Ludwig Institute for Cancer Research San Diego Branch

Publications

Garcia, M.L., Singleton, A., Hernandez, D., Ward, C.M., McClure, J., Evey, C., Sapp, P.A., Hardy, J.A., Brown, R.H., Jr., and Cleveland, D.W. (2006). Mutations in neurofilament genes are not a primary cause of non-SOD1 mediated Amyotrophic Lateral Sclerosis. Neurobiol. Dis., 21, 102-109.
Eymard-Pierre, E., Yamanaka, K., Haeussler, M., Kress, W. Combes , P., Gauthier-barichard, F. Cleveland, D.W., and Boespflug-Tanguy, O. (2006). Missense mutation in the RCC1 domain of the ALS2 protein results in infantile ascending hereditary spastic paralysis (IAHSP). Ann. Neurol., 59, 976-980.
Foltz, D.R., Janssen, L., Black, B.E., Bailey, A.O., Yates, J.R., III, and Cleveland, D.W. (2006). The human CENP-A centromeric nucleosome associated complex. Nat. Cell Biol., 458-469.
Wang, Z., Shah, J.V., Berns, M.W., and Cleveland, D.W. (2006). In vivo measurements of Cdc20 complexes reveal a pool released from the APC/C during activation of the mitotic checkpoint. Biophys. J. 91, 343-351.
Boillee, S., Yamanaka, K., Copeland, N.G., Jenkins, N.A., Kasiotis, G., Kollias, G. and Cleveland, D.W. (2006). Motor neurons and microglia as determinants of disease onset and progression in inherited ALS. Science 312, 1389-1392.
Yamanaka, K., Miller, T.M., McAlonis-Downes, M., Chun, S.J. and Cleveland, D.W. (2006). Progressive spinal axonal degeneration and slowness in ALS2-deficient mice. Ann. Neurol. 60, 95-104.
Miller, T.M., Smith, R.A. and Cleveland, D.W. (2006) Amyotrophic Lateral Sclerosis and gene therapy. Nat. Neurol. 2, 462-463.
Weaver, B.A.A., Silk, A. and Cleveland, D.W. (2006). Nondisjunction, aneuploidy and tetraploidy. Nature 441, E9-10.
Smith, R.A., Miller, T.M., Yamanaka, K., Monia, B.P, Condon,T.P., Hung, G., Lobsiger, C.S., Ward, C.M., McAlonis-Downes, M., Wei, H., Wancewica, E.V., Bennett, C.F. and Cleveland, D.W. (2006). Antisense oligonucleotide therapy of human neurodegenerative disease. J. Clin. Invest. 116, 2290-2296.
Weaver, B.A.A. and Cleveland, D.W. (2006) Does aneuploidy cause cancer? Curr. Opin. Cell. Biol. 18, 658-667.
Boillee, S., Vande Velde, C. and Cleveland, D.W. (2006) ALS: from motor neurons to the neighborhood. Neuron 52, 39-59.
Ross, C.A. and Cleveland, D.W. (2006). Intercellular miscommunication in polyglutamine pathogenesis. Nat. Neurosci. 9, 1205-1206.
Sok, J. C., Coppelli, F. M., Thomas, S. M., Lango, M, N., Xi, S., Hunt, J. L., Freilino, M. L., Graner, M. W., Wikstrand, C. J., Bigner, D. D., Gooding, W. E., Furnari, F. B., Grandi, J. R. Mutant Epidermal Growth Factor Receptor (EGFRvIII) Contributes to Head and Neck Cancer Growth and Resistance to EGFR Targeting. Clinical Cancer Research, 12: 5064-5073, 2006.
Kline S*, Cheeseman I*, Hori T, Fukagawa T, Desai A. 2006. The human Mis12 complex is required for kinetochore assembly and proper chromosome segregation. J. Cell Biol. 173: 9 -17. *joint first authors
Budde PP, Desai A, Heald R. 2006. Analysis of microtubule polymerization in vitro and during the cell cycle in Xenopus egg extracts. Methods 38:29-34.
