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Genomes and Genes | Lanlan ShenSummaryAffiliation: The University of Texas Country: USA Publications
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Publications
DNA methylation changes after 5-aza-2'-deoxycytidine therapy in patients with leukemiaAllen S Yang
Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
Cancer Res 66:5495-503. 2006..In conclusion, we show dose-dependent hypomethylation after decitabine at low doses. Increasing the dose, which has been shown previously to result in a reduced response rate, was not accompanied by further hypomethylation...- Optimizing annealing temperature overcomes bias in bisulfite PCR methylation analysisLanlan Shen
Department of Leukemia, M.D. Anderson Cancer Center, Houston, TX 77030, USA
Biotechniques 42:48, 50, 52 passim. 2007 - Drug sensitivity prediction by CpG island methylation profile in the NCI-60 cancer cell line panelLanlan Shen
Department of Leukemia, The University of Texas M D Anderson Cancer Center, Houston, Texas 77030, USA
Cancer Res 67:11335-43. 2007..Our results confirm that epigenetic profiles are useful in identifying molecular mediators for cancer drug sensitivity (pharmaco-epigenomics)... 
Genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promotersLanlan Shen
Department of Leukemia, The University of Texas at M D Anderson Cancer Center, Houston, Texas, USA
PLoS Genet 3:2023-36. 2007....
Gene silencing in cancer by histone H3 lysine 27 trimethylation independent of promoter DNA methylationYutaka Kondo
Department of Leukemia, University of Texas M D Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA
Nat Genet 40:741-50. 2008..These data establish EZH2-mediated H3K27triM as a mechanism of tumor-suppressor gene silencing in cancer that is potentially independent of promoter DNA methylation...- Identification of novel tumor markers in prostate, colon and breast cancer by unbiased methylation profilingWoonbok Chung
Department of Leukemia, Baylor College of Medicine, Houston, Texas, United States of America
PLoS ONE 3:e2079. 2008..Our data identify new targets of transcriptional silencing in cancer, and provide new biomarkers that could be useful in screening for prostate cancer and other cancers... - Integrated genetic and epigenetic analysis identifies three different subclasses of colon cancerLanlan Shen
Department of Leukemia, University of Texas M D Anderson Cancer Center, Houston, TX 77030
Proc Natl Acad Sci U S A 104:18654-9. 2007..Together, our integrated genetic and epigenetic analysis reveals that colon cancers correspond to three molecularly distinct subclasses of disease... - DNA methylation profiles of primary colorectal carcinoma and matched liver metastasisKazuo Konishi
Department of Leukemia, Division of Cancer Medicine, The University of Texas M D Anderson Cancer Center, Houston, Texas, United States of America
PLoS ONE 6:e27889. 2011..The contribution of DNA methylation to the metastatic process in colorectal cancers (CRCs) is unclear... - High-throughput methylation profiling by MCA coupled to CpG island microarrayMarcos R H Estecio
Department of Leukemia, UT M D Anderson Cancer Center, Houston, Texas 77030, USA
Genome Res 17:1529-36. 2007..In summary, MCAM is a suitable technique to discover methylated genes and to profile methylation changes in clinical samples in a high-throughput fashion... - Epigenetic-genetic interactions in the APC/WNT, RAS/RAF, and P53 pathways in colorectal carcinomaYutaka Suehiro
Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
Clin Cancer Res 14:2560-9. 2008.... - Rare CpG island methylator phenotype in ulcerative colitis-associated neoplasiasKazuo Konishi
Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
Gastroenterology 132:1254-60. 2007..Whether this translates into hypermethylation in UC-associated cancers (UC-Cs) is not known... - DNA methylation predicts survival and response to therapy in patients with myelodysplastic syndromesLanlan Shen
Department of Leukemia and Biostatistics, The University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
J Clin Oncol 28:605-13. 2010..Epigenetic therapy using decitabine, a DNA hypomethylating agent, is clinically effective for the treatment of MDS. Therefore, we investigated the association between DNA methylation and clinical outcome in MDS... - Sensitive and specific detection of early gastric cancer with DNA methylation analysis of gastric washesYoshiyuki Watanabe
Department of Leukemia, The University of Texas M D Anderson Cancer Center, Houston, Texas 77030, USA
Gastroenterology 136:2149-58. 2009..We hypothesized that methylation analysis of DNA recovered from gastric washes could be used to detect gastric cancer... - LINE-1 hypomethylation in cancer is highly variable and inversely correlated with microsatellite instabilityMarcos R H Estecio
Department of Leukemia, University of Texas M D Anderson Cancer Center, Houston, Texas, United States of America
PLoS ONE 2:e399. 2007..This study was performed to determine the relationship between DNA hypomethylation, hypermethylation and microsatellite instability in cancer... - Epigenetic maturation in colonic mucosa continues beyond infancy in miceRichard Kellermayer
