Publications

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2026

Zhong G, Gu H, Huo Z, Zhu M, Gingold JA, Lee DF, Huang G, Shen J, Tu J. Comparison of the effectiveness of neoadjuvant chemotherapy versus upfront surgery for osteosarcoma: A target trial emulation study. Eur J Surg Oncol. 2026 Jun 2;52(8):111915. doi: 10.1016/j.ejso.2026.111915
Huo Z, Tu J, Yang WL, Huang MF, Wang R, Chu CW, Xu A, Yu Y, Tavakol TN, Kizilbash M, Fisher ME, Huang YW, Phan TTT, Shoemaker R, Chen YW, Zhang Y, Huff CD, Chen SY, Liu TJ, Xiao H, Lee DF, Zhao R. An artificial intelligence optimized hepatic differentiation unveils NR5A2 and AP-1 transcriptional regulation in hepatic maturation. J Biol Chem. 2026 Apr 8:111435. doi: 10.1016/j.jbc.2026.111435.
Huo Z, Tu J, Shoemaker R, Lee DF, Zhao R. Engineering Mutation Clones in Mammalian Cells with CRISPR/Cas9. Methods Mol Biol. 2026;2983:343-359.

2025

Suzuki S, Acosta Sandoval NV, Doddipalli S, Hassan DM, Barillà C, Rab A, Huang MF, Avila JM, Tabak B, Lu J, Derebery BC, Garay MG, Winkler SL, Ponnaluri SS, Forcioli-Conti N, Rea-Moreno M, Chen YW, Kim J, Lee CM, Nakayama N, Li W, Mahoney JE, Lee DF, Sorscher EJ, Chen J, Davis BR, Huang SX. Generation of Region-specific Airway Basal Stem Cells from Human Pluripotent Stem Cells via Regulation of BMP-NOGGIN Axis. bioRxiv [Preprint]. 2025 Oct 1:2025.10.01.657190.
Cadena LA, Luo KL, Otero-Perez CA, Fernandez SM, Huang YW, Zhao R, Lee DF, Ting AH, Ye F, You MJ, Lee SH. A TP53 Intron-Derived Peptide Promotes Tumor Survival. bioRxiv [Preprint]. 2025 Sep 9:2025.09.04.674312.
Itai T, Dai Y, Liu W, Lee DF, Zhao Z. Investigating prognostic features in high-grade serous ovarian cancer through gene regulatory network inference with single-cell transcriptomic profiles. Sci Rep. 2025 Nov 10;15(1):39345.
Large-Scale CRISPR Screening in Primary Human 3D Gastric Organoids Enables Comprehensive Dissection of Gene-Drug Interactions. Lo YH, Horm HT, Huang MF, Yu WC, Liu Q, Tomaske M, Tower M, Dominguez Am Bassik MC, Lee DF, Qi LS, Weissman JS, Chen J, Kuo CJ. Nat Commun. 2025 Aug 14;16(1):7566.
Liu J, Zhao C, Chen J, Zeng P, Li Q, Dai R, Lai X, Song W, Chen J, Zhu X, Liu X, Sun J, Wang J, Fang P, Wang T, Chen W, Guallar D, Cao N, Zhao J, Su S, Xiang AP, Zeng YA, Li J, Cai J, Lee DF, Bei J, Huo Y, Hu H, Suo S, Huang DF, Bai J, Ding J. Human iPSC-based breast cancer model identifies S100P-dependent cancer stemness induced by BRCA1 mutation. Sci Adv. 2025 Jul 25;11(30):eadi2370
Hu B, Shi Y, Xiong F, Chen YT, Zhu X, Wen X, Drolet N, Ghosh A, Xu XM, Lee DF, Soto C, Zhong S, Zheng H, Li W. Rewired m6A methylation of promoter antisense RNAs in Alzheimer’s disease regulates global gene transcription in the 3D nucleome. Nat Commun. 2025 Jun 6;16(1):5251.
Luo H, Huang MF, Xu A, Wang D, Chen YH, Gingold JA, Tu J, Wang R, Huo Z, Chiang YT, Tsai KL, Su J, Bazer DA, Hung MC, Xie C, Guo Y, Lee DF, Yang H, Zhao R. Mutant p53 confers chemoresistance by activating KMT5B-mediated DNA repair pathway in nasopharyngeal carcinoma. Cancer Lett. 2025 Apr 30:217736.
Huang MF, Fisher ME, Phan TTT, Zhao R, Lee DF. Decoding Cancer Etiology with Cellular Reprogramming. Curr Opin Genet Dev. 2025 Feb;90:102301.

