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Dechen Lin, PhD

Assistant Professor

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Overview

Dr. Dechen Lin is an Assistant Professor at the Herman Ostrow School of Dentistry of the USC and serves as the Associate Director of Research for the USC Head and Neck Center at the Keck School of Medicine. At the USC Center for Craniofacial Molecular Biology, he leads a research program focused on cancer genomics, transcriptional regulation, and epigenomics, particularly in head and neck squamous cell carcinoma (HNSCC) and esophageal cancers.

Dr. Lin earned his B.S. in Biology from Nanjing University in 2005 and his Ph.D. in Cell Biology from the Chinese Academy of Medical Sciences in 2010. He completed postdoctoral training at the Cancer Science Institute of Singapore and Cedars-Sinai Medical Center. Prior to joining USC in 2022, he held faculty positions at Cedars-Sinai and served as an Adjunct Associate Professor at UCLA.

His research employs advanced genomic and organoid-based models to investigate the molecular mechanisms driving cancer progression and immune evasion. Notably, his recent work identified the gene KMT2C as a key regulator of tumor-infiltrating lymphocytes, enhancing the efficacy of immune checkpoint blockade therapies in HNSCC.

Dr. Lin’s contributions have been recognized with several awards, including the NIH/NCI R37 MERIT Award (2020), the Ming Hsieh Research Award (2023), and he has authored over 100 peer-reviewed publications.

Awards

  • Sigma Xi: Elected full member, 2024
  • Ming Hsieh Institute: Ming Hsieh Research Award, 2023
  • NIH/NCI: NCI R37 MERIT Award, 2020
  • Springer Nature Publishing Group (Oncogene): Readers’ Choice: The best of Oncogene 2019, 2020
  • American Association for Cancer Research (AACR): Best of AACR Award: most-cited research article in Cancer Research, 2019
  • American Society of Hematology: ASH Fellow Scholar Award, 2015
  • American Association for Cancer Research (AACR): Incorporated Scholar-in-Training Award, 2014