Department of Pediatrics, Baylor College of Medicine, USDA ARS Children s Nutrition Research Center, Houston, TX 77030, USA
Hum Mol Genet 19:2168-76. 2010..Transcript Profiling: Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/), accession numbers: GSE18031 (DNA methylation arrays), GSE19506 (gene expression arrays)... - Aberrant CpG island methylation in acute myeloid leukemia is accentuated at relapseHeike Kroeger
Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
Blood 112:1366-73. 2008..0% to 15.2% (median 10.6%) genes in relapse (P < .001). Our data suggest that DNA methylation is involved in AML progression and provide a rationale for the use of epigenetic agents in remission maintenance... - RIL, a LIM gene on 5q31, is silenced by methylation in cancer and sensitizes cancer cells to apoptosisYanis A Boumber
Department of Leukemia, The University of Texas M D Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
Cancer Res 67:1997-2005. 2007..In MDS, RIL methylation is a marker of adverse prognosis independent of chromosome 5 and 7 deletions. Our data suggest that RIL is a good candidate TSG silenced by hypermethylation in cancer... - An Sp1/Sp3 binding polymorphism confers methylation protectionYanis A Boumber
Department of Leukemia, MD Anderson Cancer Center, University of Texas, Houston, Texas, United States of America
PLoS Genet 4:e1000162. 2008..Our finding demonstrates that, in some genes, hypermethylation in cancer is dictated by protein-DNA interactions at the promoters and provides a novel mechanism by which genetic polymorphisms can influence an epigenetic state... - Association between DNA methylation and shortened survival in patients with advanced colorectal cancer treated with 5-fluorouracil based chemotherapyLanlan Shen
The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
Clin Cancer Res 13:6093-8. 2007..We sought to determine the prognostic significance of CIMP in advanced colorectal cancer patients treated with 5-fluorouracil (5-FU) in an Eastern Cooperative Oncology Group clinical trial... - Concordant DNA methylation in synchronous colorectal carcinomasKazuo Konishi
Department of Leukemia, The University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
Cancer Prev Res (Phila) 2:814-22. 2009..Screening for and secondary prevention of colon cancer should take this fact into account... - CpG island methylation profiling in human melanoma cell linesCarmen S Tellez
Department of Leukemia, The University of Texas M D Anderson Cancer Center, Houston, Texas, USA
Melanoma Res 19:146-55. 2009..We conclude that aberrant hypermethylation, is frequent in melanoma cell lines, directly correlated with global DNA methylation, and independent of BRAF and NRAS mutations... - Genome architecture marked by retrotransposons modulates predisposition to DNA methylation in cancerMarcos R H Estecio
Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
Genome Res 20:1369-82. 2010.... - MGMT promoter methylation and field defect in sporadic colorectal cancerLanlan Shen
Department of Leukemia, The University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
J Natl Cancer Inst 97:1330-8. 2005..The DNA repair gene O6-methylguanine-DNA methyltransferase (MGMT) is frequently methylated in colorectal cancer. We hypothesized that MGMT methylation could be one of the mediators of field cancerization in the colon mucosa... - Chromatin immunoprecipitation microarrays for identification of genes silenced by histone H3 lysine 9 methylationYutaka Kondo
Department of Leukemia, University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA
Proc Natl Acad Sci U S A 101:7398-403. 2004..This unbiased approach confirms the tight coupling between DNA methylation and histone modifications in cancer and could be used to probe gene silencing in nonneoplastic conditions as well... - Hypomethylation of long interspersed nuclear element-1 in hepatocellular carcinomasMi Jung Kim
Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
Mod Pathol 22:442-9. 2009..In hepatocellular carcinomas, hypermethylation of CpG islands, and CpG island methylator phenotype status seems to correlate with levels of long interspersed nuclear element-1 hypomethylation... - Widespread and tissue specific age-related DNA methylation changes in miceShinji Maegawa
Department of Leukemia, The University of Texas M D Anderson Cancer Center, Houston, Texas 77030, USA
Genome Res 20:332-40. 2010..We conclude that epigenetic deregulation is a common feature of aging in mammals... - Induction of hypomethylation and molecular response after decitabine therapy in patients with chronic myelomonocytic leukemiaYasuhiro Oki
Department of Leukemia, University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
Blood 111:2382-4. 2008..Our data suggest a predominantly noncytotoxic mechanism of action for decitabine, leading to altered biology of the neoplastic clone and/or normal cells. This trial was registered at www.ClinicalTrials.gov as #NCT00067808... - Repetitive elements and enforced transcriptional repression co-operate to enhance DNA methylation spreading into a promoter CpG-islandYan Zhang
