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Items: 46

1.

DNA methylation at an enhancer of the three prime repair exonuclease 2 gene (TREX2) is linked to gene expression and survival in laryngeal cancer.

Weigel C, Chaisaingmongkol J, Assenov Y, Kuhmann C, Winkler V, Santi I, Bogatyrova O, Kaucher S, Bermejo JL, Leung SY, Chan TL, Lasitschka F, Bohrer MH, Marx A, Haußen RH, Herold-Mende C, Dyckhoff G, Boukamp P, Delank KW, Hörmann K, Lippert BM, Baier G, Dietz A, Oakes CC, Plass C, Becher H, Schmezer P, Ramroth H, Popanda O.

Clin Epigenetics. 2019 May 3;11(1):67. doi: 10.1186/s13148-019-0666-5.

2.

Genome-wide promoter methylation of hairy cell leukemia.

Arribas AJ, Rinaldi A, Chiodin G, Kwee I, Mensah AA, Cascione L, Rossi D, Kanduri M, Rosenquist R, Zucca E, Johnson PW, Gaidano G, Oakes CC, Bertoni F, Forconi F.

Blood Adv. 2019 Feb 12;3(3):384-396. doi: 10.1182/bloodadvances.2018024059.

3.

Genome-wide association study identifies an acute myeloid leukemia susceptibility locus near BICRA.

Walker CJ, Oakes CC, Genutis LK, Giacopelli B, Liyanarachchi S, Nicolet D, Eisfeld AK, Scholz M, Brock P, Kohlschmidt J, Mrózek K, Bill M, Carroll AJ, Kolitz JE, Powell BL, Wang ES, Niederwieser DW, Stone RM, Byrd JC, Schwind S, de la Chapelle A, Bloomfield CD.

Leukemia. 2019 Mar;33(3):771-775. doi: 10.1038/s41375-018-0281-z. Epub 2018 Oct 5. No abstract available.

4.

Insight into origins, mechanisms, and utility of DNA methylation in B-cell malignancies.

Oakes CC, Martin-Subero JI.

Blood. 2018 Sep 6;132(10):999-1006. doi: 10.1182/blood-2018-02-692970. Epub 2018 Jul 23. Review.

PMID:
30037886
5.

Epigenetic and Posttranscriptional Regulation of CD16 Expression during Human NK Cell Development.

Victor AR, Weigel C, Scoville SD, Chan WK, Chatman K, Nemer MM, Mao C, Young KA, Zhang J, Yu J, Freud AG, Oakes CC, Caligiuri MA.

J Immunol. 2018 Jan 15;200(2):565-572. doi: 10.4049/jimmunol.1701128. Epub 2017 Dec 11.

6.

Drug-perturbation-based stratification of blood cancer.

Dietrich S, Oleś M, Lu J, Sellner L, Anders S, Velten B, Wu B, Hüllein J, da Silva Liberio M, Walther T, Wagner L, Rabe S, Ghidelli-Disse S, Bantscheff M, Oleś AK, Słabicki M, Mock A, Oakes CC, Wang S, Oppermann S, Lukas M, Kim V, Sill M, Benner A, Jauch A, Sutton LA, Young E, Rosenquist R, Liu X, Jethwa A, Lee KS, Lewis J, Putzker K, Lutz C, Rossi D, Mokhir A, Oellerich T, Zirlik K, Herling M, Nguyen-Khac F, Plass C, Andersson E, Mustjoki S, von Kalle C, Ho AD, Hensel M, Dürig J, Ringshausen I, Zapatka M, Huber W, Zenz T.

J Clin Invest. 2018 Jan 2;128(1):427-445. doi: 10.1172/JCI93801. Epub 2017 Dec 11.

7.

Erratum: DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats.

Brocks D, Schmidt CR, Daskalakis M, Jang HS, Shah NM, Li D, Li J, Zhang B, Hou Y, Laudato S, Lipka DB, Schott J, Bierhoff H, Assenov Y, Helf M, Ressnerova A, Islam MS, Lindroth AM, Haas S, Essers M, Imbusch CD, Brors B, Oehme I, Witt O, Lübbert M, Mallm JP, Rippe K, Will R, Weichenhan D, Stoecklin G, Gerhäuser C, Oakes CC, Wang T, Plass C.

