Table of Services

Genomics Facility Publications

2010

  • Altomare DA, Rybak SM, Pei J, Maizel JV, Cheung M, Testa JR, Shogen K. Onconase responsive genes in human mesothelioma cells: implications for an RNA damaging therapeutic agent. BMC Cancer. 2010;10:34. PMID: 20137089
  • Cheung M, Pei J, Pei Y, Jhanwar SC, Pass HI, Testa J.R. The promyelocytic leukemia zinc-finger gene, PLZF, is frequently downregulated in malignant mesothelioma cells and contributes to cell survival. Oncogene. 2010;29:1633-40. PMID: 20010871
  • Dorgan JF, Spittle CS, Egleston BL, Shaw CM, Kahle LL, Brinton LA. Assay reproducibility and within-person variation of mullerian inhibiting substance. Fertil Steril. 2010;94:301-4. PMID: 19409547

2009

  • Altomare DA, Menges CW, Pei J, Zhang L, Skele-Stump KL, Carbone M. Kane, AB, Testa JR. Activated TNFα/NFκB signaling via down regulation of Fas-associated factor 1 in asbestos-induced mesotheliomas from Arf knockout mice. Proc Natl Acad Sci USA. 2009;106:3420-5. PMCID: PMC2644256
  • Belinsky MG, Skorobogatko YV, Rink L, Pei J, Cai KQ, Vanderveer LA, Ridell D, Merkel E, Tarn C, Eisenberg BL, von Mehren M, Testa JR, Godwin AK. High density DNA array analysis reveals distinct genomic profiles in a subset of gastrointestinal stromal tumors. Genes Chromosomes Cancer 2009;48:886-96. NIHMSID: NIHMS 133073
  • Boquoi A, Jover R, Chen T, Pennings M, Enders GH. Transgenic expression of VEGF in intestinal epithelium drives mesenchymal cell interactions and epithelial neoplasia. Gastroenterology 2009 136:596-606. PMCID: PMC2824597
  • Capo-Chichi CD, Cai KQ, Testa JR, Godwin AK, Xu XX. Loss of GATA6 leads to nuclear deformation and aneuploidy in ovarian cancer. Mol Cell Biol. 2009;29:4766-77. PMCID: PMC2725711
  • Dorgan J.F., Stanczyk F.Z., Egleston B.L., Kahle L.L., Shaw C.M., Spittle C.S., Godwin A.K., Brinton L.A. Prospective case-control study of serum mullerian inhibiting substance and breast cancer risk. J Natl Cancer Inst. 101:1501-1509, 2009. PMCID: PMC2773186
  • Fazlieva R, Spittle CS, Morrissey D, Hayashi H, Yan H, Matsumoto Y. Proofreading exonuclease activity of human DNA polymerase delta and its effects on lesion-bypass DNA synthesis. Nucleic Acids Res. 2009;37:2854-66. PMCID: PMC2685094
  • Hartman TR, Liu D, Zilfou JT, Robb V, Morrison T, Watnick T, Henske EP. The tuberous sclerosis proteins regulate formation of the primary cilium via a rapamycin-insensitive and polycystin 1-independent pathway. Hum Mol Genet. 2009;18:151-63. PMCID: PMC2644647
  • Hartman TR, Nicolas E, Klein-Szanto A, Al-Saleem T, Cash TP, Simon MC, Henske EP. The role of the Birt-Hogg-Dubé protein in mTOR activation and renal tumorigenesis. Oncogene. 2009;28:1594-1604. PMCID: PMC2664853
  • Ivanov SV, Miller J, Lucito R, Tang C, Ivanova AV, Pei J, Carbone M, Cruz C, Beck A, Webb C, Nonaka D, Testa JR, Pass HI. Genomic events associated with progression of pleural malignant mesothelioma. Int J Cancer. 2009;124:589-99. NIHMSID: NIHMS70933
  • Izumchenko E, Singh MK, Plotnikova OV, Tikhmyanova N, Little JL, Serebriiskii IG, Seo S, Kurokawa M, Egleston BL, Klein-Szanto A, Pugacheva EN, Hardy RR, Wolfson M, Connolly DC, Golemis EA. NEDD9 promotes oncogenic signaling in mammary tumor development. Cancer Res. 2009;69:7198-7206. PMCID: PMC2758619
  • Karbowniczek M, Zitserman D, Khabibullin D, Hartman T, Yu J, Morrison T, Nicolas E, Squillace R, Roegiers F, Henske EP. The evolutionarily conserved TSC/Rheb pathway activates Notch in tuberous sclerosis complex and Drosophila external sensory organ development. J Clin Invest. 2009;120:93-102. PMCID: PMC2798691
  • Timakhov RA, Tan Y, Rao M, Liu Z, Altomare DA, Pei J, Wiest DL, Favorova OO, Knepper JE, Testa JR. Recurrent chromosomal rearrangements implicate oncogenes contributing to T-cell lymphomagenesis in Lck-MyrAkt2 transgenic mice. Genes Chromosomes Cancer. 2009;48:786-94. PMCID: PMC2739734
  • Xu J, Testa JR. DLX5 (distal-less homeobox 5) promotes tumor cell proliferation by transcriptionally regulating MYC. J Biol Chem. 2009;284:20593-601. PMCID: PMC2742824
  • Yu JJ, Robb VA, Morrison TA, Ariazi EA, Karbowniczek M, Astrinidis A, Wang C, Hernandez-Cuebas L, Seeholzer LF, Nicolas E, Hensley H, Jordan VC, Walker CL, Henske EP. Estrogen promotes the survival and pulmonary metastasis of tuberin-null cells. Proc Natl Acad Sci U.S.A. 2009;106:2635-2640. PMCID: PMC2637277