Publications

  • The MLL3/GRHL2 complex regulates malignant transformation and anti-tumor immunity in squamous cancer J Exp Med. 2025 Apr 07; 222(4). . View in PubMed
  • Genetically Defined Organoid Models Reveal Mechanisms Driving Squamous Cell Neoplastic Evolution and Identify Potential Therapeutic Vulnerabilities bioRxiv. 2025 Jan 22. . View in PubMed
  • Comprehensive analysis of H3K27me3 LOCKs under different DNA methylation contexts reveal epigenetic redistribution in tumorigenesis Epigenetics Chromatin. 2025 Jan 20; 18(1):6. . View in PubMed
  • Patient-derived tumor organoids to model drug response in gastric cancer Cell Rep Med. 2024 Jul 16; 5(7):101650. . View in PubMed
  • Genomic and single-cell characterization of patient-derived tumor organoid models of head and neck squamous cell carcinoma bioRxiv. 2024 Jul 02. . View in PubMed
  • 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. . View in PubMed
  • Super-enhancer trapping by the nuclear pore via intrinsically disordered regions of proteins in squamous cell carcinoma cellsCell Chem Biol. 2024 Apr 18; 31(4):792-804. e7. . View in PubMed
  • Nat Commun. 2024 Mar 20; 15(1):2484. . View in PubMed
  • Epigenomic analyses identify FOXM1 as a key regulator of anti-tumor immune response in esophageal adenocarcinoma Cell Death Dis. 2024 02 19; 15(2):152. . View in PubMed
  • Establishing mouse and human oral esophageal organoids to investigate the tumor immune response Dis Model Mech. 2024 Jan 01; 17(1). . View in PubMed
  • ARID1A Deficiency Regulates Anti-Tumor Immune Response in Esophageal Adenocarcinoma Cancers (Basel). 2023 Nov 12; 15(22). . View in PubMed
  • Moving closer towards a comprehensive view of tumor biology and microarchitecture using spatial transcriptomics Nat Commun. 2023 11 02; 14(1):7017. . View in PubMed
  • Comprehensive analyses of partially methylated domains and differentially methylated regions in esophageal cancer reveal both cell-type- and cancer-specific epigenetic regulation Genome Biol. 2023 08 24; 24(1):193. . View in PubMed
  • Comparative impact of grade on mortality across salivary cancers: A novel, unifying staging system Head Neck. 2023 08; 45(8):2028-2039. . View in PubMed
  • Treatment for ovarian clear cell carcinoma with combined inhibition of WEE1 and ATR J Ovarian Res. 2023 Apr 22; 16(1):80. . View in PubMed
  • Targeting RNA Exonuclease XRN1 Potentiates Efficacy of Cancer Immunotherapy Cancer Res. 2023 03 15; 83(6):922-938. . View in PubMed
  • Large-scale genomic analyses reveal alterations and mechanisms underlying clonal evolution and immune evasion in esophageal cancer Nat Commun. 2023 02 17; 14(1):893. . View in PubMed
  • A novel role of master regulator transcription factor in anti-tumor immunity and cancer immunotherapy Theranostics. 2023; 13(6):1823-1825. . View in PubMed
  • Single-cell genomics identifies immune response to neoadjuvant chemoradiotherapy EBioMedicine. 2022 12; 86:104389. . View in PubMed
  • Generation and multiomic profiling of a TP53/CDKN2A double-knockout gastroesophageal junction organoid model Sci Transl Med. 2022 11 30; 14(673):eabq6146. . View in PubMed
  • Exercise impacts the epigenome of cancer Prostate Cancer Prostatic Dis. 2022 09; 25(3):379-380. . View in PubMed
  • Genomic and Epigenomic Characterization of Tumor Organoid Models Cancers (Basel). 2022 Aug 24; 14(17). . View in PubMed
  • Quantitative Nodal Burden and Mortality Across Solid Cancers J Natl Cancer Inst. 2022 07 11; 114(7):1003-1011. . View in PubMed
  • Chemotherapy predictors and a time-dependent chemotherapy effect in metastatic esophageal cancer World J Gastrointest Oncol. 2022 Feb 15; 14(2):511-524. . View in PubMed
  • Comparative Proteomic Analysis of HPV(+) Oropharyngeal Squamous Cell Carcinoma Recurrence J Proteome Res. 2022 01 07; 21(1):200-208. . View in PubMed
  • Investigation of early neoplastic transformation and premalignant biology using genetically engineered organoid models Comput Struct Biotechnol J. 2022; 20:5309-5315. . View in PubMed
