Keck School Faculty

Albumin levels predict prognosis in advanced renal cell carcinoma treated with tyrosine kinase inhibitors: a systematic review and meta-analysisUrol Oncol. 2022 01; 40(1):12. e13-12. e22. . View in PubMed

Reply by Authors J Urol. 2023 05; 209(5):862. . View in PubMed

A Urine-based DNA Methylation Marker Test to Detect Upper Tract Urothelial Carcinoma: A Prospective Cohort Study J Urol. 2023 05; 209(5):854-862. . View in PubMed

RNA mis-splicing drives viral mimicry response after DNMTi therapy in SETD2-mutant kidney cancer Cell Rep. 2023 01 31; 42(1):112016. . View in PubMed

FOXC1 Binds Enhancers and Promotes Cisplatin Resistance in Bladder Cancer Cancers (Basel). 2022 Mar 28; 14(7). . View in PubMed

Characterizing DNA methylation signatures of retinoblastoma using aqueous humor liquid biopsy Nat Commun. 2022 09 21; 13(1):5523. . View in PubMed

DNMT and EZH2 inhibitors synergize to activate therapeutic targets in hepatocellular carcinoma Cancer Lett. 2022 11 01; 548:215899. . View in PubMed

The Role of DNA Methylation and DNA Methyltransferases in Cancer Adv Exp Med Biol. 2022; 1389:317-348. . View in PubMed

Characterizing DNA methylation signatures and their potential functional roles in Merkel cell carcinoma Genome Med. 2021 08 16; 13(1):130. . View in PubMed

Immunogenic cell death pathway polymorphisms for predicting oxaliplatin efficacy in metastatic colorectal cancer J Immunother Cancer. 2020 11; 8(2). . View in PubMed

Epigenetic plasticity potentiates a rapid cyclical shift to and from an aggressive cancer phenotype Int J Cancer. 2020 06 01; 146(11):3065-3076. . View in PubMed

Telomerase Variants in Patients with Cirrhosis Awaiting Liver Transplantation Hepatology. 2019 06; 69(6):2652-2663. . View in PubMed

Impact of polymorphisms within genes involved in regulating DNA methylation in patients with metastatic colorectal cancer enrolled in three independent, randomised, open-label clinical trials: a meta-analysis from TRIBE, MAVERICC and FIRE-3 Eur J Cancer. 2019 04; 111:138-147. . View in PubMed

The Roles of Human DNA Methyltransferases and Their Isoforms in Shaping the Epigenome Genes (Basel). 2019 02 23; 10(2). . View in PubMed

AMPK variant, a candidate of novel predictor for chemotherapy in metastatic colorectal cancer: A meta-analysis using TRIBE, MAVERICC and FIRE3 Int J Cancer. 2019 10 15; 145(8):2082-2090. . View in PubMed

Data integration by multi-tuning parameter elastic net regression BMC Bioinformatics. 2018 Oct 10; 19(1):369. . View in PubMed

Quantitative Contour Analysis as an Image-based Discriminator Between Benign and Malignant Renal Tumors Urology. 2018 Apr; 114:121-127. . View in PubMed

Integrative Epigenetic Analysis Reveals Therapeutic Targets to the DNA Methyltransferase Inhibitor Guadecitabine (SGI-110) in Hepatocellular Carcinoma Hepatology. 2018 10; 68(4):1412-1428. . View in PubMed

DNA methylation aberrancies delineate clinically distinct subsets of colorectal cancer and provide novel targets for epigenetic therapies Oncogene. 2018 02 01; 37(5):566-577. . View in PubMed

Improving needle biopsy accuracy in small renal mass using tumor-specific DNA methylation markers Oncotarget. 2017 Jan 17; 8(3):5439-5448. . View in PubMed

Identifying aggressive prostate cancer foci using a DNA methylation classifier Genome Biol. 2017 01 12; 18(1):3. . View in PubMed

Nucleosome Positioning and NDR Structure at RNA Polymerase III Promoters Sci Rep. 2017 02 08; 7:41947. . View in PubMed

DNA methylation aberrancies as a guide for surveillance and treatment of human cancers Epigenetics. 2017 06 03; 12(6):416-432. . View in PubMed