2024

Chao TC, Chen SF, Kim HJ, Tang HC, Tseng HC, Xu A, Palao III L, Khadka S, Li T, Huang MF, Lee DF, Murakami K, Boyer TG, Tsai KL. Structural basis of the human transcriptional Mediator regulated by its dissociable kinase module. Mol Cell. 2024 Oct 17;84(20):3932-3949.e10.
Shoemaker R, Huang MF, Wu YS, Hung CS, Lee DF. Decoding the molecular symphony: Interactions between the m6A and p53 signaling pathways in cancer. NAR Cancer. 2024 Sep 26;6(3):zcae037. #Featured Article as Editor’s Choice
Malla S, Kumari K, Garcia-Prieto CA, Caroli J, Nordin A, Phan TTT, Bhattarai DP, Marthinez-Gamero C, Dorafshan E, Stransky S, Álvarez-Errico D, Saiki PA, Lai W, Lyu C, Lizana L, Gilthorpe JD, Wang H, Sidoli S, Mateus A, Lee DF, Cantù C, Esteller M, Mattevi A, Roman A, Aguilo F. The scaffolding function of LSD1 controls DNA methylation in mouse ESCs. Nat Commun. 2024 Sep 5;15(1):7758. doi: 10.1038/s41467-024-51966-7.
Zhu D, Huang MF, Xu A, Gao X, Huang YW, Phan TTT, Lu L, Chi TY, Dai Y, Pang LK, Gingold JA, Tu J, Huo Z, Bazer DA, Shoemaker R, Wang J, Ambrose CG, Shen J, Kameoka J, Zhao Z, Wang LL, Zhang Y, Zhao R, Lee DF. Systematic Transcriptome Profiling of hPSC-derived Osteoblasts Unveils CORIN's Mastery in Governing Osteogenesis Through CEBPD Modulation. J Biol Chem. 2024 Jun 24:107494. doi: 10.1016/j.jbc.2024.107494.
Lien S, Whitbread TP, Shastri SO, Contreras JA, Zhao R, Zhu Y. Cancer-associated MDM2 W329G mutant attenuates ribosomal stress-mediated p53 responses to promote cell survival and glycolysis. Am J Cancer Res. 2024 May 15;14(5):2141-2156
Huang MF, Wang YX, YT Chou, Lee DF. Therapeutic Strategies for RB1-Deficient Cancers: Intersecting Gene Regulation and Targeted Therapy. Cancers (Basel). 2024 Apr 19;16(8):1558.

2023

DLX2 promotes osteosarcoma epithelial-mesenchymal transition and doxorubicin resistance by enhancing HOXC8-CDH2 axis Zhang B, Du X, Fan Y, Qu G, Pang LK, Zhao R, Yao W. iScience. 2023 Oct 19;26(11):108272. doi: 10.1016/j.isci.2023.108272. eCollection 2023 Nov 17.
Unveiling the prognostic implications of RPLP1 upregulation in osteosarcoma. Du X, Wei H, Zhang B, Pang LK, Zhao R, Zhang XD, Yao W. Am J Cancer Res. 2023 Oct 15;13(10):4822-4831. eCollection 2023.
Batra JS, Chi TY, Huang MF, Zhu D, Chen Z, Lee DF, Kameoka J. Wearable Biosensor with Molecularly Imprinted Conductive Polymer Structure to Detect Lentivirus in Aerosol. Biosensors (Basel). 2023 Aug 31;13(9):861
Chachad D, Patel LR, Recio CV, Pourebrahim R, Whitley EM, Wang W, Su X, Xu A, Lee DF, Lozano G. Unique transcriptional profiles underlie osteosarcomagenesis driven by different p53 mutants. Cancer Res. 2023 Jul 14;83(14):2297-2311.
Choe JH, Kawase T, Xu A, Guzman A, Tong DR, Obraadovic AZ, Low-Calle AM, Alaghebandan B, Raghavan A, Long K, Hwang PM, Schiffman JD, Zhu Y, Zhao R, Lee DF*, Katz C*, Prives C*. Li-Fraumeni Syndrome-associated dimer-forming mutant p53 promotes transactivation-independent mitochondrial cell death. Cancer Discov. 2023 May 4;13(5):1250-1273. doi: 10.1158/2159-8290.CD-22-0882. (*Corresponding Author) #Commentary by Stieg et al., Cancer Discov. 2023 May 4;13(5):1046-1048. doi: 10.1158/2159-8290.CD-23-0200.
Du X, Wei H, Zhang B, Wang B, Li Z, Pang LK, Zhao R, Yao W. Molecular mechanisms of osteosarcoma metastasis and possible treatment opportunities. Front Oncol. 2023 May 1;13:1117867.
Xu A, Liu M, Hung MF, Zhang Y, Hu R, Gingold JA, Liu Y, Zhu D, Chien CS, Wang WC, Liao Z, Yuan F, Hsu CW, Tu J, Yu Y, Rosen T, Xiong F, Jia P, Yang YP, Bazer DA, Chen YW, Li W, Huff CD, Zhu JJ, Aguilo F, Chiou SH, Boles NC, Lai CC, Hung MC, Zhao Z, Van Nostrand EL, Zhao R*, Lee DF*. Rewired m6A epitranscriptomic networks link mutant p53 to neoplastic transformation. Nat Commun. 2023 Mar 27;14(1):1694. doi: 10.1038/s41467-023-37398-9. (*Corresponding Author) #Featured Article by Nat Commun Editor Dr. Stephanie Koo
Lee DF, Pereira CF. Reprogramming Stars #10: Modeling Cancer with Cellular Reprogramming-An Interview with Dr. Dung-Fang Lee. Cell Reprogram. 2023 Jan 31. doi: 10.1089/cell.2023.29081.dfl

