Dechen Lin, Ph.D.

De-chen Lin

Assistant Professor
Herman Ostrow School of Dentistry of USC

Associate Director of Research for the USC Head and Neck Center
Keck School of Medicine of USC

 

2250 Alcazar St.
CSA 207D – HSC 9062
Los Angeles, CA 90089
Phone: (323) 442-1220
Fax: (323) 442-2981
dechenli@usc.edu
Lab website:
sites.usc.edu/linlab

Education
Experience
Awards
Research
Publications

Nanjing University, China
B.S., 2005
Biology

Chinese Academy of Medical Sciences, China
Ph.D., 2010
Cell Biology

  • 2023 – present – Associate Director of Research for the USC Head and Neck Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
  • 2022 – present – Assistant Professor – Ostrow School of Dentistry of USC, University of Southern California, Los Angeles, CA
  • 2020 – 2021 – Adjunct Associate Professor – UCLA School of Medicine, Los Angeles, CA
  • 2016 – 2021 – Assistant Professor – Cedars-Sinai Medical Center, Los Angeles, CA
  • 2014 – 2015 – Project Scientist – Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA
  • 2013 – 2014 – Post-doctoral Fellow – Cedars-Sinai Medical Center, CA
  • 2011 – 2013 – Post-doctoral Fellow – Cancer Science Institute of Singapore, National University of Singapore, Singapore
  • 2020 – Readers Choice: The best of Oncogene 2019 (Agency: Nature Publishing Group)
  • 2019 – The Best of AACR Award: most-cited research article in Cancer Research 2018 (Agency: American Association for Cancer Research (AACR))
  • 2018-2020 – Clinical and Translational Science Institute (CTSI) Core Voucher Award
  • 2018-2020 – DeGregorio Foundation Award for Cancers of the Esophagus and Stomach (Agency: DeGregorio Family Foundation)
  • 2017-2019 – Tower Foundation Career Development Award (Agency: Tower Cancer Research Foundation)
  • 2015-2017 – Donna and Jesse Garber Awards for Cancer Research (Agency: Cedars-Sinai Medical Center)
  • 2015-2017 – American Society of Hematology (ASH) Fellow Scholar Award (Agency: American Society of Hematology)
  • 2015-2017 – MDS Young Investigator Award (Agency: THE MDS FOUNDATION)
  • 2014 – Incorporated Scholar-in-Training Award, AACR-Aflac (Agency: American Association for Cancer Research (AACR))

Modeling Pathways of Early Growth Dysregulation at the GEJ – Grant #5 R01 DK135562

  • Principal Investigator: Stephen J Meltzer, Ph.D. and Dechen Lin, Ph.D.
  • Sponsor: National Institutes of Health
  • Period: 05/01/2024 – 02/28/2029
  • Goal: The application will test the hypothesis that dysregulated Platelet Activating Factor (PTAF) and free fatty-acid (FFA) metabolism, via a novel epigenetic crosstalk featuring aberrant HNF4A transcription factor activation, is involved in growth dysregulation and early neoplastic evolution in cardia columnar cells at the human gastroesophageal junction (GEJ-cardia).

Pharmacological and dietary inhibition of a novel metabolic-epigenetic crosstalk in head and neck cancer – Grant #5 R01 CA033648

  • Principal Investigator: Dechen Lin, Ph.D.
  • Sponsor: National Institutes of Health
  • Period: 03/01/2024 – 01/31/2029
  • Goal: Head neck squamous cell carcinoma (HNSCC) is common and aggressive cancer without effective therapy. In this proposal, we will: i) focus on the crosstalk between cancer metabolism and epigenetic regulation to study the primary forces transforming normal oral cells into HNSCC using advanced organoid technology and mouse models; ii) investigate the pharmacological and dietary inhibition of the link between methionine metabolism and epigenetic network.

Development of genome-guided immunotherapeutic strategies for head neck cancer

  • Principal Investigator: Dechen Lin, Ph.D.
  • Sponsor: Ming Hsieh Institute Research Award
  • Period: 08/01/2023 – 08/31/2024
  • Goal: The major goal of this project is to develop MLL3 mutations as biomarkers to predict immunotherapeutic response in patients with head and neck squamous cancer using both animal models and patient-derived tumor organoids.

