3c194:: AID-CYTO1163%3e3.0.CO;2-C.
41. Rondeau, S., Vacher, S., De Koning, L., Briaux, A., Schnitzler, A., Chemlali, W., Callens, C., Lidereau, R., and Bieche, I. 2015. ATM has a major role in the double-strand break repair pathway dysregulation in sporadic breast carcinomas and is an independent prognostic marker at both mRNA and protein levels. Br. J. Cancer 112: 1059-1066. doi: 10.1038/bjc.2015.60.
42. Tario, J.D., Jr., Muirhead, K.A., Pan, D., Munson, M.E., andWallace, P.K. 2011. Tracking immune cell proliferation and cytotoxic potential using flow cytometry. Methods Mol. Biol. 699: 119-164. doi: 10.1007/978-1-61737-950-5_7.
43. Trask, B., van den Engh, G., Landegent, J., in de Wal, N.J., and van der Ploeg, M. 1985. Detection of DNA sequences in nuclei in suspension by in situ hybridization and dual beam flow cytometry. Science 230: 1401-1403. doi: 10.1126/science. 2416058.
44. Tsukamoto, T., Kusakabe, M., and Saga, Y. 1991. In situ hybridization with non-radioactive digoxigenin-11-UTP-labeled cRNAprobes: Localization of developmentally regulated mouse tenascin mRNAs. Int. J. Dev. Biol. 35: 25-32.
45. Tyakht, A.V., Ilina, E.N., Alexeev, D.G., Ischenko, D.S., Gorbachev, A.Y., Semashko, T.A., Larin, A.K., Selezneva, O.V., Kostryukova, E.S., Karalkin, P.A., Vakhrushev, I.V., Kurbatov, L.K., Archakov, A.I., and Govorun, V.M. 2014. RNASeq gene expression profiling of HepG2 cells: The influence of experimental factors and comparison with liver tissue. BMC Genomics 15: 1108. doi: 10.1186/1471-2164-15-1108.
46. Ukpo, O.C., Flanagan, J.J., Ma, X.J., Luo, Y., Thorstad,W.L., and Lewis, J.S., Jr. 2011. Highrisk human papillomavirus E6/E7 mRNA detection by a novel in situ hybridization assay strongly correlates with p16 expression and patient outcomes in oropharyngeal squamous cell carcinoma. Am. J. Surg. Pathol. 35: 1343-1350. doi: 10.1097/PAS.0b013e318220e59d.
47. Unwin, R.D. and Whetton, A.D. 2006. Systematic proteome and transcriptome analysis of stem cell populations. Cell Cycle 5: 1587-1591. doi: 10.4161/cc.5.15.3101.
48. van Dekken, H., Arkesteijn, G.J., Visser, J.W., and Bauman, J.G. 1990. Flow cytometric quantification of human chromosome specific repetitive DNA sequences by single and bicolor fluorescent in situ hybridization to lymphocyte interphase nuclei. Cytometry 11: 153-164. doi: 10.1002/cyto.990110118.
49. Van Hoof, D., Lomas, W., Hanley, M.B., and Park, E. 2014. Simultaneous flow cytometric analysis of IFN-gamma and CD4 mRNA and protein expression kinetics in human peripheral blood mononuclear cells during activation. Cytometry A 85: 894-900. doi: 10.1002/cyto.a.22521.
50. Walter, R.F., Mairinger, F.D., Ting, S., Vollbrecht, C., Mairinger, T., Theegarten, D., Christoph, D.C., Schmid, K.W., and Wohlschlaeger, J. 2015. MDM2 is an important prognostic and predictive factor for platin-pemetrexed therapy in malignant pleural mesotheliomas and deregulation of P14/ARF (encoded by CDKN2A) seems to contribute to an MDM2-driven inactivation of P53. Br. J. Cancer 112: 883-890. doi: 10.1038/bjc.2015.27.