Heterogeneous patterns of DNA methylation-based field effects in histologically normal prostate tissue from cancer patients Sci Rep. 2017 01 13; 7:40636. . View in PubMed

epiG: statistical inference and profiling of DNA methylation from whole-genome bisulfite sequencing data Genome Biol. 2017 02 21; 18(1):38. . View in PubMed

Down-regulation of ARID1A is sufficient to initiate neoplastic transformation along with epigenetic reprogramming in non-tumorigenic endometriotic cells Cancer Lett. 2017 08 10; 401:11-19. . View in PubMed

Genetic and Epigenetic Alterations in Bladder Cancer Int Neurourol J. 2016 Nov; 20(Suppl 2):S84-94. . View in PubMed

Isoform switching and exon skipping induced by the DNA methylation inhibitor 5-Aza-2'-deoxycytidine Sci Rep. 2016 Apr 19; 6:24545. . View in PubMed

The Role of DNA Methylation in Cancer Adv Exp Med Biol. 2016; 945:151-172. . View in PubMed

Bivalent Regions of Cytosine Methylation and H3K27 Acetylation Suggest an Active Role for DNA Methylation at Enhancers Mol Cell. 2016 05 05; 62(3):422-431. . View in PubMed

Identification of DNA Methylation-Independent Epigenetic Events Underlying Clear Cell Renal Cell Carcinoma Cancer Res. 2016 04 01; 76(7):1954-64. . View in PubMed

DNMT3B isoforms without catalytic activity stimulate gene body methylation as accessory proteins in somatic cells Nat Commun. 2016 04 28; 7:11453. . View in PubMed

Vitamin C increases viral mimicry induced by 5-aza-2'-deoxycytidine Proc Natl Acad Sci U S A. 2016 09 13; 113(37):10238-44. . View in PubMed

Linker histone H12 establishes chromatin compaction and gene silencing through recognition of H3K27me3. Sci Rep. 2015 Nov 19; 5:16714. . View in PubMed

Hypermethylation of the VTRNA1-3 Promoter is Associated with Poor Outcome in Lower Risk Myelodysplastic Syndrome Patients Genes (Basel). 2015 Oct 14; 6(4):977-90. . View in PubMed

Unique Role for a DNA Methyltransferase Isoform in Lung Cancer EBioMedicine. 2015 Oct; 2(10):1272-3. . View in PubMed

CT prediction of the Fuhrman grade of clear cell renal cell carcinoma (RCC): towards the development of computer-assisted diagnostic method Abdom Imaging. 2015 Oct; 40(8):3168-74. . View in PubMed

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

Outlining the limits of partial nephrectomy Transl Androl Urol. 2015 Jun; 4(3):294-300. . View in PubMed

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

Epigenetic alterations and microRNA misexpression in cancer and autoimmune diseases: a critical review Clin Rev Allergy Immunol. 2014 Oct; 47(2):128-35. . View in PubMed

A panel of three markers hyper- and hypomethylated in urine sediments accurately predicts bladder cancer recurrence Clin Cancer Res. 2014 Apr 01; 20(7):1978-89. . View in PubMed

Reprogramming of the human intestinal epigenome by surgical tissue transposition Genome Res. 2014 Apr; 24(4):545-53. . View in PubMed

miR-30d, miR-181a and miR-199a-5p cooperatively suppress the endoplasmic reticulum chaperone and signaling regulator GRP78 in cancer Oncogene. 2013 Sep 26; 32(39):4694-701. . View in PubMed

Alterations in deoxyribonucleic acid (DNA) methylation patterns of Calca, Timp3, Mmp2, and Igf2r are associated with chronic cystitis in a cyclophosphamide-induced mouse modelUrology. 2013 Jul; 82(1):253. e9-15. . View in PubMed

Diagnostic markers of urothelial cancer based on DNA methylation analysis BMC Cancer. 2013 Jun 04; 13:275. . View in PubMed

SNF5 is an essential executor of epigenetic regulation during differentiation PLoS Genet. 2013 Apr; 9(4):e1003459. . View in PubMed