Nat Genet. 2017 Oct 27;49(11):1661. doi: 10.1038/ng1117-1661c.

PMID:
29074949
8.

BET-bromodomain inhibitors modulate epigenetic patterns at the diacylglycerol kinase alpha enhancer associated with radiation-induced fibrosis.

Valinciute G, Weigel C, Veldwijk MR, Oakes CC, Herskind C, Wenz F, Plass C, Schmezer P, Popanda O.

Radiother Oncol. 2017 Oct;125(1):168-174. doi: 10.1016/j.radonc.2017.08.028. Epub 2017 Sep 12.

PMID:
28916223
9.

Charting the dynamic epigenome during B-cell development.

Martin-Subero JI, Oakes CC.

Semin Cancer Biol. 2018 Aug;51:139-148. doi: 10.1016/j.semcancer.2017.08.008. Epub 2017 Aug 26. Review.

PMID:
28851627
10.

Genomic analysis of hairy cell leukemia identifies novel recurrent genetic alterations.

Durham BH, Getta B, Dietrich S, Taylor J, Won H, Bogenberger JM, Scott S, Kim E, Chung YR, Chung SS, Hüllein J, Walther T, Wang L, Lu SX, Oakes CC, Tibes R, Haferlach T, Taylor BS, Tallman MS, Berger MF, Park JH, Zenz T, Abdel-Wahab O.

Blood. 2017 Oct 5;130(14):1644-1648. doi: 10.1182/blood-2017-01-765107. Epub 2017 Aug 11.

11.

DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats.

Brocks D, Schmidt CR, Daskalakis M, Jang HS, Shah NM, Li D, Li J, Zhang B, Hou Y, Laudato S, Lipka DB, Schott J, Bierhoff H, Assenov Y, Helf M, Ressnerova A, Islam MS, Lindroth AM, Haas S, Essers M, Imbusch CD, Brors B, Oehme I, Witt O, Lübbert M, Mallm JP, Rippe K, Will R, Weichenhan D, Stoecklin G, Gerhäuser C, Oakes CC, Wang T, Plass C.

Nat Genet. 2017 Jul;49(7):1052-1060. doi: 10.1038/ng.3889. Epub 2017 Jun 12. Erratum in: Nat Genet. 2017 Oct 27;49(11):1661.

12.

Prognostic and biological significance of the proangiogenic factor EGFL7 in acute myeloid leukemia.

Papaioannou D, Shen C, Nicolet D, McNeil B, Bill M, Karunasiri M, Burke MH, Ozer HG, Yilmaz SA, Zitzer N, Behbehani GK, Oakes CC, Steiner DJ, Marcucci G, Powell BL, Kolitz JE, Carter TH, Wang ES, Mrózek K, Croce CM, Caligiuri MA, Bloomfield CD, Garzon R, Dorrance AM.

Proc Natl Acad Sci U S A. 2017 Jun 6;114(23):E4641-E4647. doi: 10.1073/pnas.1703142114. Epub 2017 May 22.

13.

Emerging insights on the pathogenesis and treatment of extranodal NK/T cell lymphomas (ENKTL).

Haverkos BM, Coleman C, Gru AA, Pan Z, Brammer J, Rochford R, Mishra A, Oakes CC, Baiocchi RA, Freud AG, Porcu P.

Discov Med. 2017 Mar;23(126):189-199. Review.

14.

EGR2 mutations define a new clinically aggressive subgroup of chronic lymphocytic leukemia.

Young E, Noerenberg D, Mansouri L, Ljungström V, Frick M, Sutton LA, Blakemore SJ, Galan-Sousa J, Plevova K, Baliakas P, Rossi D, Clifford R, Roos-Weil D, Navrkalova V, Dörken B, Schmitt CA, Smedby KE, Juliusson G, Giacopelli B, Blachly JS, Belessi C, Panagiotidis P, Chiorazzi N, Davi F, Langerak AW, Oscier D, Schuh A, Gaidano G, Ghia P, Xu W, Fan L, Bernard OA, Nguyen-Khac F, Rassenti L, Li J, Kipps TJ, Stamatopoulos K, Pospisilova S, Zenz T, Oakes CC, Strefford JC, Rosenquist R, Damm F.

