H. Earl Ruley, Ph.D.


Faculty Appointments
Professor of Pathology, Microbiology and Immunology
Ph.D., Microbiology, University of North Carolina, Chapel Hill, North CarolinaB.A., Anthropology, Stanford University, Stanford, California
Office Address
A-4210A MCN
TN 2363
Research Description
My laboratory uses genetic and biochemical approaches to study mechanisms important in growth control and cancer. We have developed gene trapping strategies for genome-wide, biallelic mutagenesis of mammalian cells. Mutations in embryonic stem cells that affect specific genes of interest may be introduced into the germline; alternatively biallelic mutagens may be used in phenotype driven screens to identify genes responsible for recessive phenotypes in mammalian cells. We have used the to first approach to generate mice and cells defective in genes that are potentially involved in post-transcriptional gene regulation, [Ran GTPase activating protein, hnRNP A2/B1, hnRNP C, hnRNP U, TLS/Fus (hnRNP P2) and arginine methytransferase 1 (Prmt1)]. The genetic analysis of TLS/Fus, a gene translocated in human cancer, led to the unexpected discovery implicating this RNA binding protein in the maintenance of genome stability. The second approach has been used to identify candidate genes involved in Reovirus infection.
Studies to develop gene trap vectors provided basic information about transcript quality control, notably exon definition and nonsense-mediated decay, that govern the expression of gene segments inserted at ectopic sites in the genome. In addition, the collection of mutant stem cells has been used in genome-wide studies of spontaneous and carcinogen-induced LOH (loss of heterozygosity). The extent of LOH was remarkably high approaching 1% of the genome after brief exposure to nontoxic levels of carcinogens. These results highlight the importance of LOH as a somatic mutation and suggest that much of the LOH in cancer cells may result from prior exposure to genotoxic agents rather than from a state of chromosome instability during carcinogenesis. In addition this work underscores the importance of genome maintenance in stem cells that serve as the normal cellular precursors to cancer. Current work in the lab is investigating the mechanisms of carcinogen-induced LOH.
Research Keywords
Genetic analysis of growth control and development
Lin Q, Donahue SL, Ruley HE. Genome maintenance and mutagenesis in embryonic stem cells. Cell Cycle [print-electronic]. 2006 Dec; 5(23): 2710-4. PMID: 17172854, PII: 3517, ISSN: 1551-4005.

Donahue SL, Lin Q, Cao S, Ruley HE. Carcinogens induce genome-wide loss of heterozygosity in normal stem cells without persistent chromosomal instability. Proc. Natl. Acad. Sci. U.S.A [print-electronic]. 2006 Aug 8/1/2006; 103(31): 11642-6. PMID: 16868089, PMCID: PMC1544223, PII: 0510741103, DOI: 10.1073/pnas.0510741103, ISSN: 0027-8424.

Lin Q, Donahue SL, Moore-Jarrett T, Cao S, Osipovich AB, Ruley HE. Mutagenesis of diploid mammalian genes by gene entrapment. Nucleic Acids Res [print-electronic]. 2006; 34(20): e139. PMID: 17062627, PMCID: PMC1635309, PII: gkl728, DOI: 10.1093/nar/gkl728, ISSN: 1362-4962.

Roshon MJ, Ruley HE. Hypomorphic mutation in hnRNP U results in post-implantation lethality. Transgenic Res. 2005 Apr; 14(2): 179-92. PMID: 16022389, ISSN: 0962-8819.

Osipovich AB, Singh A, Ruley HE. Post-entrapment genome engineering: first exon size does not affect the expression of fusion transcripts generated by gene entrapment. Genome Res. 2005 Mar; 15(3): 428-35. PMID: 15741512, PMCID: PMC551569, PII: 15/3/428, DOI: 10.1101/gr.3258105, ISSN: 1088-9051.

Organ EL, Sheng J, Ruley HE, Rubin DH. Discovery of mammalian genes that participate in virus infection. BMC Cell Biol. 2004 Nov 11/2/2004; 5(1): 41. PMID: 15522117, PMCID: PMC534806, PII: 1471-2121-5-41, DOI: 10.1186/1471-2121-5-41, ISSN: 1471-2121.

Lin Q, Jo D, Gebre-Amlak KD, Ruley HE. Enhanced cell-permeant Cre protein for site-specific recombination in cultured cells. BMC Biotechnol. 2004 Oct 10/22/2004; 4: 25. PMID: 15500682, PMCID: PMC529453, PII: 1472-6750-4-25, DOI: 10.1186/1472-6750-4-25, ISSN: 1472-6750.

