Validation and implementation of a method for microarray gene expression profiling of minor B-cell subpopulations in man

BMC Immunology

Volumn 15, Issue 1, 2014, Pages

  Bergkvist, Kim S ^a   Nyegaard, Mette ^a,b   Bøgsted, Martin ^a,c   Schmitz, Alexander ^a   Bødker, Julie S ^a   Rasmussen, Simon M ^a   Perez Andres, Martin ^a   Falgreen, Steffen ^a   Bilgrau, Anders E ^a,c   Kjeldsen, Malene K ^a   Gaihede, Michael ^a,c   Nørgaard, Martin A ^a   Bæch, John ^a   Grønholdt, Marie Louise ^a   Jensen, Frank S ^a   Johansen, Preben ^a   Dybkær, Karen ^a,c   Johnsen, Hans E ^a,c  

^a AALBORG UNIVERSITY HOSPITAL   (Denmark)

^b AARHUS UNIVERSITY   (Denmark)

^c AALBORG UNIVERSITY   (Denmark)

Author keywords

B cell subpopulations; Fluorescence activated cell sorting; Microarray gene expression profiling; RNA purification

Indexed keywords

ACTIVATION INDUCED CYTIDINE DEAMINASE; B LYMPHOCYTE INDUCED MATURATION PROTEIN 1; CHEMOKINE RECEPTOR CXCR4; COMPLEMENTARY RNA; INTERFERON REGULATORY FACTOR 4; MESSENGER RNA; PROTEIN BCL 6; RNA POLYMERASE; X BOX BINDING PROTEIN 1; COMPLEMENTARY DNA; GENOMIC DNA;

ARTICLE; B LYMPHOCYTE; B LYMPHOCYTE SUBPOPULATION; CARCINOGENESIS; CELL COUNT; COMPARATIVE STUDY; CONTROLLED STUDY; CYTOLYSIS; FLOW CYTOMETRY; FLUORESCENCE ACTIVATED CELL SORTING; FREEZING; GENE AMPLIFICATION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE REARRANGEMENT; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; IMMUNOPHENOTYPING; LYMPHOCYTE SUBPOPULATION; LYMPHOID TISSUE; LYMPHOPOIESIS; MICROARRAY ANALYSIS; NUCLEIC ACID AMPLIFICATION; RNA EXTRACTION; RNA PURIFICATION; STORAGE; TONSIL; ADOLESCENT; ADULT; AGED; BONE MARROW; CELL SORTER; CLINICAL ARTICLE; DNA MICROARRAY; FEMALE; HUMAN TISSUE; INTERMETHOD COMPARISON; MALE; MULTIPLE MYELOMA CELL LINE; POLYMERASE CHAIN REACTION SYSTEM; THYMUS; WORKFLOW;

ANTIGENS, CD; B-LYMPHOCYTE SUBSETS; FLOW CYTOMETRY; GENE EXPRESSION PROFILING; HUMANS; LYMPHOID TISSUE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ORGAN SPECIFICITY; REAL-TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS;

EID: 84893168174     PISSN: None     EISSN: 14712172     Source Type: Journal    
DOI: 10.1186/1471-2172-15-3     Document Type: Article

References (37)