2022

Huang MF, Shoemaker R, Lee DF. Bcl11b and Atoh8 Coordinate Cellular Plasticity for Reprogramming and Transformation. Cell Reprogram. 2022 Nov 21. doi: 10.1089/cell.2022.0128.
Li HB, Huang G, Tu J, Lv DM, Jin QL, Chen JK, Zou YT, Lee DF, Xie D, Shen JN, Xie XB. METTL14-mediated epitranscriptome modification of MN1 mRNA promotes tumorigenicity and all-trans-retinoic acid resistance in osteosarcoma. EBioMedicine. 2022 Jul 7;82:104142.
Tu J, Huo Z, Yu Y, Zhu D, Xu A, Huang MF, Hu R, Wang R, Gingold JA, Chen YH, Tsai KL, Forcioli-Conti NR, Huang SXL, Webb TR, Su J, Bazer DA, Jia P, Yustein JT, Wang LL, Hung MC, Zhao Z, Huff CD, Shen J, Zhao R, Lee DF. Hereditary retinoblastoma iPSC model reveals aberrant spliceosome function driving bone malignancies. Proc Natl Acad Sci U S A. 2022 Apr 19;119(16):e2117857119.
Malla S, Prasad Bhattarai D, Groza P, Melguizo-Sanchis D, Atanasoai I, Martinez-Gamero C, Román ÁC, Zhu D, Lee DF, Kutter C, Aguilo F. ZFP207 sustains pluripotency by coordinating OCT4 stability, alternative splicing and RNA export. EMBO Rep. 2022 Jan 17:e53191.

2021

Jewell BE, Xu A, Zhu D, Huang MF, Lu L, Liu M, Underwood EL, Park JH, Gingold JA, Zhou R, Tu J, Huo Z, Liu Y, Jin W, Chen YH, Xu Y, Chen SH, Rainusso N, Berg NK, Bazer DA, Vellano C, Jones P, Eltzschig HK, Kaipparettu BA, Zhao R, Wang LL, Lee DF. Patient-derived iPSCs Link Elevated Mitochondrial Respiratory Complex I Function to Osteosarcoma in Rothmund-Thomson Syndrome. PLoS Genet. 2021, 17(12): e1009971.
Huang MF, Pang LK, Chen YH, Zhao R, Lee DF. Cardiotoxicity of Antineoplastic Therapies and Applications of Induced Pluripotent Stem Cell-Derived Cardiomyocytes. Cells. 2021, 10(11), 2823.
Chiang YT, Chien YC, Lin YH, Wu HH, Lee DF, Yu YL. The Function of the Mutant p53-R175H in Cancer. Cancers (Basel). 2021 Aug 13;13(16):4088. doi: 10.3390/cancers131640
Huang PS, Wen MH, Xie X, Xu A, Lee DF, Chen TY. Generation of a homozygous knock-in human embryonic stem cell line expressing SNAP-tagged SOD1. Stem Cell Res. 2021 Jul;54:102415. doi: 10.1016/j.scr.2021.102415
Xiong F, Wang R, Lee JH, Li S, Chen SF, Liao Z, Hasani LA, Nguyen PT, Zhu X, Krakowiak J, Lee DF, Han L, Tsai KL, Liu Y, Li W.RNA m6A modification orchestrates a LINE-1-host interaction that facilitates retrotransposition and contributes to long gene vulnerability. Cell Res. 2021 Aug;31(8):861-885. doi: 10.1038/s41422-021-00515-8
Sevilla A, Papatsenko D, Mazloom AR, Xu H, Vasileva A, Unwin RD, LeRoy G, Chen EY, Garrett-Bakelman FE, Lee DF, Trinite B, Webb RL, Wang Z, Su J, Gingold J, Melnick A, Garcia BA, Whetton AD, MacArthur BD, Ma'ayan A, Lemischka IR. An Esrrb and Nanog Cell Fate Regulatory Module Controlled by Feed Forward Loop Interactions. Front Cell Dev Biol. 2021 Mar 19;9:630067. doi: 10.3389/fcell.2021.630067. eCollection 2021.
Papapetrou EP, Lee DF. Reprogramming and cancer. Stem Cell Res. 2021 Apr;52:102249.
Chou PC, Choi HH, Huang Y, Fuentes-Mattei E, Velazquez-Torres G, Zhang F, Phan L, Lee J, Shi Y, Bankson JA, Wu Y, Wang H, Zhao R, Yeung SJ, Lee MH. Impact of diabetes on promoting the growth of breast cancer. Cancer Commun (Lond). 2021 Feb 20. doi: 10.1002/cac2.12147.
Xu A, Huang MF, Zhu D, Gingold JA, Bazer DA, Chang B, Wang D, Lai CC, Lemischka IR, Zhao R, Lee DF. LncRNA H19 Suppresses Osteosarcomagenesis by Regulating snoRNAs and DNA Repair Protein Complexes. Front Genet. 2021 Jan 15;11:611823.

2020

Pang LK, Pena M, Zhao R, Lee DF. Modeling of Osteosarcoma with Induced Pluripotent Stem Cells. Stem Cell Res. 2020 Dec;49:102006.
Chen L, Xiong L, Hong S, Li J, Huo Z, Li Y, Chen S, Zhang Q, Zhao R, Gingold JA, Zhu X, Lv W, Li Y, Yu S, Xiao H. Circulating Myeloid-derived Suppressor Cells Facilitate Invasion of Thyroid Cancer Cells by Repressing miR-486-3p. J Clin Endocrinol Metab. 2020 Aug 1;105(8):dgaa344.
Li H, Tu J, Zhao Z, Chen L, Qu Y, Li H, Yao H, Wang X, Lee DF, Shen J, Wen L, Huang G, Xie X. Molecular signatures of BRCAness analysis identifies PARP inhibitor Niraparib as a novel targeted therapeutic strategy for soft tissue Sarcomas. Theranostics. 2020 Jul 25;10(21):9477-9494.
Li A, Mallik S, Luo H, Jia P, Lee DF, Zhao Z. H19, a Long Non-coding RNA, Mediates Transcription Factors and Target Genes through Interference of MicroRNAs in Pan-Cancer. Mol Ther Nucleic Acids. 2020 Sep 4; 21:180-191.
Huo Z, Tu J, Lee DF, Zhao R. Engineering Mutation Clones in Mammalian Cells with CRISPR/Cas9. Methods Mol Biol. 2108:355-369, 2020.