2008

  • Carbone M, Pannuti A, Zhang L, Testa JR, Bocchetta M. A novel mechanism of late gene silencing drives SV40 transformation of human mesothelial cells. Cancer Res. 2008;68:9488-96. PMCID: PMC2666620
  • Chai N, Chang HE, Nicolas E, Han Z, Jarnik M, Taylor J. Properties of subviral particles of hepatitis B virus. J Virol. 2008;82:7812-7. PMCID: PMC2519590
  • Gudima S, He Y, Chai N, Bruss V, Urban S, Mason W, Taylor J. Primary human hepatocytes are susceptible to infection by hepatitis delta virus assembled with envelope proteins of woodchuck hepatitis virus. J Virol. 2008;82:7276-83. PMCID: PMC2493318
  • He X, Park K, Wang H, He X, Zhang Y, Hua X, Li Y, Kappes DJ. CD4-CD8 lineage commitment is regulated by a silencer element at the ThPOK transcription-factor locus. Immunity. 2008;28:346-58.
  • Karbowniczek M, Spittle CS, Morrison T, Wu H, Henske EP. mTOR is activated in the majority of malignant melanomas. J Invest Dermatol. 2008;128:980-7.
  • McDaniel AS, Allen JD, Park SJ, Jaffer ZM, Michels EG, Burgin SJ, Chen S, Bessler WK, Hofmann C, Ingram DA, Chernoff J., Clapp DW. Pak1 regulates multiple c-Kit mediated Ras-MAPK gain-in-function phenotypes in Nf1+/- mast cells. Blood. 2008;112:4646-54. PMCID: PMC2597131
  • Poleshko A, Palagin I, Zhang R, Boimel P, Castagna C, Adams PD, Skalka AM, Katz RA. Identification of cellular proteins that maintain retroviral epigenetic silencing: evidence for an antiviral response. J Virol. 2008;82:2313-23. PMCID: PMC2258957
  • Singh MK, Dadke D, Nicolas E, Serebriiskii IG, Apostolou S, Canutescu A, Egleston BL, Golemis EA. A novel Cas family member, HEPL, regulates FAK and cell spreading. Mol Biol Cell. 2008;19:1627-36. PMCID: PMC2291417
  • Smith SD, Jaffer ZM, Chernoff J, Ridley AJ. PAK1-mediated activation of ERK1/2 regulates lamellipodial dynamics. J Cell Sci. 2008;121:3729-36. PMCID: PMC2702775
  • Tan Y, Timakhov RA, Rao M, Altomare DA, Xu J, Liu Z, Gao Q, Jhanwar SC, Di Cristofano A, Wiest DL, Knepper JE, Testa JR. A novel recurrent chromosomal inversion implicates the homeobox gene Dlx5 in T-cell lymphomas from Lck-Akt2 transgenic mice. Cancer Res. 2008;68:1296-1302. Accepted prior to April 7, 2008
  • Tseng M, Olufade T, Kurzer MS, Wahala K, Fang CY, van der Schouw YT, Daly MB. Food frequency questionnaires and overnight urines are valid indicators of daidzein and genistein intake in U.S. women relative to multiple 24-h urine samples. Nutr Cancer. 2008;60:619-26. PMID: 18791925

