A strategy to identify genomic expression at single-cell level or a small number of cells

Electronic Journal of Biotechnology

Volumn 8, Issue 1, 2005, Pages 71-81

  Li, Biaoru ^a  

^a CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Genome; Genomic expression; Genomic expression analysis at single cell; Single cell

Indexed keywords

CELL CULTURE; CELLS; CLONING; ELECTROPHORESIS; GELS; GENES;

DIFFERENTIAL DISPLAY (DD); EXPRESSED TAG SEQUENCING (EST); GENOMIC EXPRESSION; MICROARRAYS;

GENETIC ENGINEERING;

DNA; MESSENGER RNA;

CARCINOGENESIS; DIFFERENTIAL DISPLAY; DNA MICROARRAY; GENE EXPRESSION; GENOME ANALYSIS; LASER CAPTURE MICRODISSECTION; MAMMALIAN GENETICS; MASS SPECTROMETRY; NONHUMAN; POLYMERASE CHAIN REACTION; PROTEIN ISOLATION; PROTEIN MICROARRAY; REVIEW; SERIAL ANALYSIS OF GENE EXPRESSION; SOLID TUMOR; TWO DIMENSIONAL GEL ELECTROPHORESIS;

MAMMALIA; SALVIA;

EID: 19344374851     PISSN: 07173458     EISSN: 07173458     Source Type: Journal    
DOI: 10.2225/vol8-issue1-fulltext-3     Document Type: Review

References (46)

