Application of genomic resources and gene expression profiles to identify genes that regulate bone destiny

Current Genomics

Volumn 4, Issue 1, 2003, Pages 75-102

  Gu, W K ^a,b   Li, X M ^a   Roe, B A ^c   Lau, K H William ^a   Mohan, S ^a   Baylink, D J ^a  

^a LOMA LINDA UNIVERSITY   (United States)

^b UNIVERSITY OF TENNESSEE HEALTH SCIENCE CENTER   (United States)

^c UNIVERSITY OF OKLAHOMA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

4 CARBOXYGLUTAMIC ACID; APOLIPOPROTEIN E; CALCITONIN; CALCIUM SENSING RECEPTOR; DNA; ESTROGEN RECEPTOR ALPHA; ESTROGEN RECEPTOR BETA; INTERLEUKIN 1 RECEPTOR BLOCKING AGENT; INTERLEUKIN 6; OSTEOCALCIN; OSTEOPROTEGERIN; PARATHYROID HORMONE; PARATHYROID HORMONE RECEPTOR; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA; PROCOLLAGEN; SOMATOMEDIN C; TRANSFORMING GROWTH FACTOR BETA1; TUMOR NECROSIS FACTOR RECEPTOR 2; VITAMIN D RECEPTOR;

BIOINFORMATICS; BONE DENSITY; DNA MICROARRAY; EXPRESSED SEQUENCE TAG; FRAGILITY FRACTURE; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC DATABASE; GENETIC VARIABILITY; GENOME ANALYSIS; HEREDITY; HUMAN; NONHUMAN; NUCLEOTIDE SEQUENCE; OSTEOPOROSIS; PATHOGENESIS; POPULATION RESEARCH; QUANTITATIVE TRAIT LOCUS; REGULATORY MECHANISM; REVIEW; SEQUENCE ANALYSIS; UNINDEXED SEQUENCE;

EUKARYOTA;

EID: 0037245165     PISSN: 13892029     EISSN: None     Source Type: Journal    
DOI: 10.2174/1389202033350146     Document Type: Review

References (67)