2019

Wen MH, Xie X, Tu J, Lee DF, Chen TY. Generation of a genetically modified human embryonic stem cells expressing fluorescence tagged ATOX1. Stem Cell Res. 2019 Dec;41:101631.
Su J, Zhu D, Huo Z, Gingold JA, Ang YS, Tu J, Zhou R, Lin Y, Luo H, Yang H, Zhao R, Schaniel C, Moore KA, Lemischka IR, Lee DF. Genomic Integrity Safeguards Self-Renewal in Embryonic Stem Cells. Cell Rep. Aug 6;28(6):1400-1409.e4, 2019.
Wang D, Luo H, Huo Z, Chen M, Han Z, Hung M, Su B, Li Y, Wang X, Guo X, Xiao H, Lee D, Zhao R, Yang H. Irradiation-induced dynamic changes of gene signatures reveal gain of metastatic ability in nasopharyngeal carcinoma. Am J Cancer Res. Mar 1;9(3):479-495, 2019.
Huo Z, Tu J, Xu A, Li Y, Wang D, Liu M, Zhou R, Zhu D, Lin Y, Gingold JA, Yen CJ, Xiao H, Zhao R. Generation of a heterozygous p53 R249S mutant human embryonic stem cell line by TALEN-mediated genome editing. Stem Cell Res. 2019 Jan;34:101360.

2018

Jewell BE, Liu M, Lu L, Zhou R, Tu J, Zhu D, Huo Z, Xu A, Wang D, Mata H, Jin W, Xia W, Rao PH, Zhao R, Hung MC, Wang LL, Lee DF. Generation of an induced pluripotent stem cell line from an individual with a heterozygous RECQL4 mutation. Stem Cell Res. Dec;33:36-40, 2018.
Kim HS, Yoo S, Zhou R, Xu A, Bernitz JM, Yuan Y, Gomes AM, Daniel MG, Su J, Demicco EG, Zhu J, Moore, KA, Lee DF, Lemischka IR, Schaniel C. Oncogenic role of SFRP2 in p53-mutant osteosarcoma development via autocrine and paracrine mechanism. Proc Natl Acad Sci U S A. Nov 20:115(47):E11128-E11137, 2018.
Zhu D, Kong CSL, Gingold JA, Zhao R, Lee DF. Induced pluripotent stem cells and induced pluripotent cancer cells in cancer disease modeling. Adv Exp Med Biol. 1119:169-183, 2018.
Liu M, Tu J, Gingold JA, Kong CSL, Lee DF. Cancer in a dish: Progress using stem cells a platform for cancer research. Am J Cancer Res. Jun 1;8(6):944-954,2018.
Zhou R, Xu A, Tu J, Liu M, Gingold JA, Zhao R, Lee DF. Modeling osteosarcoma using Li-Fraumeni syndrome patient-derived induced pluripotent stem cells. J Vis Exp. Jun 13;(136), 2018
Xu A, Zhou R, Tu J, Huo Z, Zhu D, Wang D, Gingold JA, Mata H, Rao PH, Liu M, Mohamed AMT, Kong CSL, Jewell BE, Xia W, Zhao R, Hung MC, Lee DF. Establishment of a human embryonic stem cell line with homozygous TP53 R248W mutant by TALEN mediated gene editing. Stem Cell Res. Apr 27;29:215-219, 2018
Gingold JA, Zhu D, Lee DF, Kaseb A, Chen J. Genomic Profiling and Metabolic Homeostasis in Primary Liver Cancer. Trends Mol Med. Apr;24(4):395-411, 2018
Zhou R, Xu A, Wang D, Zhu D, Mata H, Huo Z, Tu J, Liu M, Mohamed AMT, Jewell BE, Gingold J, Xia W, Rao PH, Hung MC, Zhao R, Lee DF. A homozygous p53 R282W mutant human embryonic stem cell line generated using TALEN-mediated precise gene editing. Stem Cell Res. Jan 26;27:131-135, 2018.
Tu J, Huo Z, Liu M, Wang D, Xu A, Zhou R, Zhu D, Gingold J, Shen J, Zhao R, Lee DF. Generation of human embryonic stem cell line with heterozygous RB1 deletion by CRISPR/Cas9 nickase. Stem Cell Res. Feb 2;28:29-32, 2018

2017

Zhou R, Xu A, Gingold J, Strong LC, Zhao R, Lee DF. Li-Fraumeni syndrome disease model: A platform to develop precision cancer therapy targeting oncogenic p53. Trends Pharmacol Sci. 38(10):908-927, 2017.
Lin YH, Jewell BE, Gingold J, Lu L, Zhao R, Wang LL, Lee DF. Osteosarcoma: Molecular pathogenesis and iPSC modeling. Trends Mol Med. 23(8):737-755, 2017.
Freire AG, Waghray A, Soares-da-Silva F, Resende TP, Lee DF, Pereira CF, Nascimento DS, Lemischka IR, Pinto-do-Ó P. Transient HES5 activity instructs mesodermal cells toward a cardiac fate. Stem Cell Reports. 9(1):136-148, 2017.
Lu J, Song G, Tang Q, Yin J, Zou C, Zhao Z, Xie X, Xu H, Huang G, Wang J, Lee DF, Khokha R, Yang H, Shen J. MiR-26a inhibits stem cell-like phenotype and tumor growth of osteosarcoma by targeting Jagged1. Oncogene.12;36(2):231-241, 2017.
Tu J, Huo Z, Gingold J, Zhao R, Shen J, Lee DF. The histogenesis of Ewing sarcoma. Cancer Rep Rev. 1(2): 1, 2017.

