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Rosann Farber, PhD
Professor
Associate Chair

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Research Interests
Key words: Human molecular genetics, somatic-cell genetics, instability of simple sequence repeats


The general interest of my lab is in genetic instability in the development and progression of cancer. We are using a tissue culture system to study mutations that result in changes in the lengths of microsatellite sequences in mammalian cells. Microsatellites are tandem repeats of short sequences (usually from one to five base pairs per repeat unit, with tract lengths up to about 30 units); they are abundant and widely dispersed throughout mammalian and other eucaryotic genomes. There is extensive length polymorphism at most human microsatellite loci. Microsatellite instability has been shown to be a hallmark of certain cancers, including those that occur in families with hereditary nonpolyposis colorectal cancer (HNPCC) and a subset of related sporadic cancers. The hypermutability of microsatellites in these cancers results in at least some families from a defect in DNA mismatch repair

We have developed a plasmid vector into which various microsatellite sequences can be cloned. The cloning site is located within a fusion gene, composed of the Herpes simplex virus thymidine kinase (tk) gene fused to the 5' end of a bacterial neomycin-resistance (neo) gene. The cloning site is located near the 3' end of the tk gene, such that inserts affect the reading frame of the neo gene. Inserts that position the gene out-of-frame and consist of tandem repeats that are not multiples of three bases are being studied. Plasmids containing microsatellites are introduced by transfection into mammalian cells, where they integrate into the cellular genome, and clones resistant to the neomycin analogue G418 are selected. Increases and decreases in specific numbers of repeating units restore the reading frame of the neo gene, leading to drug-resistance.

We are using these microsatellites as markers of genetic instability in neoplasia. We are asking questions about the rates and kinds of mutations that occur in neoplastic cells with and without mismatch repair defects and about genes other than those involved in mismatch repair that may affect the stability of these sequences. The effects of microsatellite length and sequence composition on mutation rates and the nature of these mutations are being studied. A similar system yeast is being used to learn about the effects of the position in the genome on microsatellite mutations.


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Publications
Farber, R.A., Gene dosage and the expression of electrophoretic patterns in heteroploid mouse cell lines, Genetics 74: 521-531 (1973).

Gartler, S.M., and Farber, R.A., Biochemical identification of cells in culture, A. Human cell lines by enzyme polymorphism, in Tissue Culture: Methods and Applications, eds. Kruse, P.F., Jr., and Patterson, M.K., New York: Academic Press, Inc., pp. 797-804 (1973).

Farber, R.A., and Liskay, R.M., Karyotypic analysis of a near-diploid established mouse cell line, Cytogenet. Cell Genet. 13: 384-396 (1974).

Petes, T.D., Farber, R.A., Tarrant, G.M., and Holliday, R., Altered rate of DNA replication in aging human fibroblasts, Nature 251: 434-435 (1974).

Farber, R.A., and Unrau, P., Isolation of cold-sensitive Chinese hamster cells, Molec. Gen. Genet. 138: 233-242 (1975).

Farber, R.A., and Deutscher, M.P., Physiological and biochemical properties of a temperature-sensitive leucyl-tRNA synthetase mutant (tsH1) and revertant from Chinese hamster cells, Somat. Cell Genet. 2: 509-520 (1976).

Farber, R.A., and Unrau, P., Induction and isolation of cold-sensitive lines of Chinese hamster cells, Methods in Cell Biol. 14: 265-271 (1976).

Farber, R.A., and Davidson, R.L., Differences in the order of termination of DNA replication in human chromosomes in peripheral blood lymphocytes and skin fibroblasts from the same individual, Cytogenet. Cell Genet. 18: 349-363 (1977).

Farber, R.A., and Davidson, R.L., Altered pattern of replication of human chromosomes in a human fibroblast-mouse cell hybrid, Proc. Natl. Acad. Sci. (U.S.) 75: 1470-1474 (1978).

Farber, R.A., Maintenance of replication patterns in human x mouse hybrids with different chromosomal compositions, Cytogenet. Cell Genet. 27: 246-253 (1980).