Department of Leukemia, The University of Texas MD Anderson Cancer Center, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
Nucleic Acids Res 40:7257-68. 2012.... - Understanding the development of human bladder cancer by using a whole-organ genomic mapping strategyTadeusz Majewski
Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
Lab Invest 88:694-721. 2008..These analyses provided new insights on the involvement of several non-coding sequences mapping to the region and identified novel target genes, termed forerunner (FR) genes, involved in early phases of cancer development... - Frequent alteration of MLL3 frameshift mutations in microsatellite deficient colorectal cancerYoshiyuki Watanabe
Department of Leukemia, The University of Texas M D Anderson Cancer Center, Houston, Texas, United States of America
PLoS ONE 6:e23320. 2011..Mutations in MLL3 were found in a whole genome analysis of colorectal cancer but have not been confirmed by a separate study... - Silencing of bidirectional promoters by DNA methylation in tumorigenesisJingmin Shu
Department of Leukemia, M.D. Anderson Cancer Center, Houston, Texas 77030, USA
Cancer Res 66:5077-84. 2006.... - Aberrant DNA methylation of p57KIP2 identifies a cell-cycle regulatory pathway with prognostic impact in adult acute lymphocytic leukemiaLanlan Shen
Department of Leukemia, University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
Blood 101:4131-6. 2003..02). Our results indicate that p57KIP2 is frequently methylated in adult patients with ALL, and that inactivation of a pathway composed of p73, p15, and p57KIP2 predicts for poor prognosis in Ph-negative patients... - Correlation between CpG methylation profiles and hormone receptor status in breast cancersWeiwei Feng
Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
Breast Cancer Res 9:R57. 2007..The present study was undertaken to determine whether methylation of a set of growth-suppressor genes would correlate to the expression of estrogen receptors (ERs) and progesterone receptors (PRs)... - 15-Lipoxygenase-1 transcriptional silencing by DNA methyltransferase-1 independently of DNA methylationXiangsheng Zuo
Department of Clinical Cancer Prevention, The University of Texas M D Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030 4009, USA
FASEB J 22:1981-92. 2008..DNMT-1 has a direct suppressive role in 15-LOX-1 transcriptional silencing that is independent of 15-LOX-1 promoter DNA methylation... - Delta DNMT3B variants regulate DNA methylation in a promoter-specific mannerJie Wang
Department of Thoracic Head and Neck Medical Oncology, The University of Texas M D Anderson Cancer Center, Houston, Texas 77030, USA
Cancer Res 67:10647-52. 2007..We conclude that promoter DNA methylation can be differentially regulated and DeltaDNMT3Bs are involved in regulation of such promoter-specific de novo DNA methylation... - Age-related DNA methylation changes in normal human prostate tissuesBernard Kwabi-Addo
Department of Pathology, Baylor College of Medicine, The University of Texas M D Anderson Cancer Center, Houston, Texas, USA
Clin Cancer Res 13:3796-802. 2007..We examined the extent of gene methylation in pathologically normal human prostate as a function of age... - Critical role of histone methylation in tumor suppressor gene silencing in colorectal cancerYutaka Kondo
Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston 77030, USA
Mol Cell Biol 23:206-15. 2003..Our results suggest that reduced H3 Lys-4 methylation and increased H3 Lys-9 methylation play a critical role in the maintenance of promoter DNA methylation-associated gene silencing in colorectal cancer... - Season of conception in rural gambia affects DNA methylation at putative human metastable epiallelesRobert A Waterland
Department of Pediatrics, Baylor College of Medicine, USDA ARS Children s Nutrition Research Center, Houston, Texas, United States of America
PLoS Genet 6:e1001252. 2010..MEs should therefore facilitate an improved understanding of the role of interindividual epigenetic variation in human disease... - Methods of DNA methylation analysisLanlan Shen
Department of Leukemia, University of Texas MD Anderson Cancer Center, USA
Curr Opin Clin Nutr Metab Care 10:576-81. 2007..To provide guidance for investigators who are new to the field of DNA methylation analysis... - Phenotype of microsatellite-stable colorectal carcinomas with CpG island methylationLucian R Chirieac
Department of Pathology, Division of Pathology and Laboratory Medicine, University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA
Am J Surg Pathol 29:429-36. 2005..5, P = 0.03). Our epigenotype-phenotype correlation study shows that microsatellite-stable CRC with CpG island methylation have a distinctive pathologic phenotype with both similarities to and differences from MSI-H tumors... - Effects of TET2 mutations on DNA methylation in chronic myelomonocytic leukemiaJumpei Yamazaki
Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