1. Smith, D.M., Nance, W.E., Kang, K.W., Christian, J.C., Johnston, C.C. Jr. Genetic factors in determining bone mass. Journal of Clinical Investigation, 1973, 52: 2800-8.
2. Slemenda, C.W., Christian, J.C., Williams, C.J., Norton, J.A., Johnston, C.C. Jr. Genetic determinants of bone mass in adult women: a reevaluation of the twin model and the potential importance of gene interaction on heritability estimates. J. Bone Miner Res., 1998, 6: 561-7.
3. Eisman, J.A. Genetics of osteoporosis. Endocr. Rev., 1999, 20: 788-804.
4. Kroger, H., Tuppurainen, M., Honkanen, R., Alhava, E., Saarikoski, S. Bone mineral density and risk factors for osteoporosis: a population-based study of 1600 perimenopausal women. Calcif. Tissue Int., 1994, 55: 1-7.
5. Seeman, E., Tsalamandris, C., Formica, C., Hopper, J.L., McKay, J. Reduced femoral neck bone density in the daughters of women with hip fractures: the role of low peak bone density in the pathogenesis of osteoporosis. J. Bone Miner Res., 1994, 9: 739-43.
6. Ryan, P.J., Blake, G.M., Herd, R., Parker, J., Fogelman, I. Distribution of bone mineral density in the lumbar spine in health and osteoporosis. Osteoporos. Int., 1994, 4: 67-71.
7. Turner, J.G., Gilchrist, N.L., Ayling, E.M., Hassall, A.J., Hooke, E.A., Sadler, W.A. Factors affecting bone mineral density in high school girls. N. Z. Med. J., 1992, 105: 95-6.
8. Yeap, S.S., Beaumont, M., Bennett, A., Keating, N.A., White, D.A., Hosking, D.J. Genetic and environmental factors affecting bone mineral density in large families. Postgraduate Medical Journal, 1998, 74: 349-54.
9. Jouanny, P., Guillemin, F., Kuntz, C., Jeandel, C., Pourel, J. Environmental and genetic factors affecting bone mass. Similarity of bone density among members of healthy families. Arthritis & Rheumatism, 1995, 38: 61-7.
10. Beamer, W.G., Shultz, K.L., Churchill, G.A., Frankel, W.N., Baylink, D.J., Rosen, C.J., Donahue, L.R. Quantitative trait loci for bone density in C57BL/6J and CAST/EiJ inbred mice. Mamm. Genome, 1999, 10: 1043-9.
11. Koller, D.L., Econs, M.J., Morin, P.A., Christian, J.C., Hui, S.L., Parry, P., Curran, M.E., Rodriguez, L.A., Conneally, P.M., Joslyn, G., Peacock, M., Johnston, C.C., Foroud, T. Genome screen for QTLs contributing to normal variation in bone mineral density and osteoporosis. J. Clin. Endocrinol. Metab., 2000, 85: 3116-20.
12. Devoto, M., Shimoya, K., Caminis, J., Ott, J., Tenenhouse, A., Whyte, M.P., Sereda, L., Hall, S., Considine, E., Williams, C.J., Tromp, G., Kuivaniemi, H., Ala-Kokko, L., Prockop, D.J., Spotila, L.D. First-stage autosomal genome screen in extended pedigrees suggests genes predisposing to low bone mineral density on chromosomes 1p, 2p and 4q. Eur. J. Hum. Genet., 1998, 6:151-7.
13. Niu, T., Chen, C., Cordell, H., Yang, J., Wang, B., Wang, Z., Fang, Z., Schork, N.J., Rosen, C.J., Xu, X. A genome-wide scan for loci linked to forearm bone mineral density. Hum. Genet., 1999, 104: 226-33.
14. Shimizu, M., Higuchi, K., Bennett, B., Xia, C., Tsuboyama, T., Kasai, S., Chiba, T., Fujisawa, H., Kogishi, K., Kitado, H., Kimoto, M., Takeda, N., Matsushita, M., Okumura, H., Serikawa, T., Nakamura, T., Johnson, T.E., Identification of peak bone mass QTL in a spontaneously osteoporotic mouse strain. Mamm. Genome, 1999, 10: 81-7.
15. Benes, H., Weinstein, R.S., Zheng, W., Thaden, J.J., Jilka, R.L., Manolagas, S.C., Shmookler Reis. R.J. Chromosomal mapping of osteopenia-associated quantitative trait loci using closely related mouse strains. J. Bone Miner Res., 2000 15: 626-33.
16. Klein, R.F., Mitchell, S.R., Phillips, T.J., Belknap, J.K., Orwoll, E.S. Quantitative trait loci affecting peak bone mineral density in mice. J. Bone Miner Res., 1998, 13: 1648-56.
17. Ho, N.C., Jia, L., Driscoll, C.C., Gutter, E.M., Francomano, C.A. A skeletal gene database. J. Bone Miner Res., 2000, 15: 2095-122.