Master regulator transcription factors promote esophageal neoplastic evolution – Grant #5 R37 CA237022

  • Principal Investigator: Dechen Lin, Ph.D.
  • Sponsor: National Institutes of Health
  • Period: 06/01/2020-05/31/2025
  • Goal: To establish primary driving forces of BE-associated neoplasia evolution and uncover epigenomic mechanisms underlying esophagus transformation, which will fundamentally transform our insights into the biology of esophageal cancer.

Window pre-operative study of FID-007 in patients with squamous cell carcinoma of the head and neck

  • Principal Investigator: Jacob Thomas MD; Co-Principal Investigator: Dechen Lin, Ph.D.
  • Sponsor: Ming Hsieh Institute Research Award
  • Period: 08/01/2023 – 08/31/2024
  • Goal: The major goal of this project is to 1) conduct a clinical trial evaluating the combination of Taxane-based drugs and ICB therapies in HNSCC patients; 2) study the immune-modulating function of Taxane-based drugs using single-cell RNA-seq and patient-derived tumor organoids.

A central regulator and predictive biomarker for head neck cancer immunotherapy

  • Principal Investigator: Uttum Sinha MD, Dechen Lin, Ph.D.
  • Sponsor: The Wright Foundation
  • Period: 08/01/2023 – 07/31/2024
  • Goal: The major goal of this project is to perform single-cell RNA-seq analyses of HNSCC tumor microenvironment to understand the role on STAT1-IFN pathway in anti-tumor immune regulation and to develop biomarkers using multiplexed immunofluorescence of HNSCC tumor samples.

  1. Vistoso Monreal A, Zhao H, Sedghizadeh PP, Lin DC*. Patient-derived tumor organoids to model drug response in gastric cancer. Cell Reports Medicine. July 16;5(7):101650. https://doi.org/10.1016/j.xcrm.2024.101650.

  2. Nam C, Li LY, Yang Q, Ziman B, Zhao H, Hu B, Collet C, Jing P, Lei Q, Xu LY, Li EM, Koeffler HP, Sinha UK, Lin DC*. A druggable cascade links methionine metabolism to epigenomic reprogramming in squamous cell carcinoma. Proc Natl Acad Sci U S A. 2024 Jun 25;121(26):e2320835121. doi: 10.1073/pnas.2320835121. Epub 2024 Jun 20. PMID: 38900797.

  3. Ziman B, Yang Q, Zheng Y, Sheth M, Nam C, Zhao H, Zhang L, Hu B, Bhowmick NA, Sinha UK, Lin DC*. Epigenomic analyses identify FOXM1 as a key regulator of anti-tumor immune response in esophageal adenocarcinoma. Cell Death Dis. 2024 Feb 19;15(2):152. PMID: 38373993.

  4. Park, Y.M., Lin, DC. (2023) Moving closer towards a comprehensive view of tumor biology and microarchitecture using spatial transcriptomics. Nat Commun 14, 7017 (2023). https://doi.org/10.1038/s41467-023-42960-6.

  5. Zheng, Y., Ziman, B., Ho, A. S., Sinha, U. K., Xu, L.-Y., Li, E.-M., Koeffler, H. P., Berman, B. P., & Lin, D.-C.. (2023) Comprehensive analyses of partially methylated domains and differentially methylated regions in esophageal cancer reveal both cell-type- and cancer-specific epigenetic regulation. Genome Biology, 2023 Aug 24;24(1):193. doi: 10.1186/s13059-023-03035-3. PMID: 37620896.

  6. Lin DC. Large-scale genomic analyses reveal alterations and mechanisms underlying clonal evolution and immune evasion in esophageal cancer. Nat Commun. Feb 17; (2023) 14:893. PMID: 36807265.

  7. Sinha UK, Lin DC*. A novel role of master regulator transcription factor in anti-tumor immunity and cancer immunotherapy. Theranostics. 2023; 13(6):1823-1825. doi:10.7150/thno.83486.

  8. Zhao H, Cheng Y, Kalra A, Ma K, Zheng Y, Ziman B, Tressler C, Glunde K, Shin EJ, Ngamruengphong S, Khashab M, Singh V, Anders RA, Jit S, Wyhs N, Chen W, Li X, Lin DC, Meltzer SJ. Generation and multiomic profiling of a TP53/CDKN2A double-knockout gastroesophageal junction organoid model. Sci Transl Med. 2022 Nov 30;14(673):eabq6146. doi: 10.1126/scitranslmed.abq6146. Epub 2022 Nov 30. PMID: 36449602.