Okada M, Cheeseman I, Hori T, Okawa K, McLeod I, Yates J, Desai A, Fukagawa T. 2006. The CENP-H/I complex is required for the efficient incorporation of newly synthesized CENP-A into centromeres. Nat Cell Biol. 8:446-57.
Maddox P, Portier N, Desai A, Oegema K. 2006. Molecular analysis of mitotic chromosome condensation using a quantitative time-resolved fluorescence microscopy assay. Proc. Natl. Acad. Sci. USA 103:15097-102.
Smolka M, Chen S, Maddox P, Enserink J, Albuquerque C, Wei X, Desai A, Kolodner R, Zhou H. An FHA domain-mediated protein interaction network reveals a role of Rad53 in the regulation of morphogenesis. J. Cell Biol. 175:743-753.
Cheeseman I, Chappie J, Wilson-Kubalek E, Desai A. 2006. The conserved KMN network constitutes the core microtubule binding site of the kinetochore. Cell 127:983-97.
Sato, K., Sato, M., Audhya, A., Oegema, K., Schweinsberg, P. and B.D. Grant. Dynamic Regulation of Caveolin-1 Trafficking in the Germ Line and Embryo of Caenorhabditis elegans. 2006. Mol. Biol. Cell 7:3085-3094.
Olson, S.K., Bishop, J.R., Yates, J.R., Oegema, K., and J.D. Esko. Identification of novel chondroitin proteoglycans in Caenorhabditis elegans: embryonic cell division depends on CPG-1 and CPG-2. 2006. J. Cell Biol. 173: 985-994.
Sandall, S., Severin, F., McLeod, I.X., Yates, J.R. 3rd, Oegema, K., Hyman, A. and A. Desai. A Bir1-Sli15 complex connects centromeres to microtubules and is required to sense kinetochore tension. 2006. Cell. 127:1179-91.
McNally, K., Audhya, A., Oegema, K., McNally, F.J. Katanin controls mitotic and meiotic spindle length. 2006. J Cell Biol. 2006 175:881-91.
Yang C, Zhou W, Jeon MS, Demydenko D, Harada Y, Zhou H, Liu YC. Negative regulation of the E3 ubiquitin ligase itch via Fyn-mediated tyrosine phosphorylation. Mol Cell. 2006 Jan 6;21(1):135-41.
Hashimoto, N., Kido, Y., Uchida, T., Asahara, S., Shigeyama, Y., Matsuda, T., Takeda, A., Tsuchihashi, D., Nishizawa, A., Ogawa, W., Fujimoto, Y., Okamura, H., Arden, K.C., Herrera, P. L., Noda, T., Kasuga, M. Ablation of PDK1 in pancreaticÿ² cells induces diabetes as a result of loss ofÿb-cell mass. Nat Genet. 38:589-93 (2006).
Arden, K.C. Multiple roles of FOXO transcription factors in mammalian cells point to multiple roles in cancer. Exp Gerontol. 41:709-17 (2006).