Sheng J, Organ EL, Hao C, Wells KS, Ruley HE, Rubin DH. Mutations in the IGF-II pathway that confer resistance to lytic reovirus infection. BMC Cell Biol. 2004 Aug 8/27/2004; 5: 32. PMID: 15333144, PMCID: PMC517494, PII: 1471-2121-5-32, DOI: 10.1186/1471-2121-5-32, ISSN: 1471-2121.

Osipovich AB, White-Grindley EK, Hicks GG, Roshon MJ, Shaffer C, Moore JH, Ruley HE. Activation of cryptic 3' splice sites within introns of cellular genes following gene entrapment. Nucleic Acids Res [electronic-print]. 2004; 32(9): 2912-24. PMID: 15155860, PMCID: PMC419606, PII: 32/9/2912, DOI: 10.1093/nar/gkh604, ISSN: 1362-4962.

Cao S, Bendall H, Hicks GG, Nashabi A, Sakano H, Shinkai Y, Gariglio M, Oltz EM, Ruley HE. The high-mobility-group box protein SSRP1/T160 is essential for cell viability in day 3.5 mouse embryos. Mol. Cell. Biol. 2003 Aug; 23(15): 5301-7. PMID: 12861016, PMCID: PMC165710, ISSN: 0270-7306.

Jo D, Lin Q, Nashabi A, Mays DJ, Unutmaz D, Pietenpol JA, Ruley HE. Cell cycle-dependent transduction of cell-permeant Cre recombinase proteins. J. Cell. Biochem. 2003 Jul 7/1/2003; 89(4): 674-87. PMID: 12858334, DOI: 10.1002/jcb.10542, ISSN: 0730-2312.

Roshon M, DeGregori JV, Ruley HE. Gene trap mutagenesis of hnRNP A2/B1: a cryptic 3' splice site in the neomycin resistance gene allows continued expression of the disrupted cellular gene. BMC Genomics [print-electronic]. 2003 Jan 1/20/2003; 4(1): 2. PMID: 12546712, PMCID: PMC149352, ISSN: 1471-2164.

Pawlak MR, Banik-Maiti S, Pietenpol JA, Ruley HE. Protein arginine methyltransferase I: substrate specificity and role in hnRNP assembly. J. Cell. Biochem. 2002; 87(4): 394-407. PMID: 12397599, DOI: 10.1002/jcb.10307, ISSN: 0730-2312.

White EK, Moore-Jarrett T, Ruley HE. PUM2, a novel murine puf protein, and its consensus RNA-binding site. RNA. 2001 Dec; 7(12): 1855-66. PMID: 11780640, PMCID: PMC1370223, ISSN: 1355-8382.

Jo D, Nashabi A, Doxsee C, Lin Q, Unutmaz D, Chen J, Ruley HE. Epigenetic regulation of gene structure and function with a cell-permeable Cre recombinase. Nat. Biotechnol. 2001 Oct; 19(10): 929-33. PMID: 11581657, PII: nbt1001-929, DOI: 10.1038/nbt1001-929, ISSN: 1087-0156.

Ruley HE. Functional genomics of the murine immune system. Immunol. Res. 2001; 23(2-3): 289-99. PMID: 11444394, PII: IR:23:2-3:289, DOI: 10.1385/IR:23:2-3:289, ISSN: 0257-277X.

Peck SR, Ruley HE. Ly108: a new member of the mouse CD2 family of cell surface proteins. Immunogenetics. 2000 Nov; 52(1-2): 63-72. PMID: 11132158, ISSN: 0093-7711.

Williamson DJ, Banik-Maiti S, DeGregori J, Ruley HE. HnRNP C is required for postimplantation mouse development but Is dispensable for cell viability. Mol. Cell. Biol. 2000 Jun; 20(11): 4094-105. PMID: 10805751, PMCID: PMC85779, ISSN: 0270-7306.

Hicks, G.G., Singh, N, Nashabi, A., Mai, S., Gracjan Bozek, Klewes, L., Arapovic, D., White, E.K., Koury, M.J., Oltz, E.M., Van Kaer, L.V., and Ruley, H.E. Fus deficiency in mice results in defective B lymphocyte development and activation, high levels of chromosomal instability and perinatal death. Nature Genetics. 2000; 24: 176-9.

Pawlak, M.R., Scherer, C.A., Chen, J., Roshon, M.J., Ruley, H.E. Arginine methyltransferase 1 is required for early post- implantation mouse development, but cells deficient in the enzyme are viable. Mol. Cell. Biol. 2000; 20: 4859-69.