2016

Gingold J, Zhou R, Lemischka IR, Lee DF. Modeling cancer with pluripotent stem cells. Trends Cancer. 2(9):485-494, 2016.
Lee DF, Walsh MJ, Aguilo F. ZNF217/ZFP217 meets chromatin and RNA. Trends Biochem Sci. 41(12):986-988, 2016.
Li CW, Xia W, Lim SO, Hsu JL, Huo L, Wu Y, Li LY, Lai CC, Chang SS, Hsu YH, Sun HL, Kim J, Yamaguchi H, Lee DF, Wang H, Wang Y, Chou CK, Hsu JM, Lai YJ, LaBaff AM, Ding Q, Ko HW, Tsai FJ, Tsai CH, Hortobagyi GN, Hung MC. AKT1 Inhibits Epithelial-to-Mesenchymal Transition in Breast Cancer through Phosphorylation-Dependent Twist1 Degradation. Cancer Res. 76(6):1451-62, 2016.

2015

Aguilo F, Zhang F, Sancho A, Fidalgo M, Di Cecilia S, Vashisht A, Lee DF, Chen CH, Rengasamy M, Andino B, Jahouh F, Roman A, Krig SR, Wang R, Zhang W, Wohlschlegel JA, Wang J, Walsh MJ. Coordination of m(6)A mRNA Methylation and Gene Transcription by ZFP217 Regulates Pluripotency and Reprogramming. Cell Stem Cell. 2015 Dec 3;17(6):689-704.
Mulero-Navarro S, Sevilla A, Roman AC, Lee DF, D'Souza SL, Pardo S, Riess I, Su J, Cohen N, Schaniel C, Rodriguez NA, Baccarini A, Brown BD, Cavé H, Caye A, Strullu M, Yalcin S, Park CY, Dhandapany PS, Yongchao G, Edelmann L, Bahieg S, Raynal P, Flex E, Tartaglia M, Moore KA, Lemischka IR, Gelb BD. Myeloid Dysregulation in a Human Induced Pluripotent Stem Cell Model of PTPN11-Associated Juvenile Myelomonocytic Leukemia. Cell Rep. 2015 Oct 20;13(3):504-515.
Gingold JA, Coakley ES, Su J, Lee DF, Lau Z, Zhou H, Felsenfeld DP, Schaniel C, Lemischka IR. Distribution Analyzer, a methodology for identifying and clustering outlier conditions from single-cell distributions, and its application to Nanog reporter RNAi screen. BMC Bioinformatics. 2015 Jul 22;16:225.
Waghray A, Saiz N, Jayaprakash AD, Freire AG, Papatsenko D, Pereira CF, Lee DF, Brosh R, Chang B, Darr H, Gingold J, Kelley K, Schaniel C, Hadjantonakis AK, Lemischka IR. Tbx3 Controls Dappa3 Levels and Exit from Pluripotency toward Mesoderm. Stem Cell Reports. 2015 Jul 14;5(1):97-110.
Ding J, Huang X, Shao N, Zhou H, Lee DF, Faiola F, Fidalgo M, Guallar D, Saunders A, Shliaha PV, Wang H, Waghray A, Papatsenko D, Sánchez-Priego C, Li D, Yuan Y, Lemischka IR, Shen L, Kelley K, Deng H, Shen X, Wang J. Tex10 Coordinates Epigenetic Control of Super-Enhancer Activity in Pluripotency and Reprogramming. Cell Stem Cell. 2015 Jun 4;16(6):653-68.
Lee DF†, Su J, Kim HS, Chang B, Papatsenko D, Zhao R, Ye Yuan, Gingold J, Xia W, Darr H, Mirzayans R, Hung MC, Schaniel C, Lemischka IR†. Modeling Familial Cancer with Induced Pluripotent Stem Cells. Cell. 2015 Apr 9;161(2):240-54. (†Corresponding authors)

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2014

Chen J, Shin JH, Zhao R, Phan L, Wang H, Xue Y, Post SM, Ho Choi H, Chen JS, Wang E, Zhou Z, Tseng C, Gully C, Velazquez-Torres G, Fuentes-Mattei E, Yeung G, Qiao Y, Chou PC, Su CH, Hsieh YC, Hsu SL, Ohshiro K, Shaikenov T, Wang H, Yeung SC, Lee MH. CSN6 drives carcinogenesis by positively regulating Myc stability. Nat Commun. 2014 Nov 14;5:5384.
Kim HS, Bernitz J, Lee DF, Lemischka IR. Genomic editing tools to model human disease with isogenic pluripotent stem cells. Stem Cells Dev. 2014 Nov 15;23(22):2673-86.
Huo L, Li CW, Huang TH, Lam YC, Xia W, Tu C, Chang WC, Hsu JL, Lee DF, Nie L, Yamaguchi H, Wang Y, Lang J, Li LY, Chen CH, Mishra L, Hung MC. Activation of Keap1/Nrf2 signaling pathway by nuclear epidermal growth factor receptor in cancer cells. Am J Transl Res. 2014 Nov 22;6(6):649-63.
Gingold JA, Fidalgo M, Guallar D, Lau Z, Sun Z, Zhou H, Faiola F, Huang X, Lee DF, Waghray A, Schaniel C, Felsenfeld DP, Lemischka IR, Wang J. A genome-wide RNAi screen identifies opposing functions of Snail1 and Snail2 on the Nanog dependency of establishing pluripotency. Mol Cell. 2014 Oct 2;56(1):140-52.
Fuentes-Mattei E, Velazquez-Torres G, Phan L, Zhang F, Chou PC, Shin JH, Choi HH, Chen JS, Zhao R, Chen J, Gully C, Carlock C, Qi Y, Zhang Y, Wu Y, Esteva FJ, Luo Y, McKeehan WL, Ensor J, Hortobagyi GN, Pusztai L, Fraser Symmans W, Lee MH, Yeung SC. Effects of obesity on transcriptomic changes and cancer hallmarks in estrogen receptor-positive breast cancer. J Natl Cancer Inst. 2014 Jun 23;106(7).