2007

  • Balogh GA, Heulings R, Russo IH, Mailo D, Li, Y-S, Russo J. Methodological approach to study the genomic profile of the human breast. Int J Oncol. 2007;31:253-60.
  • Balogh GA, Russo IH, Spittle C, Heulings R, Russo J. Immune-surveillance and programmed cell death-related genes are significantly overexpressed in the normal breast epithelium of postmenopausal parous women. Int J Oncol. 2007;31:303-12.
  • Balogh GA, Russo J, Mailo DA, Heulings R, Russo PA, Morrison P, Sheriff F, Russo IH. The breast of parous women without cancer has a different genomic profile than those with cancer. Int J Oncol. 2007;31:1165-75.
  • Chai N, Chang HE, Nicolas E, Gudima S, Chang J, Taylor J. Assembly of hepatitis B virus envelope proteins onto a lentivirus pseudotype that infects primary human hepatocytes. J Virol. 2007;81:10897-904.
  • Chai N, Gudima S, Chang J, Taylor J. Immunoadhesins containing pre-S domains of hepatitis B virus large envelope protein are secreted and inhibit virus infection. J Virol. 2007;81:4912-8.
  • Chang WC, Coudry RA, Clapper ML, Zhang X, Williams KL, Spittle CS, Li T, Cooper HS. Loss of p53 enhances the induction of colitis-associated neoplasia by dextran sulfate sodium. Carcinogenesis. 2007;28:2375-81.
  • Coudry RA, Meireles SI, Stoyanova R, Cooper HS, Carpino A, Wang X, Engstrom PF, Clapper ML. Successful application of microarray technology to microdissected, formalin-fixed, paraffin-embedded tissue. J Mol Diagn. 2007;9:70-9.
  • Gudima S, He Y, Meier A, Chang J, Chen R, Jarnik M, Nicolas E, Bruss V, Taylor J. Assembly of hepatitis delta virus: particle characterization, including the ability to infect primary human hepatocytes. J Virol. 2007;81:3608-17.
  • Johnson JE, Gettings EJ, Schwalm J, Pei J, Testa JR, Litwin S, von Mehren M, Broccoli D. Whole-genome profiling in liposarcomas reveals genetic alterations common to specific telomere maintenance mechanisms. Cancer Res. 2007;67:9221-8.
  • Katz RA, Jack-Scott E, Narezkina A, Palagin I, Boimel P, Kulkosky J, Nicolas E, Greger JG, Skalka AM. High-frequency epigenetic repression and silencing of retroviruses can be antagonized by histone deacetylase inhibitors and transcriptional activators, but uniform reactivation in cell clones is restricted by additional mechanisms. J Virol. 2007;81:2592-2604.
  • Mabuchi S, Altomare DA, Connolly DC, Klein-Szanto A, Litwin S, Hoelzle MK, Hensley HH, Hamilton TC, Testa JR. RAD001 (Everolimus) delays tumor onset and progression in a transgenic mouse model of ovarian cancer. Cancer Res. 2007;67:2408-13.
  • Page RE, Klein-Szanto AJ, Litwin S, Nicolas E, Al-Jumaily R, Alexander P, Godwin AK, Ross EA, Schilder RJ, Bassi DE. Increased expression of the pro protein convertase furin predicts decreased survival in ovarian cancer. Cell Oncol. 2007;29:289-99.
  • Rose RW, Vorobyeva AG, Skipworth JD, Nicolas E, Rall GF. Altered levels of STAT1 and STAT3 influence the neuronal response to interferon gamma. J Neuroimmunol. 2007;192:145-56.
  • Singh MK, Nicolas E, Gherraby W, Dadke D, Lessin S, Golemis EA. HEI10 negatively regulates cell invasion by inhibiting cyclin B/Cdk1 and other promotility proteins. Oncogene. 2007;26:4825-32.
  • Spittle C, Ward MR, Nathanson KL, Gimotty PA, Rappaport E, Brose MS, Medina A, Letrero R, Herlyn M, Edwards RH. Application of a BRAF pyrosequencing assay for mutation detection and copy number analysis in malignant melanoma. J Mol Diagn. 2007;9:464-71.
  • van Slegtenhorst M, Khabibullin D, Hartman TR, Nicolas E, Kruger WD, Henske EP. The Birt-Hogg-Dube and tuberous sclerosis complex homologs have opposing roles in amino acid homeostasis in Schizosaccharomyces pombe. J Biol Chem. 2007;282:24583-90.
  • Xu C, Yamamoto Y, Zhou T, Aldrich CE, Frank K, Cullen JM, Jilbert AR, Mason WS. The liver of woodchucks chronically infected with woodchuck hepatitis virus contains foci of virus core antigen negative hepatocytes with both altered and normal morphology. Virology. 2007;359:283-94.