Leukemia. 2017 Jul;31(7):1547-1554. doi: 10.1038/leu.2016.359. Epub 2016 Nov 28.

PMID:
27890934
15.

IL-10 production by CLL cells is enhanced in the anergic IGHV mutated subset and associates with reduced DNA methylation of the IL10 locus.

Drennan S, D'Avola A, Gao Y, Weigel C, Chrysostomou E, Steele AJ, Zenz T, Plass C, Johnson PW, Williams AP, Packham G, Stevenson FK, Oakes CC, Forconi F.

Leukemia. 2017 Aug;31(8):1686-1694. doi: 10.1038/leu.2016.356. Epub 2016 Nov 28.

PMID:
27890932
16.

Genomic disruption of the histone methyltransferase SETD2 in chronic lymphocytic leukaemia.

Parker H, Rose-Zerilli MJ, Larrayoz M, Clifford R, Edelmann J, Blakemore S, Gibson J, Wang J, Ljungström V, Wojdacz TK, Chaplin T, Roghanian A, Davis Z, Parker A, Tausch E, Ntoufa S, Ramos S, Robbe P, Alsolami R, Steele AJ, Packham G, Rodríguez-Vicente AE, Brown L, McNicholl F, Forconi F, Pettitt A, Hillmen P, Dyer M, Cragg MS, Chelala C, Oakes CC, Rosenquist R, Stamatopoulos K, Stilgenbauer S, Knight S, Schuh A, Oscier DG, Strefford JC.

Leukemia. 2016 Nov;30(11):2179-2186. doi: 10.1038/leu.2016.134. Epub 2016 May 20.

17.

Dissection of CD20 regulation in lymphoma using RNAi.

Słabicki M, Lee KS, Jethwa A, Sellner L, Sacco F, Walther T, Hüllein J, Dietrich S, Wu B, Lipka DB, Oakes CC, Mamidi S, Pyrzyńska B, Winiarska M, Oleś M, Seifert M, Plass C, Kirschfink M, Boettcher M, Gołąb J, Huber W, Fröhling S, Zenz T.

Leukemia. 2016 Dec;30(12):2409-2412. doi: 10.1038/leu.2016.230. Epub 2016 Aug 18. No abstract available.

PMID:
27560109
18.

Surface IgM expression and function are associated with clinical behavior, genetic abnormalities, and DNA methylation in CLL.

D'Avola A, Drennan S, Tracy I, Henderson I, Chiecchio L, Larrayoz M, Rose-Zerilli M, Strefford J, Plass C, Johnson PW, Steele AJ, Packham G, Stevenson FK, Oakes CC, Forconi F.

Blood. 2016 Aug 11;128(6):816-26. doi: 10.1182/blood-2016-03-707786. Epub 2016 Jun 14.

19.

High-content screening identifies kinase inhibitors that overcome venetoclax resistance in activated CLL cells.

Oppermann S, Ylanko J, Shi Y, Hariharan S, Oakes CC, Brauer PM, Zúñiga-Pflücker JC, Leber B, Spaner DE, Andrews DW.

Blood. 2016 Aug 18;128(7):934-47. doi: 10.1182/blood-2015-12-687814. Epub 2016 Jun 13.

20.

Hsp90 inhibition increases SOCS3 transcript and regulates migration and cell death in chronic lymphocytic leukemia.

Chen TL, Gupta N, Lehman A, Ruppert AS, Yu L, Oakes CC, Claus R, Plass C, Maddocks KJ, Andritsos L, Jones JA, Lucas DM, Johnson AJ, Byrd JC, Hertlein E.

Oncotarget. 2016 May 10;7(19):28684-96. doi: 10.18632/oncotarget.8760.

21.

Epigenetic regulation of diacylglycerol kinase alpha promotes radiation-induced fibrosis.

Weigel C, Veldwijk MR, Oakes CC, Seibold P, Slynko A, Liesenfeld DB, Rabionet M, Hanke SA, Wenz F, Sperk E, Benner A, Rösli C, Sandhoff R, Assenov Y, Plass C, Herskind C, Chang-Claude J, Schmezer P, Popanda O.

