Faculty

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Peter Anthony Jones, PhD
Professor of Urology
Mark A., J. Ruth and Stillman F. Sawyer Chair in Cancer Research
Urology
NOR 7341 Health Sciences Campus Los Angeles
+1 323 442 8065

Overview

Peter A. Jones, Ph.D., D.Sc., former Director of the USC Norris Comprehensive Cancer Center, is a Distinguished Professor of Urology and Biochemistry & Molecular Biology at the Keck School of Medicine of the University of Southern California, and the H. Leslie Hoffman and Elaine S. Hoffman Chair in Cancer Research.

He is known for his studies on the molecular biology of cancer and of basic mechanisms of DNA methylation and its role in cancer and differentiation. In 1980, Dr. Jones made a seminal discovery that the drug 5-azacytidine could induce profound changes in gene expression at the same time as being a powerful inhibitor of DNA methylation. This discovery was the first to causally link DNA cytosine methylation, differentiation, and gene expression and played a large part in opening the now burgeoning field of epigenetics. The discovery of the mechanism of action of this drug led directly to the isolation of the first mammalian determination gene and also to the discovery of a large number of tumor suppressor genes which become epigenetically silenced in human cancer. The drug has now been approved for use in the treatment of myelodysplastic syndrome by the FDA. In addition to this work, Dr. Jones’ laboratory has played a seminal role in the delineation of molecular pathways leading to human bladder cancer, to the realization that DNA methylation sites are hotspots for cancer causing mutations and to the growing realization that epigenetic silencing plays a major role in human carcinogenesis. Dr. Jones’ work has been recognized as a “milestone” in gene expression and a “milestone” in cancer by Nature magazine. He was recently selected to co-lead one of the five prestigious “Dream Teams” selected by Stand Up 2 Cancer, an initiative dedicated to funding cutting-edge research designed to bring new cancer treatment to patients in an accelerated timeframe.

Dr. Jones was born in South Africa, raised and attended school in Rhodesia (now Zimbabwe), and received his Doctor of Philosophy Degree from the University of London in 1973. He joined the University of Southern California in 1977, attaining the rank of Professor in 1985, and becoming Director of the USC Norris Comprehensive Cancer Center in 1993. In 1999, he was named Distinguished Professor of Urology and Biochemistry and Molecular Biology at USC. He has received a variety of honors, including a MERIT Award from the National Cancer Institute, the AACR Kirk A. Landon Prize for Basic Cancer Research in 2009 and the David Workman Memorial Award from the Samuel Waxman Cancer Research Foundation in 2008. He was named a Fellow of the American Association for the Advancement of Science in 2010. He is the past President of the American Association for Cancer Research. He is the author of more than 250 journal publications and book chapters, and he serves on several national and international committees, panels, and editorial boards.

Publications

Miranda TB, Kelly TK, Bouazoune K, Jones PA. Methylation-sensitive single-molecule analysis of chromatin structure. Curr Protoc Mol Biol. 2010 Jan; Chapter 21:Unit 21. 17. 1-16. View in: PubMed

Jones PA, Issa JP, Baylin S. Targeting the cancer epigenome for therapy. Nat Rev Genet. 2016 Sep 15; 17(10):630-41. View in: PubMed

Liu M, Ohtani H, Zhou W, Ørskov AD, Charlet J, Zhang YW, Shen H, Baylin SB, Liang G, Grønbæk K, Jones PA. Vitamin C increases viral mimicry induced by 5-aza-2'-deoxycytidine. Proc Natl Acad Sci U S A. 2016 Sep 13; 113(37):10238-44. View in: PubMed

Charlet J, Duymich CE, Lay FD, Mundbjerg K, Dalsgaard Sørensen K, Liang G, Jones PA. Bivalent Regions of Cytosine Methylation and H3K27 Acetylation Suggest an Active Role for DNA Methylation at Enhancers. Mol Cell. 2016 May 5; 62(3):422-31. View in: PubMed

Becket E, Chopra S, Duymich CE, Lin JJ, You JS, Pandiyan K, Nichols PW, Siegmund KD, Charlet J, Weisenberger DJ, Jones PA, Liang G. Identification of DNA Methylation-Independent Epigenetic Events Underlying Clear Cell Renal Cell Carcinoma. Cancer Res. 2016 Apr 1; 76(7):1954-64. View in: PubMed

Duymich CE, Charlet J, Yang X, Jones PA, Liang G. DNMT3B isoforms without catalytic activity stimulate gene body methylation as accessory proteins in somatic cells. Nat Commun. 2016; 7:11453. View in: PubMed

Baylin SB, Jones PA. Epigenetic Determinants of Cancer. Cold Spring Harb Perspect Biol. 2016; 8(9). View in: PubMed

