Expression profiling using human tissues in combination with RNA amplification and microarray analysis: Assessment of Langerhans cell histiocytosis

Amino Acids

Volumn 28, Issue 3, 2005, Pages 279-290

  McClain, K L ^a   Cai, Y H ^a   Hicks, J ^a   Peterson, L E ^a   Yan, X T ^a   Che, S ^b,c   Ginsberg, S D ^b,c  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

^b NATHAN S KLINE INSTITUTE FOR PSYCHIATRIC RESEARCH   (United States)

^c NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Cancer genomics; cDNA microarray; Molecular fingerprint; Postmortem human brain; Translational neuroscience

Indexed keywords

COMPLEMENTARY RNA; RNA;

BIOPSY; CELL POPULATION; COMPARATIVE STUDY; CONTROLLED STUDY; GENE AMPLIFICATION; GENE EXPRESSION; GENE SEQUENCE; GENETIC ANALYSIS; GENOME; HISTIOCYTOSIS; HISTOCHEMISTRY; HOMEOSTASIS; HUMAN; HUMAN TISSUE; IMMUNOCYTOCHEMISTRY; LANGERHANS CELL; LASER CAPTURE MICRODISSECTION; METHODOLOGY; MOLECULAR GENETICS; PATHOGENESIS; PHYSIOLOGY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; RNA EXTRACTION; SHORT SURVEY; TISSUE MICROARRAY;

GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HISTIOCYTOSIS, LANGERHANS-CELL; HUMANS; NUCLEIC ACID AMPLIFICATION TECHNIQUES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 20044394041     PISSN: 09394451     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00726-005-0177-x     Document Type: Short Survey

References (73)