2013

Kuo HP, Wang Z, Lee DF, Iwasaki M, Duque-Afonso J, Wong SH, Lin CH, Figueroa ME, Su J, Lemischka IR, Cleary ML. Epigenetic roles of MLL oncoproteins are dependent on NF-κB. Cancer Cell. 2013 Oct 14;24(4):423-37.

2012

Singer S, Zhao R, Barsotti AM, Ouwehand A, Fazollahi M, Coutavas E, Breuhahn K, Neumann O, Longerich T, Pusterla T, Powers MA, Giles KM, Leedman PJ, Hess J, Grunwald D, Bussemaker HJ, Singer RH, Schirmacher P, Prives C. Nuclear pore component Nup98 is a potential tumor suppressor and regulates posttranscriptional expression of select p53 target genes. Mol Cell. 2012 Dec 14;48(5):799-810.
Lee DF, Su J, Ang YS, Carvajal-Vergara X, Mulero-Navarro S, Pereira CF, Gingold J, Wang HL, Zhao R, Sevilla A, Darr H, Williamson AJ, Chang B, Niu X, Aguilo F, Flores ER, Sher YP, Hung MC, Whetton AD, Gelb BD, Moore KA, Snoeck HW, Ma'ayan A, Schaniel C, Lemischka IR. Regulation of Embryonic and Induced Pluripotency by Aurora Kinase-p53 Signaling. Cell Stem Cell. 2012 Aug 3;11(2):179-94.
Lee DF†, Su J, Sevilla A, Gingold J, Schaniel C, Lemischka IR†. Combining competition assays with genetic complementation strategies to dissect mouse embryonic stem cell self-renewal and pluripotency. Nat Protoc. 2012 Mar 22;7(4):729-48. (†Corresponding authors)
Wang Y, Ding QQ, Yen CJ, Xia W, Izzo JG, Lang JY, Li CW, Miller SA, Wang X, Lee DF, Hsu JL, Hsu JM, Huo LF, LaBaff AM, Liu DP, Huang TH, Lai CC, Tsai FU, Chang WC, Chen CH, Wu TT, Buttar NS, Wang KK, Wu Y, Wang H, Ajani J, Hung MC. The crosstalk of mTOR/S6K1 and Hedgehog pathways. Cancer Cell. 2012 Mar 20;21(3):374-87.
Ling J, Kang Y, Zhao R, Xia Q, Lee DF, Chang Z, Peng B, Fleming JB, Wang H, Lemischka IR, Hung MC, Chiao PJ. KrasG12D-Induced IKK2/beta/NF-kappaB Activation by IL-1alpha and p62 Feedforward Loops is Required for Development of Pancreatic Ductal Adenocarcinoma. Cancer Cell. 2012 Jan 17;21(1):105-20.
Liu M, Lee DF, Chen CT, Yen CJ, Li LY, Lee HJ, Chang CJ, Chang WC, Hsu JM, Kuo HP, Xia W, Wei Y, Chiu PC, Chou CK, Du Y, Dhar D, Karin M, Chen CH, Hung MC. IKKalpha activation of NOTCH links tumorigenesis via FOXA2 suppression. Mol Cell. 2012 Jan 27;45(2):171-84.