  9. Lin, DC*. Large-scale genomic analyses reveal alterations and mechanisms underlying clonal evolution and immune evasion in esophageal cancer. Nat Commun 14, 893 (2023). https://doi.org/10.1038/s41467-023-36557-2.

  10. Uttam K. Sinha, W. Martin Kast, De-Chen Lin*. (2022) Single-cell genomics identifies immune response to neoadjuvant chemoradiotherapy. eBioMedicine, Volume 86. 2022, 104389, ISSN 2352-3964, https://doi.org/10.1016/j.ebiom.2022.104389.

  11. Zhao H, Collet C, Peng D, Sinha UK, Lin DC. (2022) Investigation of early neoplastic transformation and premalignant biology using genetically engineered organoid models. Computational and Structural Biotechnology Journal. https://doi.org/10.1016/j.csbj.2022.09.026.

  12. Nam C, Ziman B, Sheth M, Zhao H, D-C. Lin. (2022) Genomic and Epigenomic Characterization of Tumor Organoid Models. Cancers. 2022, 14, 4090. https://doi.org/10.3390/cancers14174090.

  13. Dinh H.Q, Pan F, Wang G, Q Huang, C Olingy, Z Wu, S Wang, X Xu, X Xu, J He, Q Yang, S Orsulic, M Haro, L Li, G Huang, J Breunig, H Koeffler, C Hedrick, L Xu, Lin DC, E Li. (2021) Integrated single-cell transcriptome analysis reveals heterogeneity of esophageal squamous cell carcinoma microenvironment. Nat Commun. 2021 Dec 17;12(1):7335. doi: 10.1038/s41467-021-27599-5. PMID: 34921160; PMCID: PMC8683407.

  14. Ho AS, Robinson A, Shon W, Laury A, Raedschelders K, Venkatraman V, Holewinski R, Zhang Y, Shiao SL, Chen MM, Mallen-St Clair J, Lin DC, Zumsteg ZS, Van Eyk JE. (2021) Comparative Proteomic Analysis of HPV(+) Oropharyngeal Squamous Cell Carcinoma Recurrence. J Proteome Res. 2021 Nov 30. doi: 10.1021/acs.jproteome.1c00757. Epub ahead of print. PMID: 34846153.

  15. Ho AS, Luu M, Shafqat I, Mallen-St Clair J, Chen MM, Chen Y, Jain M, Ali N, Patio C, Filarski CF, Lin DC, Bankston H, Braunstein GD, Sacks WL, Zumsteg ZS. (2021) Predictive Impact of Metastatic Lymph Node Burden on Distant Metastasis Across Papillary Thyroid Cancer Variants. Thyroid. 2021 Oct;31(10):1549-1557. doi:10.1089/thy.2021.0131. PMID: 34470466.

  16. Lin DC. (2021) A closer look at esophageal cancer through different lenses. EBioMedicine. 2021 Sep;71:103545. doi: 10.1016/j.ebiom.2021.103545. Epub 2021 Aug 19. PMID: 34419929; PMCID: PMC8385164.

  17. Li LY, Yang Q, Jiang YY, Yang W, Jiang Y, Li X, Hazawa M, Zhou B, Huang GW, Xu XE, Gery S, Zhang Y, Ding LW, Ho AS, Zumsteg ZS, Wang MR, Fullwood MJ, Freedland SJ, Meltzer SJ, Xu LY, Li EM, Koeffler HP, Lin DC. (2021) Interplay and cooperation between SREBF1 and master transcription factors regulate lipid metabolism and tumor-promoting pathways in squamous cancer. Nat Commun. 2021 Jul 16;12(1):4362. doi: 10.1038/s41467-021-24656-x. PMID: 34272396; PMCID:PMC8285542.

  18. Zheng Y, Huang G, Silva TC, Yang Q, Jiang YY, Koeffler HP, Lin DC, Berman BP. (2021) A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb target genes. Nat Commun. 2021 Apr 30;12(1):2485. doi:10.1038/s41467-021-22720-0. Erratum in: Nat Commun. 2021 Jun 28;12(1):4106.PMID: 33931649; PMCID: PMC8087678.

  19. Lin DC. (2021) Exercise impacts the epigenome of cancer. Prostate Cancer Prostatic Dis. 2021 May 27. doi: 10.1038/s41391-021-00396-3. Epub ahead of print. PMID: 34045658.