Roulois D, Loo Yau H, Singhania R, Wang Y, Danesh A, Shen SY, Han H, Liang G, Jones PA, Pugh TJ, O'Brien C, De Carvalho DD. DNA-Demethylating Agents Target Colorectal Cancer Cells by Inducing Viral Mimicry by Endogenous Transcripts. Cell. 2015 Aug 27; 162(5):961-73. View in: PubMed

Lay FD, Liu Y, Kelly TK, Witt H, Farnham PJ, Jones PA, Berman BP. The role of DNA methylation in directing the functional organization of the cancer epigenome. Genome Res. 2015 Apr; 25(4):467-77. View in: PubMed

Statham AL, Taberlay PC, Kelly TK, Jones PA, Clark SJ. Genome-wide nucleosome occupancy and DNA methylation profiling of four human cell lines. Genom Data. 2015 Mar; 3:94-6. View in: PubMed

Yang X, Han H, De Carvalho DD, Lay FD, Jones PA, Liang G. Gene body methylation can alter gene expression and is a therapeutic target in cancer. Cancer Cell. 2014 Oct 13; 26(4):577-90. View in: PubMed

Taberlay PC, Statham AL, Kelly TK, Clark SJ, Jones PA. Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer. Genome Res. 2014 Sep; 24(9):1421-32. View in: PubMed

Su SF, de Castro Abreu AL, Chihara Y, Tsai Y, Andreu-Vieyra C, Daneshmand S, Skinner EC, Jones PA, Siegmund KD, Liang G. A panel of three markers hyper- and hypomethylated in urine sediments accurately predicts bladder cancer recurrence. Clin Cancer Res. 2014 Apr 1; 20(7):1978-89. View in: PubMed

Lay FD, Triche TJ, Tsai YC, Su SF, Martin SE, Daneshmand S, Skinner EC, Liang G, Chihara Y, Jones PA. Reprogramming of the human intestinal epigenome by surgical tissue transposition. Genome Res. 2014 Apr; 24(4):545-53. View in: PubMed

Pedersen JS, Valen E, Velazquez AM, Parker BJ, Rasmussen M, Lindgreen S, Lilje B, Tobin DJ, Kelly TK, Vang S, Andersson R, Jones PA, Hoover CA, Tikhonov A, Prokhortchouk E, Rubin EM, Sandelin A, Gilbert MT, Krogh A, Willerslev E, Orlando L. Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome. Genome Res. 2014 Mar; 24(3):454-66. View in: PubMed

Li H, Chiappinelli KB, Guzzetta AA, Easwaran H, Yen RW, Vatapalli R, Topper MJ, Luo J, Connolly RM, Azad NS, Stearns V, Pardoll DM, Davidson N, Jones PA, Slamon DJ, Baylin SB, Zahnow CA, Ahuja N. Immune regulation by low doses of the DNA methyltransferase inhibitor 5-azacitidine in common human epithelial cancers. Oncotarget. 2014 Feb 15; 5(3):587-98. View in: PubMed

Jeong KW, Andreu-Vieyra C, You JS, Jones PA, Stallcup MR. Establishment of active chromatin structure at enhancer elements by mixed-lineage leukemia 1 to initiate estrogen-dependent gene expression. Nucleic Acids Res. 2014 Feb 1; 42(4):2245-56. View in: PubMed

Jones PA. At the tipping point for epigenetic therapies in cancer. J Clin Invest. 2014 Jan 2; 124(1):14-6. View in: PubMed

Wrangle J, Wang W, Koch A, Easwaran H, Mohammad HP, Vendetti F, Vancriekinge W, Demeyer T, Du Z, Parsana P, Rodgers K, Yen RW, Zahnow CA, Taube JM, Brahmer JR, Tykodi SS, Easton K, Carvajal RD, Jones PA, Laird PW, Weisenberger DJ, Tsai S, Juergens RA, Topalian SL, Rudin CM, Brock MV, Pardoll D, Baylin SB. Alterations of immune response of non-small cell lung cancer with Azacytidine. Oncotarget. 2013 Nov; 4(11):2067-79. View in: PubMed

Choi IS, Yu K, Kim J, De Guzman E, Weisenberger DJ, Oghamian S, Kim HJ, Lee KH, Carroll C, Trinh BN, Kim M, Houshdaran S, Laird PW, Jones PA, Warburton D, Liang G, Koh CJ. Alterations in deoxyribonucleic acid (DNA) methylation patterns of Calca, Timp3, Mmp2, and Igf2r are associated with chronic cystitis in a cyclophosphamide-induced mouse model. Urology. 2013 Jul; 82(1):253. e9-15. View in: PubMed

Gumus M, Gumus H, Jones SE, Jones PA, Sever AR, Weeks J. How long will I be blue? Prolonged skin staining following sentinel lymph node biopsy using intradermal patent blue dye. Breast Care (Basel). 2013 Jun; 8(3):199-202. View in: PubMed