1. AMBION CATALOG. Macromolecular Components of E. coli and Hela Cells. 2004, p. 192.
2. BAHN, S.; AUGOOD, S.J.; RYAN, M.; STANDAERT, D.G.; STARKEY, M. and EMSON, P.C. Gene expression profiling in the post-mortem human brain - no cause for dismay. Journal of Chemistry Neuroanatomy, 2001, vol.22, no. 1-2, p. 79-94.
3. BOSCH, I.; MELICHAR, H. and PARDEE, A.B. Highly sensitive differential display (DD) using small amounts of RNA. Qiagen News. 2000, no. 3, p. 3.
4. BOULTWOOD, J. and WAINSCOAT, J.S. Clonality in the myelodysplastic syndromes. International Journal of Hematology, June 2001, vol. 73, no. 4, p. 411-415.
5. BRANDT, S.; KLOSKA, S.; ALTMANN, T. and KEHR, J. Using array hybridization to monitor gene expression at the single cell level. Journal of Experimental Botany, December 2002, vol. 53, no. 379, p. 2315-2323.
6. CARULLI, J.P.; ARTINGER, M.; SWAIN, P.M.; ROOT, C.D.; CHEE, L.; TULIG, C.; GUERIN. J.; OSBORNE, M.; STEIN, G.; LIAN, J. and LOMEDICO, P.T. High throughput analysis of differential gene expression. Journal of Cellular Biochemistry, suppl., 1998, vol. 30-31, p. 286-296.
7. CHEN, Y. and TALMAGE, D.A. Subtractive cDNA cloning and characterization of genes induced by all-trans retinoic acid. Annals of New York Academy Sciences, 1999, vol. 886, p. 225-228.
8. CLAUDIO, J.O.; LIEW, C.C.; DEMPSEY, A.A.; CUKERMAN, E.; STEWART, A.K.; NA, E.; ATKINS, H.L.; ISCOVE, N.N. and HAWLEY, R.G. Identification of sequence-tagged transcripts differentially expressed within the human hematopoietic hierarchy. Genomics, May 1998, vol. 50, no. 1, p. 44-52.
9. CORDWELL, S.J.; NOUWENS, A.S.; VERRILLS, N.M.; BASSEAL, D.J. and WALSH, B.J. Subproteomics based upon protein cellular location and relative solubilities in conjunction with composite two-dimensional electrophoresis gels. Electrophoresis, April 2000, vol. 21, no. 6, p.1094-1103.
10. DEAN, F.B.; HOSONO, S.; FANG, L.; WU, X.; FARUQI, A.F.; BRAY, WARD P.; SUN, Z.; ZONG, Q.; DU, Y.; DU, J.; DRISCOLL, M.; SONG, W.; KINGSMORE, S.F.; EGHOLM, M. and LASKEN, R.S. Comprehensive human genome amplification using multiple displacement amplification. Proceedings of National Academy of Sciences of the United States of America, 2002, vol. 99, no.8, p. 5261-5266.
11. DIXON, A.K.; RICHARDSON, P.J.; LEE, K.; CARTER, N.P. and FREEMAN, T.C. Expression profiling of single cells using 3 prime end amplification (TPEA) PCR. Nucleic Acids Research, October 1998, vol. 26, no. 19, p. 4426-4431.
12. EBERWINE, J. Amplification of mRNA populations using aRNA generated from immobilized oligo(dT)-T7 primed cDNA. Biotechniques, April 1996, vol. 20, no. 4, p. 584-591.
13. EBERWINE, J.; YEH, H.; MIYASHIRO, K.; CAO, Y.; NAIR, S.; FINNELL, R.; ZETTEL, M. and COLEMAN, P. Analysis of gene expression in single live neurons. Proceedings of National Academy of Sciences of the United States of America, April 1992, vol. 89, no. 7, p. 3010-3014.
14. EMMERT-BUCK, M.R.; BONNER, R.F.; SMITH, P.D.; CHUAQUI, R.F.; ZHUANG, Z.; GOLDSTEIN, S.R.; WEISS, R.A. and LIOTTA, L.A. Laser capture microdissection. Science, November 1996, vol. 274, no.5289, p. 998-1001.
15. EPSTEIN, J.R.; LEUNG, A.P.; LEE, K.H. and WALT, D.R. High-density, microsphere-based fiber optic DNA microarrays. Biosensors and Bioelectronics, May 2003, vol. 18, no. 5-6, p. 501-546.
16. FEND, F.; EMMERT-BUCK, M.R.; CHUAQUI, R.; COLE, K.; LEE, J.; LIOTTA, L.A. and RAFFELD, M. Immuno-LCM: laser capture microdissection of immunostained frozen sections for mRNA analysis. American Journal of Pathology, June 1999, vol. 154, no. 6,p. 1857-1866.
17. FORDE, C.E. and MCCUTCHEN-MALONEY, S.L. Characterization of transcription factors by mass spectrometry and the role of SELDI-MS. Mass Spectrometry Review, November-December 2002, vol. 21, no. 6, p. 419-439.
18. GEY, A.; HAMDI, S.; VIELH, P.; MEHTALI, M.; FRIDMAN, W.H. and TARTOUR, E. Development of a direct in situ RT-PCR method using labeled primers to detect cytokine mRNA inside cells. Journal of Immunology Methods, July 1999, vol. 227, no. 1-2, p. 149-160.
19. GINSBERG, S.D. and CHE, S. RNA amplification in brain tissues. Neurochemistry Research, 2002, vol. 27, no. 10, p.981-992.
20. HAHN, S.; ZHONG, X.Y. and HOLZGREVE, W. Single cell PCR in laser capture microscopy. Methods of Enzymology, 2002, vol. 356, p. 295-301.
21. KLEBE, R.J.; RODRIGUEZ, S.A.; VERBEEK, M.L. and GIAMBERNARDI, T.A. RT-PCR without RNA isolation. Biotechniques, December 1996, vol. 21, no. 6, p. 1094-1100.
22. KIM, J.H. Bioinformatics and genomic medicine. Genetics in Medicine, November-December 2002, vol. 4, no. 6, p.62S-65S.
23. LEVSKY, J.M.; SHENOY, S.M.; PEZO, R.C. and SINGER, R.H. Single-cell gene expression profiling. Science, August 2002, vol. 297, no. 5582, p. 836-840.
24. LI, B.; PERABEKAM, S.; LIU, G.; YIN, M.; SONG, S. and LARSON, A. Experimental and bioinformatics comparison of gene expression between T cells from TIL of liver cancer and T cells from UniGene. Journal of Gastroenterology, 2002, vol. 37, no. 4, p. 275-282.