1. Aittokallio T, Kurki M, Nevalainen O, Nikula T, West A, Lahesmaa R (2003) Computational strategies for analyzing data in gene expression microarray experiments. J Bioinform Comput Biol 1: 541-586
2. Arenzana-Seisdedos F, Barbey S, Virelizier JL, Kornprobst M, Nezelof C (1986) Histiocytosis X. Purified (T6+) cells from bone granuloma produce interleukin 1 and prostaglandin E2 in culture. J Clin Invest 77: 326-329
3. Blumberg DD (1987) Creating a ribonuclease-free environment. Methods Enzymol 152: 20-24
4. Bonner RF Emmert-Buck M, Cole K, Pohida T, Chuaqui R, Goldstein S, Liotta LA (1997) Laser capture microdissection: molecular analysis of tissue. Science 278: 1481-1483
5. Brown PO, Botstein D (1999) Exploring the new world of the genome with DNA microarrays. Nat Genet 21 [Suppl]: 33-37
6. Carstensen H, Ornvold K (1993) Langerhans-cell histiocytosis (histiocytosis X) in children. Ugeskr Laeger 155: 1779-1783
7. Che S, Ginsberg SD (2004a) Amplification of transcripts using terminal continuation. Lab Invest 84: 131-137
8. Che S, Ginsberg SD (2004b) RNA amplification methodologies. In: Progress in RNA research. Nova Science Publishing (in press)
9. Craven RA, Totty N, Harnden P, Selby PJ, Banks RE (2002) Laser capture microdissection and two-dimensional polyacrylamide gel electrophoresis: evaluation of tissue preparation and sample limitations. Am J Pathol 160: 815-822
10. Dafforn A, Chen P, Deng G, Herrler M, Iglehart D, Koritala S, Lato S, Pillarisetty S, Purohit R, Wang M, et al. (2004) Linear mRNA amplification from as little as 5 ng total RNA for global gene expression analysis. Biotechniques 37: 854-857
11. Dolter KE, Braman JC (2001) Small-sample total RNA purification: laser capture microdissection and cultured cell applications. Biotechniques 30: 1358-1361
12. Eberwine J, Kacharmina JE, Andrews C, Miyashiro K, McIntosh T, Becker K, Barrett T, Hinkle D, Dent G, Marciano P (2001) mRNA expression analysis of tissue sections and single cells. J Neurosci 21: 8310-8314
13. Eberwine J, Yeh H, Miyashiro K, Cao Y, Nair S, Finnell R, Zettel M, Coleman P (1992) Analysis of gene expression in single live neurons. Proc Natl Acad Sci USA 89: 3010-3014
14. Egeler RM, Favara BE, van Meurs M, Laman JD, Claassen E (1999) Differential In situ cytokine profiles of Langerhans-like cells and T cells in Langerhans cell histiocytosis: abundant expression of cytokines relevant to disease and treatment. Blood 94: 4195-4201
15. Ehrig T, Abdulkadir SA, Dintzis SM, Milbrandt J, Watson MA (2001) Quantitative amplification of genomic DNA from histological tissue sections after staining with nuclear dyes and laser capture microdissection. J Mol Diagn 3: 22-25
16. Eisen MB, Brown PO (1999) DNA arrays for analysis of gene expression. Methods Enzymol 303: 179-205
17. Emmert-Buck MR, Bonner RF, Smith PD, Chuaqui RF, Zhuang Z, Goldstein SR, Weiss RA, Liotta LA (1996) Laser capture microdissection. Science 274: 998-1001
18. Farrell RE Jr (1998) RNA Methodologies, 2nd edn. Academic Press, San Diego
19. Fasulo WH, Hemby SE (2003) Time-dependent changes in gene expression profiles of midbrain dopamine neurons following haloperidol administration. J Neurochem 87: 205-219
20. Favara BE, Jaffe R, Egeler RM (2002) Macrophage activation and hemophagocytic syndrome in Langerhans cell histiocytosis: report of 30 cases. Pediatr Dev Pathol 5: 130-140
21. Fend F, Emmert-Buck MR, Chuaqui R, Cole K, Lee J, Liotta LA, Raffeld M (1999) Immuno-LCM: laser capture microdissection of immunostained frozen sections for mRNA analysis. Am J Pathol 154: 61-66
22. Florell SR, Coffin CM, Holden JA, Zimmermann JW, Gerwels JW, Summers BK, Jones DA, Leachman SA (2001) Preservation of RNA for functional genomic studies: a multidisciplinary tumor bank protocol. Mod Pathol 14: 116-128
23. Freeman WM, Hemby SE (2004) Proteomics for protein expression profiling in neuroscience. Neurochem Res 29: 1065-1081
24. Galvin JE, Ginsberg SD (2004) Expression profiling and pharmacotherapeutic development in the central nervous system. Alzheimer Dis Assoc Disord 18: 264-269
25. Geissmann F, Revy P, Regnault A, Lepelletier Y, Dy M, Brousse N, Amigorena S, Hermine O, Durandy A (1999) TGF-beta 1 prevents the noncognate maturation of human dendritic Langerhans cells. J Immunol 162: 4567-4575
26. Geissmann F, Lepelletier Y, Fraitag S, Valladeau J, Bodemer C, Debre M, Leborgne M, Saeland S, Brousse N (2001) Differentiation of Langerhans cells in Langerhans cell histiocytosis. Blood 97: 1241-1248