You JS, De Carvalho DD, Dai C, Liu M, Pandiyan K, Zhou XJ, Liang G, Jones PA. SNF5 is an essential executor of epigenetic regulation during differentiation. PLoS Genet. 2013 Apr; 9(4):e1003459. View in: PubMed

Pandiyan K, You JS, Yang X, Dai C, Zhou XJ, Baylin SB, Jones PA, Liang G. Functional DNA demethylation is accompanied by chromatin accessibility. Nucleic Acids Res. 2013 Apr; 41(7):3973-85. View in: PubMed

Chihara Y, Kanai Y, Fujimoto H, Sugano K, Kawashima K, Liang G, Jones PA, Fujimoto K, Kuniyasu H, Hirao Y. Diagnostic markers of urothelial cancer based on DNA methylation analysis. BMC Cancer. 2013; 13:275. View in: PubMed

Beck S, Bernstein BE, Campbell RM, Costello JF, Dhanak D, Ecker JR, Greally JM, Issa JP, Laird PW, Polyak K, Tycko B, Jones PA. A blueprint for an international cancer epigenome consortium. A report from the AACR Cancer Epigenome Task Force. Cancer Res. 2012 Dec 15; 72(24):6319-24. View in: PubMed

Kelly TK, Liu Y, Lay FD, Liang G, Berman BP, Jones PA. Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules. Genome Res. 2012 Dec; 22(12):2497-506. View in: PubMed

Sever AR, Mills P, Weeks J, Jones SE, Fish D, Jones PA, Mali W. Preoperative needle biopsy of sentinel lymph nodes using intradermal microbubbles and contrast-enhanced ultrasound in patients with breast cancer. AJR Am J Roentgenol. 2012 Aug; 199(2):465-70. View in: PubMed

You JS, Jones PA. Cancer genetics and epigenetics: two sides of the same coin? Cancer Cell. 2012 Jul 10; 22(1):9-20. View in: PubMed

Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet. 2012 Jul; 13(7):484-92. View in: PubMed

De Carvalho DD, Sharma S, You JS, Su SF, Taberlay PC, Kelly TK, Yang X, Liang G, Jones PA. DNA methylation screening identifies driver epigenetic events of cancer cell survival. Cancer Cell. 2012 May 25; 21(5):655-67. View in: PubMed

Yang X, Noushmehr H, Han H, Andreu-Vieyra C, Liang G, Jones PA. Gene Reactivation by 5-Aza-2'-Deoxycytidine-Induced Demethylation Requires SRCAP-Mediated H2A. Z Insertion to Establish Nucleosome Depleted Regions. PLoS Genet. 2012 Mar; 8(3):e1002604. View in: PubMed

Sever AR, Mills P, Hyvelin JM, Weeks J, Gumus H, Fish D, Mali W, Jones SE, Jones PA, Devalia H. Percutaneous removal of sentinel lymph nodes in a swine model using a breast lesion excision system and contrast-enhanced ultrasound. Eur Radiol. 2012 Mar; 22(3):545-50. View in: PubMed

Treppendahl MB, Qiu X, Søgaard A, Yang X, Nandrup-Bus C, Hother C, Andersen MK, Kjeldsen L, Möllgaard L, Hellström-Lindberg E, Jendholm J, Porse BT, Jones PA, Liang G, Grønbæk K. Allelic methylation levels of the noncoding VTRNA2-1 located on chromosome 5q31. 1 predict outcome in AML. Blood. 2012 Jan 5; 119(1):206-16. View in: PubMed

Sharma S, Gerke DS, Han HF, Jeong S, Stallcup MR, Jones PA, Liang G. Lysine methyltransferase G9a is not required for DNMT3A/3B anchoring to methylated nucleosomes and maintenance of DNA methylation in somatic cells. Epigenetics Chromatin. 2012; 5(1):3. View in: PubMed

Taberlay PC, Kelly TK, Liu CC, You JS, De Carvalho DD, Miranda TB, Zhou XJ, Liang G, Jones PA. Polycomb-Repressed Genes Have Permissive Enhancers that Initiate Reprogramming. Cell. 2011 Dec 9; 147(6):1283-94. View in: PubMed

Andreu-Vieyra C, Lai J, Berman BP, Frenkel B, Jia L, Jones PA, Coetzee GA. Dynamic nucleosome-depleted regions at androgen receptor enhancers in the absence of ligand in prostate cancer cells. Mol Cell Biol. 2011 Dec; 31(23):4648-62. View in: PubMed

Han H, Cortez CC, Yang X, Nichols PW, Jones PA, Liang G. DNA methylation directly silences genes with non-CpG island promoters and establishes a nucleosome occupied promoter. Hum Mol Genet. 2011 Nov 15; 20(22):4299-310. View in: PubMed