  • Integrated single-cell transcriptome analysis reveals heterogeneity of esophageal squamous cell carcinoma microenvironment Nat Commun. 2021 12 17; 12(1):7335. . View in PubMed
  • Predicting master transcription factors from pan-cancer expression data Sci Adv. 2021 Nov 26; 7(48):eabf6123. . View in PubMed
  • Predictive Impact of Metastatic Lymph Node Burden on Distant Metastasis Across Papillary Thyroid Cancer Variants Thyroid. 2021 10; 31(10):1549-1557. . View in PubMed
  • A closer look at esophageal cancer through different lenses EBioMedicine. 2021 09; 71:103545. . View in PubMed
  • Interplay and cooperation between SREBF1 and master transcription factors regulate lipid metabolism and tumor-promoting pathways in squamous cancer Nat Commun. 2021 07 16; 12(1):4362. . View in PubMed
  • Publisher Correction: A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb target genes Nat Commun. 2021 Jun 28; 12(1):4106. . View in PubMed
  • Nodal staging convergence for HPV- and HPV+ oropharyngeal carcinoma Cancer. 2021 05 15; 127(10):1590-1597. . View in PubMed
  • A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb target genes Nat Commun. 2021 04 30; 12(1):2485. . View in PubMed
  • Prognostic Impact of Histologic Grade for Papillary Thyroid Carcinoma Ann Surg Oncol. 2021 Mar; 28(3):1731-1739. . View in PubMed
  • A Transcriptional Regulatory Loop of Master Regulator Transcription Factors, PPARG, and Fatty Acid Synthesis Promotes Esophageal Adenocarcinoma Cancer Res. 2021 03 01; 81(5):1216-1229. . View in PubMed
  • Super-enhancer-mediated core regulatory circuitry in human cancer Comput Struct Biotechnol J. 2021; 19:2790-2795. . View in PubMed
  • Complete response to neoadjuvant pembrolizumab and capecitabine in microsatellite stable, Epstein-Barr virus-positive, locally advanced gastric adenocarcinoma: case report AME Case Rep. 2021; 5:30. . View in PubMed
  • EWS-FLI1 regulates and cooperates with core regulatory circuitry in Ewing sarcoma Nucleic Acids Res. 2020 11 18; 48(20):11434-11451. . View in PubMed
  • TP63, SOX2, and KLF5 Establish a Core Regulatory Circuitry That Controls Epigenetic and Transcription Patterns in Esophageal Squamous Cell Carcinoma Cell LinesGastroenterology. 2020 10; 159(4):1311-1327. e19. . View in PubMed
  • Characterization of super-enhancer-associated functional lncRNAs acting as ceRNAs in ESCC Mol Oncol. 2020 09; 14(9):2203-2230. . View in PubMed
  • Lineage-Specific Epigenomic and Genomic Activation of Oncogene HNF4A Promotes Gastrointestinal Adenocarcinomas Cancer Res. 2020 07 01; 80(13):2722-2736. . View in PubMed
  • Enhancer-Driven lncRNA BDNF-AS Induces Endocrine Resistance and Malignant Progression of Breast Cancer through the RNH1/TRIM21/mTOR Cascade Cell Rep. 2020 06 09; 31(10):107753. . View in PubMed
  • Master transcription factors form interconnected circuitry and orchestrate transcriptional networks in oesophageal adenocarcinoma Gut. 2020 04; 69(4):630-640. . View in PubMed
  • dbInDel: a database of enhancer-associated insertion and deletion variants by analysis of H3K27ac ChIP-Seq Bioinformatics. 2020 03 01; 36(5):1649-1651. . View in PubMed
  • Disease-specific alteration of karyopherin-a subtype establishes feed-forward oncogenic signaling in head and neck squamous cell carcinoma Oncogene. 2020 03; 39(10):2212-2223. . View in PubMed
  • Identification of key genes by integrating DNA methylation and next-generation transcriptome sequencing for esophageal squamous cell carcinoma Aging (Albany NY). 2020 01 21; 12(2):1332-1365. . View in PubMed
  • RNA-Binding Protein ZFP36L1 Suppresses Hypoxia and Cell-Cycle Signaling Cancer Res. 2020 01 15; 80(2):219-233. . View in PubMed
  • EuRBPDB: a comprehensive resource for annotation, functional and oncological investigation of eukaryotic RNA binding proteins (RBPs) Nucleic Acids Res. 2020 01 08; 48(D1):D307-D313. . View in PubMed