  20. Jiang Y, Jiang YY, Lin DC. (2021) Super-enhancer-mediated core regulatory circuitry in human cancer. Comput Struct Biotechnol J. 2021 May 5;19:2790-2795. doi:10.1016/j.csbj.2021.05.006. PMID: 34093993; PMCID: PMC8138668.

  21. Ho AS, Luu M, Kim S, Tighiouart M, Mita AC, Scher KS, Mallen-St Clair J, Walgama ES, Lin DC, Nguyen AT, Zumsteg ZS. (2021) Nodal staging convergence for HPV-and HPV+ oropharyngeal carcinoma. Cancer. 2021 May 15;127(10):1590-1597. doi:10.1002/cncr.33414. Epub 2021 Feb 17. PMID: 33595897.

  22. Guo Z, Pan F, Peng L, Tian S, Jiao J, Liao L, Lu C, Zhai G, Wu Z, Dong H, Xu X, Wu J, Chen P, Bai X, Lin D, Xu L, Li E, Zhang K. (2021) Systematic Proteome and Lysine Succinylome Analysis Reveals the Enhanced Cell Migration by Hyposuccinylation in Esophageal Squamous Cell Cancer. Mol Cell Proteomics. 2021 Feb 6;20:100053. doi: 10.1074/mcp.RA120.002150. Epub ahead of print. PMID:33561546; PMCID: PMC7970140.

  23. Ma S, Zhou B, Yang Q, Pan Y, Yang W, Freedland SJ, Ding LW, Freeman MR, Breunig JJ, Bhowmick NA, Pan J, Koeffler HP, Lin DC. (2021) A Transcriptional Regulatory Loop of Master Regulator Transcription Factors, PPARG, and Fatty Acid Synthesis Promotes Esophageal Adenocarcinoma. Cancer Res. 2021 Mar 1;81(5):1216-1229. doi: 10.1158/0008-5472.CAN-20-0652. Epub 2021 Jan 5. PMID:33402390; PMCID: PMC8026506.

  24. Shi X, Zheng Y, Jiang L, Zhou B, Yang W, Li L, Ding L, Huang M, Gery S, Lin DC, Koeffler HP. (2020) EWS-FLI1 regulates and cooperates with core regulatory circuitry in Ewing sarcoma. Nucleic Acids Res. 2020 Nov 18;48(20):11434-11451. doi: 10.1093/nar/gkaa901. PMID: 33080033; PMCID: PMC7672457.

  25. Ho AS, Luu M, Barrios L, Balzer BL, Bose S, Fan X, Walgama E, Mallen-St Clair J, Alam U, Shafqat I, Lin DC, Chen Y, Van Eyk JE, Maghami EG, Braunstein GD, Sacks WL, Zumsteg ZS. (2020) Prognostic Impact of Histologic Grade for Papillary Thyroid Carcinoma. Ann Surg Oncol. 2021 Mar;28(3):1731-1739. doi:10.1245/s10434-020-09023-2. Epub 2020 Aug 17. PMID: 32808161.

  26. Jiang YY, Jiang Y, Li CQ, Zhang Y, Dakle P, Kaur H, Deng JW, Lin RY, Han L, Xie JJ, Yan Y, Doan N, Zheng Y, Mayakonda A, Hazawa M, Xu L, Li Y, Aswad L, Jeitany M, Kanojia D, Guan XY, Said JW, Yang W, Fullwood MJ, Lin DC, Koeffler HP. (2020) TP63, SOX2, and KLF5 Establish a Core Regulatory Circuitry That Controls Epigenetic and Transcription Patterns in Esophageal Squamous Cell Carcinoma Cell Lines. Gastroenterology. 2020 Oct;159(4):1311-1327.e19. doi:10.1053/j.gastro.2020.06.050. Epub 2020 Jun 30. PMID: 32619460.

  27. Wang QY, Peng L, Chen Y, Liao LD, Chen JX, Li M, Li YY, Qian FC, Zhang YX, Wang F, Li CQ, Lin DC, Xu LY, Li EM. (2020) Characterization of super-enhancer-associated functional lncRNAs acting as ceRNAs in ESCC. Mol Oncol. 2020 Sep;14(9):2203-2230. doi: 10.1002/1878-0261.12726. Epub 2020 Jun 20. PMID:32460441; PMCID: PMC7463357.

