Northwestern University Feinberg School of Medicine

Jindan Yu Lab

Publications

2017

59. Kim J, Jin H, Zhao JC, Yang YA, Li Y, Yang X, Dong X, Yu J. FOXA1 inhibits prostate cancer neuroendocrine differentiation.  Oncogene. 2017 March 20. PMID: 28319070

58. Qadir AS, Ceppi P, Brockway S, Law C, Mu L, Khodarev NN, Kim J, Zhao JC, Putzbach W, Murmann AE, Chen Z, Chen W, Liu X, Salomon AR, Liu H, Weichselbaum RR, Yu J, Peter ME.  CD95/Fas Increases Stemness in Cancer Cells by Inducing a STAT1-Dependent Type I Interferon Response.  Cell Rep. 2017 March 07. PMID: 28273453

2016

57. Fong KW, Zhao JC, Kim J, Li S, Yang YA, Song B, Rittie L, Hu M, Yang X, Perbal B, Yu J. Polycomb-mediated disruption of an androgen receptor feedback loop drives castration-resistant prostate cancer.  Cancer Res. 2016 Nov 4. PMID: 27815387

56. Kim JY, Yu J, Abdulkadir SA, Chakravarti D.  KAT8 regulates androgen signaling in prostate cancer cells.  Mol Endocrinol. 2016 June 07. PMID: 27257062

55. Yang YA, Zhao JC, Fong KW, Kim J, Li S, Song C, Song B, Zheng B, He C, Yu J. FOXA1 potentiates lineage-specific enhancer activation through modulating TET1 expression and function.  Nucleic Acids Res. 2016 June 01. PMID: 27268279

54. Zhao JC, Li XY, Guo MX, Yu J, Yan C. The common stress responsive transcription factor ATF3 binds genomic sites enriched with p300 and H3K27ac for transcriptional regulation.  BMC Genomics. 2016 May 04. PMID: 27146783

53. Zhao JC, Fong KW, Jin HJ, Yang YA, Kim J, Yu JFOXA1 acts upstream of GATA2 and AR in hormonal regulation of gene expression.  Oncogene. 2016 Jan 11. PMID: 26751772

2015

52. Wang L, Song G, Tan W, Qi M, Zhang L, Chan J, Yu J, Han J, Han B. miR-573 inhibits prostate cancer metastasis by regulating epithelial-mesenchymal transition.  Oncotarget. 2015 Oct 03. PMID: 26451614

51. Zhang A, Zhao JC, Kim J, Fong KW, Yang YA, Chakravarti D, Mo YY, Yu J. LncRNA HOTAIR Enhances the Androgen-Receptor-Mediated Transcriptional Program and Drives Castration-Resistant Prostate Cancer.  Cell Reports. 2015 Aug.

50. Shen S, Guo X, Yan H, Lu Y, Ji X, Li L, Liang T, Zhou D, Feng XH, Zhao JC, Yu J, Gong XG, Zhang L, Zhao B. A miR-130a-YAP positive feedback loop promotes organ size and tumorigenesis.  Cell Res. 2015 Aug 14. PMID: 26272168

49. Xue XY, Yang YA, Zhang A, Fong KW, Kim J, Song B, Li S, Zhao JC, Yu J. LncRNA HOTAIR enhances ER signaling and confers tamoxifen resistance in breast cancer.  Oncogene. 2015 Sep 14. PMID: 26364613

48. Yang YA, Yu J. Current perspectives on FOXA1 regulation of androgen receptor signaling and prostate cancer.  Genes Dis. 2015 June

2014

47. Wang L, Song G, Chang X, Tan W, Pan J, Zhu X, Liu Z, Qi M, Yu J, Han B. The role of TXNDC5 in castration-resistant prostate cancer-involvement of androgen receptor signaling pathway.  Oncogene. 2014 Dec 15. PMID: 25500540

46. Jin HJ, Zhao JC, Wu L, Kim J, Yu J. Cooperativity and equilibrium with FOXA1 define the androgen receptor transcriptional program.  Nat Commun. 2014 May 30. PMID: 24875621

