Xu Lab | Unversity of California, San Diego | Division of Biological Sciences

2013

Lu, X., Mazur, S. J., Lin, T., Appella, E, & Xu, Y. The pluripotency factor Nanog promotes breast cancer tumorigenesis and metastasis. Oncogene, In press.

2012

Westenskow, P.D., Moreno, S.K., Krohne, T.U., Kurihara, T., Zhu, S., Zhang, Z.N., Zhao, T., Xu, Y., Ding, S., & Friedlander, M. (2012). Using flow cytometry to compare the dynamics of photoreceptor outer segment phagocytosis in iPS-Derived RPE cells. Investigative Opthalmology and Visual Science 53(10): 6282-90,
Rong, Z., Fu, X., Wang, M., & Xu, Y. (2012). A scalable approach to prevent teratoma formation of human embryonic stem cells. J Biol Chem. [Epub ahead of print]
Fu, X. & Xu, Y. (2012). Challenges to the clinical application of pluripotent stem cells: Towards genomic and functional stability. Genome Med. 4(6):55. [Epub ahead of print]
Won, K.J., Xu, Z., Zhang, X., Whitaker, J.W., Shoemaker, R., Ren, B., Xu, Y., Wang, W. (2012). Global identification of transcriptional regulators of pluripotency and differentiation in embryonic stem cells. Nucleic Acids Res. [Epub ahead of print]
Lu, X., Liu, D., and Xu, Y. (2012). The gain-of-function of p53 cancer mutant in promoting mammary tumorigenesis. Oncogene, In press.
Zhang, Z. and Xu, Y. (2012). Progress and bottleneck in induced pluripotency. Cell Regeneration, In press.
Boyd, A.S., Rodrigues, N.P., Lui, K.O., Fu, X., and Xu, Y. (2012). Concise review: Immune recognition of induced pluripotent stem cells. Stem Cells 30(5): 797-803.
Chen, Z., Zhao, T., and Xu, Y. (2012). The genomic stability of induced pluripotent stem cells. Protein Cell 3(4): 271-7.
Lake, B., Fink, J., Klemetsaune, L., Fu, X., Jeffers, J., Zambetti, G. and Xu Y. (2012). Context-dependent enhancement of induced pluripotent stem cell reprogramming by silencing Puma. Stem Cells 30(5): 888-97.
Xu, Z., Hou, T., Li, N., Xu, Y., and Wang, W. (2012). Proteome-wide detection of AbI1 SH3-binding peptides by integrating computational prediction and peptide microarray. Mol Cell Proteomics 11(1):O111.0101389.

2011

Zhao, T., Zhang, Z.N., Rong, Z., and Xu, Y. (2011). Immunogenicity of induced pluripotent stem cells. Nature 474: 212-215. (42).
Fu, X. and Xu, Y. (2011). Self-renewal and scalability of human embryonic stem cells for human therapy. Regen. Med. 6: 327-34.

2010

Liu, D., Xu, Y. (2010). p53, oxidative stress and aging. Antioxid Redox Signal. Sep 15;15(6):1669-78. Epub 2011 Feb 7.
Liu, D., Ou, L., Clemenson Jr, G.D., Chao, C., Lutske, M.E., Zambetti, G.P., Gage, F.H. and Xu, Y. (2010). Puma is required for p53-induced depletion of adult stem cells. Nat. Cell Biol. 12:993-8.
Moretto-Zita, M., Jin1, H., Zhouxin Shen, Z., Tongbiao Zhao, T., Briggs, S.P. and Xu, Y. (2010). Phosphorylation stabilizes Nanog by promoting its interaction with Pin1. Proc Natl Acad Sci USA. 107(30):13312-7.
Song, H. and Xu, Y. (2010). Disease Research and Drug Development Models Based on Genetically Altered Human Embryonic Stem Cells. Discov. Med. 9(49):500-503.
Lee, K., Li, M, Michalowski, A.M, Zhang, X., Liao, H., Chen, L., Xu, Y., Wu, X. and Huang, J. (2010). A genome-wide study identifies the Wnt signaling pathway as a major target of p53 in murine embryonic stem cells, Proc Natl Acad Sci USA. 107:69-74.
Zhao, T. and Xu, Y. (2010). p53 and Stem cells: new developments and new concerns. Trends Cell Biol. 20: 170-175.
Jankovic M, Robbiani DF, Dorsett Y, Eisenreich T, Xu Y, Tarakhovsky A, Nussenzweig A, Nussenzweig MC. (2010). Role of the translocation partner in protection against AID-dependent chromosomal translocations. Proc Natl Acad Sci U S A. 107: 187-192.
Song, H., Chung, S.K. and Xu, Y. (2010). Modeling disease in human ESCs using an efficient BAC-based homologous recombination system. Cell Stem Cell 6: 80-89.
Liu, D.P., Song, H. and Xu, Y. (2010) A common Gain of function of p53 cancer mutants in inducing genetic instability. Oncogene 29:949-56.