Sun, P., Xiong, H., Kim, T.H., Ren, B., and Zhang Z., Positive inter-regulation between beta-catenin/T cell factor-4 signaling and endothelin-1 signaling potentiates proliferation and survival of prostate cancer cells. Molelular Pharmacology, 69:520-31, 2006
Toyo-oka, K., Bowen T.J., Hirotsune S., Li, Z., Jain, S., Ota, S., Lozach, L.E., Bassett, I.G., Lozach, J., Rosenfeld, M.G., Glass, C.K., Eisenman, R., Ren, B., Hurlin, P. and Wynshaw-Boris, A., Mnt-deficient mammary glands exhibit impaired involution and tumors with characteristics of Myc overexpression. Cancer Research, 66:5565-73, 2006
Zheng, M., Barrera, L.O., Ren, B. and Wu, Y., ChIP-chip: data, model, and analysis. Biometrics, (in press)
Heintzman N.D., Stuart R.K., Hon G., Fu Y., Barrera L.O., Van Calcar S., Qu C., Ching K.A., Wang W., Weng Z., Green R.D., Crawford G. and Ren B., Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nature Genetics, (in press)
Kim T.H., Abdullayev Z., Smith A., Ching K.A., Loukinov D., Green R.D., Zhang M.Q., Lobanenkov V., and Ren B., Analysis of the vertebrate insulator protein CTCF binding in the human genome. Cell, (in press)
Kim, T.H. and Ren, B., Genome-wide Analysis of Protein-DNA Interactions. Annual Review of Genomics and Human Genetics, 7, 2006
Barrera, L.O. and Ren, B., The transcriptional regulatory code of eukaryotic cells - Insights from Genome-wide Analysis of Chromatin Organization and Transcription Factor Binding. Current Opinion in Cell Biology, 18:1-8, 2006
Hawkins, R.D. and Ren, B., Genome-wide Location Analysis: insights on transcriptional regulation. Human Molecular Genetics, 15:R1-R7, 2006
Kim, T.H. and Ren, B., An all-round view of eukaryotic transcription. Genome Biology 7:323, 2006
Heintzman N.D. and Ren, B., The Gateway to Transcription: Identifying, Characterizing, and Understanding Promoters in the Eukaryotic Genome, Cellular and Molecular Life Sciences, (in press)
Schmidt, KH, Pennaneach, V, Putnam, CD, and Kolodner, RD. Analysis of gross chromosomal rearrangements in Saccharomyces cerevisiae. Methods in Enzymology. 2006;409:462-476.
Pennaneach, V, Putnam, CD, and Kolodner, RD. Chromosome healing by de novo telomere addition in Saccharomyces cerevisiae. Mol. Microbiology. 2006;59:1357-1368.
Hess, MT, Mendillo, ML, Mazur, DJ, and Kolodner, RD. Biochemical basis for dominant mutations in the Saccharomyces cerevisiae MSH6 gene. Proc. Natl. Acad. Sci. USA. 2006;103:558-563.
Kats, E, Albuquerque, CP, Zhou, H, and Kolodner, RD. Checkpoint functions are required for normal S-phase progression in Saccharomyces cerevisiae RCAF- and CAF-I-defective mutants. Proc. Natl. Acad. Sci. USA. 2006;103:3710-3715.
Mazur, DJ, Mendillo, ML, and Kolodner, RD. Inhibition of Msh6 ATPase activity by mispaired DNA induces a Msh2(ATP)-Msh6(ATP) state that is capable of hydrolysis independent movement along DNA. Mol. Cell. 2006;22:39-49.
Schmidt, KH, Wu, J, and Kolodner, RD. Control of translocations between highly diverged genes by Sgs1, the Saccharomyces cerevisiae homolog of the Bloom's Syndrome protein. Mol. Cell. Biol. 2006;26:5406-5420.
Cooper, AA, Gitler, AD, Cashikar, A, Haynes, CM, Hill, KJ, Bhullar, B, Liu, K, Xu, K, Strathearn, KE, Liu, F, Cao, S, Caldwell, KA, Caldwell, GA, Marsischky, G, Kolodner, RD, LaBaer, J, Rochet, J-C, Bonini, NM, and Lindquist, S. a-Synuclein blocks ER to Golgi trafficking and Rab1 ameliorates neuron loss in Parkinson's disease models. Science. 2006;313:324-328.
Schmidt, KH, and Kolodner, RD. Suppression of spontaneous genome rearrangements in Saccharomyces cerevisiae DNA helicase mutants. Proc. Natl. Acad. Sci. USA. 2006;103:18196-18201.
Chen, CC, Motegi, A, Hasegawa, Y, Myung, K, Kolodner, RD and D’Andrea, AD. REV3, RAD18/SIZ1 and RAD5/SRS2 define distinct pathways mediating ionizing radiation-induced mutagenesis in Saccharomyces cerevisiae. DNA Repair. 2006;5:1475-1488.
Enserink, JM, Smolka, MB, Zhou, H, and Kolodner, RD. Checkpoint proteins control morphogenetic events during DNA replication stress in Saccharomyces cerevisiae. J. Cell Biol. 2006;175:729-741.