Epigenetics 7:201-7. 2012..0% and 9.8%, respectively) (p = 0.016). Thus, TET2 mutations affect global methylation in CMML but most of the changes are likely to be outside gene promoters... - P14 methylation in human colon cancer is associated with microsatellite instability and wild-type p53Lanlan Shen
Department of Leukemia, The University of Texas at M. D. Anderson Cancer Center, Houston, Texas 77030, USA
Gastroenterology 124:626-33. 2003..The results provide a possible explanation for the paucity of p53 mutations in colon cancers with microsatellite instability... - Epigenomic profiling indicates a role for DNA methylation in early postnatal liver developmentRobert A Waterland
Department of Pediatrics, Baylor College of Medicine, USDA Children s Nutrition Research Center, 1100 Bates St, Ste 5080, Houston, TX 77030, USA
Hum Mol Genet 18:3026-38. 2009..These in vivo data clearly indicate a role for DNA methylation in mammalian differentiation, and provide the novel insight that critical windows in mammalian developmental epigenetics extend well beyond early embryonic development... - DNA methylation and environmental exposures in human hepatocellular carcinomaLanlan Shen
Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, 77030, USA
J Natl Cancer Inst 94:755-61. 2002..6%; P<.001). CONCLUSION: Geographic variations in the methylation status of various CpG islands indicate that environmental factors may influence the frequent and concordant degree of hypermethylation in multiple genes in HCC tumors... - Foxa1 functions as a pioneer transcription factor at transposable elements to activate Afp during differentiation of embryonic stem cellsJoseph H Taube
Department of Biochemistry and Molecular Biology, Graduate School of Biomedical Sciences, Center for Stem Cell and Developmental Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
J Biol Chem 285:16135-44. 2010.... - Decitabine improves patient outcomes in myelodysplastic syndromes: results of a phase III randomized studyHagop Kantarjian
Department of Leukemia, University of Texas M D Anderson Cancer Center, Houston, Texas 77030, USA
Cancer 106:1794-803. 2006..Decitabine indirectly depletes methylcytosine and causes hypomethylation of target gene promoters... - Forerunner genes contiguous to RB1 contribute to the development of in situ neoplasiaSangkyou Lee
Department of Pathology, University of Texas M D Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
Proc Natl Acad Sci U S A 104:13732-7. 2007..We also show that homozygous inactivation of P2RY5 was antecedent to the loss of RB1 during tumor development, and that nucleotide substitutions in P2RY5 represent a cancer predisposing factor... - Vascular endothelial growth factor receptor-1 activation mediates epithelial to mesenchymal transition in human pancreatic carcinoma cellsAnthony D Yang
Department of Surgical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77230-1402, USA
Cancer Res 66:46-51. 2006..Given our previous finding of VEGFR-1-mediated tumor cell invasion and migration in pancreatic carcinoma cells, we hypothesize that VEGFR-1 plays a role in tumor progression in pancreatic cancer through the induction of EMT... - Downregulation of histone H3 lysine 9 methyltransferase G9a induces centrosome disruption and chromosome instability in cancer cellsYutaka Kondo
Division of Molecular Oncology, Aichi Cancer Center Research Institute, Nagoya, Japan
PLoS ONE 3:e2037. 2008..Cancer cells are characterized by prominent epigenetic dysregulation, including histone modifications. However, the functional roles of the histone methyltransferases (HMT) in cancer remain unclear... - Epigenetic inactivation of EGFR by CpG island hypermethylation in cancerAlberto J Montero
Division of Hematology Oncology, Medical University of South Carolina, Charleston, South Carolina, USA
Cancer Biol Ther 5:1494-501. 2006..In conclusion, EGFR is hypermethylated and silenced in a subset of solid tumor cell lines and primary tumor specimens, and cotreatment with decitabine and gefitinib has an additive effect only in EGFR methylated breast cancer cell lines... - Variable DNA methylation patterns associated with progression of disease in hepatocellular carcinomasWentao Gao
Division of Molecular Oncology, Aichi Cancer Center Research Institute, 1 1 Kanokoden, Chikusa ku, Nagoya 464 8681, Japan
Carcinogenesis 29:1901-10. 2008..Our global epigenome analysis reveals distinct patterns of methylation that are probably to represent different pathophysiologic processes in HCCs... - HLTF gene silencing in human colon cancerHelen R Moinova
Cancer Center and Department of Medicine at Case Western Reserve University, Cleveland, OH 44106, USA
Proc Natl Acad Sci U S A 99:4562-7. 2002..These findings show that HLTF is a common target for methylation and epigenetic gene silencing in colon cancer and suggest HLTF is a candidate colon cancer suppressor gene... - Lack of p21(CIP1) DNA methylation in acute lymphocytic leukemiaLanlan Shen
Blood 100:3432-3; author reply 3433-4. 2002 - CIMP, at lastJean-Pierre J Issa
Gastroenterology 129:1121-4. 2005