2009

Gaidarenko, O. and Xu, Y. (2009). Transcription activity is required for p53-dependent tumor suppression. Oncogene 28:4397-401.
Deng W. and Xu, Y. (2009). Genome integrity: linking pluripotency and tumorgenicity. Trends Genet. 25:425-7.
Hou, T., Xu, Z., Zhang, W., McLaughlin, W.A., Case, D.A., Xu, Y. and Wang W. (2009). Characterization of domain-peptide interaction interface: a generic structure-based model to decipher the binding specificity of SH3 domains. Mol Cell Proteomics 8:639-49.

2008

Xu, Y. (2008). Induction of genetic instability by p53 cancer mutants. Oncogene 27:3501-7.
Hewitt, S.L., Farmer, D., Marszalek, K., Cadera, E., Liang, H.E., Xu, Y., Schlissel, M.S. and Skok, J.A. (2008). Association between the Igk and Igh immunoglobulin loci mediated by the 3' Igk enhancer induces 'decontraction' of the Igh locus in pre-B cells. Nat Immunol. 9:396-404.
Jenkins LM, Mazur SJ, Rossi M, Gaidarenko O, Xu Y and Appella E. (2008). Quantitative proteomics analysis of the effects of ionizing radiation in wild type and p53 K317R knock-in mouse thymocytes. Mol Cell Proteomics. 7:716-27.

2007

Song, H. and Xu, Y. (2007). Gain of function of p53 cancer mutants in disrupting critical DNA damage response pathways. Cell Cycle 6: 1570-1573.
Song,J., Chao, C. and Xu, Y. (2007). Ser18 and Ser23 phosphorylation plays synergistic roles in activating p53-dependent neuronal apoptosis. Cell Cycle 6: 1412-1414.
Song, H., Hollstein, M. and Xu, Y. (2007) p53 gain-of-function cancer mutants induce genetic instability by inactivating ATM. Nat. Cell. Biol. 9:573-80.

2006

Xu, Y. (2006) DNA Damage: a Trigger of Innate Immunity but Essential for Adaptive Immune Homeostasis. Nature Reviews Immunology, 6:261-70.
Chao, C., Wu, Z., Mazur, SJ, Borges, H., Rossi, M., Lin, T., Wang, JYJ, Anderson, CW, Appella, E and Xu, Y. (2006). Acetylation of Mouse p53 at Lysine 317 Negatively Regulates p53 Apoptotic Activities after DNA Damage. Mole. Cell. Biol. 26, 6859-69.
Feng, L. Hollstein, M and Xu, Y. (2006) Ser46 Phosphorylation Regulates p53-dependent Apoptosis and Celular Senescence. Cell Cycle, 5(23):2812-9
Inlay, M.A., Gao,H., Lin, T., and Xu, Y. (2006). Critical roles of the immunoglobulin heavy and kappa light chain intronic enhancers in maintaining the sequential rearrangement of immunoglobulin loci. J. of Exp. Med., June 19th [Epub ahead of print].
Inlay, M.A, Gao, H., Odegard, V.H., Lin, T., Schatz, D.G. and Xu, Y. (2006). Roles of the immunoglobulin kappa light chain intronic and 3' enhancers in Igk somatic hypermutation. J. of Immunol. 177, 1146-1151.
Chao, C., Herr, D., Chun, J. and Xu, Y. (2006). Phosphorylation of p53 at Ser18 and 23 is required for p53-dependent apoptosis and tumor suppression in aging animals. EMBO J. 25, 2615-22.