18. Yamada, Y. Association of a Leu(10)-->Pro polymorphism of the transforming growth factor-beta I with genetic susceptibility to osteoporosis and spinal osteoarthritis. Mech. Ageing Dev., 2000, 116: 113-23.
19. Yamada, Y., Miyauchi, A., Takagi, Y., Tanaka, M., Mizuno, M., Harada, A. Association of the C-509-->T polymorphism, alone or in combination with the T869-->C polymorphism, of the transforming growth factor-beta1 gene with bone mineral density and genetic susceptibility to osteoporosis in Japanese women. J. Mol. Med., 2001, 79: 149-56.
20. Keen, R.W., Snieder, H., Molloy, H., Daniels, J., Chiano, M., Gibson, F., Fairbairn, L., Smith, P., MacGregor, A.J., Gewert, D., Spector, T.D. Evidence of association and linkage disequilibrium between a novel polymorphism in the transforming growth factor beta 1 gene and hip bone mineral density: a study of female twins. Rheumatology (Oxford), 2001, 40: 48-54.
21. Spotila, L.D., Rodriguez, H., Koch, M., Adams, K., Caminis, J., Tenenhouse, H.S., Tenenhouse, A. Association of a polymorphism in the TNFR2 gene with low bone mineral density. J. Bone Miner Res., 2000, 15: 1376-83.
22. Albagha, O.M., McGuigan, F.E., Reid, D.M., Ralston, S.H. Estrogen receptor alpha gene polymorphisms and bone mineral density: haplotype analysis in women from the United Kingdom. J. Bone Miner Res., 2001, 16: 128-34.
23. Ho, A.Y., Yeung, S.S., Kung, A.W. PvuII polymorphisms of the estrogen receptor alpha and bone mineral density in healthy southern Chinese women. Calcif Tissue Int., 2000, 66: 405-8.
24. Ogawa, S., Hosoi, T., Shiraki, M., Orimo, H., Emi, M., Muramatsu, M., Ouchi, Y., Inoue, S. Association of estrogen receptor beta gene polymorphism with bone mineral density. Biochem. Biophys. Res. Commun., 2000, 269: 537-41.
25. Bell, N.H., Morrison, N.A., Nguyen, T.V., Eisman, J., Hollis, B.W. ApaI polymorphisms of the vitamin D receptor predict bone density of the lumbar spine and not racial difference in bone density in young men. J. Lab. Clin. Med., 2001, 137: 133-40.
26. McGuigan, F.E., Reid, D.M., Ralston, S.H. Susceptibility to osteoporosic fracture is determined by allelic variation at the Sp1 site, rather than other polymorphic sites at the COL1A1 locus. Osteoporos. Int., 2000, 11: 338-43.
27. Willing, M.C., Torner, J.C., Burns, T.L., Segar, E.T., Werner, J.R. Determinants of bone mineral density in postmenopausal white Iowans. J. Gerontol. A. Biol. Sci. Med. Sci., 1997, 52: 337-42.
28. Ogawa, S., Urano, T., Hosoi, T., Miyao, M., Hoshino, S., Fujita, M., Shiraki, M., Orimo, H., Ouchi, Y., Inoue, S. Association of bone mineral density with a polymorphism of the peroxisome proliferator-activated receptor gamma gene: PPARgamma expression in osteoblasts. Biochem. Biophys. Res. Commun., 1999, 260: 122-6.
29. Ferrari, S.L., Garnero, P., Emond, S., Montgomery, H., Humphries, S.E., Greenspan, S.L. A functional polymorphic variant in the interleukin-6 gene promoter associated with low bone resorption in postmenopausal women. Arthritis. Rheum., 2001, 44: 196-201.
30. Murray, R.E., McGuigan, F., Grant, S.F., Reid, D.M., Ralston, S.H. Polymorphisms of the interleukin-6 gene are associated with bone mineral density. Bone, 1997, 21: 89-92.
31. Langdahl, B.L., Lokke, E., Carstens, M., Stenkjaer, L.L., Eriksen, E.F. Osteoporotic fractures are associated with an 86-base pair repeat polymorphism in the interleukin-1--receptor antagonist gene but not with polymorphisms in the interleukin-1beta gene. J. Bone Miner Res., 2000, 15: 402-14.
32. Bajnok, E., Takacs, I., Vargha, P., Speer, G., Nagy, Z., Lakatos, P. Lack of association between interleukin-1 receptor antagonist protein gene polymorphism and bone mineral density in Hungarian postmenopausal women. Bone, 2000, 27: 559-62.