Eves, E.M., and Farber, R.A., Chromosome segregation is frequently associated with the expression of recessive mutations in mouse cells, Proc. Natl. Acad. Sci. (U.S.) 78: 1768-1772 (1981).

Lindgren, V., and Farber, R.A., Chromosome replication in aging human diploid fibroblasts, Exptl. Cell Res. 142: 301-308 (1982).

Dubnick, M., Chou, J., Petes, T.D., and Farber, R.A., Relationships among DNA sequences of the 1.3 kb EcoRI family of mouse DNA, J. Molec. Evol. 19: 115-121 (1983).

Lindgren, V., and Farber, R.A., Chromosome replication in normal and transformed human lymphocytes, Cancer Genet. Cytogenet. 9: 71-79 (1983).

Eves, E.M., and Farber, R.A., Expression of recessive Aprt- mutations in mouse CAK cells resulting from chromosome loss and duplication, Somat. Cell Genet. 9: 771-778 (1983).

Samuelson, L., and Farber, R.A., Cytological localization of the adenosine kinase, nucleoside phosphorylase-1 and esterase-10 genes on mouse chromosome 14, Somat. Cell Molec. Genet. 11: 157-165 (1985).

Farber, R.A., and Zielinski, D., Assignment of a processed mouse Aprt pseudogene to the same chromosome as the functional gene, Cytogenet. Cell Genet. 42: 198-201 (1986).

Strauss, B., Sagher, D., Karrison, T., Larson, R., Meier, P., Schwartz, J., Farber, R., and Weichselbaum, R., The response of human cells to in vivo methylation damage, in Proceedings of the International Congress on DNA Damage and Repair, ed. A. Castellani, New York: Plenum Press, pp. 107-123 (1988).

Farber, R.A., Phalen, T., Neuman,. W.L., Le Beau, M.M., Wasmuth, J.J., and Dobbs, M. An anonymous DNA segment (pTP5E) maps to the long arm of chromosome 5 and identifies a Taq I polymorphism (D5S70), Nuc. Acids Res. 16:2360 (1988).

McCormick, J.J., Yang, D., Maher, V.M., Farber, R., Neuman, W., Peterson, W.D., Jr., and Pollack, M.S., The HuT series of 'carcinogen-transformed' human fibroblast cell lines are derived from the human fibrosarcoma cell line 8387, Carcinogenesis 9:2073-2079 (1988).

Neuman, W.L., Ponto, K., Farber, R., and Shangold, G.A., DNA analysis of unilateral twin ectopic gestation, Obstetrics and Gynecology 75:479-483 (1990).

Highsmith, W.E., Jr., Chong, G., Orr, H.T., Perry, T.R., Schaid, D., Farber, R., Wagner, K., Knowles, M.R., Warwick, W.J., Silverman, L.M., and Thibodeau, S.N., Frequency of the DPhe508 mutation and correlation with XV.2c/KM-19 haplotypes in an American population of cystic fibrosis patients: Results of a collaborative study, Clin. Chem.36:1741-1746 (1990).

Perlman, E.J., Stetten, G., Tuck-Miller, C.M., Farber, R.A., Neuman, W.L., Blakemore, K.J., and Hutchins, G.M., Sexual discordance in monozygotic twins, Amer. J. Med. Genet. 37:551-557 (1990).

Witt, M., Erickson, R.P., Ober, C., Howatt, W.F., and Farber, R., Correlation of phenotypic and genetic heterogeneity in cystic fibrosis: variability in sweat electrolyte levels contributes to heterogeneity, Amer. J. Med. Genet. 39:137-143 (1991).

Neuman, W.L., Rubin, C.M., Rios, R.B., Larson, R., Le Beau, M.M., Rowley, J.D., Vardiman, J.W., Schwartz, J.L., and Farber, R.A., Chromosomal loss and deletion are the most common mechanisms for loss of heterozygosity from chromosomes 5 and 7 in malignant myeloid disorders, Blood 79:1501-1510 (1992).