2011

Ding Q, Chang CJ, Xie X, Xia W, Yang JY, Wang SC, Wang Y, Xia J, Chen L, Cai C, Li H, Yen CJ, Kuo HP, Lee DF, Lang J, Huo L, Cheng X, Chen YJ, Li CW, Jeng LB, Hsu JL, Li LY, Tan A, Curley SA, Ellis LM, Dubois RN, Hung MC. APOBEC3G promotes liver metastasis in an orthotopic mouse model of colorectal cancer and predicts human hepatic metastasis. J Clin Invest. 2011 Nov;121(11):4526-36.
Su JL, Cheng X, Yamaguchi H, Chang YW, Hou CF, Lee DF, Ko HW, Hua KT, Wang YN, Hsiao M, Chen PB, Hsu JM, Bast RC Jr, Hortobagyi GN, Hung MC. FOXO3a-Dependent Mechanism of E1A-Induced Chemosensitization. Cancer Res. 2011 Nov 1;71(21):6878-87.
Li C, Ao J, Fu J, Lee DF, Xu J, Lonard D, O’Malley BW. Tumor-suppressor role for the SPOP ubiquitin ligase in signal-dependent proteolysis of the oncogenic co-activator SRC-3/AIB1. Oncogene. 2011 Oct 20;30(42):4350-64.
Zhang X, Yalcin S, Lee DF, Yeh TY, Lee SM, Su J, Mungamuri SK, Pimmele P, Kennedy M, Sellers R, Landthaler M, Tuschl T, Chi NW, Lemischka I, Keller G, Ghaffari S. FOXO1 is an essential regulator of pluripotency in human embryonic stem cells. Nat Cell Biol. 2011 Jul 31;13(9):1092-9.
Tsai SY, Bouwman BA, Ang YS, Kim SJ, Lee DF, Lemischka IR, Rendl M. Single transcription factor reprogramming of hair follicle dermal papilla cells to induced pluripotent stem cells. Stem Cells. 2011 Jun;29(6):964-71.
Aguilo F, Avagyan S, Labar AS, Sevilla A, Lee DF, Kumar P, Lemischka IR, Zhou BY, Snoeck HW. Prdm16 is a physiological regulator of hematopoietic stem cells. Blood. 2011 May 12;117(19):5057-66.
Ang YS, Tsai SY, Lee DF, Monk J, Su J, Ratnakumar K, Ding J, Ge Y, Darr H, Chang B, Wang J, Rendl M, Bernstein E, Schaniel C, Lemischka IR. Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network. Cell. 2011 Apr 15;145(2):183-97.
Zhao R, Yeung SC, Chen J, Iwakuma T, Su CH, Chen B, Qu C, Zhang F, Chen YT, Lin YL, Lee DF, Jin F, Zhu R, Shaikenov T, Sarbassov D, Sahin A, Wang H, Wang H, Lai CC, Tsai FJ, Lozano G, Lee MH. Subunit 6 of the COP9 signalsome promotes tumorigenesis in mice through stabilization of MDM2 and is upregulated in human cancer. J Clin Invest. 2011 Mar;121(3):851-65.

2010

Carvajal-Vergara X, Sevilla A, D'Souza SL, Ang YS, Schaniel C, Lee DF, Yang L, Kaplan AD, Adler ED, Rozov R, Ge Y, Cohen N, Edelmann LJ, Chang B, Waghray A, Su J, Pardo S, Lichtenbelt KD, Tartaglia M, Gelb BD, Lemischka IR. Patient-specific induced pluripotent stem-cell-derived models of LEOPARD syndrome. Nature. 2010 Jun 10;465(7299):808-12.
Kuo HP, Lee DF, Chen CT, Liu M, Chou CK, Lee HJ, Du Y, Xie X, Wei Y, Xia W, Weihua Z, Yang JY, Yen CJ, Huang TH, Tan M, Xing G, Zhao Y, Lin CH, Tsai SF, Fidler IJ, Hung MC. ARD1 stabilization of TSC2 suppresses tumorigenesis through the mTOR signaling pathway. Sci Signal. 2010 Feb 9;3(108):ra9.
Tsai SY, Clavel C, Kim S, Ang YS, Grisanti L, Lee DF, Kelley K, Rendl M. Oct4 and Klf4 reprogram dermal papilla cells into induced pluripotent stem cells. Stem Cells. 2010 Feb;28(2):221-8.
Schaniel C, Lee DF, Lemischka IR. Exploration of self-renewal and pluripotency in ES cells using RNAi. Method Enzymol. 2010;477:351-65.

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2009

Kuo HP, Lee DF, Xia W, Wei Y, Hung MC. TNFalpha induces HIF-1alpha expression through activation of IKKbeta. Biochem Biophys Res Commun. 2009 Nov 27;389(4):640-4.
Kuo HP, Lee DF, Xia W, Lai CC, Li LY, Hung MC. (2009). Phosphorylation of ARD1 by IKKbeta contributes to its destabilization and degradation. Biochem Biophys Res Commun. 2009 Nov 6;389(1):156-61.
Chou CK, Lee DF, Sun HL, Li LY, Lin CY, Huang WC, Hsu JM, Kuo HP, Yamaguchi H, Wang YN, Liu M, Wu HY, Liao PC, Yen CJ, Hung MC. The suppression of MAD1 by AKT-mediated phosphorylation activates MAD1 target genes transcription. Mol Carcinog. 2009 Nov;48(11):1048-58.
Lee DF, Kuo HP, Liu M, Chou CK, Xia W, Du Y, Shen J, Huo L, Chen CT, Hsu MC, Li CW, Ding Q, Liao TL, Lai CC, Lin AC, Chang YH, Tsai SF, Li LY, Hung MC. KEAP1 E3 ligase-mediated down regulation of NF-KappaB signaling by targeting IKKbeta. Mol Cell. 2009 Oct 9;36(1):131-40.

2008

Lee DF, Kuo HP, Chen CT, Wei Y, Chou CK, Hung JY, Yen CJ, Hung MC. IKKbeta suppression of TSC1 function links the mTOR pathway with insulin resistance. Int J Mol Med. 2008 Nov;22(5):633-8.
Lee DF and Hung MC. Advances in targeting IKK and IKK-related kinases for cancer therapy. Clin Cancer Res. 2008 Sep 15;14(18):5656-62
Ding Q, Huo L, Yang JY, Xia W, Wei Y, Liao Y, Chang CJ, Yang Y, Lai CC, Lee DF, Yen CJ, Chen YJ, Hsu JM, Kuo HP, Lin CY, Tsai FJ, Li LY, Tsai CH, Hung MC. Down-regulation of myeloid cell leukemia-1 through inhibiting Erk/Pin 1 pathway by sorafenib facilitates chemosensitization in breast cancer. Cancer Res. 2008 Aug 1;68(15):6109-17.
Yen CJ, Izzo JG, Lee DF, Guha S, Wei Y, Wu TT, Chen CT, Kuo HP, Hsu JM, Sun HL, Chou CK, Buttar NS, Wang KK, Huang P, Ajani J, Hung MC. Bile salt exposure up-regulates tuberous sclerosis complex 1/mammalian target of rapamycin pathway in Barrett’s-associated esophageal adenocarcinoma. Cancer Res. 2008 Apr 15;68(8):2632-40.
Yang JY, Zong CS, Xia W, Yamaguchi H, Ding Q, Xie X, Lang JY, Lai CC, Chang CJ, Huang WC, Huang H, Kuo HP, Lee DF, Li LY, Lien HC, Cheng X, Chang KJ, Hsiao CD, Tsai FJ, Tsai CH, Sahin AA, Muller WJ, Mills GB, Yu D, Hortobagyi GN, Hung MC. ERK promotes tumorigenesis by inhibiting FOXO3a via MDM2-mediated degradation. Nat Cell Biol. 2008 Feb;10(2):138-48.