Chen J, Ruley HE. An enhancer element in the EphA2 (Eck) gene sufficient for rhombomere-specific expression is activated by HOXA1 and HOXB1 homeobox proteins. J. Biol. Chem. 1998 Sep 9/18/1998; 273(38): 24670-5. PMID: 9733765, ISSN: 0021-9258.

Kelly, L.L., Hicks, G.G., Hsieh, F.F., Green, W.F., Miller, M.D., Eide, E.J. and Ruley, H.E. Wild-type p53 regulation and function in early stage tumor progression differs from that following DNA damage. Oncogene. 1998; 17: 1119-30.

Chen, J. and Ruley, H.E. An enhancer element in the EphA2 (Eck) gene is sufficient for rhombomere-specific gene expression and is activated by HOXA1 and HOXB1 homeobox proteins. J. Biol. Chem. 1998; 273: 64670-5.

Hicks GG, Shi EG, Li XM, Li CH, Pawlak M, Ruley HE. Functional genomics in mice by tagged sequence mutagenesis. Nat. Genet. 1997 Aug; 16(4): 338-44. PMID: 9241269, DOI: 10.1038/ng0897-338, ISSN: 1061-4036.

Hicks, G.G., Shi, E., Li, X., Li, C., Pawlak, M. and Ruley, H.E. Functional Genomics in Mice by Tagged Sequence Mutagenesis. Nature Genetics. 1997; 16: 338-44.

Chen J, Nachabah A, Scherer C, Ganju P, Reith A, Bronson R, Ruley HE. Germ-line inactivation of the murine Eck receptor tyrosine kinase by gene trap retroviral insertion. Oncogene. 1996 Mar 3/7/1996; 12(5): 979-88. PMID: 8649815, ISSN: 0950-9232.

Martin WD, Hicks GG, Mendiratta SK, Leva HI, Ruley HE, Van Kaer L. H2-M mutant mice are defective in the peptide loading of class II molecules, antigen presentation, and T cell repertoire selection. Cell. 1996 Feb 2/23/1996; 84(4): 543-50. PMID: 8598041, PII: S0092-8674(00)81030-2, ISSN: 0092-8674.

Ruley HE. P53 and response to chemotherapy and radiotherapy. Important Adv. Oncol. 1996; 37-56. PMID: 8791127, ISSN: 0883-5896.

Ruley, H.E. P53 and response to chemotherapy and radiotherapy. Important Advances in Oncology 1996. DeVita, V.T., Hellman, S. and Rosenberg, S.A. eds. J.B. Lippincott Co., Philadelphia. 1996; 37-56.

Chen, J., Nachebeh, A., Scherer, C., Ganju, P., Reith, A., Bronson, R., Ruley, H.E. Germ-line inactivation of the murine Eck receptor tyrosine kinase gene by retroviral insertion. Oncogene. 1996; 12: 979-88.

Martin, W. D., Hicks, G.G., Mediratta, S.K., Leva, H.I., Ruley, H.E., and Van Kaer, L. H-2M mutant mice are defective in the peptide loading of class II molecules, antigen presentation, and T cell repertoire selection. Cell. 1996; 84: 543-50.

Scherer, C.A., Chen, J., Nachabeh, A., Hopkins, N., and Ruley, H.E. Transcriptional specificity of the pluripotent embryonic stem cell. Cell Growth Diff. 1996; 7: 1393-401.

Hicks GG, Shi EG, Chen J, Roshon M, Williamson D, Scherer C, Ruley HE. Retrovirus gene traps. Meth. Enzymol. 1995; 254: 263-75. PMID: 8531691, ISSN: 0076-6879.

Kelley LL, Green WF, Hicks GG, Bondurant MC, Koury MJ, Ruley HE. Apoptosis in erythroid progenitors deprived of erythropoietin occurs during the G1 and S phases of the cell cycle without growth arrest or stabilization of wild-type p53. Mol. Cell. Biol. 1994 Jun; 14(6): 4183-92. PMID: 8196656, PMCID: PMC358784, ISSN: 0270-7306.

DeGregori J, Russ A, von Melchner H, Rayburn H, Priyaranjan P, Jenkins NA, Copeland NG, Ruley HE. A murine homolog of the yeast RNA1 gene is required for postimplantation development. Genes Dev. 1994 Feb 2/1/1994; 8(3): 265-76. PMID: 8314081, ISSN: 0890-9369.

Chen, J., Degregori, J., Hicks, G., Roshon, M., Shi, E-G, Scherer, S. and Ruley H.E. Gene Trap Retroviruses. Meth. Mol. Genet. 1994; 4: 123-40.