Baylin SB, Jones PA. A decade of exploring the cancer epigenome - biological and translational implications. Nat Rev Cancer. 2011 Oct; 11(10):726-34. View in: PubMed

You JS, Kelly TK, De Carvalho DD, Taberlay PC, Liang G, Jones PA. OCT4 establishes and maintains nucleosome-depleted regions that provide additional layers of epigenetic regulation of its target genes. Proc Natl Acad Sci U S A. 2011 Aug 30; 108(35):14497-502. View in: PubMed

Molognoni F, Cruz AT, Meliso FM, Morais AS, Souza CF, Xander P, Bischof JM, Costa FF, Soares MB, Liang G, Jones PA, Jasiulionis MG. Epigenetic reprogramming as a key contributor to melanocyte malignant transformation. Epigenetics. 2011 Apr; 6(4):450-64. View in: PubMed

Sever AR, Mills P, Jones SE, Cox K, Weeks J, Fish D, Jones PA. Preoperative sentinel node identification with ultrasound using microbubbles in patients with breast cancer. AJR Am J Roentgenol. 2011 Feb; 196(2):251-6. View in: PubMed

Kelly TK, Jones PA. Role of nucleosomes in mitotic bookmarking. Cell Cycle. 2011 Feb 1; 10(3):370-1. View in: PubMed

Taberlay PC, Jones PA. DNA methylation and cancer. Prog Drug Res. 2011; 67:1-23. View in: PubMed

Osorio N, Delmas P, Jones PA. Patch clamp recording from enteric neurons in situ. Nat Protoc. 2011 Jan; 6(1):15-27. View in: PubMed

Jones P. Out of Africa and into epigenetics: discovering reprogramming drugs. Nat Cell Biol. 2011 Jan; 13(1):2. View in: PubMed

Sharma S, De Carvalho DD, Jeong S, Jones PA, Liang G. Nucleosomes containing methylated DNA stabilize DNA methyltransferases 3A/3B and ensure faithful epigenetic inheritance. PLoS Genet. 2011; 7(2):e1001286. View in: PubMed

Yang X, Lay F, Han H, Jones PA. Targeting DNA methylation for epigenetic therapy. Trends Pharmacol Sci. 2010 Nov; 31(11):536-46. View in: PubMed

Wolff EM, Chihara Y, Pan F, Weisenberger DJ, Siegmund KD, Sugano K, Kawashima K, Laird PW, Jones PA, Liang G. Unique DNA methylation patterns distinguish noninvasive and invasive urothelial cancers and establish an epigenetic field defect in premalignant tissue. Cancer Res. 2010 Oct 15; 70(20):8169-78. View in: PubMed

De Carvalho DD, You JS, Jones PA. DNA methylation and cellular reprogramming. Trends Cell Biol. 2010 Oct; 20(10):609-17. View in: PubMed

Kelly TK, De Carvalho DD, Jones PA. Epigenetic modifications as therapeutic targets. Nat Biotechnol. 2010 Oct; 28(10):1069-78. View in: PubMed

Kelly TK, Miranda TB, Liang G, Berman BP, Lin JC, Tanay A, Jones PA. H2A. Z maintenance during mitosis reveals nucleosome shifting on mitotically silenced genes. Mol Cell. 2010 Sep 24; 39(6):901-11. View in: PubMed

Chuang JC, Warner SL, Vollmer D, Vankayalapati H, Redkar S, Bearss DJ, Qiu X, Yoo CB, Jones PA. S110, a 5-Aza-2'-deoxycytidine-containing dinucleotide, is an effective DNA methylation inhibitor in vivo and can reduce tumor growth. Mol Cancer Ther. 2010 May; 9(5):1443-50. View in: PubMed

Wolff EM, Byun HM, Han HF, Sharma S, Nichols PW, Siegmund KD, Yang AS, Jones PA, Liang G. Hypomethylation of a LINE-1 promoter activates an alternate transcript of the MET oncogene in bladders with cancer. PLoS Genet. 2010 Apr; 6(4):e1000917. View in: PubMed

Qiu X, Hother C, Ralfkiær UM, Søgaard A, Lu Q, Workman CT, Liang G, Jones PA, Grønbæk K. Equitoxic doses of 5-azacytidine and 5-aza-2'deoxycytidine induce diverse immediate and overlapping heritable changes in the transcriptome. PLoS One. 2010; 5(9). View in: PubMed

Sharma S, Kelly TK, Jones PA. Epigenetics in cancer. Carcinogenesis. 2010 Jan; 31(1):27-36. View in: PubMed

Ricca TI, Liang G, Suenaga AP, Han SW, Jones PA, Jasiulionis MG. Tissue inhibitor of metalloproteinase 1 expression associated with gene demethylation confers anoikis resistance in early phases of melanocyte malignant transformation. Transl Oncol. 2009 Dec; 2(4):329-40. View in: PubMed