  28. Pan J, Silva TC, Gull N, Yang Q, Plummer JT, Chen S, Daigo K, Hamakubo T, Gery S, Ding LW, Jiang YY, Hu S, Xu LY, Li EM, Ding Y, Klempner SJ, Gayther SA, Berman BP, Koeffler HP, Lin DC. (2020) Lineage-Specific Epigenomic and Genomic Activation of Oncogene HNF4A Promotes Gastrointestinal Adenocarcinomas. Cancer Res. 2020 Jul 1;80(13):2722-2736. doi: 10.1158/0008-5472.CAN-20-0390. Epub 2020 Apr 24. PMID: 32332020.

  29. Huang M, Wang Y, Yang M, Yan J, Yang H, Zhuang W, Xu Y, Koeffler HP, Lin DC, Chen X. (2020) dbInDel: a database of enhancer-associated insertion and deletion variants by analysis of H3K27ac ChIP-Seq. Bioinformatics. 2020 Mar 1;36(5):1649-1651. doi: 10.1093/bioinformatics/btz770. PMID: 31603498; PMCID:PMC7703781.

  30. Chen Y, Liao LD, Wu ZY, Yang Q, Guo JC, He JZ, Wang SH, Xu XE, Wu JY, Pan F, Lin DC, Xu LY, Li EM. (2020) Identification of key genes by integrating DNA methylation and next-generation transcriptome sequencing for esophageal squamous cell carcinoma. Aging (Albany NY). 2020 Jan 21;12(2):1332-1365. doi:10.18632/aging.102686. Epub 2020 Jan 21. PMID: 31962291; PMCID: PMC7053602.

  31. Liao JY, Yang B, Zhang YC, Wang XJ, Ye Y, Peng JW, Yang ZZ, He JH, Zhang Y, Hu K, Lin DC, Yin D. (2020) EuRBPDB: a comprehensive resource for annotation, functional and oncological investigation of eukaryotic RNA binding proteins (RBPs). Nucleic Acids Res. 2020 Jan 8;48(D1):D307-D313. doi: 10.1093/nar/gkz823. PMID: 31598693; PMCID: PMC6943034.

  32. Howard LE, Zhang J, Fishbane N, Hoedt AM, Klaassen Z, Spratt DE, Vidal AC, Lin D, Hitchins MP, You S, Freeman MR, Yamoah K, Davicioni E, Freedland SJ. (2020) Validation of a genomic classifier for prediction of metastasis and prostate cancer-specific mortality in African-American men following radical prostatectomy in an equal access healthcare setting. Prostate Cancer Prostatic Dis. 2020 Sep;23(3):419-428. doi: 10.1038/s41391-019-0197-3. Epub 2019 Dec 16. PMID: 31844180.

  33. Hazawa M, Sakai K, Kobayashi A, Yoshino H, Iga Y, Iwashima Y, Lim KS, Chih-Cheng Voon D, Jiang YY, Horike SI, Lin DC, Wong RW. (2020) Disease-specific alteration of karyopherin-a subtype establishes feed-forward oncogenic signaling in head and neck squamous cell carcinoma. Oncogene. 2020 Mar;39(10):2212-2223. doi:10.1038/s41388-019-1137-3. Epub 2019 Dec 10. PMID: 31822798; PMCID: PMC7056645.

  34. Loh XY, Sun QY, Ding LW, Mayakonda A, Venkatachalam N, Yeo MS, Silva TC, Xiao JF, Doan NB, Said JW, Ran XB, Zhou SQ, Dakle P, Shyamsunder P, Koh AP, Huang RY, Berman BP, Tan SY, Yang H, Lin DC, Koeffler HP. (2020) RNA-Binding Protein ZFP36L1 Suppresses Hypoxia and Cell-Cycle Signaling. Cancer Res. 2020 Jan 15;80(2):219-233. doi: 10.1158/0008-5472.CAN-18-2796. Epub 2019 Sep 24. PMID:31551365.

  35. Chen L, Huang M, Plummer J, Pan J, Jiang YY, Yang Q, Silva TC, Gull N, Chen S, Ding LW, An O, Yang H, Cheng Y, Said JW, Doan N, Dinjens WN, Waters KM, Tuli R, Gayther SA, Klempner SJ, Berman BP, Meltzer SJ, Lin DC, Koeffler HP. (2020) Master transcription factors form interconnected circuitry and orchestrate transcriptional networks in oesophageal adenocarcinoma. Gut. 2020 Apr;69(4):630-640. doi: 10.1136/gutjnl-2019-318325. Epub 2019 Aug 13. PMID:31409603; PMCID: PMC8108390.