2006

  • Balogh GA, Heulings R, Mailo DA, Russo PA, Sheriff F, Russo IH, Moral R, Russo J. Genomic signature induced by pregnancy in the human breast. Int J Oncol. 2006;28:399-410.
  • Caslini C, Capo-chichi CD, Roland IH, Nicolas E, Yeung AT, Xu X-X. Histone modifications silence the GATA transcription factor genes in ovarian cancer. Oncogene. 2006;25:5446-61.
  • Chen G, Lin W, Shen F, Iloeje UH, London WT, Evans AA. Past HBV viral load as predictor of mortality and morbidity from HCC and chronic liver disease in a prospective study. Am J Gastroenterol. 2006;101:1797-1803.
  • Lian Z, De Luca P, Di Cristofano A. Gene expression analysis reveals a signature of estrogen receptor activation upon loss of Pten in a mouse model of endometrial cancer. J Cell Physiol. 2006;208:255-66.
  • Pei J, Kruger WD, Testa JR. High resolution analysis of 9p loss in human cancer cells using SNP-based mapping arrays. Cancer Genet Cytogenet. 2006;170:65-8.
  • Rumfelt LL, Zhou Y, Rowley BM, Shinton SA, Hardy RR. Lineage specification and plasticity in CD19-negative early B-cell precursors. J Exp Med. 2006;203:675-87.
  • Shatalova EG, Loginov VI, Braga EA, Kazubskaia TP, Sudomoina MA, Blanchard RL, Favorova OO. Association of polymorphisms in SULT1A1 and UGT1A1 genes with breast cancer risk and phenotypes in Russian women. Mol Biol (Mosk). 2006;40:263-70.
  • Vilgelm A, Lian Z, Wang H, Beauparlant SL, Klein-Szanto A, Ellenson LH, Di Cristofano A. Akt-mediated phosphorylation and activation of estrogen receptor alpha is required for endometrial neoplastic transformation in Pten+/- mice. Cancer Res. 2006;66:3375-80.
  • Yang DH, Fazili Z, Smith ER, Cai KQ, Klein-Szanto A, Cohen C, Horowitz IR, Xu XX. Disabled-2 heterozygous mice are predisposed to endometrial and ovarian tumorigenesis and exhibit sex-biased embryonic lethality in a p53-null background. Am J Pathol. 2006;169:258-67.
  • Yang H, Bocchetta M, Kroczynska B, Elmishad AG, Chen Y, Liu Z, Bubici C, Mossman BT, Pass HI, Testa JR, Franzoso G, Carbone M. TNF-α inhibits asbestos induced cytotoxicity via a NF-κB dependent pathway, a possible mechanism for asbestos-induced oncogenesis. Proc Natl Acad Sci U.S.A. 2006;103:10397-402.

2005

  • Capo-Chichi CD, Rula ME, Smedberg JL, Vanderveer L, Parmacek MS, Morrisey EE, Godwin AK, Xu XX. Perception of differentiation cues by GATA factors in primitive endoderm lineage determination of mouse embryonic stem cells. Dev Biol. 2005;286:574-586.
  • Carlini LE, Meropol NJ, Bever J, Andria ML, Hill T, Gold P, Rogatko A, Wang H, Blanchard RL. UGT1A7 and UGT1A9 polymorphisms predict response and toxicity in colorectal cancer patients treated with capecitabine/irinotecan. Clin Cancer Res. 2005;11:1226-36.
  • Cooper HS, Chang W-C, Coudry R, Gary M, Everley L, Spittle CS, Wang H, Litwin S, Clapper ML. Generation of a unique strain of multiple intestinal neoplasia (Apc+/Min-FCCC) mice with significantly increased numbers of colorectal adenomas. Mol Carcinog. 2005;44:31-41.
  • Fernandez SV, Russo IH, Lareef MH, Balsara B, Russo J. Comparative genomic hybridization of human breast epithelial cells transformed by estrogen and its metabolites. Int J Oncol. 2005;26:691-5.
  • Hayashi J, Stoyanova R, Seeger C. The transcriptome of HCV replicon expressing cell lines in the presence of alpha interferon. Virology. 2005;335:264-75.
  • Li, X., Dumont, P., Della Pietra, A.C., Shetler, C., Murphy, M.E. The codon 47 polymorphism in p53 is functionally significant. J Biol Chem. 2005;280:24245-51.
  • Pasche B, Knobloch TJ, Bian Y, Liu J, Phukan S, Rosman D, Kaklamani V, Baddi L, Siddiqui FS, Frankel W, Prior TW, Schuller DE, Agrawal A, Lang J, Dolan ME, Vokes EE, Lane WS, Huang CC, Caldes T, Di Cristofano A, Hampel H, Nilsson I, von Heijne G, Fodde R, Murty VV, de la Chapelle A, Weghorst CM. Somatic acquisition and signaling of TGFBR1*6A in cancer. JAMA. 2005;294:1634-46.
  • Xiao G-H, Gallagher R, Shetler J, Skele K, Altomare DA, Pestell RG, Jhanwar S, Testa J.R. The NF2 tumor suppressor gene product, Merlin, Inhibits cell proliferation and cell cycle progression by repressing cyclin D1 expression. Mol Cell Biol. 2005;25:2384-94.