45. Yang YA, Kim J, Yu J. Influence of oncogenic transcription factors on chromatin conformation and implications in prostate cancer.  Appl Clin Genet. 2014 May 12. PMID: 24876790

2013

44. Kim J, Wu L, Zhao JC, Jin HJ, Yu J. TMPRSS2-ERG gene fusions induce prostate tumorigenesis by modulating microRNA miR-200c.  Oncogene. 2013 Nov 4. [Epub ahead of print] PMID: 24186205

43. Jin HJ, Kim J, Yu J. Androgen receptor genomic regulation.  Translational Andrology and Urology. 2013;2(3):158-177

42. Wu L, Zhao JC, Kim J, Jin HJ, Wang CY, Yu J. ERG is a critical regulator of Wnt/LEF1 signaling in prostate cancer.  Cancer Research. 2013 Aug 1. [Epub ahead of print] PMID: 23913826

41. Yang YA, Yu J. EZH2, an epigenetic driver of prostate cancer.  Protein Cell. 2013 Apr 30. [Epub ahead of print] PMID: 23636686

40. Wang L, Zeng X, Chen S, Ding L, Zhong J, Zhao JC, Wang L, Sarver A, Koller A, Zhi J, Ma Y, Yu J, Chen J, Huang H. BRCA1 is a negative modulator of the PRC2 complex.  EMBO J. 2013 Apr 26. [Epub ahead of print] PMID: 23624935

39. Jin HJ, Zhao JC, Ogden I, Bergan R, Yu J. Androgen-receptor independent function of FoxA1 in prostate cancer metastasis.  Cancer Research. 2013 Mar 28. [Epub ahead of print] PMID: 23539448

38. Wu L, Runkle C, Jin HJ, Yu JJ, Li J, Yang X, Kuzel T, Lee C, Yu J. CCN3/NOV gene expression in human prostate cancer is directly suppressed by the androgen receptor.  Oncogene. 2013 Jan 14. [Epub ahead of print] PMID: 23318417

2012

37. Ezponda T, Popovic R, Shah MY, Martinez-Garcia E, Zheng Y, Min DJ, Will C, Neri A, Kelleher NL, Yu J, Licht JD. The histone methyltransferase MMSET/WHSC1 activates TWIST1 to promote an epithelial-mesenchymal transition and invasive properties of prostate cancer.  Oncogene. 2012 July 16. [Epub ahead of print] PMID: 22797064

36. Kim J, Yu J. Interrogating genomic and epigenomic data to understand prostate cancer.  BBA-Reviews on Cancer. 2012 Apr;1825(2):186-96. Epub 2012 Jan 3. PMID: 22240201

35. Zhao B, Li L, Wang L, Wang CY, Yu J, Guan KL. Cell detachment activates the Hippo pathway via cytoskeleton reorganization to induce anoikis.  Genes Dev. 2012 Jan 1;26(1):54-68. PMID: 22215811

34. Zhao JC, Yu JJ, Runkle C, Wu L, Hu M, Wu D, Liu JS, Wang Q, Qin ZS, Yu J. Cooperation between Polycomb and androgen receptor during oncogenic transformation.  Genome Res. 2012 Feb;22(2):322-31. Epub 2011 Dec 16. PMID: 22179855

2011

33. Zhang C, Wang L, Wu D, Chen H, Chen Z, Thomas-Ahner J, Zynger D, Eeckhoute J, Yu J, Luo J, Brown M, Clinton SK, Nephew KP, Huang TH, Li W, Wang Q. Definition of a FoxA1 Cistrome that is Crucial for G1-S Phase Cell- Cycle Transit in Castration-Resistant Prostate Cancer.  Cancer Res. 2011 Sep 7. PMID: 21900400