  • Cancer Res. 2019 Dec 01; 79(23):5930-5943. . View in PubMed
  • Biological Significance of Tumor Heterogeneity in Esophageal Squamous Cell Carcinoma Cancers (Basel). 2019 Aug 12; 11(8). . View in PubMed
  • SOX7 regulates MAPK/ERK-BIM mediated apoptosis in cancer cells Oncogene. 2019 08; 38(34):6196-6210. . View in PubMed
  • SEanalysis: a web tool for super-enhancer associated regulatory analysis Nucleic Acids Res. 2019 07 02; 47(W1):W248-W255. . View in PubMed
  • ELMER v2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles. Bioinformatics. 2019 06 01; 35(11):1974-1977. . View in PubMed
  • LNK suppresses interferon signaling in melanoma Nat Commun. 2019 05 20; 10(1):2230. . View in PubMed
  • Mutational and transcriptomic profiling of acute leukemia of ambiguous lineage reveals obscure but clinically important lineage bias Haematologica. 2019 05; 104(5):e200-e203. . View in PubMed
  • Clonality and clonal evolution analysis of paediatric ALL based on B-cell receptor/T-cell receptor rearrangement Br J Haematol. 2019 03; 184(5):829-833. . View in PubMed
  • Super-enhancer-associated MEIS1 promotes transcriptional dysregulation in Ewing sarcoma in co-operation with EWS-FLI1 Nucleic Acids Res. 2019 02 20; 47(3):1255-1267. . View in PubMed
  • Super-Enhancer-Associated Long Noncoding RNA HCCL5 Is Activated by ZEB1 and Promotes the Malignancy of Hepatocellular Carcinoma Cancer Res. 2019 02 01; 79(3):572-584. . View in PubMed
  • ARID1A and CEBPa cooperatively inhibit UCA1 transcription in breast cancer Oncogene. 2018 11; 37(45):5939-5951. . View in PubMed
  • Maftools: efficient and comprehensive analysis of somatic variants in cancer Genome Res. 2018 11; 28(11):1747-1756. . View in PubMed
  • Modeling Wnt signaling by CRISPR-Cas9 genome editing recapitulates neoplasia in human Barrett epithelial organoids Cancer Lett. 2018 11 01; 436:109-118. . View in PubMed
  • Identification of distinct mutational patterns and new driver genes in oesophageal squamous cell carcinomas and adenocarcinomas Gut. 2018 10; 67(10):1769-1779. . View in PubMed
  • Profiling the B/T cell receptor repertoire of lymphocyte derived cell lines BMC Cancer. 2018 Oct 01; 18(1):940. . View in PubMed
  • Co-activation of super-enhancer-driven CCAT1 by TP63 and SOX2 promotes squamous cancer progression Nat Commun. 2018 09 06; 9(1):3619. . View in PubMed
  • The c-MYC-BMI1 axis is essential for SETDB1-mediated breast tumourigenesis J Pathol. 2018 09; 246(1):89-102. . View in PubMed
  • Cell Mol Life Sci. 2018 07; 75(14):2643-2661. . View in PubMed
  • Super-Enhancer-Driven Long Non-Coding RNA LINC01503, Regulated by TP63, Is Over-Expressed and Oncogenic in Squamous Cell CarcinomaGastroenterology. 2018 06; 154(8):2137-2151. e1. . View in PubMed
  • ROCK-dependent phosphorylation of NUP62 regulates p63 nuclear transport and squamous cell carcinoma proliferation EMBO Rep. 2018 01; 19(1):73-88. . View in PubMed
  • Genomic and Epigenomic Aberrations in Esophageal Squamous Cell Carcinoma and Implications for Patients Gastroenterology. 2018 01; 154(2):374-389. . View in PubMed
  • Degalactotigonin, a Natural Compound from Solanum nigrum L, Inhibits Growth and Metastasis of Osteosarcoma through GSK3ß Inactivation-Mediated Repression of the Hedgehog/Gli1 Pathway. Clin Cancer Res. 2018 01 01; 24(1):130-144. . View in PubMed
  • Non-malignant epithelial cells preferentially proliferate from nasopharyngeal carcinoma biopsy cultured under conditionally reprogrammed conditions Sci Rep. 2017 12 12; 7(1):17359. . View in PubMed
  • Super-Enhancers Promote Transcriptional Dysregulation in Nasopharyngeal Carcinoma Cancer Res. 2017 12 01; 77(23):6614-6626. . View in PubMed
  • Circadian clock cryptochrome proteins regulate autoimmunity Proc Natl Acad Sci U S A. 2017 11 21; 114(47):12548-12553. . View in PubMed
  • Genomic lesions drive the metastasis of esophageal squamous cell carcinoma J Thorac Dis. 2017 Oct; 9(10):3523-3524. . View in PubMed