33. Rosen, C.J., Kurland, E.S., Vereault, D., Adler, R.A., Rackoff, P.J., Craig, W.Y., Witte, S., Rogers, J., Bilezikian, J.P. Association between serum insulin growth factor-I (IGF-I) and a simple sequence repeat in IGF-I gene: implications for genetic studies of bone mineral density. J. Clin. Endocrinol. Metab., 1998, 83: 2286-90.
34. Takacs, I., Koller, D.L., Peacock, M., Christian, J.C., Hui, S.L., Conneally, P.M., Johnston, C.C. Jr. Foroud, T., Econs, M.J. Sibling pair linkage and association studies between bone mineral density and the insulin-like growth factor I gene locus. J. Clin. Endocrinol. Metab., 1999, 84: 4467-71.
35. Cole, D.E., Vieth, R., Trang, H.M., Wong, B.Y., Hendy, G.N., Rubin, L.A. Association between total serum calcium and the A986S polymorphism of the calcium-sensing receptor gene. Mol. Genet. Metab., 2001, 72: 168-74.
36. Nakamura, M., Morimoto, S., Zhang, Z., Utsunomiya, H., Inagami, T., Ogihara, T., Kakudo, K. Calcitonin receptor gene polymorphism in japanese women: correlation with body mass and bone mineral density. Calcif Tissue Int., 2001, 68: 211-5.
37. Tsukamoto, K., Orimo, H., Hosoi, T., Miyao, M., Yoshida, H., Watanabe, S., Suzuki, T., Emi, M. Association of bone mineral density with polymorphism of the human matrix Gla protein locus in elderly women. J. Bone Miner Metab., 2000, 18: 27-30.
38. Miyao, M., Hosoi, T., Emi, M., Nakajima, T., Inoue, S., Hoshino, S., Shiraki, M., Orimo, H., Ouchi, Y. Association of bone mineral density with a dinucleotide repeat polymorphism at the calcitonin (CT) locus. J. Hum. Genet., 2000, 45: 346-50.
39. Kanzawa, M., Sugimoto, T., Kobayashi, T., Kobayashi, A., Chihara, K. Association between parathyroid hormone (PTH)/PTH-related peptide receptor gene polymorphism and the extent of bone mass reduction in primary hyperparathyroidism. Horm. Metab. Res., 2000, 32: 355-8.
40. Golan, I., Preising, M., Wagener, H., Baumert, U., Niederdellmann, H., Lorenz, B., Mussig, D. A novel missense mutation of the CBFA1 gene in a family with cleidocranial dysplasia (CCD) and variable expressivity. J. Craniofac Genet. Dev. Biol., 2000, 20: 113-20.
41. Wuyts, W., Van Wesenbeeck, L., Morales-Piga, A., Ralston, S., Hocking, L., Vanhoenacker, F., Westhovens, R., Verbruggen, L., Anderson, D., Hughes, A., Van Hul, W. Evaluation of the role of RANK and OPG genes in Paget's disease of bone. Bone, 2001, 28: 104-7.
42. Cauley, J.A., Zmuda, J.M., Yaffe, K., Kuller, L.H., Ferrell, R.E., Wisniewski, S.R., Cummings, S.R. Apolipoprotein E polymorphism: A new genetic marker of hip fracture risk-the study of osteoporotic fractures. J. Bone Miner Res., 1999, 14: 1175-81.
43. Semprini, S., Mango, R., Brancati, F., Dallapiccola, B., Becherini, L., Novelli, G., De Lorenzo, A., Brandi, M.L., Gennari, L. Absence of correlation between BMP-4 polymorphism and postmenopausal osteoporosis in Italian women. Calcif. Tissue Int., 2000, 67: 93-4.
44. Huizenga, N.A., Koper, J.W., De Lange, P., Pols, H.A., Stolk, R.P., Burger, H., Grobbee, D.E., Brinkmann, A.O., De Jong, F.H., Lamberts, S.W. A polymorphism in the glucocorticoid receptor gene may be associated with and increased sensitivity to glucocorticoids in vivo. J. Clin. Endocrinol. Metab., 1998, 83: 144-51.
45. Bouras, M., Tabone, E., Bertholon, J., Sommer, P., Bouvier, R., Droz, J.P., Benahmed, M. A novel SMAD4 gene mutation in seminoma germ cell tumors. Cancer Res., 2000, 60: 922-8.
46. Iwao, K., Miyoshi, Y., Nawa, G., Yoshikawa, H., Ochi, T., Nakamura, Y. Frequent beta-catenin abnormalities in bone and soft-tissue tumors. Jpn. J. Cancer Res., 1999, 90: 205-9.
47. Cheng, L., Wing, H.W. Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection. Proc. Natl. Acad. Sci. USA, 2001, 98: 31-36.
48. Burke, H.B. Discovering patterns in microarray data. Mol. Diagn., 2000, 5: 349-57.
49. Rimm, D.L., Camp, R.L., Charette, L.A., Costa, J., Olsen, D.A., Reiss, M. Tissue microarray: a new technology for amplification of tissue resources. Cancer J., 2001, 7: 24-31.