32. Cao Q, Mani RS, Ateeq B, Dhanasekaran SM, Asangani IA, Prensner JR, Kim JH, Brenner JC, Jing X, Cao X, Wang R, Li Y, Dahiya A, Wang L, Pandhi M, Lonigro RJ, Wu YM, Tomlins SA, Palanisamy N, Qin Z, Yu J, Maher CA, Varambally S, Chinnaiyan AM. Coordinated Regulation of Polycomb Group Complexes through microRNAs in Cancer.  Cancer Cell. 2011 Aug 16;20(2):187-99. PMID: 21840484

31. Kim JH, Dhanasekaran SM, Prensner JR, Cao X, Robinson D, Kalyana-Sundaram S, Huang C, Shankar S, Jing X, Iyer M, Hu M, Sam L, Grasso C, Maher CA, Palanisamy N, Mehra R, Kominsky HD, Siddiqui J, Yu J, Qin ZS, Chinnaiyan AM. Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer.  Genome Res. 2011 Jul;21(7):1028-41. PMID: 21724842

30. Brenner JC, Ateeq B, Li Y, Yocum AK, Cao Q, Asangani IA, Patel S, Wang X, Liang H, Yu J, Palanisamy N, Siddiqui J, Yan W, Cao X, Mehra R, Sabolch A, Basrur V, Lonigro RJ, Yang J, Tomlins SA, Maher CA, Elenitoba-Johnson KS, Hussain M, Navone NM, Pienta KJ, Varambally S, Feng FY, Chinnaiyan AM. Mechanistic Rationale for Inhibition of Poly(ADP-Ribose) Polymerase in ETS Gene Fusion-Positive Prostate Cancer.  Cancer Cell. 2011 May 17;19(5):664-78. PMID: 21575865

29. Kappes F, Waldmann T, Mathew V, Yu J, Zhang L, Khodadoust MS, Chinnaiyan AM, Luger K, Erhardt S, Schneider R, Markovitz DM. The DEK oncoprotein is a Su(var) that is essential to heterochromatin integrity.  Genes Dev. 2011 Apr 1;25(7):673-8. PMID: 21460035

28. Corey SJ, Yu J.  Cancer cell migration: when red light switched to green.  Asian J Androl. 2011 Mar;13(2):177-8. Epub 2011 Jan 17. PMID: 21240294

2010

27. Rickman DS, Chen YB, Banerjee S, Pan Y, Yu J, Vuong T, Perner S, Lafargue CJ, Mertz KD, Setlur SR, Sircar K, Chinnaiyan AM, Bismar TA, Rubin MA, Demichelis F. ERG Cooperates with Androgen Receptor in Regulating Trefoil Factor 3 in Prostate Cancer Disease Progression.  Neoplasia. 2010 Dec;12(12):1031-40 PMID: 21170267

26. Pichot CS, Arvanitis C, Hartig SM, Jensen SA, Bechill J, Marzouk S, Yu J, Frost JA, Corey SJ. Cdc42-Interacting Protein 4 Promotes Breast Cancer Cell Invasion and Formation of Invadopodia through Activation of N-WASp.  Cancer Res. 2010 Nov 1;70(21):8347-56. Epub 2010 Oct 12. PMID: 20940394

25. Yu J*, Cao Q, Yu JJ, Wu L, Dallol A, Li J, Chen G, Grasso C, Cao X, Lonigro RJ, Varambally S, Mehra R, Palanisamy N, Wu JY, Latif F, Chinnaiyan AM. The neuronal repellent SLIT2 is a target for repression by EZH2 in prostate cancer.  Oncogene. 2010 Jul 12. PMID: 20622896 *also a corresponding author.

24. Qin ZS, Yu JJ, Shen J, Maher CA, Hu M, Kalyana-Sundaram S, Yu J, Chinnaiyan AM. HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data.  BMC Bioinformatics. 2010 Jul 2;11(1):369. PMID: 20598134

23. Lian I, Kim J, Okazawa H, Zhao J, Zhao B, Yu J, Chinnaiyan AM, Israel M, Goldstein L, Abujarour R, Ding S, Guan KL. The role of YAP transcription co-activator in regulating stem cells self-renewal and differentiation.  Genes Dev. 2010 Jun 1;24(11):1106-18. PMID: 20516196