Nat Commun. 2016 Mar 11;7:10893. doi: 10.1038/ncomms10893.

22.

Longitudinal copy number, whole exome and targeted deep sequencing of 'good risk' IGHV-mutated CLL patients with progressive disease.

Rose-Zerilli MJ, Gibson J, Wang J, Tapper W, Davis Z, Parker H, Larrayoz M, McCarthy H, Walewska R, Forster J, Gardiner A, Steele AJ, Chelala C, Ennis S, Collins A, Oakes CC, Oscier DG, Strefford JC.

Leukemia. 2016 Jun;30(6):1301-10. doi: 10.1038/leu.2016.10. Epub 2016 Feb 5.

23.

DNA methylation dynamics during B cell maturation underlie a continuum of disease phenotypes in chronic lymphocytic leukemia.

Oakes CC, Seifert M, Assenov Y, Gu L, Przekopowitz M, Ruppert AS, Wang Q, Imbusch CD, Serva A, Koser SD, Brocks D, Lipka DB, Bogatyrova O, Weichenhan D, Brors B, Rassenti L, Kipps TJ, Mertens D, Zapatka M, Lichter P, Döhner H, Küppers R, Zenz T, Stilgenbauer S, Byrd JC, Plass C.

Nat Genet. 2016 Mar;48(3):253-64. doi: 10.1038/ng.3488. Epub 2016 Jan 18.

24.

p53-dependent non-coding RNA networks in chronic lymphocytic leukemia.

Blume CJ, Hotz-Wagenblatt A, Hüllein J, Sellner L, Jethwa A, Stolz T, Slabicki M, Lee K, Sharathchandra A, Benner A, Dietrich S, Oakes CC, Dreger P, te Raa D, Kater AP, Jauch A, Merkel O, Oren M, Hielscher T, Zenz T.

Leukemia. 2015 Oct;29(10):2015-23. doi: 10.1038/leu.2015.119. Epub 2015 May 14.

PMID:
25971364
25.

Epigenetic silencing of miR-708 enhances NF-κB signaling in chronic lymphocytic leukemia.

Baer C, Oakes CC, Ruppert AS, Claus R, Kim-Wanner SZ, Mertens D, Zenz T, Stilgenbauer S, Byrd JC, Plass C.

Int J Cancer. 2015 Sep 15;137(6):1352-61. doi: 10.1002/ijc.29491. Epub 2015 Mar 13.

26.

Transient DNMT1 suppression reveals hidden heritable marks in the genome.

McGraw S, Zhang JX, Farag M, Chan D, Caron M, Konermann C, Oakes CC, Mohan KN, Plass C, Pastinen T, Bourque G, Chaillet JR, Trasler JM.

Nucleic Acids Res. 2015 Feb 18;43(3):1485-97. doi: 10.1093/nar/gku1386. Epub 2015 Jan 10.

27.

Lag times between lymphoproliferative disorder and clinical diagnosis of chronic lymphocytic leukemia: a prospective analysis using plasma soluble CD23.

Kaaks R, Sookthai D, Łuczyńska A, Oakes CC, Becker S, Johnson T, Johansson A, Melin B, Sjöberg K, Trichopoulos D, Trichopoulou A, Lagiou P, Mattiello A, Tumino R, Masala G, Agnoli C, Boeing H, Aleksandrova K, Brennan P, Franceschi S, Roulland S, Casabonne D, de Sanjose S, Sánchez MJ, Huerta JM, Ardanaz E, Sala N, Overvad K, Tjønneland A, Halkjær J, Weiderpass E, Bueno-de-Mesquita HB, Vermeulen R, Peeters PH, Vineis P, Kelly RS, Khaw KT, Travis RC, Key TJ, Riboli E, Nieters A.

Cancer Epidemiol Biomarkers Prev. 2015 Mar;24(3):538-45. doi: 10.1158/1055-9965.EPI-14-1107. Epub 2014 Dec 26.

28.

BAZ2A (TIP5) is involved in epigenetic alterations in prostate cancer and its overexpression predicts disease recurrence.