50. Patankar, S., Munasinghe, A., Shoaibi, A., Cummings, L.M., Wirth, D.F. Serial analysis of gene expression in plasmodium falciparum reveals the global expression profile of erythrocytic stages and the presence of antisense transcripts in the malarial parasite. Mol. Biol. Cell, 2001, 10: 3114-25.
51. Stanton, L.W. Methods to profile gene expression. Trends Cardiovasc. Med., 2001, 11: 49-54.
52. Weindruch, R., Kayo, T., Lee, C.K., Prolla, T.A. Microarray profiling of gene expression in aging and its alteration by caloric restriction in mice. J. Nutr., 2001, 131: 918S-923S.
53. Blohm, D.H., Guiseppi-Elie, A. New developments in microarray technology. Curr. Opin. Biotechnol., 2001, 12: 41-7.
54. Snijders, A.M., Meijer, G.A., Brakenhoff, R.H., van den Brule, A.J., van Diest, P.J. Microarray techniques in pathology: tool or toy? Mol. Pathol., 2000, 53: 289-94.
55. Bednar, M. DNA microarray technology and application. Med. Sci. Monit., 2000, 6: 796-800.
56. Diehn, M., Relman, D.A. Comparing functional genomic datasets: lessons from DNA microarray analyses of host-pathogen interactions. Curr. Opin. Microbiol., 2001, 4: 95-101.
57. Alizadeh, A., Eisen, M., Davis, R.E., Ma, C., Sabet, H., Tran, T., Powell, J.I., Yang, L., Marti, G.E., Moore, D.T., Hudson, J.R. Jr., Chan, W.C., Greiner, T., Weisenburger, D., Armitage, J.O., Lossos, I., Levy, R., Botstein, D., Brown, P.O., Staudt, L.M. The lymphochip: a specialized cDNA microarray for the genomic-scale analysis of gene expression in normal and malignant lymphocytes. Cold Spring Harb. Symp. Quant. Biol., 1999, 64: 71-8.
58. Rikke, B.A., Johnson, T.E. Towards the cloning of genes underlying murine QTLs. Mamm. Genome, 1998, 9: 963-8.
59. Crabbe, J.C., Phillips, T.J., Buck, K.J., Cunningham, C.L., Belknap, J.K. Identifying genes for alcohol and drug sensitivity: recent progress and future directions. Trends Neurosci., 1999, 22: 173-9.
60. Dominiczak, A.F., Negrin, D.C., Clark, J.S., Brosnan, M.J., McBride, M.W., Alexander, M.Y. Genes and hypertension: from gene mapping in experimental models to vascular gene transfer strategies. Hypertension, 2000, 35: 164-72.
61. Legare, M.E., Bartlett, F.S. 2nd., Frankel, W.N. A major effect QTL determined by multiple genes in epileptic EL mice. Genome Res., 2000, 10: 42-8.
62. Beck, G.R. Jr., Zerler, B., Moran, E. Gene array analysis of osteoblast differentiation. Cell Growth Differ., 2001, 12: 61-83.
63. Lomri, A., Lemonnier, J., Delannoy, P. and Marie, P.J. Increased expression of protein kinase C alpha, interleukin-1 alpha, and RhoA guanosine 5′-triphosphatase in osteoblasts expressing the Ser252Trp fibroblast growth factor 2 Apert mutation: identification by analysis of complementary DNA microarray. J. Bone Miner Res., 2001, 16: 705-12.
64. Chen, J., Zhong, Q., Wang, J., Cameron, R.S., Borke, J.L., Isales, C.M., Bollag, R.J. Microarray analysis of Tbx2-directed gene expression: a possible role in osteogenesis. Mol. Cell. Endocrinol., 2001, 177: 43-54.
65. Xynos, I.D., Edgar, A.J., Buttery, L.D., Hench, L.L., Polak, J.M. Gene-expression profiling of human osteoblasts following treatment with the ionic products of Bioglass 45S5 dissolution. J. Biomed. Mater Res., 2001, 55: 151-7.
66. Huang, W., Carlsen, B., Rudkin, G.H., Shah, N., Chung, C., Ishida, K., Yamaguchi, D.T., Miller, T.A. Effect of serial passage on gene expression in MC3T3-E1 preosteoblastic cells: a microarray study. Biochem. Biophys. Res. Commun., 2001, 281: 1120-6.
67. Gu, W-K., Li, X., Lau, K-H.W., Edderkaoui, B., Donahae, L.R., Rosen, C.J., Beamer, W.G., Shultz, K.L., Srivastava, A., Mohan, S., Baylink, D.J. Gene expression between a congenic strain that contains a QTL locus of high bone density from CAST/EiJ and its wild type strain C57BL/6J. Functional and Integrative Genomics, 2002, 1: 375-86.