2005

Xu, Y. (2005). A New Role of p53 in Maintaining Genetic Stability in Embryonic Stem Cells. Cell Cycle 4, 3.
Lin, T., Chao, C., Saito, S., Muzar, S., Murphy, M., Appela, E. and Xu, Y. (2005). p53 induces differentiation of mouse embryonic stem cells by suppressing Nanog expression. Nat. Cell Biol. 7, 165-171.
Jones, R.G., Plas, D.R., Kubek, S., Buzzai, M., Mu, J., Xu, Y., Birnbaum, M.J. and Thompson, C.B. (2005). AMP-Activated Protein Kinase Induces a p53-Dependent Metabolic Checkpoint. Mol. Cell 18, 283-293.
Feng, L., Lin, T., Uranishi, H., Gu, W., and Xu, Y. (2005). Functional analysis of the posttranslational modifications at p53 C-terminus in regulating p53 stability and activity. Mol. Cell. Biol. 25:5389-5395.
Kang, J., Ferguson, D., Song, H., Bassing, C., Eckersdorff, M., Alt, F.W. and Xu, Y. (2005). Functional interaction of H2AX, NBS1 and p53 in ATM-dependent DNA damage responses and tumor suppression. Mol. Cell.Biol. 25(2), 661-670.

2004

Borges, HL, Chao, C., Xu, Y, Linden, R. and Wang J.Y. (2004). Rdiation-Induced Apoptosis in Developing Mouse Retina Exhibits Dose-Dependent Requirement for ATM Phosphorylation of p53. Cell Death Differ. 11, 494-502.
Inlay, M., Tian, H., Lin, T. and Xu, Y. (2004). Functional dissection of the immunoglobulin kappa light chain intronic enhancer reveals important roles for E protein binding sites in activating VkappaJkappa rearrangement. J. Exp. Med. 200, 1205-1211.

2003

Inlay, M. and Xu, Y. (2003). Epigenetic Regulation of Antigen Receptor Rearrangement. Clinical Immunology, 109, 29-36.
Chao, C., Hergenhahn, M., Kaeser, M.D.,Wu, Z., Saito, S., Iggo, R., Hollstein, M., Appella, E. and Xu, Y. (2003). Cell type- and promoter-specific roles of Ser18 phosphorylation in Regulating p53 responses. J Biol. Chem. 278, 41028-41033.
Xu Y. (2003). Regulation of p53 Responses by Posttranslational Modifications. Cell Death Differ. 10, 400-403.

2002

Inlay, M., Alt, F.W., Baltimore, D., and Xu, Y. (2002). Essential roles of the kappa light chain intronic enhancer and 3' enhancer in kappa rearrangement and demethylation. Nat. Immunol. 3:463-468.
Kang, J., Bronson, R.T. and Xu, Y. (2002). Targeted Disruption of NBS1 Reveals Its Roles in Mouse Development and DNA Repair. EMBO J. 21, 1447-1455
Wu, Z., Earle, J., Saito, S., Anderson, C.W., Appella, E., and Xu, Y. (2002). Mutation of Mouse p53Ser23 and the response to DNA damage. Mol. Cell. Biol. 22, 2441-2449.
Woo, R.A., Jack, M.T., Xu, Y., Burma, S., Chen, D.J., Lee, P.W. (2002). DNA damage-induced apoptosis requires the DNA-dependent protein kinase, and is mediated by the latent population of p53. EMBO J. 21, 3000-3008.
Chin, A. I., Dempsey, P. W., Bruhn, K., Miller, J. F., Xu, Y., and Cheng, G. (2002). Involvement of Receptor Interacting Protein 2 in Innate and Adaptive Immune Responses. Nature 416, 190-194.

2001

Post, S., Weng, Y-C., Cimprich K., Chen, L. B., Xu Y., and Lee, E.Y.-H.P. (2001). Phosphorylation serines 635 and 645 of human Rad17 is cell cycle regulated and is required for G1/S checkpoint activation in response to DNA damage. Proc. Natl. Acad. Sci. USA 98, 13102-13107.
Sekiguchi, J., Ferguson, D.O., Chen, H.T., Yang, E.M., Earle, J., Frank, K., Whitlow, S., Gu, Y.S., Xu, Y., Nussenzweig, A. and Alt, F.W. (2001). Genetic interactions between ATM and the nonhomologous end-joining factors in genomic stability and development. Proc. Natl. Acad. Sci. USA 98, 3243-3248.

2000

Chao, C., Saito, S., Anderson, C.W., Appella, E. and Xu, Y. (2000). Phosphorylation of Murine p53 at Ser18 regulates the p53 Responses to DNA Damage. Proc. Natl. Acad. Sci. USA 97, 11936-11941.
Chao, C., Saito, S., Kang, J., Anderson, C.W., Appella, E. and Xu, Y. (2000). p53 transcriptional activity is essential for p53-dependent apoptosis following DNA damage. EMBO J., 19, 4967-4975.
Ellmeier, W., Jung, S., Sunshine, M.J., Hatam, F., Xu, Y., Baltimore, D., Mano, H., Littman, D.R. (2000). Severe B cell deficiency in mice lacking the tec kinase family members tec and Btk. J Exp Med. 192, 1611-1624.
Chao, C., Yang, E.M. and Xu, Y. (2000). Rescue of defective T cell development and function in Atm-/- mice by a functional Tcrab transgene. J. Immunol. 164, 345-349.