  36. You R, Liu YP, Lin DC, Li Q, Yu T, Zou X, Lin M, Zhang XL, He GP, Yang Q, Zhang YN, Xie YL, Jiang R, Wu CY, Zhang C, Cui C, Wang JQ, Wang Y, Zhuang AH, Guo GF, Hua YJ, Sun R, Yun JP, Zuo ZX, Liu ZX, Zhu XF, Kang TB, Qian CN, Mai HQ, Sun Y, Zeng MS, Feng L, Zeng YX, Chen MY. (2019) Clonal Mutations Activate the NF-KB Pathway to Promote Recurrence of Nasopharyngeal Carcinoma. Cancer Res. 2019 Dec 1;79(23):5930-5943. doi: 10.1158/0008-5472.CAN-18-3845. Epub 2019 Sep 4. PMID:31484669.

  37. Lin L, Lin DC. (2019) Biological Significance of Tumor Heterogeneity in Esophageal Squamous Cell Carcinoma. Cancers (Basel). 2019 Aug 12;11(8):1156. doi: 10.3390/cancers11081156. PMID: 31409002; PMCID: PMC6721624.

  38. Sun QY, Ding LW, Johnson K, Zhou S, Tyner JW, Yang H, Doan NB, Said JW, Xiao JF, Loh XY, Ran XB, Venkatachalam N, Lao Z, Chen Y, Xu L, Fan LF, Chien W, Lin DC, Koeffler HP. (2019) SOX7 regulates MAPK/ERK-BIM mediated apoptosis in cancer cells. Oncogene. 2019 Aug;38(34):6196-6210. doi: 10.1038/s41388-019-0865-8. Epub 2019 Jul 22. PMID: 31332289.

  39. Qian FC, Li XC, Guo JC, Zhao JM, Li YY, Tang ZD, Zhou LW, Zhang J, Bai XF, Jiang Y, Pan Q, Wang QY, Li EM, Li CQ, Xu LY, Lin DC. (2019) SEanalysis: a web tool for super-enhancer associated regulatory analysis. Nucleic Acids Res. 2019 Jul 2;47(W1):W248-W255. doi: 10.1093/nar/gkz302. PMID: 31028388; PMCID: PMC6602466.

  40. Silva TC, Coetzee SG, Gull N, Yao L, Hazelett DJ, Noushmehr H, Lin DC, Berman BP. (2019) ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles. Bioinformatics. 2019 Jun 1;35(11):1974-1977. doi: 10.1093/bioinformatics/bty902. PMID: 30364927; PMCID:PMC6546131.

  41. Ding LW, Sun QY, Edwards JJ, Fernández LT, Ran XB, Zhou SQ, Scolyer RA, Wilmott JS, Thompson JF, Doan N, Said JW, Venkatachalam N, Xiao JF, Loh XY, Pein M, Xu L, Mullins DW, Yang H, Lin DC, Koeffler HP. (2019) LNK suppresses interferon signaling in melanoma. Nat Commun. 2019 May 20;10(1):2230. doi:10.1038/s41467-019-09711-y. PMID: 31110180; PMCID: PMC6527565.

  42. Lin L, Huang M, Shi X, Mayakonda A, Hu K, Jiang YY, Guo X, Chen L, Pang B, Doan N, Said JW, Xie J, Gery S, Cheng X, Lin Z, Li J, Berman BP, Yin D, Lin DC, Koeffler HP. (2019) Super-enhancer-associated MEIS1 promotes transcriptional dysregulation in Ewing sarcoma in co-operation with EWS-FLI1. Nucleic Acids Res. 2019 Feb 20;47(3):1255-1267. doi: 10.1093/nar/gky1207. PMID: 30496486; PMCID:PMC6379679.

  43. Lao ZT, Ding LW, An O, Hattori N, Sun QY, Tan KT, Mayakonda A, Chuan WG, Madan V, Lin DC, Yang H, Koeffler HP. (2019) Mutational and transcriptomic profiling of acute leukemia of ambiguous lineage reveals obscure but clinically important lineage bias. Haematologica. 2019 May;104(5):e200-e203. doi:10.3324/haematol.2018.202911. Epub 2018 Dec 4. PMID: 30514800; PMCID:PMC6518916.