DeGregori, J.V., Russ, A., von Melchner, H., Rayburn, H., Priyaranjan, P., Jenkins, N., Copeland, N.and Ruley, H.E. A murine homolog of the yeast RNA1 gene is required for postimplantation development. Genes and Dev. 1994; 8: 265-76.

Lowe, S.W., Jacks, T., and Housman and Ruley, H.E. Abrogation of oncogene associated apoptosis allows transformation of p53 deficient cells. Proc. Natl. Acad. Sci. (USA). 1994; 91: 2026-30.

Hubbard, S.C., Walls, L., Ruley, H.E., and Muchmore, E.A. Generation of Chineses hamster ovary cell glycosylation mutants by retroviral insertional mutagenesis: integration into a discrete locus generates mutants expressing high levels of N-glycolyneuraminic acid. J. Biol. Chem. 1994; 269: 3713-24.

Kelly, L.L., Green, W.F., Hicks, G.G., Bondurant, M.C., Koury, M.J. and Ruley, H.E. Apoptosis in erythroid progenitors deprived of erythropoietin occurs during G1 and S phases of the cell cycle without growth arrest or stabilization of wild-type p53. Mol. Cell. Biol. 1994; 14: 4183-92.

Lowe, S.W., Bodis, S., McClatchey, A., Remington, L., Ruley, H.E., Fisher, D., Housman, D., and Jacks, T. P53 status and the efficacy of cancer therapy in vivo. Science. 1994; 266: 807-10.

Chang, W., Fridel, C. and Ruley, H.E. Enrichment of insertional mutants following retrovirus gene trap selection. Virology. 1993; 193: 737-47.

Lowe, S.W. and Ruley, H.E. Stabilization of the p53 tumor suppressor is induced by adenovirus-5 E1A and accompanies apoptosis. Genes Dev. 1993; 7: 535-45.

Lowe, S.W., Ruley, H.E., Jacks, T., and Housman, D.E. P53-dependent apoptosis modulates the cytoxicity of anticancer agents. Cell. 1993; 74: 957-67.

von Melchner, H., DeGregori, J.V., Raybrun, H., Reddy, S. ,Fridel, C., and Ruley, H.E. Selective disruption of genes expressed in totipotent embryonal stem cells. Genes Dev. 1992; 6: 919-26.

Reddy, S., Rayburn, H., von Melchner, H., and Ruley, H.E. Fluorescence activated sorting of totipotent embryonic stem cells expressing developmentally regulated lacZ fusion genes. Proc. Natl. Acad. Sci. U.S.A. 1992; 89: 6721-5.

Reddy, S., DeGregori, J.V., von Melchner, H. and Ruley, H.E. Retrovirus promoter trap vector to induce lacZ gene fusions in mammalian cells. J. Virol. 1991; 65: 1507-15.

Ravid, K., Beeler, D.L. Rabin, M.S., Ruley, H.E. and Rosenberg, R.D. Selective targeting of gene products with megakarocyte PF4 promoter. Proc. Natl Acad. Sci. U.S.A. 1991; 88: 1521-5.

Hirakawa, T., Maruyama, K., Kohl, N.E., Kodama, T. and Ruley, H.E. Massive accumulation of neutral lipids in cells conditionally transformed by an activated H-ras oncogene. Oncogene. 1990; 6: 289-95.

Hirakawa, T. and H.E. Ruley. Rescue of cells from ras-oncogene induced growth arrest by a second, complementing oncogene. Proc. Natl. Acad. Sci. (USA). 1988; 85: 1519-23.

Whyte, P., Ruley, H.E. and Harlow, E. Two regions of the adenovirus early region proteins required for transformation. J. Virol. 1988; 62: 257-65.

Zerler, B., B.Moran, K.Maruyama, J.Moomaw, T.Grodzicker, and H.E.Ruley. Adenovirus E1A coding sequences that enable ras and pmt oncogenes to transform cultured primary cells. Mol. Cell Biol. 1986; 6: 887-99.

Franza, B.R. Jr.,K. Maruyama, J.I.Garrels, and H.E. Ruley. In vitro establishment is not a sufficient prerequisite for transformation by activated ras oncogenes. Cell. 1986; 44: 409-18.

Ruley, H.E. and Fried, M. Clustered illegitimate recombination events in mammalian cells involving very short sequence homologies. Nature. 1983; 304: 181-4.

Ruley, H.E. and Fried, M. Sequence repeats in a polyoma virus DNA region important for gene expression. J. Virol. 1983; 47: 233-7.

Ruley, H.E. Adenovirus early region 1A enables viral and cellular transforming genes to transform primary cells in culture. Nature. 1983; 304: 602-6.