Smolka, MB, Chen, S-h, Maddox, PS, Enserink, JM, Albuquerque, CP, Wei, XX, Desai, A, Kolodner, RD, and Zhou, H. An FHA domain-mediated protein interaction network reveals its role in polarized cell growth. J. Cell Biol. 2006;175:743-753.
Wu A-h, Xiao J, Anker L, Hall WA, Gregerson DS, Cavenee WK, Chen W and Low WC. Identification of EGFRvIII-Derived CTL Epitopes Restricted by HLA A0201 for Dendritic Cell Based Immunotherapy of Gliomas. Journal of Neuro-Oncology 76: 23-30, 2006.
Carrasco DR, Fenton T, Protopopova M, Sukhdeo K, German M, You M, DiVizio D, Nogueira C, Stommel J, Fletcher C, Hornick J, Cavenee W, Furnari F and DePinho RA. The PTEN and Ink4a/Arf Tumor Suppressors Maintain a Myelolymphoid Hematopoietic Compartment and Cooperate to Constrain Histiocytic Sarcoma Development. Cancer Cell 9: 379-390, 2006.
Nagane M, Cavenee WK and Shiokawa Y. Activation of Multiple Apoptosis Pathways in Human Glioma Cells by Combination Treatment with Ionizing Irradiation and TRAIL/Apo2L Leads to Synergistic Cytotoxicity. Journal of Neurosurgery (in press).
Wang MY, Lu KV, Zhu S, Dia EQ, Vivanco I, Shackleford GM, Cavenee WK, Mellinghoff IK, Cloughesy TF, Sawyers CL and Mischel PS. mTOR Inhibition Promotes Response to EGFR Kinase Inhibitors in PTEN-Deficient and PTEN-Intact Glioblastoma Cells. Cancer Research 66: 7864-7869, 2006.
Okumura K, Mendoza M, Bachoo RM, DePinho RA, Cavenee WK and Furnari FB. PCAF (p300/CBP Associated Factor) Modulates PTEN (Phosphatase and Tensin Homolog Deleted on Chromosome Ten) Activity. Journal of Biological Chemistry 281: 26562-26568, 2006.
Finckenstein FG, Davicioni E, Osborn KG, Cavenee WK, Arden KC and Anderson MJ. PAX3-FKHR Expression in the Developing Mouse Reveals a Unique Role for this Tumor-Specific Fusion Protein in Regulating Skeletal Muscle Development. Transgenic Research 15: 595-614, 2006.
Johns TG, Perera RM, Vernes S, Vitali AA, Cao D, Cavenee WK, Scott AM and Furnari FB. The Efficacy of EGFR-Specific Antibodies Against Glioma Xenografts is Influenced by Receptor Levels, Activation Status and Heterodimerization. Clinical Cancer Research.
Louis DN, Ohgaki H, Wiestler OD and Cavenee WK, eds. Pathology and Genetics of Tumours of the Nervous System 3rd Edition. IARC Press, Lyon, France, 2007 (in press).
Kleihues P, Burger PC, Cavenee WK, Ohgaki H, Aldape KD, Plate KH, Brat DJ and Bigner DD. Glioblastoma. In Pathology and Genetics of Tumours of the Nervous System 3rd Edition. D. Louis, H. Ohgaki, O. Wiestler and W. Cavenee, eds. IARC Press, Lyon, France, 2007 (in press).
Cavenee W, Burger PC, Leung SY and Van Meir EG. Turcot Syndrome. In Pathology and Genetics of Tumours of the Nervous System 3rd Edition. D. Louis, H. Ohgaki, O. Wiestler and W. Cavenee, eds. IARC Press, Lyon, France, 2007 (in press).
Eberhart C, Cavenee W and Pietsch T. Naevoid Basal Cell Carcinoma Syndrome. In Pathology and Genetics of Tumours of the Nervous System 3rd Edition. D. Louis, H. Ohgaki, O. Wiestler and W. Cavenee, eds. IARC Press, Lyon, France, 2007 (in press).