Jones PA, Liang G. Rethinking how DNA methylation patterns are maintained. Nat Rev Genet. 2009 Nov; 10(11):805-11. View in: PubMed

Jeong S, Liang G, Sharma S, Lin JC, Choi SH, Han H, Yoo CB, Egger G, Yang AS, Jones PA. Selective anchoring of DNA methyltransferases 3A and 3B to nucleosomes containing methylated DNA. Mol Cell Biol. 2009 Oct; 29(19):5366-76. View in: PubMed

Rademeyer C, Jones PA, Dalziel S, Clearwater G, Foley B, Ghafel M. Emergency Department utilisation: a natural experiment. N Z Med J. 2009 Sep 11; 122(1302):29-39. View in: PubMed

Bouazoune K, Miranda TB, Jones PA, Kingston RE. Analysis of individual remodeled nucleosomes reveals decreased histone-DNA contacts created by hSWI/SNF. Nucleic Acids Res. 2009 Sep; 37(16):5279-94. View in: PubMed

Friedman JM, Jones PA. MicroRNAs: critical mediators of differentiation, development and disease. Swiss Med Wkly. 2009 Aug 22; 139(33-34):466-72. View in: PubMed

Friedman JM, Jones PA, Liang G. The tumor suppressor microRNA-101 becomes an epigenetic player by targeting the polycomb group protein EZH2 in cancer. Cell Cycle. 2009 Aug; 8(15):2313-4. View in: PubMed

Miranda TB, Cortez CC, Yoo CB, Liang G, Abe M, Kelly TK, Marquez VE, Jones PA. DZNep is a global histone methylation inhibitor that reactivates developmental genes not silenced by DNA methylation. Mol Cancer Ther. 2009 Jun; 8(6):1579-88. View in: PubMed

Friedman JM, Liang G, Liu CC, Wolff EM, Tsai YC, Ye W, Zhou X, Jones PA. The putative tumor suppressor microRNA-101 modulates the cancer epigenome by repressing the polycomb group protein EZH2. Cancer Res. 2009 Mar 15; 69(6):2623-9. View in: PubMed

Youssef RF, Mitra AP, Bartsch G, Jones PA, Skinner DG, Cote RJ. Molecular targets and targeted therapies in bladder cancer management. World J Urol. 2009 Feb; 27(1):9-20. View in: PubMed

Yoo CB, Valente R, Congiatu C, Gavazza F, Angel A, Siddiqui MA, Jones PA, McGuigan C, Marquez VE. Activation of p16 gene silenced by DNA methylation in cancer cells by phosphoramidate derivatives of 2'-deoxyzebularine. J Med Chem. 2008 Dec 11; 51(23):7593-601. View in: PubMed

Cortez CC, Jones PA. Chromatin, cancer and drug therapies. Mutat Res. 2008 Dec 1; 647(1-2):44-51. View in: PubMed

Gal-Yam EN, Egger G, Iniguez L, Holster H, Einarsson S, Zhang X, Lin JC, Liang G, Jones PA, Tanay A. Frequent switching of Polycomb repressive marks and DNA hypermethylation in the PC3 prostate cancer cell line. Proc Natl Acad Sci U S A. 2008 Sep 2; 105(35):12979-84. View in: PubMed

Yoo CB, Chuang JC, Byun HM, Egger G, Yang AS, Dubeau L, Long T, Laird PW, Marquez VE, Jones PA. Long-term epigenetic therapy with oral zebularine has minimal side effects and prevents intestinal tumors in mice. Cancer Prev Res (Phila). 2008 Sep; 1(4):233-40. View in: PubMed

Wolff EM, Liang G, Cortez CC, Tsai YC, Castelao JE, Cortessis VK, Tsao-Wei DD, Groshen S, Jones PA. RUNX3 methylation reveals that bladder tumors are older in patients with a history of smoking. Cancer Res. 2008 Aug 1; 68(15):6208-14. View in: PubMed

Weisenberger DJ, Trinh BN, Campan M, Sharma S, Long TI, Ananthnarayan S, Liang G, Esteva FJ, Hortobagyi GN, McCormick F, Jones PA, Laird PW. DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight. Nucleic Acids Res. 2008 Aug; 36(14):4689-98. View in: PubMed

Gal-Yam EN, Saito Y, Egger G, Jones PA. Cancer epigenetics: modifications, screening, and therapy. Annu Rev Med. 2008; 59:267-80. View in: PubMed

George B, Datar RH, Wu L, Cai J, Patten N, Beil SJ, Groshen S, Stein J, Skinner D, Jones PA, Cote RJ. p53 gene and protein status: the role of p53 alterations in predicting outcome in patients with bladder cancer. J Clin Oncol. 2007 Dec 1; 25(34):5352-8. View in: PubMed