25. LI, B.; CHANG, T.; LARSON, A. and DING, J. Identification of mRNAs expressed in tumor-infiltrating lymphocytes by a strategy for rapid and high throughput screening. Gene, September 2000, vol. 255, no. 2, p. 273-279.
26. LILLEBERG, S.L. In-depth mutation and SNP discovery using DHPLC gene scanning. Current Opinion of Drug Discovery and Development, 2003, vol.6, p. 237-252.
27. LISS, B. Improved quantitative real-time RT-PCR for expression profiling of individual cells. Nucleic Acids Research, 2002, vol. 30, no. 17, p. e89.
28. MEEHAN, W.J. and WELCH, D.R. Breast cancer metastasis suppressor 1: update. Clinical Experimental Metastasis, 2003, vol. 20, no. 1, p. 45-50.
29. MEIER-RUGE, W.; BIELSER, W.; REMY, E.; HILLENKAMP, F.; NITSCHE, R. and UNSOLD, R. The laser in the Lowry technique for microdissection of freezedried tissue slices. Histochemistry Journal, July 1976, vol. 8, no. 4, p. 387-401.
30. MCKIE, A.; SAMUEL, D.; COHEN, B. and SAUNDERS, N.A. Development of a quantitative immuno-PCR assay and its use to detect mumps-specific IgG in serum. Journal of Immunology Methods, March 2002, vol. 261, no. 1-2, p.167-175.
31. MORITA, M.; HACHISUKA, H. and SASAI, Y. Detection of genomic DNA with a high sensitivity in tissue sections using a two step cycling in situ PCR procedure. Kurume Medical Journal, 1994, vol. 41, no.4, p. 215-220.
32. MICHAEL, K.L. and WALT, D.R. Combined imaging and chemical sensing of fertilization-induced acid release from single sea urchin eggs. Analytical Biochemistry, September 1999, vol. 273, no. 2, p. 168-178.
33. MURRAY, J.; GILKERSON, R. and CAPALDI, R.A. Quantitative proteomics: the copy number of pyruvate dehydrogenase is more than 10(2)-fold lower than that of complex III in human mitochondria. FEBS Letter, October 2002, vol. 9, no. 2-3, p. 173-178.
34. OPPERMANN, M.; COLS, N.; NYMAN, T.; HELIN, J.; SAARINEN, J.; BYMAN, I.; TORAN, N.; ALAIYA, A.A.; BERGMAN, T.; KALKKINEN, N.; GONZÀLEZDUARTE, R. and JÖRNVALL, H. Identification of foetal brain proteins by two-dimensional gel electrophoresis and mass spectrometry. Comparison of samples from individuals with or without chromosome 21 trisomy. European Journal of Biochemistry, 2000, vol. 267, p. 4713-4719.
35. ORMEROD, M. Flow Cytometry: A Practical Approach. Oxford University Press, Oxford, UK. 2000, p. 276. ISBN 0199638241.
36. REN, Z.P.; SALLSTROM, J.; SUNDSTROM, C.; NISTER, M. and OLSSON, Y. Recovering DNA and optimizing PCR conditions from microdissected formalinfixed and paraffin-embedded materials. Pathobiology, 2000, vol. 68, no. 4-5, p. 215-217.
37. RENNER, C.; TRUMPER, L.; PFITZENMEIER, J.P.; LOFTIN, U.; GERLACH, K.; STEHLE, I.; WADLE, A. and PFREUNDSCHUH, M. Differential mRNA display at the single-cell level. Biotechniques, May 1998, vol. 24, no. 5, p. 720-722.
38. SCHUTZE, K. and LAHR, G. Identification of expressed genes by laser-mediated manipulation of single cells. Nature Biotechnology, August 1998, vol. 16, no. 8, p. 737-742.
39. SHAKNOVICH, R.; CELESTINE, A.; YANG, L. and CATTORETTI, G. Novel relational database for tissue microarray analysis. Archives of Pathology and Laboratory Medicine, 2003, vol. 127, no. 4, p. 492-494.
40. STEINERT, R.; BUSCHMANN, T.; VAN DER LINDEN, M.; FELS, L.M.; LIPPERT, H. and REYMOND, M.A. The role of proteomics in the diagnosis and outcome prediction in colorectal cancer. Technology in Cancer Research and Treatment. August 2002, vol. 1, no. 4, p. 297-304.
41. TOELLNER, K.M.; GULBRANSON-JUDGE, A.; TAYLOR, D.R.; SZE, D.M. and MACLENNAN, I.C. Immunoglobulin switch transcript production in vivo related to the site and time of antigen-specific B cell activation. Journal of Experimental Medicine, May 1996, vol. 183, no. 5, p. 2303-2312.
42. TRENDELENBURG, G.; PRASS, K.; PRILLER, J.; KAPINYA, K.; POLLEY, A.; MUSELMANN, C.; RUSCHER, K.; KANNBLEY, U.; SCHMITT, A.O.; CASTELL, S.; WIEGAND, F.; MEISEL, A.; ROSENTHAL, A. and DIRNAGL, U. Serial analysis of gene expression identifies metallothionein-II as major neuroprotective gene in mouse focal cerebral ischemia. The Journal of Neuroscience, July 15, 2002, vol. 22, no. 14, p.5879-5888.
43. WEIGL, B.H.; BARDELL, R.L. and CABRERA, C.R. Lab-on-a-chip for drug development. Advanced Drug Delivery Reviews, February 2003, vol. 55, no. 3, p. 349-377.
44. WOOD, G.S. Analysis of clonality in cutaneous T cell lymphoma and associated diseases. Annals of New York Academy Sciences, 2001, vol. 941, p. 26-30.
45. ZHANG, W.; QU, Y.; PRETLOW TP. and LI, B. Gene cloning and genomic expression analysis from ACF-A study on pre-colon cancer. In: Cancer Genetics and Tumor suppressor genes. (18 - 22 August, 2004, New York, USA). Cold Spring Harbor Laboratory, 2004, p. 234.
46. ZHANG, H.T.; KACHARMINA, J.E.; MIYASHIRO, K.; GREENE, M.I. and EBERWINE, J. Protein quantification from complex protein mixtures using a proteomics methodology with single-cell resolution. Proceedings of National Academy of Sciences of the United States of America, May 2001, vol. 98, no. 10, p. 5497-5502. Note: This paper for a memory of Dr. Harvey D. Preisler, who contributed his whole life to study tumorigenesis of AML, He was a director of Rush Cancer Institute from 1990 to 2002.