2007

Lee DF and Hung MC. All roads lead to mTOR: Integrating inflammation and tumor angiogenesis. Cell Cycle. 2007 Dec 15;6(24):3011-4.
Lee DF, Kuo HP, Chen CT, Hsu JM, Chou CK, Wei Y, Sun, HL, Li LY, Huang WC, He X, Ping B, Hung JY, Lai CC, Ding Q, Su JL, Yang JY, Sahin AA, Hortobagyi GN, Tsai FJ, Tsai CH, Hung MC. IKKbeta suppression of TSC1 links inflammation and tumor angiogenesis via the mTOR pathway. Cell. 2007 Aug 10;130(3):440-55.
Ding Q, He X, Hsu JM, Xia W, Chen CT, Li LY, Lee DF, Liu JC, Zhong Q, Wang X, Hung MC. Degradation of Mcl-1 by beta-TrCP mediates glycogen synthase kinase 3-induced tumor suppression and chemosensitization. Mol Cell Biol. 2007 Jun;27(11):4006-17.
Ding Q, He X, Xia W, Hsu JM, Chen CT, Li LY, Lee DF, Liu JC, Hung MC. Myeloid cell leukemia-1 inversely correlates with glycogen synthase kinase-3beta activity and associates with poor prognosis in human breast cancer. Cancer Res. 2007 May 15;67(10):4564-71.

2006

Ping B, He X, Xia W, Lee DF, Wei Y, Yu D, Mills G, Shi D, Hung MC. Cytoplasmic expression of p21CIP1/WAF1 is correlated with IKKbeta overexpression in human breast cancers. Int J Oncol. 2006 Nov;29(5):1103-10.

2005

Lin KA, Chen JH, Lee DF, Lin LY. Alkaline induces metallothionein gene expression and potentiates cell proliferation in Chinese hamster ovary cells. J Cell Physiol. 2005 Dec;205(3):428-36.
Giri DK, Ali-Seyed M, Li LY, Lee DF, Ling P, Bartholomeusz G, Wang SC, Hung MC. Endosomal transport of ErbB-2: mechanism for nuclear entry of the cell surface receptor. Mol Cell Biol. 2005 Dec;25(24):11005-18.
Ding Q, Xia W, Liu JC, Yang JY, Lee DF, Xia J, Bartholomeusz G, Li Y, Pan Y, Li Z, Bargou RC, Qin J, Lai CC, Tsai FJ, Tsai CH, Hung MC. Erk associates with and primes GSK-3beta for its inactivation resulting in upregulation of beta-catenin. Mol Cell. 2005 Jul 22;19(2):159-70.
Shao R, Lee DF, Wen Y, Ding Y, Xia W, Ping B, Yagita H, Spohn B, Hung MC. E1A sensitizes cancer cells to TRAIL-induced apoptosis through enhancement of caspase activation. Mol Cancer Res. 2005 Apr;3(4):219-26.

2004

Wang SC, Lien HC, Xia W, Chen IF, Lo HW, Wang Z, Ali-Seyed M, Lee DF, Bartholomeusz G, Ou-Yang F, Giri DK, Hung MC. Binding at and transactivaiton of the COX-2 promoter by nuclear tyrosine kinase receptor ErbB-2. Cancer Cell. 2004 Sep;6(3):251-61.
Xia W, Chen JS, Zhou X, Sun PR, Lee DF, Liao Y, Zhou BP, Hung MC. Phosphorylation /cytoplasmic localization of p21Cip1/WAF1 is associated with HER2/neu overexpression and provides a novel combination predictor for poor prognosis in breast cancer patients. Clin Cancer Res. 2004 Jun 1;10(11):3815-24.
Hu MC, Lee DF, Xia W, Golfman LS, Ou-Yang F, Yang JY, Zou Y, Bao S, Hanada N, Saso H, Kobayashi R, Hung MC. IkappaB kinase promotes tumorigenesis through inhibition of forkhead FOXO3a. Cell. 2004 Apr 16;117(2):225-37.
Yang DH, Wen Y, Su LK, Xia W, Wang SC, Zhang S, Gan L, Lee DF, Spohn B, Frey JA, Hortobagyi GN, Hung MC. A delayed chemically induced tumorigenesis in Brca2 mutant mice. Oncogene. 2004 Mar 11;23(10):1896-901.

2000

Lee DF, Chen CC, Hsu TA, Juang JL. A baculovirus superinfection system: efficient vehicle for gene transfer into Drosophila S2 cells. J Virol. 2000 2000 Dec;74(24):11873-80. doi: 10.1128/jvi.74.24.11873-11880.2000.