Functional DNA demethylation is accompanied by chromatin accessibility Nucleic Acids Res. 2013 Apr; 41(7):3973-85. . View in PubMed

Nucleosome occupancy and gene regulation during tumorigenesis Adv Exp Med Biol. 2013; 754:109-34. . View in PubMed

Synergistic re-activation of epigenetically silenced genes by combinatorial inhibition of DNMTs and LSD1 in cancer cells PLoS One. 2013; 8(9):e75136. . View in PubMed

Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules Genome Res. 2012 Dec; 22(12):2497-506. . View in PubMed

DNA methylation screening identifies driver epigenetic events of cancer cell survival Cancer Cell. 2012 May 15; 21(5):655-667. . View in PubMed

Lysine methyltransferase G9a is not required for DNMT3A/3B anchoring to methylated nucleosomes and maintenance of DNA methylation in somatic cells Epigenetics Chromatin. 2012 Jan 27; 5(1):3. . View in PubMed

Allelic methylation levels of the noncoding VTRNA2-1 located on chromosome 5q311 predict outcome in AML. Blood. 2012 Jan 05; 119(1):206-16. . View in PubMed

Epigenetic alterations in bladder cancer and their potential clinical implications Adv Urol. 2012; 2012:546917. . View in PubMed

Gene reactivation by 5-aza-2'-deoxycytidine-induced demethylation requires SRCAP-mediated H2AZ insertion to establish nucleosome depleted regions. PLoS Genet. 2012; 8(3):e1002604. . View in PubMed

Polycomb-repressed genes have permissive enhancers that initiate reprogramming Cell. 2011 Dec 09; 147(6):1283-94. . View in PubMed

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

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

Creating a flexible multiple microRNA expression vector by linking precursor microRNAs Biochem Biophys Res Commun. 2011 Jul 29; 411(2):276-80. . View in PubMed

Conditional inactivation of the CXCR4 receptor in osteoprecursors reduces postnatal bone formation due to impaired osteoblast development J Biol Chem. 2011 Jul 29; 286(30):26794-805. . View in PubMed

Epigenetic reprogramming as a key contributor to melanocyte malignant transformation Epigenetics. 2011 Apr; 6(4):450-64. . View in PubMed

Nucleosomes containing methylated DNA stabilize DNA methyltransferases 3A/3B and ensure faithful epigenetic inheritance PLoS Genet. 2011 Feb 03; 7(2):e1001286. . View in PubMed

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

Equitoxic doses of 5-azacytidine and 5-aza-2'deoxycytidine induce diverse immediate and overlapping heritable changes in the transcriptome PLoS One. 2010 Sep 29; 5(9). . View in PubMed

H2AZ maintenance during mitosis reveals nucleosome shifting on mitotically silenced genes. Mol Cell. 2010 Sep 24; 39(6):901-11. . View in PubMed

Hypomethylation of a LINE-1 promoter activates an alternate transcript of the MET oncogene in bladders with cancer PLoS Genet. 2010 Apr 22; 6(4):e1000917. . View in PubMed

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

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

Changes in DNA methylation of tandem DNA repeats are different from interspersed repeats in cancer Int J Cancer. 2009 Aug 01; 125(3):723-9. . View in PubMed

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

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

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

Epigenetic therapy upregulates the tumor suppressor microRNA-126 and its host gene EGFL7 in human cancer cells Biochem Biophys Res Commun. 2009 Feb 13; 379(3):726-31. . View in PubMed

Rethinking how DNA methylation patterns are maintained Nat Rev Genet. 2009 11; 10(11):805-11. . View in PubMed

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 02; 105(35):12979-84. . View in PubMed

DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight Nucleic Acids Res. 2008 Aug; 36(14):4689-98. . View in PubMed

RUNX3 methylation reveals that bladder tumors are older in patients with a history of smoking Cancer Res. 2008 Aug 01; 68(15):6208-14. . View in PubMed

Examination of IGF2 and H19 loss of imprinting in bladder cancer Cancer Res. 2007 Nov 15; 67(22):10753-8. . View in PubMed

Role of nucleosomal occupancy in the epigenetic silencing of the MLH1 CpG island Cancer Cell. 2007 Nov; 12(5):432-44. . View in PubMed