Miranda TB, Jones PA. DNA methylation: the nuts and bolts of repression. J Cell Physiol. 2007 Nov; 213(2):384-90. View in: PubMed

Lin JC, Jeong S, Liang G, Takai D, Fatemi M, Tsai YC, Egger G, Gal-Yam EN, Jones PA. Role of nucleosomal occupancy in the epigenetic silencing of the MLH1 CpG island. Cancer Cell. 2007 Nov; 12(5):432-44. View in: PubMed

Grønbaek K, Hother C, Jones PA. Epigenetic changes in cancer. APMIS. 2007 Oct; 115(10):1039-59. View in: PubMed

Yoo CB, Jeong S, Egger G, Liang G, Phiasivongsa P, Tang C, Redkar S, Jones PA. Delivery of 5-aza-2'-deoxycytidine to cells using oligodeoxynucleotides. Cancer Res. 2007 Jul 1; 67(13):6400-8. View in: PubMed

Chuang JC, Jones PA. Epigenetics and microRNAs. Pediatr Res. 2007 May; 61(5 Pt 2):24R-29R. View in: PubMed

Jones PA, Jones SE. The critique of sentinel node biopsy as an acceptable way of locally staging breast cancer. Breast. 2007 Apr; 16(2):110. View in: PubMed

Jones PA, Baylin SB. The epigenomics of cancer. Cell. 2007 Feb 23; 128(4):683-92. View in: PubMed

Egger G, Aparicio AM, Escobar SG, Jones PA. Inhibition of histone deacetylation does not block resilencing of p16 after 5-aza-2'-deoxycytidine treatment. Cancer Res. 2007 Jan 1; 67(1):346-53. View in: PubMed

Jia L, Shen HC, Wantroba M, Khalid O, Liang G, Wang Q, Gentzschein E, Pinski JK, Stanczyk FZ, Jones PA, Coetzee GA. Locus-wide chromatin remodeling and enhanced androgen receptor-mediated transcription in recurrent prostate tumor cells. Mol Cell Biol. 2006 Oct; 26(19):7331-41. View in: PubMed

Saito Y, Jones PA. Epigenetic activation of tumor suppressor microRNAs in human cancer cells. Cell Cycle. 2006 Oct; 5(19):2220-2. View in: PubMed

van Rietschoten JG, Verzijlbergen KF, Gringhuis SI, van der Pouw Kraan TC, Bayley JP, Wierenga EA, Jones PA, Kooter JM, Verweij CL. Differentially methylated alleles in a distinct region of the human interleukin-1alpha promoter are associated with allele-specific expression of IL-1alpha in CD4+ T cells. Blood. 2006 Oct 1; 108(7):2143-9. View in: PubMed

Gal-Yam EN, Jeong S, Tanay A, Egger G, Lee AS, Jones PA. Constitutive nucleosome depletion and ordered factor assembly at the GRP78 promoter revealed by single molecule footprinting. PLoS Genet. 2006 Sep 22; 2(9):e160. View in: PubMed

Egger G, Jeong S, Escobar SG, Cortez CC, Li TW, Saito Y, Yoo CB, Jones PA, Liang G. Identification of DNMT1 (DNA methyltransferase 1) hypomorphs in somatic knockouts suggests an essential role for DNMT1 in cell survival. Proc Natl Acad Sci U S A. 2006 Sep 19; 103(38):14080-5. View in: PubMed

Saito Y, Liang G, Egger G, Friedman JM, Chuang JC, Coetzee GA, Jones PA. Specific activation of microRNA-127 with downregulation of the proto-oncogene BCL6 by chromatin-modifying drugs in human cancer cells. Cancer Cell. 2006 Jun; 9(6):435-43. View in: PubMed

Yoo CB, Jones PA. Epigenetic therapy of cancer: past, present and future. Nat Rev Drug Discov. 2006 Jan; 5(1):37-50. View in: PubMed

Jones PA, Martienssen R. A blueprint for a Human Epigenome Project: the AACR Human Epigenome Workshop. Cancer Res. 2005 Dec 15; 65(24):11241-6. View in: PubMed

Friedrich MG, Chandrasoma S, Siegmund KD, Weisenberger DJ, Cheng JC, Toma MI, Huland H, Jones PA, Liang G. Prognostic relevance of methylation markers in patients with non-muscle invasive bladder carcinoma. Eur J Cancer. 2005 Nov; 41(17):2769-78. View in: PubMed

Marquez VE, Kelley JA, Agbaria R, Ben-Kasus T, Cheng JC, Yoo CB, Jones PA. Zebularine: a unique molecule for an epigenetically based strategy in cancer chemotherapy. Ann N Y Acad Sci. 2005 Nov; 1058:246-54. View in: PubMed