27. Ginsberg SD, Che S (2002) RNA amplification in brain tissues. Neurochem Res 27: 981-992
28. Ginsberg SD, Che S (2004) Combined histochemical staining, RNA amplification, regional, and single cell analysis within the hippocampus. Lab Invest 84: 952-962
29. Ginsberg SD, Che S (2005) Expression profile analysis within the human hippocampus: comparison of CA1 and CA3 pyramidal neurons. J Comp Neurol (in press)
30. Ginsberg SD, Crino PB, Lee VM-Y, Eberwine JH, Trojanowski JQ (1997) Sequestration of RNA in Alzheimer's disease neurofibrillary tangles and senile plaques. Ann Neurol 41: 200-209
31. Ginsberg SD, Galvin JE, Chiu T-S, Lee VM-Y, Masliah E, Trojanowski JQ (1998) RNA sequestration to pathological lesions of neurodegenerative disorders. Acta Neuropathol 96: 487-494
32. Ginsberg SD, Crino PB, Hemby SE, Weingarten JA, Lee VM-Y, Eberwine JH, Trojanowski JQ (1999) Predominance of neuronal mRNAs in individual Alzheimer's disease senile plaques. Ann Neurol 45: 174-181
33. Ginsberg SD, Hemby SE, Lee VM-Y, Eberwine JH, Trojanowski JQ (2000) Expression profile of transcripts in Alzheimer's disease tangle-bearing CA1 neurons. Ann Neurol 48: 77-87
34. Ginsberg SD, Elarova I, Ruben M, Tan F, Counts SE, Eberwine JH, Trojanowski JQ, Hemby SE, Mufson EJ, Che S (2004) Single cell gene expression analysis: implications for neurodegenerative and neuropsychiatric disorders. Neurochem Res 29: 1054-1065
35. Goldsworthy SM, Stockton PS, Trempus CS, Foley JF, Maronpot RR (1999) Effects of fixation on RNA extraction and amplification from laser capture microdissected tissue. Mol Carcinog 25: 86-91
36. Gottwald E, Muller O, Polten A (2001) Semiquantitative reverse transcription-polymerase chain reaction with the Agilent 2100 Bioanalyzer. Electrophoresis 22: 4016-4022
37. Grotzer MA, Patti R, Geoerger B, Eggert A, Chou TT, Phillips PC (2000) Biological stability of RNA isolated from RNAlater-treated brain tumor and neuroblastoma xenografts. Med Pediatr Oncol 34: 438-442
38. Hemby SE, Ginsberg SD, Brunk B, Arnold SE, Trojanowski JQ, Eberwine JH (2002) Gene expression profile for schizophrenia: discrete neuron transcription patterns in the entorhinal cortex. Arch Gen Psychiat 59: 631-640
39. Hemby SE, Trojanowski JQ, Ginsberg SD (2003) Neuron-specific age-related decreases in dopamine receptor subtype mRNAs. J Comp Neurol 456: 176-183
40. Heyer LJ, Kruglyak S, Yooseph S (1999) Exploring expression data: identification and analysis of coexpressed genes. Genome Res 9: 1106-1115
41. Iscove NN, Barbara M, Gu M, Gibson M, Modi C, Winegarden N (2002) Representation is faithfully preserved in global cDNA amplified exponentially from sub-picogram quantities of mRNA. Nat Biotechnol 20: 940-943
42. Islinger RB, Kuklo TR, Owens BD, Horan PJ, Choma TJ, Murphey MD, Temple HT (2000) Langerhans' cell histiocytosis in patients older than 21 years. Clin Orthop 379: 231-235
43. Kacharmina JE, Crino PB, Eberwine J (1999) Preparation of cDNA from single cells and subcellular regions. Methods Enzymol 303: 3-18
44. Klimecki WT, Futscher BW, Dalton WS (1994) Effects of ethanol and paraformaldehyde on RNA yield and quality. Biotechniques 16: 1021-1023
45. Klur S, Toy K, Williams MP, Certa U (2004) Evaluation of procedures for amplification of small-size samples for hybridization on microarrays. Genomics 83: 508-517
46. Kotlyar M, Fuhrman S, Ableson A, Somogyi R (2002) Spearman correlation identifies statistically significant gene expression clusters in spinal cord development and injury. Neurochem Res 27: 1133-1140
47. Lehmann U, Bock O, Glockner S, Kreipe H (2000) Quantitative molecular analysis of laser-microdissected paraffin-embedded human tissues. Pathobiology 68: 202-208
48. Lewis F, Maughan NJ, Smith V, Hillan K, Quirke P (2001) Unlocking the archive-gene expression in paraffin-embedded tissue. J Pathol 195: 66-71
49. Lockhart DJ, Barlow C (2001) Expressing what's on your mind: DNA arrays and the brain. Nat Rev Neurosci 2: 63-68
50. Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H, Brown EL (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 14: 1675-1680
51. McClain K, Hutter J, Cassady J (1994) Langerhan's cell histiocytosis. In: Cassady J (ed) Radiation therapy in pediatric oncology. Springer, New York, pp 337-350