22. Yu J, Yu JJ, Mani RS, Cao Q, Brenner CJ, Cao X, Wang GX, Wu L ...Qin ZS, Chinnaiyan AM. An Integrated Network of Androgen Receptor, Polycomb, and TMPRSS2-ERG Gene Fusions in Prostate Cancer Progression.  Cancer Cell. 2010 May 18;17(5):443-54. Cover Article. PMID: 20478527

21. Hu M, Yu J, Chinnaiyan AM, Qin Z. On the detection and refinement of transcription factor binding sites using ChIP-Seq data.  Nucleic Acids Res. 2010 Jan 6. PMID: 20056654

2009

20. Vellaichamy A, Sreekumar A, Strahler JR, Rajendiran TM, Yu J, Varambally S, Li Y, Omenn GS, Chinnaiyan AM, Nesvizhskii AII. Proteomic Interrogation of Androgen Action in Prostate Cancer Cells Reveals Roles of Aminoacyl tRNA Synthetases.  PLoS One. 2009 Sep 18;4(9):e7075. PMID: 19763266

19. Maher CA, Palanisamy N, Brenner JC, Cao, X, Kalyana-Sundaram S, Lou S, Khrebtukova I, Barrette T, Grasso C, Yu J, Lonigro R, Schroth G, Kumar-Sinha C, Chinnaiyan AM. Chimeric transcript discovery by paired-end transcriptome sequencing.  Proc Natl Acad Sci U S A. 2009 Jul 28;106(30):12353-8. Epub 2009 Jul 10. PMID: 19592507

18. Wang Q, Li W, Zhang Y, Yuan X, Xu K, Yu J, Chen Z, Beoukhim R, Wang H, Lupien M, Wu T, Regan MM, Meyer CA, Carroll JS, Manrai AK, Janne OA, Balk SP, Mehra R, Han B, Chinnaiyan AM, Rubin MA, True L, Fiorentino M, Fiore C, Loda M, Kantoff PW, Liu XS, Brown M. Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer.  Cell. 2009 Jul 23;138(2):245-56. PMID: 19632176

17. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM. Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression.  Nature. 2009 Feb 12;457(7231):910-4. PMID: 19212411

2008

16. Varambally S, Cao Q, Mani RS, Shankar S, Wang X, Ateeq B, Laxman B, Cao X, Jing X, Ramnarayanan K, Brenner JC, Yu J, Kim JH, Han B, Tan P, Kumar-Sinha C, Lonigro RJ, Palanisamy N, Maher CA, Chinnaiyan AM. Genomic Loss of microRNA-101 Leads to Overexpression of Histone Methyltransferase EZH2 in Cancer.  Science. 2008 Nov 13. PMID: 19008416

15. Cao Q, Yu J, Tomlins SA, Mehra R, Dhanasekaran SM, Laxman B, Cao X, Yu JJ, Kleer CG, Varambally S, Chinnaiyan AM. Repression of E_cadherin by the Polycomb group protein EZH2 in Cancer.  Oncogene. 2008 Sep 22. PMID: 18806826

14. Han B, Mehra R, Dhanasekaran S, Yu J, Lonigro B, Wang X, Laxman B, LeBlanc M, Wang L, Menon A, Tsodikov A, Shah RB, Palanisamy N, Tomlins SA, Chinnaiyan AM. A fluorescence in situ hybridization screen for E26 transformation-specific aberrations: identification of DDX5-ETV4 fusion protein in prostate cancer.  Cancer Res. 2008 Sep 15;68(18):7629-37. PMID: 18794152

13. Zhao B, Ye X, Yu J, Li L, Li W, Chinnaiyan AM, Lin J, Lai Z, Guan K. TEAD mediates YAP dependent gene induction and growth control.  Genes & Development. 2008 Jul 15;22(14):1962-71. Epub 2008 Jun 25. PMID: 18794152

12. Tomlins SA, Laxman B, Varambally S, Cao X, Yu J, Helgeson BE, Cao Q, Prensner JR, Rubin MA, Shah RB, Mehra R, Chinnaiyan AM. Role of the TMPRSS2-ERG gene fusion in prostate cancer.  Neoplasia. 2008 Feb; 10(2):177-188. PMID: 18283340