Wolff EM, Liang G, Jones PA. Mechanisms of Disease: genetic and epigenetic alterations that drive bladder cancer. Nat Clin Pract Urol. 2005 Oct; 2(10):502-10. View in: PubMed

Chuang JC, Yoo CB, Kwan JM, Li TW, Liang G, Yang AS, Jones PA. Comparison of biological effects of non-nucleoside DNA methylation inhibitors versus 5-aza-2'-deoxycytidine. Mol Cancer Ther. 2005 Oct; 4(10):1515-20. View in: PubMed

Jones PA. Overview of cancer epigenetics. Semin Hematol. 2005 Jul; 42(3 Suppl 2):S3-8. View in: PubMed

Takai N, Kawamata N, Walsh CS, Gery S, Desmond JC, Whittaker S, Said JW, Popoviciu LM, Jones PA, Miyakawa I, Koeffler HP. Discovery of epigenetically masked tumor suppressor genes in endometrial cancer. Mol Cancer Res. 2005 May; 3(5):261-9. View in: PubMed

Sever AR, O'Brien ME, Humphreys S, Singh I, Jones SE, Jones PA. Radiopaque coil insertion into breast cancers prior to neoadjuvant chemotherapy. Breast. 2005 Apr; 14(2):108-17. View in: PubMed

Fatemi M, Pao MM, Jeong S, Gal-Yam EN, Egger G, Weisenberger DJ, Jones PA. Footprinting of mammalian promoters: use of a CpG DNA methyltransferase revealing nucleosome positions at a single molecule level. Nucleic Acids Res. 2005; 33(20):e176. View in: PubMed

Marquez VE, Barchi JJ, Kelley JA, Rao KV, Agbaria R, Ben-Kasus T, Cheng JC, Yoo CB, Jones PA. Zebularine: a unique molecule for an epigenetically based strategy in cancer chemotherapy. The magic of its chemistry and biology. Nucleosides Nucleotides Nucleic Acids. 2005; 24(5-7):305-18. View in: PubMed

Friedrich MG, Weisenberger DJ, Cheng JC, Chandrasoma S, Siegmund KD, Gonzalgo ML, Toma MI, Huland H, Yoo C, Tsai YC, Nichols PW, Bochner BH, Jones PA, Liang G. Detection of methylated apoptosis-associated genes in urine sediments of bladder cancer patients. Clin Cancer Res. 2004 Nov 15; 10(22):7457-65. View in: PubMed

Cheng JC, Yoo CB, Weisenberger DJ, Chuang J, Wozniak C, Liang G, Marquez VE, Greer S, Orntoft TF, Thykjaer T, Jones PA. Preferential response of cancer cells to zebularine. Cancer Cell. 2004 Aug; 6(2):151-8. View in: PubMed

Chatterjee SJ, George B, Goebell PJ, Alavi-Tafreshi M, Shi SR, Fung YK, Jones PA, Cordon-Cardo C, Datar RH, Cote RJ. Hyperphosphorylation of pRb: a mechanism for RB tumour suppressor pathway inactivation in bladder cancer. J Pathol. 2004 Jul; 203(3):762-70. View in: PubMed

Widschwendter M, Siegmund KD, Müller HM, Fiegl H, Marth C, Müller-Holzner E, Jones PA, Laird PW. Association of breast cancer DNA methylation profiles with hormone receptor status and response to tamoxifen. Cancer Res. 2004 Jun 1; 64(11):3807-13. View in: PubMed

Egger G, Liang G, Aparicio A, Jones PA. Epigenetics in human disease and prospects for epigenetic therapy. Nature. 2004 May 27; 429(6990):457-63. View in: PubMed

Liang G, Lin JC, Wei V, Yoo C, Cheng JC, Nguyen CT, Weisenberger DJ, Egger G, Takai D, Gonzales FA, Jones PA. Distinct localization of histone H3 acetylation and H3-K4 methylation to the transcription start sites in the human genome. Proc Natl Acad Sci U S A. 2004 May 11; 101(19):7357-62. View in: PubMed

Takai D, Jones PA. Origins of bidirectional promoters: computational analyses of intergenic distance in the human genome. Mol Biol Evol. 2004 Mar; 21(3):463-7. View in: PubMed

Cheng JC, Weisenberger DJ, Gonzales FA, Liang G, Xu GL, Hu YG, Marquez VE, Jones PA. Continuous zebularine treatment effectively sustains demethylation in human bladder cancer cells. Mol Cell Biol. 2004 Feb; 24(3):1270-8. View in: PubMed

Weisenberger DJ, Velicescu M, Cheng JC, Gonzales FA, Liang G, Jones PA. Role of the DNA methyltransferase variant DNMT3b3 in DNA methylation. Mol Cancer Res. 2004 Jan; 2(1):62-72. View in: PubMed