Gu L, Frommel SC, Oakes CC, Simon R, Grupp K, Gerig CY, Bär D, Robinson MD, Baer C, Weiss M, Gu Z, Schapira M, Kuner R, Sültmann H, Provenzano M; ICGC Project on Early Onset Prostate Cancer, Yaspo ML, Brors B, Korbel J, Schlomm T, Sauter G, Eils R, Plass C, Santoro R.

Nat Genet. 2015 Jan;47(1):22-30. doi: 10.1038/ng.3165. Epub 2014 Dec 8.

PMID:
25485837
29.

p19-INK4d inhibits neuroblastoma cell growth, induces differentiation and is hypermethylated and downregulated in MYCN-amplified neuroblastomas.

Dreidax D, Bannert S, Henrich KO, Schröder C, Bender S, Oakes CC, Lindner S, Schulte JH, Duffy D, Schwarzl T, Saadati M, Ehemann V, Benner A, Pfister S, Fischer M, Westermann F.

Hum Mol Genet. 2014 Dec 20;23(25):6826-37. doi: 10.1093/hmg/ddu406. Epub 2014 Aug 7.

PMID:
25104850
30.

Early aberrant DNA methylation events in a mouse model of acute myeloid leukemia.

Sonnet M, Claus R, Becker N, Zucknick M, Petersen J, Lipka DB, Oakes CC, Andrulis M, Lier A, Milsom MD, Witte T, Gu L, Kim-Wanner SZ, Schirmacher P, Wulfert M, Gattermann N, Lübbert M, Rosenbauer F, Rehli M, Bullinger L, Weichenhan D, Plass C.

Genome Med. 2014 Apr 30;6(4):34. doi: 10.1186/gm551. eCollection 2014.

31.

Validation of ZAP-70 methylation and its relative significance in predicting outcome in chronic lymphocytic leukemia.

Claus R, Lucas DM, Ruppert AS, Williams KE, Weng D, Patterson K, Zucknick M, Oakes CC, Rassenti LZ, Greaves AW, Geyer S, Wierda WG, Brown JR, Gribben JG, Barrientos JC, Rai KR, Kay NE, Kipps TJ, Shields P, Zhao W, Grever MR, Plass C, Byrd JC.

Blood. 2014 Jul 3;124(1):42-8. doi: 10.1182/blood-2014-02-555722. Epub 2014 May 27. Erratum in: Blood. 2014 Sep 11;124(11):1848.

32.

Evolution of DNA methylation is linked to genetic aberrations in chronic lymphocytic leukemia.

Oakes CC, Claus R, Gu L, Assenov Y, Hüllein J, Zucknick M, Bieg M, Brocks D, Bogatyrova O, Schmidt CR, Rassenti L, Kipps TJ, Mertens D, Lichter P, Döhner H, Stilgenbauer S, Byrd JC, Zenz T, Plass C.

Cancer Discov. 2014 Mar;4(3):348-61. doi: 10.1158/2159-8290.CD-13-0349. Epub 2013 Dec 19.

33.

Loss of DNMT1o disrupts imprinted X chromosome inactivation and accentuates placental defects in females.

McGraw S, Oakes CC, Martel J, Cirio MC, de Zeeuw P, Mak W, Plass C, Bartolomei MS, Chaillet JR, Trasler JM.

PLoS Genet. 2013 Nov;9(11):e1003873. doi: 10.1371/journal.pgen.1003873. Epub 2013 Nov 21.

34.

Germline allele-specific expression of DAPK1 in chronic lymphocytic leukemia.

Wei QX, Claus R, Hielscher T, Mertens D, Raval A, Oakes CC, Tanner SM, de la Chapelle A, Byrd JC, Stilgenbauer S, Plass C.

PLoS One. 2013;8(1):e55261. doi: 10.1371/journal.pone.0055261. Epub 2013 Jan 28.

35.

Germline variants of base excision repair genes and breast cancer: A polymorphism in DNA polymerase gamma modifies gene expression and breast cancer risk.

Popanda O, Seibold P, Nikolov I, Oakes CC, Burwinkel B, Hausmann S, Flesch-Janys D, Plass C, Chang-Claude J, Schmezer P.

Int J Cancer. 2013 Jan 1;132(1):55-62. doi: 10.1002/ijc.27665. Epub 2012 Jun 26.

36.