1999

Xu, Y. (1999) Involvement of ATM in lymphoid development and tumorigenesis. Adv. in Immunol., 72, 179-189.
Kuljis, R.O., Chen, G., Lee, E.Y., Aguila, M.C. and Xu Y. (1999). ATM immunolocalization in mouse neuronal endosomes: implications for ataxia-telangiectasia. Brain Res. 25, 842(2):351-8
Chen, G., Yuan, S.S., Liu, W., Xu, Y., Trujillo, K., Song, B., Cong, F., Goff, S.P., Wu, Y., Arlinghaus, R., Baltimore, D., Gasser, P.J., Park, M.S., Sung, P. and Lee, E.Y.(1999). Radiation-induced assembly of Rad51 and Rad52 recombination complex requires ATM and c-Abl. J Biol. Chem. 274(18):12748-52.

1998

Xu, Y., Yang, E.M., Brugarolas, J., Jacks, T., and Baltimore, D. (1998). Involvement of p53 and p21 in the cellular defects and tumorigenesis in Atm-/- mice. Mol. Cell. Biol. 18, 4385-4390.

1997

Plug, A.W., Petes, A.H.F.M., Xu, Y., Keegan, K.S., Hoekstra, M.F., Baltimore, D., Boer, P. D., and Ashley, T. (1997). Involvement of ATM and RPA in meiotic chromosome synapsis and recombination. Nature Genetics 17(4): 457-461.
Kuljis, R.O., Xu, Y., Aguila, M.C., Baltimore D. (1997). Degeneration of neurons, synapses, and neuropil and glial activation in a murine Atm knockout model of ataxia-telangiectasia. Proc Natl Acad Sci USA 94(23):12688-93.
Baskaran, R., Wood, L.D., Whitaker, L.L., Canman, C.E., Morgan, S.E., Xu, Y., Barlow, C., Baltimore, D., Wynshaw-Boris, A., Kastan, M.B., and Wang, J.Y.J. (1997). Ataxia telangiectasia mutant protein acyivates c-abl tyrosine kinase in response to ionizing radiation. Nature 387, 516-520.
Porter, F.D., Drago, J., Xu, Y., Cheema, S.S., Wassif C, Huang SP, Lee E, Grinberg A, Massalas JS, Bodine D, Alt F, Westphal H. (1997). Lhx2, a LIM homeobox gene, is required for eye, forebrain, and definitive erythrocyte development. Development 124(15):2935-44.

1996

Xu, Y. and Baltimore, D. (1996). Dual roles of ATM in the cellular response to radiation and in cell growth control. Genes & Development 10, 2401-2410.
Xu. Y., Ashley, T., Brainerd, E.E., Bronson, R.T., Meyn, S.M., and Baltimore, D. (1996). Targeted disruption of ATM leads to growth retardation, chromosomal fragmentation during meiosis, immune defects and thymic lymphoma. Genes & Development 10, 2411-2422.
Xu, Y., Cheng, G., and Baltimore, D. (1996). Targeted disruption of TRAF3 leads to postnatal lethality and defective T-dependent immune responses. Immunity 5, 407-415.
Xu, Y., Davidson, L., Alt. F.W., and Baltimore, D.(1996). Deletion of the Igk light chain intronic enhancer/matrix attachment region impairs but does not abolish VkJk_rearrangement. Immunity 4, 377-385.
Xu, Y., Davidson, L., Alt, F.W., and Baltimore, D. (1996). Function of the pre-Ta chain in the T cell development and allelic exclusion at the TCRb locus. Proc. Natl. Acad. Sci. USA 93, 2169-2173.

1993

Xu, Y., Baldassare, M., Fisher, P., Rathbun, G., Oltz, E. M., Yancopoulos, G. D., Jessell, T. M., and Alt, F. W. (1993). LH-2: a LIM/homeodomain gene expressed in developing lymphocytes and neural cells. Proc. Natl. Acad. Sci. USA 90, 227-31.
Chen, J., Trounstine, M., Kurahara, C., Young, F., Kuo, C.C., Xu, Y., Loring, J.F., Alt, F.W., Huszar, D. (1993). B cell development in mice that lack one or both immunoglobulin kappa light chain genes. EMBO J. 12, 821-30.