  44. Peng L, Jiang B, Yuan X, Qiu Y, Peng J, Huang Y, Zhang C, Zhang Y, Lin Z, Li J, Yao W, Deng W, Zhang Y, Meng M, Pan X, Li C, Yin D, Bi X, Li G, Lin DC. (2019) Super-Enhancer-Associated Long Noncoding RNA HCCL5 Is Activated by ZEB1 and Promotes the Malignancy of Hepatocellular Carcinoma. Cancer Res. 2019 Feb 1;79(3):572-584. doi: 10.1158/0008-5472.CAN-18-0367. Epub 2018 Nov 27. PMID:30482773.

  45. Ding LW, Tan KT, Sun QY, Lao ZT, Yang H, Jiang N, Chien W, Xiao JF, Loh XY, Huang ML, Lill M, Lin DC, Yeoh AEJ, Koeffler HP. (2019) Clonality and clonal evolution analysis of paediatric ALL based on B-cell receptor/T-cell receptor rearrangement. Br J Haematol. 2019 Mar;184(5):829-833. doi: 10.1111/bjh.15179. Epub 2018 Mar 13. PMID: 29532914.

  46. Corces MR, Granja JM, Shams S, Louie BH, Seoane JA, Zhou W, Silva TC, Groeneveld C, Wong CK, Cho SW, Satpathy AT, Mumbach MR, Hoadley KA, Robertson AG, Sheffield NC, Felau I, Castro MAA, Berman BP, Staudt LM, Zenklusen JC, Laird PW, Curtis C; Cancer Genome Atlas Analysis Network, Greenleaf WJ, Chang HY. (2018) The chromatin accessibility landscape of primary human cancers. Science. 2018 Oct 26;362(6413):eaav1898. doi: 10.1126/science.aav1898. PMID: 30361341; PMCID:PMC6408149.

  47. Mayakonda A, Lin DC, Assenov Y, Plass C, Koeffler HP. (2018) Maftools: efficient and comprehensive analysis of somatic variants in cancer. Genome Res. 2018 Nov;28(11):1747-1756. doi: 10.1101/gr.239244.118. Epub 2018 Oct 19. PMID:30341162; PMCID: PMC6211645.

  48. Tan KT, Ding LW, Sun QY, Lao ZT, Chien W, Ren X, Xiao JF, Loh XY, Xu L, Lill M, Mayakonda A, Lin DC, Yang H, Koeffler HP. (2018) Profiling the B/T cell receptor repertoire of lymphocyte derived cell lines. BMC Cancer. 2018 Oct 1;18(1):940. doi: 10.1186/s12885-018-4840-5. PMID: 30285677; PMCID: PMC6167786.

  49. Jiang Y, Jiang YY, Xie JJ, Mayakonda A, Hazawa M, Chen L, Xiao JF, Li CQ, Huang ML, Ding LW, Sun QY, Xu L, Kanojia D, Jeitany M, Deng JW, Liao LD, Soukiasian HJ, Berman BP, Hao JJ, Xu LY, Li EM, Wang MR, Bi XG, Lin DC, Koeffler HP. (2018) Co-activation of super-enhancer-driven CCAT1 by TP63 and SOX2 promotes squamous cancer progression. Nat Commun. 2018 Sep 6;9(1):3619. doi:10.1038/s41467-018-06081-9. PMID: 30190462; PMCID: PMC6127298.

  50. Liu X, Cheng Y, Abraham JM, Wang Z, Wang Z, Ke X, Yan R, Shin EJ, Ngamruengphong S, Khashab MA, Zhang G, McNamara G, Ewald AJ, Lin D, Liu Z, Meltzer SJ. (2018) Modeling Wnt signaling by CRISPR-Cas9 genome editing recapitulates neoplasia in human Barrett epithelial organoids. Cancer Lett. 2018 Nov 1;436:109-118. doi: 10.1016/j.canlet.2018.08.017. Epub 2018 Aug 23. PMID:30144514; PMCID: PMC6152930.

  51. Xiao JF, Sun QY, Ding LW, Chien W, Liu XY, Mayakonda A, Jiang YY, Loh XY, Ran XB, Doan NB, Castor B, Chia D, Said JW, Tan KT, Yang H, Fu XY, Lin DC, Koeffler HP. (2018) The c-MYC-BMI1 axis is essential for SETDB1-mediated breast tumourigenesis. J Pathol. 2018 Sep;246(1):89-102. doi: 10.1002/path.5126. Epub 2018 Aug 3. PMID:29926931.

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