1. Greaves M, Maley CC. Clonal evolution in cancer. Nature 2012, 481:306-313. 10.1038/nature10762, 3367003, 22258609.
2. Valent P, Bonnet D, De MR, Lapidot T, Copland M, Melo JV, et al. Cancer stem cell definitions and terminology: the devil is in the details. Nat Rev Cancer 2012, 12:767-775. 10.1038/nrc3368, 23051844.
3. Johnsen HE, Kjeldsen MK, Urup T, Fogd K, Pilgaard L, Boegsted M, et al. Cancer stem cells and the cellular hierarchy in haematological malignancies. Eur J Cancer 2009, 45(Suppl 1):194-201.
4. Hoffmann MH, Klausen TW, Boegsted M, Larsen SF, Schmitz A, Leinoe EB, et al. Clinical impact of leukemic blast heterogeneity at diagnosis in cytogenetic intermediate-risk acute myeloid leukemia. Cytometry B Clin Cytom 2012, 82:123-131.
5. Chiorazzi N, Ferrarini M. Cellular origin(s) of chronic lymphocytic leukemia: cautionary notes and additional considerations and possibilities. Blood 2011, 117:1781-1791. 10.1182/blood-2010-07-155663, 3056635, 21148333.
6. Rosenwald A, Wright G, Chan WC, Connors JM, Campo E, Fisher RI, et al. The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma. N Engl J Med 2002, 346:1937-1947. 10.1056/NEJMoa012914, 12075054.
7. Rasmussen T, Jensen L, Johnsen HE. The clonal hierachy in multiple myeloma. Acta Oncol 2000, 39:765-770. 10.1080/028418600750063479, 11145430.
8. Kuppers R. The biology of Hodgkin's lymphoma. Nat Rev Cancer 2009, 9:15-27. 10.1038/nrc2542, 19078975.
9. Kjeldsen MK, Perez-Andres M, Schmitz A, Johansen P, Boegsted M, Nyegaard M, et al. Multiparametric flow cytometry for identification and fluorescence activated cell sorting of five distinct B-cell subpopulations in normal tonsil tissue. Am J Clin Pathol 2011, 136:960-969. 10.1309/AJCPDQNP2U5DZHVV, 22095383.
10. Shaffer AL, Rosenwald A, Staudt LM. Lymphoid malignancies: the dark side of B-cell differentiation. Nat Rev Immunol 2002, 2:920-932. 10.1038/nri953, 12461565.
11. Rasmussen T, Haaber J, Dahl IM, Knudsen LM, Kerndrup GB, Lodahl M, et al. Identification of translocation products but not K-RAS mutations in memory B cells from patients with multiple myeloma. Haematologica 2010, 95:1730-1737. 10.3324/haematol.2010.024778, 2948099, 20511669.
12. Matthias P, Rolink AG. Transcriptional networks in developing and mature B cells. Nat Rev Immunol 2005, 5:497-508. 10.1038/nri1633, 15928681.
13. Morgan GJ, Walker BA, Davies FE. The genetic architecture of multiple myeloma. Nat Rev Cancer 2012, 12:335-348. 10.1038/nrc3257, 22495321.
14. O'Neil J, Look AT. Mechanisms of transcription factor deregulation in lymphoid cell transformation. Oncogene 2007, 26:6838-6849. 10.1038/sj.onc.1210766, 17934490.
15. Welner RS, Pelayo R, Kincade PW. Evolving views on the genealogy of B cells. Nat Rev Immunol 2008, 8:95-106. 10.1038/nri2234, 18204470.
16. Caraux A, Klein B, Paiva B, Bret C, Schmitz A, Fuhler GM, et al. Circulating human B and plasma cells. Age-associated changes in counts and detailed characterization of circulating normal C. Haematologica 2010, 95:1016-1020. 10.3324/haematol.2009.018689, 2878802, 20081059.
17. Hystad ME, Myklebust JH, Bo TH, Sivertsen EA, Rian E, Forfang L, et al. Characterization of early stages of human B cell development by gene expression profiling. J Immunol 2007, 179:3662-3671.
18. van Zelm MC, van der Burg M, de Ridder D, Barendregt BH, de Haas EF, Reinders MJ, et al. Ig gene rearrangement steps are initiated in early human precursor B cell subsets and correlate with specific transcription factor expression. J Immunol 2005, 175:5912-5922.
19. Klein U, Tu Y, Stolovitzky GA, Keller JL, Haddad J, Miljkovic V, et al. Transcriptional analysis of the B cell germinal center reaction. Proc Natl Acad Sci USA 2003, 100:2639-2644. 10.1073/pnas.0437996100, 151393, 12604779.
20. Nakayama Y, Stabach P, Maher SE, Mahajan MC, Masiar P, Liao C, et al. A limited number of genes are involved in the differentiation of germinal center B cells. J Cell Biochem 2006, 99:1308-1325. 10.1002/jcb.20952, 16795035.