Neuman, W.L., Le Beau, M.M., Farber, R.A., Lindgren, V., and Westbrook, C.A., Somatic cell hybrid mapping of chromosome band 5q31: A region important to hematopoiesis, Cytogenet. Cell Genet. 61:103-106 (1992).

Tazelaar, J., Friedman, K.J., Kline, R., Guthrie, M., and Farber, R.A., Detection of alpha1-antitrypsin Z and S mutations by polymerase chain reaction-mediated site-directed mutagenesis, Clinical Chemistry 38:1486-1488 (1992).

Shroeder, R.E., Johnson, F.L., Silberstein, M., Neuman, W.L., Hoag, J.M., Farber, R.A., and Noguchi, A., Longitudinal follow-up of malignant osteopetrosis by skeletal radiographs and restriction fragment length polymorphism analysis after bone marrow transplantation, Pediatrics 90:986-989 (1992).

Garrett, P., Hulka, B., Kim, Y., and Farber, R.A., HRAS proto-oncogene polymorphism and breast cancer, Cancer Epidemiology, Biomarkers, and Prevention 2:131-138 (1993).

Farber, R.A., Petes, T.D., Dominska, M., Hudgens, S.S., and Liskay, R.M., Instability of simple sequence repeats in mammalian cells, Hum. Molec. Genet.3:253-256 (1994).

Heim, R.A., Silverman, L.M., Farber, R.A., Kam-Morgan, L.N.W., and Luce, M.C., Screening for truncated NF1 proteins, Nature Genet. 8:218-219 (1994).

King, S. A., Wilson, S.J., Farber, R.A., Kaufmann, W.K., and Cordeiro-Stone, M., Xeroderma pigmentosum variant: Generation and characterization of fibroblastic cell lines for the study of the molecular defect underlying this genetic disease, Exptl. Cell Res. 217:100-108 (1995).

Heim, R.A., Kam-Morgan, L.N.W., Binnie, C.G., Corns, D.D., Cayouette, M.C., Farber, R.A., Aylsworth, A.S., Silverman, L.M., and Luce, M.C., Identification of thirteen new, truncating mutations in the neurofibromatosis 1 gene, Hum. Molec. Genet. 4:975-981 (1995).

Riedinger, K.L., Hanford, M.G., and Farber, R.A., Induction of frameshift mutations in cultured mammalian cells within a transfected sequence containing a poly(dC-dA)·poly(dT-dG) microsatellite, Env. Molec. Mutagenesis 28:276-283 (1996).

Reitnauer, P.J., Callanan, N.P., Farber, R.A., and Aylsworth, A.S., Prenatal exposure to disulfiram implicated in the cause of malformations in discordant monozygotic twins, Teratology 56:358-362 (1997).

Hanford, M.G., Rushton, B.C., Gowen, L.C., and Farber, R.A., Microsatellite mutation rates in cancer cell lines deficient or proficient in mismatch repair, Oncogene 16:2389-2393 (1998).

Boyer, J.C., Risinger, J.I., and Farber, R.A., Stability of microsatellites in myeloid neoplasias, Cancer Genet. Cytogenet. 106:54-61 (1998).

Boyer, J.C., and Farber, R.A., Mutation rate of a microsatellite sequence in normal human fibroblasts, Cancer Res. 58:3946-3949 (1998).

Twerdi, C.D., Boyer, J.C., and Farber, R.A., Relative rates of insertion and deletion mutations in a microsatellite sequence in cultured cells, Proc. Natl. Acad. Sci. USA 96:2875-2879 (1999).

Passarge, E., Horsthemke, B., and Farber, R.A., Incorrect use of the term synteny, Nature Genet. 23:387 (1999).

Lee, J.S., Hanford, M.G., Genova, J.L., and Farber, R.A., Relative stabilities of dinucleotide and tetranucleotide repeats in cultured mammalian cells, Hum. Molec. Genet. 8:2567-2572 (1999).

Roques, C.N., Boyer, J.C., and Farber, R.A., Microsatellite mutation rates are equivalent in normal and telomerase-immortalized human fibroblasts, Cancer Res. 61:8405-8407 (2001).