11. Yu JJ*, Yu J*, Cordero KE, Johnson MD, Ghosh D, Rae JM, Chinnaiyan AM, Lippman ME. A transcriptional fingerprint of estrogen in human breast cancer predicts patient survival.  Neoplasia. 2008 Jan;10(1):79-88. PMID: 18231641 *Co-authors with equal contribution

2007

10. Zhao B, Li Q, Wei X, Yang Q, Xie J, Ikenoue T, Yu J, Zheng P, Ye K, Chinnaiyan AM, Lai Z, Guan K. Inactivation of YAP oncoprotein by the Hippo pathway is involved in cell contact inhibition.  Genes & Development. 2007 Nov1;21(21):2747-61. PMID: 17974916

9. Yu J, Yu JJ, Rhodes DR, Tomlins SA, Cao X, Chen G, Mehra R, Wang X, Ghosh D, Shah RB, Varambally S, Pienta KJ, Chinnaiyan AM. A polycomb repression signature in metastatic prostate cancer predicts cancer outcome.  Cancer Res. 2007;67(22):10657-63. Cover Article. PMID: 18006806

8. Yu J, Cao Q, Mehra R, Laxman B, Yu JJ, Tomlins SA, Creighton CJ, Dhanasekaran SM, Shen R, Chen G, Morris DS, Marquez VE, Shah RB, Ghosh D, Varambally S, Chinnaiyan AM. Integrative genomics analysis reveals silencing of beta-adrenergic signaling by polycomb in prostate cancer.  Cancer Cell. 2007; 12 (5). Featured Article. PMID: 17996646

7. Tomlins SA, Laxman B, Dhanasekaran SM, Helgeson BE, Cao X, Morris DS, Menon A, Jing X, Cao Q, Han B, Yu J, Wang L, Montie JE, Rubin MA, Pienta KJ, Roulston D, Shah RB, Varambally S, Mehra R, Chinnaiyan AM. Distinct classes of chromosomal rearrangements create oncogenic ETS gene fusions in prostate cancer.  Nature. 2007 Aug 2;448(7153):595-9. PMID: 17671502

6. Yu JJ, Yu J, Almal AA, Dhanasekaran SM, Ghosh D, Worzel WP, Chinnaiyan AM. Feature selection and molecular classification of cancer using genetic programming.  Neoplasia. 2007; 9(4):292-303. PMID: 17460773

5. Chen G. Wang X, Yu JJ, Varambally S, Yu J, Thomas DG, Chinnaiyan AM. Autoantibody Profiles reveal ubiquilin 1 as a humoral immune response target in lung adenocarcinoma.  Cancer Res. 2007; 67(7):3461-7. PMID: 17409457

pre2007

4. Yu J, He S, Friedman JS, Mears AJ, Ghosh D, Hicks D, Swaroop A. Altered expression of genes of the Bmp/Smad and Wnt/Ca2+ signaling pathways in the cone-only Nrl-knockout mouse retina, revealed by gene profiling using custom cDNA microarrays.  J Biol Chem. 2004 Oct 1;279(40):42211-20. PMID: 15292180

3. Yu J, Farjo R, MacNee SP, Baehr W, Stambolian DE, Swaroop A. Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina.  Genome Biol. 2003;4(10):R65. PMID: 14519200

2. Yu J, Othman MI, Farjo R, Zareparsi S, MacNee SP, Yoshida S, Swaroop A. Evaluation and optimization of procedures for target labeling and hybridization of cDNA microarrays.  Mol. Vis. 2002 Apr 26;8:130-7. PMID: 12011805

1. Farjo R*, Yu J*, Othman MI, Yoshida S, Sheth S, Baehr W, Swaroop A. Mouse eye gene microarrays for investigating ocular development and disease.  Vision Res. 2002 Feb;42(4):463-70. PMID: 11853762 *Co-authors with equal contribution.

Mol Endocrinol.