21. Vermeulen J, Derveaux S, Lefever S, De SE, De PK, Yigit N, et al. RNA pre-amplification enables large-scale RT-qPCR gene-expression studies on limiting sample amounts. BMC Res Notes 2009, 2:235. 10.1186/1756-0500-2-235, 2789097, 19930725.
22. Lauss M, Vierlinger K, Weinhaeusel A, Szameit S, Kaserer K, Noehammer C. Comparison of RNA amplification techniques meeting the demands for the expression profiling of clinical cancer samples. Virchows Arch 2007, 451:1019-1029. 10.1007/s00428-007-0522-4, 17972098.
23. Eberwine J, Yeh H, Miyashiro K, Cao Y, Nair S, Finnell R, et al. Analysis of gene expression in single live neurons. Proc Natl Acad Sci USA 1992, 89:3010-3014. 10.1073/pnas.89.7.3010, 48793, 1557406.
24. Phillips J, Eberwine JH. Antisense RNA Amplification: A linear amplification method for analyzing the mRNA population from single living cells. Methods 1996, 10:283-288. 10.1006/meth.1996.0104, 8954839.
25. Deng MY, Wang H, Ward GB, Beckham TR, McKenna TS. Comparison of six RNA extraction methods for the detection of classical swine fever virus by real-time and conventional reverse transcription-PCR. J Vet Diagn Invest 2005, 17:574-578. 10.1177/104063870501700609, 16475517.
26. Khymenets O, Ortuno J, Fito M, Covas MA, Farre M, de la Torre R. Evaluation of RNA isolation procedures from human blood and its application for gene expression studies (Sod-1, Sod-2). Anal Biochem 2005, 347:156-158. 10.1016/j.ab.2005.07.007, 16242658.
27. Ruettger A, Neumann S, Wiederanders B, Huber R. Comparison of different methods for preparation and characterization of total RNA from cartilage samples to uncover osteoarthritis in vivo. BMC Res Notes 2010, 3:7. 10.1186/1756-0500-3-7, 2841606, 20180968.
28. Rump LV, Asamoah B, Gonzalez-Escalona N. Comparison of commercial RNA extraction kits for preparation of DNA-free total RNA from Salmonella cells. BMC Res Notes 2010, 3:211. 10.1186/1756-0500-3-211, 3161365, 20663210.
29. Eldh M, Lotvall J, Malmhall C, Ekstrom K. Importance of RNA isolation methods for analysis of exosomal RNA: evaluation of different methods. Mol Immunol 2012, 50:278-286. 10.1016/j.molimm.2012.02.001, 22424315.
30. Mack E, Neubauer A, Brendel C. Comparison of RNA yield from small cell populations sorted by flow cytometry applying different isolation procedures. Cytometry A 2007, 71:404-409.
31. Lossos IS, Czerwinski DK, Wechser MA, Levy R. Optimization of quantitative real-time RT-PCR parameters for the study of lymphoid malignancies. Leukemia 2003, 17:789-795. 10.1038/sj.leu.2402880, 12682639.
32. Oettinger MA, Schatz DG, Gorka C, Baltimore D. RAG-1 and RAG-2, adjacent genes that synergistically activate V(D)J recombination. Science 1990, 248:1517-1523. 10.1126/science.2360047, 2360047.
33. Bartholdy B, Matthias P. Transcriptional control of B cell development and function. Gene 2004, 327:1-23. 10.1016/j.gene.2003.11.008, 14960357.
34. Cattoretti G, Shaknovich R, Smith PM, Jack HM, Murty VV, Alobeid B. Stages of germinal center transit are defined by B cell transcription factor coexpression and relative abundance. J Immunol 2006, 177:6930-6939.
35. Lu R, Medina KL, Lancki DW, Singh H. IRF-4,8 orchestrate the pre-B-to-B transition in lymphocyte development. Genes Dev 2003, 17:1703-1708. 10.1101/gad.1104803, 196178, 12832394.
36. Clement-Ziza M, Gentien D, Lyonnet S, Thiery JP, Besmond C, Decraene C. Evaluation of methods for amplification of picogram amounts of total RNA for whole genome expression profiling. BMC Genomics 2009, 10:246. 10.1186/1471-2164-10-246, 2700135, 19470167.
37. Viale A, Li J, Tiesman J, Hester S, Massimi A, Griffin C, et al. Big results from small samples: evaluation of amplification protocols for gene expression profiling. J Biomol Tech 2007, 18:150-161. 2062549, 17595311.