Quantitative DNA methylation analysis identifies a single CpG dinucleotide important for ZAP-70 expression and predictive of prognosis in chronic lymphocytic leukemia.

Claus R, Lucas DM, Stilgenbauer S, Ruppert AS, Yu L, Zucknick M, Mertens D, Bühler A, Oakes CC, Larson RA, Kay NE, Jelinek DF, Kipps TJ, Rassenti LZ, Gribben JG, Döhner H, Heerema NA, Marcucci G, Plass C, Byrd JC.

J Clin Oncol. 2012 Jul 10;30(20):2483-91. doi: 10.1200/JCO.2011.39.3090. Epub 2012 May 7.

37.

Epigenetic screen of human DNA repair genes identifies aberrant promoter methylation of NEIL1 in head and neck squamous cell carcinoma.

Chaisaingmongkol J, Popanda O, Warta R, Dyckhoff G, Herpel E, Geiselhart L, Claus R, Lasitschka F, Campos B, Oakes CC, Bermejo JL, Herold-Mende C, Plass C, Schmezer P.

Oncogene. 2012 Dec 6;31(49):5108-16. doi: 10.1038/onc.2011.660. Epub 2012 Jan 30.

PMID:
22286769
38.

Critical period of nonpromoter DNA methylation acquisition during prenatal male germ cell development.

Niles KM, Chan D, La Salle S, Oakes CC, Trasler JM.

PLoS One. 2011;6(9):e24156. doi: 10.1371/journal.pone.0024156. Epub 2011 Sep 19.

39.

Restriction digestion and real-time PCR (qAMP).

Oakes CC, La Salle S, Trasler JM, Robaire B.

Methods Mol Biol. 2009;507:271-80. doi: 10.1007/978-1-59745-522-0_20.

PMID:
18987821
40.

Restriction landmark genomic scanning (RLGS) spot identification by second generation virtual RLGS in multiple genomes with multiple enzyme combinations.

Smiraglia DJ, Kazhiyur-Mannar R, Oakes CC, Wu YZ, Liang P, Ansari T, Su J, Rush LJ, Smith LT, Yu L, Liu C, Dai Z, Chen SS, Wang SH, Costello J, Ioshikhes I, Dawson DW, Hong JS, Teitell MA, Szafranek A, Camoriano M, Song F, Elliott R, Held W, Trasler JM, Plass C, Wenger R.

BMC Genomics. 2007 Nov 30;8:446.

41.

Evaluation of a quantitative DNA methylation analysis technique using methylation-sensitive/dependent restriction enzymes and real-time PCR.

Oakes CC, La Salle S, Robaire B, Trasler JM.

Epigenetics. 2006 Jul-Sep;1(3):146-52. Epub 2006 Sep 8.

PMID:
17965615
42.

Loss of spermatogonia and wide-spread DNA methylation defects in newborn male mice deficient in DNMT3L.

La Salle S, Oakes CC, Neaga OR, Bourc'his D, Bestor TH, Trasler JM.

BMC Dev Biol. 2007 Sep 18;7:104.

43.

Adverse effects of 5-aza-2'-deoxycytidine on spermatogenesis include reduced sperm function and selective inhibition of de novo DNA methylation.

Oakes CC, Kelly TL, Robaire B, Trasler JM.

J Pharmacol Exp Ther. 2007 Sep;322(3):1171-80. Epub 2007 Jun 20.

PMID:
17581917
44.

Developmental acquisition of genome-wide DNA methylation occurs prior to meiosis in male germ cells.

Oakes CC, La Salle S, Smiraglia DJ, Robaire B, Trasler JM.

Dev Biol. 2007 Jul 15;307(2):368-79. Epub 2007 May 8.

45.

A unique configuration of genome-wide DNA methylation patterns in the testis.

Oakes CC, La Salle S, Smiraglia DJ, Robaire B, Trasler JM.

Proc Natl Acad Sci U S A. 2007 Jan 2;104(1):228-33. Epub 2006 Dec 26.

46.

Aging results in hypermethylation of ribosomal DNA in sperm and liver of male rats.

Oakes CC, Smiraglia DJ, Plass C, Trasler JM, Robaire B.

Proc Natl Acad Sci U S A. 2003 Feb 18;100(4):1775-80. Epub 2003 Feb 6.

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