Yamada, N.A., and Farber, R.A., Induction of a low level of
microsatellite instability by overexpression of DNA polymerase b, Cancer Res. 62:6061-6064 (2002).

Boyer, J.C., Yamada, N.A., Roques, C.N., Hatch, S.B., Riess, K., and Farber, R.A., Sequence dependent instability of mononucleotide microsatellites in cultured mismatch-repair-proficient and - deficient mammalian cells, Hum. Molec. Genet. 11:707-713 (2002).

Yamada, N.A., Smith, G.A., Castro, A., Roques, C.N., Boyer, J.C., and Farber, R.A., Relative rates of insertion and deletion mutations in dinucleotide repeats of various lengths in mismatch repair proficient and deficient mammalian cells, Mutation Res. 499:213-225 (2002).

Hatch, S.B., and Farber, R.A., Mutation rates in the complex
microsatellite MYCL1 and related simple repeats in cultured human cells, Mutation Res. 545:117-126 (2003).

Yamada, N.A., Parker, J.M., and Farber, R.A., Mutation frequency analysis of mononucleotide and dinucleotide repeats after oxidative stress, Env. Molec. Mutagenesis 42:75-84 (2003).

Yamada, N.A., Castro, A., and Farber, R.A., Variation in the extent of microsatellite instability in human cell lines with defects in different mismatch repair genes, Mutagenesis 18:277-282 (2003).

Hatch, S.B., Lightfoot, H.M., Garwacki, C.P., Moore, D.T., Calvo,
B.F., Woosley, J.T., Funkhouser, W.K., and Farber, R.A., Microsatellite instability and mismatch repair defects in sporadic colorectal cancer, Clin. Cancer Res. 11:2180-2187 (2005).

Hawk, J.D., Stefanovic, L., Boyer, J.C., Petes, T.D., and Farber, R.A., Variation in efficiency of DNA mismatch repair at different sites in the yeast genome, Proc. Natl. Acad. Sci. USA 102:8639-8643 (2005).

Fan, H., Booker, J.K., McCandless, S.E., Shashi, V., Fleming, A., and Farber, R.A., Mosaicism for an FMR1 gene deletion in a fragile X female, Am. J. Med. Genet. 136A:214-217 (2005).


H. Fan, C. Civalier, J.K. Booker, M.L. Gulley, T.W. Prior, R.A. Farber, Detection of common disease-causing mutations in mitochondrial DNA (MELAS MTTL1 3243 A>G and MERRF MTTK 8344A>G) by real-time PCR, J. Molec. Diagnostics 8:277-281 (2006).


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Current Trainees
Postdoctoral:
Natasha Butz, Ph.D., Academy of Sciences, Institute of Molecular Biology and Genetics, Kiev, Ukraine.


Prior Trainees
Postdoctoral:
Jayne Boyer, Ph.D.
Research Assistant Professor, Dept. of Pathology and Laboratory Medicine, UNC at Chapel Hill

Eva Eves, Ph.D., The University of Chicago
Present position: Senior Research Associate, Ben May Laboratories, U. of Chicago

Jung Sup Lee, Ph.D., Seoul National University
Present position: Associate Professor, Dept. of Pharmacology, Chosun University, Republic of Korea

Wilma L. Neuman, Ph.D., University of Illinois at Chicago
Present position: Full-time parent


Predoctoral:

Mark Dubnick, Ph.D.
Present position: Staff Fellow, NINDS/NIH

Stephanie Hatch, Ph.D.
Postdoctoral Fellow, Institute of Cancer Research, London

Valerie Lindgren, Ph.D.
Present position: Associate Professor, Dept. of Pathology, Loyola University Medical Center (Chicago)

Linda Samuelson, Ph.D
Present position: Professor, Dept. of Physiology, University of Michigan

Nazumi Alice Yamada, Ph.D.
Staff Scientist, Lawrence Livermore National Laboratory, CA


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Contact Information
4109C Neuroscience Research Building, CB#7525
Office: 919. 966.6920
Lab: 919. 966.6921
Fax: 919. 966.3630
Email: rosann.farber<at>pathology.unc.edu

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