51. Wang, F., Flanagan, J., Su, N., Wang, L.C., Bui, S., Nielson, A., Wu, X., Vo, H.T., Ma, X.J., and Luo, Y. 2012. RNAscope: A novel in situ RNA analysis platform for formalin-fixed, paraffinembedded tissues. J. Mol. Diagn. 14: 22-29. doi: 10.1016/j.jmoldx.2011.08.002.
52. Weng, X.Q., Shen, Y., Sheng, Y., Chen, B., Wang, J.H., Li, J.M., Mi, J.Q., Chen, Q.S., Zhu, Y.M., Jiang, C.L., Yan, H., Zhang, X.X., Huang, T., Zhu, Z., Chen, Z., and Chen, S.J. 2013. Prognostic significance of monitoring leukemiaassociated immunophenotypes by eight-color flow cytometry in adult B-acute lymphoblastic leukemia. Blood Cancer J. 3: e133. doi: 10.1038/bcj.2013.31.
53. Wiegant, J., Ried, T., Nederlof, P.M., van der Ploeg, M., Tanke, H.J., and Raap, A.K. 1991. In situ hybridization with fluoresceinated DNA. Nucleic Acids Res. 19: 3237-3241. doi: 10.1093/nar/19.12.3237.
54. Yang, G., Garhwal, S., Olson, J.C., and Vyas, G.N. 1994. Flow cytometric immunodetection of human immunodeficiency virus type 1 proviral DNA by heminested PCR and digoxigeninlabeled probes. Clin. Diagn. Lab. Immunol. 1: 26-31.
55. Yang, G., Olson, J.C., Pu, R., and Vyas, G.N. 1995. Flow cytometric detection of human immunodeficiency virus type 1 proviral DNA by the polymerase chain reaction incorporating digoxigenin- or fluorescein-labeled dUTP. Cytometry 21: 197-202. doi: 10.1002/ cyto.990210212.
56. Yu, H., Ernst, L., Wagner, M., and Waggoner, A. 1992. Sensitive detection ofRNAs in single cells by flow cytometry. Nucleic Acids Res. 20: 83-88. doi: 10.1093/nar/20.1.83.
57. Zhang, L., Zhou, W., Velculescu, V.E., Kern, S.E., Hruban, R.H., Hamilton, S.R., Vogelstein, B., and Kinzler, K.W. 1997. Gene expression profiles in normal and cancer cells. Science 276: 1268-1272. doi: 10.1126/science. 276.5316.1268.
58. Hanley et al., 2013. See above. This paper demonstrated for the first time the simultaneous analysis of multiple mRNAs at the sensitivity detection limit for a single mRNA transcript in individual cells. This was achieved by adapting a novel signal amplification technology (also known as Branched DNA) which suppressed background while amplifying specific target signals.
59. Van Hoof et al., 2014. See above. This is the first study that incorporated the simultaneous and correlated measurement of mRNA and protein species by multiparamteric flow cytometry using the Branched DNA methodology.
60. Porichis et al., 2014. See above. This paper demonstrated the potential of the Branched DNA methodology to detect mRNAs of interest, when the availability of mAb is limited. Simultaneous protein and mRNA detection was accomplished using ImageStream technology.
61. Wang et al., 2012. See above. This article provided the technical background associated with the Branched DNA assay.
62. http://www.acdbio.com/products/rnascope-assays Advanced Cell Diagnostics (ACD) originated RNAScope technology, which represents the foundation of the Branched DNA methodology. This signal-amplification platform was developed for immunohistochemistry, but has been adapted by other companies for the detection of mRNA by flow cytometry.
63. http://www.ebioscience.com/knowledge-center/ application/flowrna/technology.htm
64. This Web site provides technical background and flow cytometric applications of the Branched DNA technology, in association with the PrimeFlow RNA Kit. http://www.ebioscience.com/media/newpdf/Prime FlowRNAAssay_UM010915.pdf
65. This Web site provides a PDF version of the Prime FlowRNA assay protocol, which was written by Affymetrix, Inc.
66. http://www.ebioscience.com/resources/faq/flowrna -faq.htm
67. This Web site provides technical support for the PrimeFlow RNA Kit.