Matsukura S, Jones PA, Takai D. Establishment of conditional vectors for hairpin siRNA knockdowns. Nucleic Acids Res. 2003 Aug 1; 31(15):e77. View in: PubMed

Hsieh CL, Jones PA. Meddling with methylation. Nat Cell Biol. 2003 Jun; 5(6):502-4. View in: PubMed

Cheng JC, Matsen CB, Gonzales FA, Ye W, Greer S, Marquez VE, Jones PA, Selker EU. Inhibition of DNA methylation and reactivation of silenced genes by zebularine. J Natl Cancer Inst. 2003 Mar 5; 95(5):399-409. View in: PubMed

Jones PA. Epigenetics in carcinogenesis and cancer prevention. Ann N Y Acad Sci. 2003 Mar; 983:213-9. View in: PubMed

Jones PA. An epigenetic approach for finding tumor suppressors. Cell Cycle. 2003 Jan-Feb; 2(1):25-6. View in: PubMed

Takai D, Jones PA. The CpG island searcher: a new WWW resource. In Silico Biol. 2003; 3(3):235-40. View in: PubMed

Nguyen CT, Weisenberger DJ, Velicescu M, Gonzales FA, Lin JC, Liang G, Jones PA. Histone H3-lysine 9 methylation is associated with aberrant gene silencing in cancer cells and is rapidly reversed by 5-aza-2'-deoxycytidine. Cancer Res. 2002 Nov 15; 62(22):6456-61. View in: PubMed

Daskalakis M, Nguyen TT, Nguyen C, Guldberg P, Köhler G, Wijermans P, Jones PA, Lübbert M. Demethylation of a hypermethylated P15/INK4B gene in patients with myelodysplastic syndrome by 5-Aza-2'-deoxycytidine (decitabine) treatment. Blood. 2002 Oct 15; 100(8):2957-64. View in: PubMed

Weisenberger DJ, Velicescu M, Preciado-Lopez MA, Gonzales FA, Tsai YC, Liang G, Jones PA. Identification and characterization of alternatively spliced variants of DNA methyltransferase 3a in mammalian cells. Gene. 2002 Sep 18; 298(1):91-9. View in: PubMed

Widschwendter M, Jones PA. DNA methylation and breast carcinogenesis. Oncogene. 2002 Aug 12; 21(35):5462-82. View in: PubMed

Jones PA. DNA methylation and cancer. Oncogene. 2002 Aug 12; 21(35):5358-60. View in: PubMed

Liang G, Gonzalgo ML, Salem C, Jones PA. Identification of DNA methylation differences during tumorigenesis by methylation-sensitive arbitrarily primed polymerase chain reaction. Methods. 2002 Jun; 27(2):150-5. View in: PubMed

Jones PA, Baylin SB. The fundamental role of epigenetic events in cancer. Nat Rev Genet. 2002 Jun; 3(6):415-28. View in: PubMed

Gonzalgo ML, Jones PA. Quantitative methylation analysis using methylation-sensitive single-nucleotide primer extension (Ms-SNuPE). Methods. 2002 Jun; 27(2):128-33. View in: PubMed

Velicescu M, Weisenberger DJ, Gonzales FA, Tsai YC, Nguyen CT, Jones PA. Cell division is required for de novo methylation of CpG islands in bladder cancer cells. Cancer Res. 2002 Apr 15; 62(8):2378-84. View in: PubMed

Takai D, Jones PA. Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc Natl Acad Sci U S A. 2002 Mar 19; 99(6):3740-5. View in: PubMed

Liang G, Gonzales FA, Jones PA, Orntoft TF, Thykjaer T. Analysis of gene induction in human fibroblasts and bladder cancer cells exposed to the methylation inhibitor 5-aza-2'-deoxycytidine. Cancer Res. 2002 Feb 15; 62(4):961-6. View in: PubMed

Widschwendter M, Jones PA. The potential prognostic, predictive, and therapeutic values of DNA methylation in cancer. Commentary re: J. Kwong et al. , Promoter hypermethylation of multiple genes in nasopharyngeal carcinoma. Clin. Cancer Res. , 8: 131-137, 2002, and H-Z. Zou et al. , Detection of aberrant p16 methylation in the serum of colorectal cancer patients. Clin. Cancer Res. , 8: 188-191, 2002. Clin Cancer Res. 2002 Jan; 8(1):17-21. View in: PubMed

Liang G, Chan MF, Tomigahara Y, Tsai YC, Gonzales FA, Li E, Laird PW, Jones PA. Cooperativity between DNA methyltransferases in the maintenance methylation of repetitive elements. Mol Cell Biol. 2002 Jan; 22(2):480-91. View in: PubMed

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