52. Minkov M, Grois N, Heitger A, Potschger U, Westermeier T, Gadner H (2002) Response to initial treatment of multisystem Langerhans cell histiocytosis: an important prognostic indicator. Med Pediatr Oncol 39: 581-585
53. Mouledous L, Hunt S, Harcourt R, Harry JL, Williams KL, Gutstein HB (2003) Proteomic analysis of immunostained, laser-capture microdissected brain samples. Electrophoresis 24: 296-302
54. Mufson EJ, Counts SE, Ginsberg SD (2002) Single cell gene expression profiles of nucleus basalis cholinergic neurons in Alzheimer's disease. Neurochem Res 27: 1035-1048
55. Murakami I, Gogusev J, Fournet JC, Glorion C, Jaubert F (2002) Detection of molecular cytogenetic aberrations in Langerhans cell histiocytosis of bone. Hum Pathol 33: 555-560
56. Palucka KA, Taquet N, Sanchez-Chapuis F, Gluckman JC (1998) Dendritic cells as the terminal stage of monocyte differentiation. J Immunol 160: 4587-4595
57. Peterson LE (2002) CLUSFAVOR 5.0: hierarchical cluster and principal-component analysis of microarray-based transcriptional profiles. Genome Biol 3, SOFTWARE0002
58. Pinto A, Sarnat HB, Vogler C, Trevenen CL, Grant LH (1990) Acridine orange-RNA histofluorescence of sarcomas and small round cell tumors of childhood. Arch Pathol Lab Med 114: 585-588
59. Rieser C, Ramoner R, Bock G, Deo YM, Holtl L, Bartsch G, Thurnher M (1998) Human monocyte-derived dendritic cells produce macrophage colony-stimulating factor: enhancement of c-fms expression by interleukin-10. Eur J Immunol 28: 2283-2288
60. Sarnat HB, Curry B, Rewcastle NB, Trevenen CL (1986) Cytoplasmic RNA in nervous system tumors in children: a fluorochromic histochemical study using acridine orange. Can J Neurol Sci 13: 31-41
61. Simone NL, Remaley AT, Charboneau L, Petricoin EF 3rd, Glickman JW, Emmert-Buck MR, Fleisher TA, Liotta LA (2000) Sensitive immunoassay of tissue cell proteins procured by laser capture microdissection. Am J Pathol 156: 445-452
62. Su JM, Perlaky L, Li XN, Leung HC, Antalffy B, Armstrong D, Lau CC (2004) Comparison of ethanol versus formalin fixation on preservation of histology and RNA in laser capture microdissected brain tissues. Brain Pathol 14: 175-182
63. Suarez-Quian CA, Goldstein SR, Pohida T, Smith PD, Peterson JI, Wellner E, Ghany M, Bonner RF (1999) Laser capture microdissection of single cells from complex tissues. Biotechniques 26: 328-335
64. Tang WX, Fasulo WH, Mash DC, Hemby SE (2003) Molecular profiling of midbrain dopamine regions in cocaine overdose victims. J Neurochem 85: 911-924
65. Tecott LH, Barchas JD, Eberwine JH (1988) In situ transcription: specific synthesis of complementary DNA in fixed tissue sections. Science 240: 1661-1664
66. To MD, Done SJ, Redston M, Andrulis IL (1998) Analysis of mRNA from microdissected frozen tissue sections without RNA isolation. Am J Pathol 153: 47-51
67. Topaloglu H, Sarnat HB (1989) Acridine orange-RNA fluorescence maturing neurons in the perinatal rat brain. Anat Rec 224: 88-93
68. Van Deerlin VMD, Ginsberg SD, Lee VM-Y, Trojanowski JQ (2000) Fixed post mortem brain tissue for mRNA expression analysis in neurodegenerative diseases. In: Geschwind DH (ed) DNA microarrays: the new frontier in gene discovery and gene expression analysis. Society for Neuroscience Washington, DC, pp 118-128
69. Van Deerlin VMD, Ginsberg SD, Lee VM-Y, Trojanowski JQ (2002) The use of fixed human post mortem brain tissue to study mRNA expression in neurodegenerative diseases: applications of microdissection and mRNA amplification. In: Geschwind DH, Gregg JP (eds) Microarrays for the neurosciences: an essential guide. MIT Press Boston, pp 201-235
70. Van Gelder R, von Zastrow M, Yool A, Dement W, Barchas J, Eberwine J (1990) Amplified RNA (aRNA) synthesized from limited quantities of heterogeneous cDNA. Proc Natl Acad Sci USA 87: 1663-1667
71. Vasilyeva E, Woodard J, Taylor FR, Kretschmer M, Fajardo H, Lyubarskaya Y, Kobayashi K, Dingley A, Mhatre R (2004) Development of a chip-based capillary gel electrophoresis method for quantification of a half-antibody in immunoglobulin G4 samples. Electrophoresis 25: 3890-3896
72. Wang E, Miller LD, Ohnmacht GA, Liu ET, Marincola FM (2000) High-fidelity mRNA amplification for gene profiling. Nat Biotechnol 18: 457-459
73. Yokota K, Ariizumi K, Kitajima T, Bergstresser PR, Street NE, Takashima A (1996) Cytokine-mediated communication between dendritic epidermal T cells and Langerhans cells. In vitro studies using cell lines. J Immunol 157: 1529-1537