Delivery of 5-aza-2'-deoxycytidine to cells using oligodeoxynucleotides Cancer Res. 2007 Jul 01; 67(13):6400-8. . View in PubMed

Methylation-sensitive single-nucleotide primer extension (Ms-SNuPE) for quantitative measurement of DNA methylation Nat Protoc. 2007; 2(8):1931-6. . View in PubMed

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

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

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

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

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

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

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

Preferential response of cancer cells to zebularine Cancer Cell. 2004 Aug; 6(2):151-8. . View in PubMed

Epigenetics in human disease and prospects for epigenetic therapy Nature. 2004 May 27; 429(6990):457-63. . View in PubMed

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

Continuous zebularine treatment effectively sustains demethylation in human bladder cancer cells Mol Cell Biol. 2004 Feb; 24(3):1270-8. . View in PubMed

Role of the DNA methyltransferase variant DNMT3b3 in DNA methylation Mol Cancer Res. 2004 Jan; 2(1):62-72. . View in PubMed

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

Hypomethylation and hypermethylation of DNA in Wilms tumors Oncogene. 2002 Sep 26; 21(43):6694-702. . View in PubMed

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

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

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

Cooperativity between DNA methyltransferases in the maintenance methylation of repetitive elements Mol Cell Biol. 2002 Jan; 22(2):480-91. . View in PubMed

Susceptibility of nonpromoter CpG islands to de novo methylation in normal and neoplastic cells J Natl Cancer Inst. 2001 Oct 03; 93(19):1465-72. . View in PubMed

Global and gene-specific epigenetic patterns in human bladder cancer genomes are relatively stable in vivo and in vitro over time Cancer Res. 2001 Aug 01; 61(15):5875-84. . View in PubMed

The endothelin receptor B (EDNRB) promoter displays heterogeneous, site specific methylation patterns in normal and tumor cells Hum Mol Genet. 2001 Apr 15; 10(9):903-10. . View in PubMed

The gene for a novel transmembrane protein containing epidermal growth factor and follistatin domains is frequently hypermethylated in human tumor cells Cancer Res. 2000 Sep 01; 60(17):4907-12. . View in PubMed

PAX6 methylation and ectopic expression in human tumor cells Int J Cancer. 2000 Jul 15; 87(2):179-85. . View in PubMed

Progressive increases in de novo methylation of CpG islands in bladder cancer Cancer Res. 2000 May 01; 60(9):2473-6. . View in PubMed

DNA methylator and mismatch repair phenotypes are not mutually exclusive in colorectal cancer cell lines Oncogene. 2000 Feb 17; 19(7):943-52. . View in PubMed

Relationship between transcription and DNA methylation Curr Top Microbiol Immunol. 2000; 249:75-86. . View in PubMed

The human DNA methyltransferases (DNMTs) 1, 3a and 3b: coordinate mRNA expression in normal tissues and overexpression in tumors Nucleic Acids Res. 1999 Jun 01; 27(11):2291-8. . View in PubMed

Novel endothelin B receptor transcripts with the potential of generating a new receptor Gene. 1999 Mar 04; 228(1-2):43-9. . View in PubMed

DNA methylation differences associated with tumor tissues identified by genome scanning analysis Genomics. 1998 Nov 01; 53(3):260-8. . View in PubMed

Regioselective effect of zwitterionic DNA substitutions on DNA alkylation: evidence for a strong side chain orientational preference Biochemistry. 1997 May 20; 36(20):6024-32. . View in PubMed

Identification and characterization of differentially methylated regions of genomic DNA by methylation-sensitive arbitrarily primed PCR Cancer Res. 1997 Feb 15; 57(4):594-9. . View in PubMed

Reaction of N-(2-chloroethyl)-N-nitrosoureas with DNA: effect of buffers on DNA adduction, cross-linking, and cytotoxicity Chem Res Toxicol. 1996 Jan-Feb; 9(1):208-14. . View in PubMed

The use of 2-hydroperoxytetrahydrofuran as a reagent to sequence cytosine and to probe non-Watson-Crick DNA structures Nucleic Acids Res. 1995 Feb 25; 23(4):713-9. . View in PubMed