  • Valosin-Containing Protein/p97 as a Novel Therapeutic Target in Acute Lymphoblastic Leukemia Neoplasia. 2017 Oct; 19(10):750-761. . View in PubMed
  • Correction: Inhibition of IRE1a-driven pro-survival pathways is a promising therapeutic application in acute myeloid leukemia Oncotarget. 2017 Sep 08; 8(38):64651. . View in PubMed
  • Identification of a Novel SYK/c-MYC/MALAT1 Signaling Pathway and Its Potential Therapeutic Value in Ewing Sarcoma Clin Cancer Res. 2017 Aug 01; 23(15):4376-4387. . View in PubMed
  • Targeting super-enhancer-associated oncogenes in oesophageal squamous cell carcinoma Gut. 2017 08; 66(8):1358-1368. . View in PubMed
  • Genomic and Epigenomic Heterogeneity of Hepatocellular Carcinoma Cancer Res. 2017 05 01; 77(9):2255-2265. . View in PubMed
  • BCL6 promotes glioma and serves as a therapeutic target Proc Natl Acad Sci U S A. 2017 04 11; 114(15):3981-3986. . View in PubMed
  • Mutational profiling of acute lymphoblastic leukemia with testicular relapse J Hematol Oncol. 2017 03 02; 10(1):65. . View in PubMed
  • Mutational Landscape of Pediatric Acute Lymphoblastic Leukemia Cancer Res. 2017 01 15; 77(2):390-400. . View in PubMed
  • Spatial intratumoral heterogeneity and temporal clonal evolution in esophageal squamous cell carcinoma Nat Genet. 2016 12; 48(12):1500-1507. . View in PubMed
  • CRM1 Inhibition Promotes Cytotoxicity in Ewing Sarcoma Cells by Repressing EWS-FLI1-Dependent IGF-1 Signaling Cancer Res. 2016 05 01; 76(9):2687-97. . View in PubMed
  • Inhibition of IRE1a-driven pro-survival pathways is a promising therapeutic application in acute myeloid leukemia Oncotarget. 2016 Apr 05; 7(14):18736-49. . View in PubMed
  • Profiling of somatic mutations in acute myeloid leukemia with FLT3-ITD at diagnosis and relapse Blood. 2015 Nov 26; 126(22):2491-501. . View in PubMed
  • Genomic and Functional Analysis of the E3 Ligase PARK2 in Glioma Cancer Res. 2015 May 01; 75(9):1815-27. . View in PubMed
  • SETDB1 accelerates tumourigenesis by regulating the WNT signalling pathway J Pathol. 2015 Mar; 235(4):559-70. . View in PubMed
  • The genomic landscape of nasopharyngeal carcinoma Nat Genet. 2014 Aug; 46(8):866-71. . View in PubMed
  • Genomic and molecular characterization of esophageal squamous cell carcinoma Nat Genet. 2014 May; 46(5):467-73. . View in PubMed
  • Targeting genetic lesions in esophageal cancer Cell Cycle. 2014; 13(13):2013-4. . View in PubMed
  • An emerging role of PARK2 in cancer J Mol Med (Berl). 2014 Jan; 92(1):31-42. . View in PubMed
  • Consistent and differential genetic aberrations between esophageal dysplasia and squamous cell carcinoma detected by array comparative genomic hybridization Clin Cancer Res. 2013 Nov 01; 19(21):5867-78. . View in PubMed
  • Genomic and functional characterizations of phosphodiesterase subtype 4D in human cancers Proc Natl Acad Sci U S A. 2013 Apr 09; 110(15):6109-14. . View in PubMed
  • Adaptor protein Lnk binds to and inhibits normal and leukemic FLT3 Blood. 2012 Oct 18; 120(16):3310-7. . View in PubMed
  • Reciprocal activation between PLK1 and Stat3 contributes to survival and proliferation of esophageal cancer cellsGastroenterology. 2012 Mar; 142(3):521-530. e3. . View in PubMed
  • Genomic alterations with impact on survival in esophageal squamous cell carcinoma identified by array comparative genomic hybridization Genes Chromosomes Cancer. 2011 Jul; 50(7):518-26. . View in PubMed
  • Clin Cancer Res. 2011 Jul 01; 17(13):4285-95. . View in PubMed
  • Atypical protein kinase C? -SKP2-AKT pathway. Mol Cancer Res. 2011 Apr; 9(4):390-402.. View in PubMed
  • [Expression of cell cycle related proteins cyclin D1, p53 and p21WAF1/Cip1 in esophageal squamous cell carcinoma] Yi Chuan. 2010 May; 32(5):455-60. . View in PubMed
  • Suppression of anoikis by SKP2 amplification and overexpression promotes metastasis of esophageal squamous cell carcinoma Mol Cancer Res. 2009 Jan; 7(1):12-22. . View in PubMed

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