Research Papers:

Alterations of immune response of non-small cell lung cancer with Azacytidine

John Wrangle, Wei Wang, Alexander Koch, Hariharan Easwaran, Helai P. Mohammad, Xiaoyu Pan, Frank Vendetti, Wim VanCriekinge, Tim DeMeyer, Zhengzong Du, Princy Parsana, Kristen Rodgers, Ray-Whay Yen, Cynthia A. Zahnow, Janis M. Taube, Julie R. Brahmer, Scott S. Tykodi, Keith Easton, Richard D. Carvajal, Peter A. Jones, Peter W. Laird, Daniel J. Weisenberger, Salina Tsai, Rosalyn A. Juergens, Suzanne L. Topalian, Charles M. Rudin, Malcolm V. Brock, Drew Pardoll and Stephen B. Baylin _

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Oncotarget. 2013; 4:2067-2079. https://doi.org/10.18632/oncotarget.1542

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John Wrangle1*, Wei Wang2*, Alexander Koch3*, Hariharan Easwaran4, Helai P. Mohammad5, Xiaoyu Pan4,Frank Vendetti4, Wim VanCriekinge3, Timothy DeMeyer3, Zhengzong Du4, Princy Parsana6, Kristen Rodgers4, Ray-Whay Yen4, Cynthia A. Zahnow4, Janis M. Taube7, Julie R. Brahmer4, Scott S. Tykodi10, Keith Easton10, Richard D. Carvajal11, Peter A. Jones8, Peter W. Laird8, Daniel J. Weisenberger8, Salina Tsai9, Rosalyn A. Juergens4, Suzanne L. Topalian12, Charles M. Rudin4**, Malcolm V. Brock4**, Drew Pardoll4**, and Stephen B. Baylin4**

1 The Johns Hopkins University, School of Medicine, Oncology Center-Hematology/Medical Oncology, Baltimore, Maryland

2 The Johns Hopkins University, School of Medicine, Human Genetics Graduate Program, Baltimore, Maryland

3 Departments of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium

4 The Johns Hopkins University, School of Medicine, Oncology, Baltimore, Maryland

5 GlaxoSmithKline Pharmaceuticals, Cancer Epigenetics and Oncology, Collegeville, Pennsylvania

6 The Johns Hopkins University, Advanced Academic Bioinformatics, Baltimore, Maryland

7 The Johns Hopkins University, School of Medicine, Dermatology and Oral Pathology, Baltimore, Maryland

8 USC Epigenome Center, Keck School of Medicine, University of Southern California, Los Angeles, California

9 The Johns Hopkins University, School of Medicine, Russell H. Morgan Department of Radiology and Radiological Science, Baltimore, Maryland

10 University of Washington and Fred Hutchison Cancer Research Center, Seattle Cancer Care Alliance, Seattle, Washington

11 Memorial Sloan-Kettering Cancer Center, New York, New York

12 The Johns Hopkins University, School of Medicine, Surgery, Baltimore, Maryland

* These authors contributed equally


Stephen B. Baylin, email:

Keywords: Non-Small Cell Lung Cancer(NSCLC), Azacytidine, HDAC inhibitor

Received: October 18, 2013 Accepted: October 25, 2013 Published: October 25, 2013


Innovative therapies are needed for advanced Non-Small Cell Lung Cancer (NSCLC). We have undertaken a genomics based, hypothesis driving, approach to query an emerging potential that epigenetic therapy may sensitize to immune checkpoint therapy targeting PD-L1/PD-1 interaction. NSCLC cell lines were treated with the DNA hypomethylating agent azacytidine (AZA - Vidaza) and genes and pathways altered were mapped by genome-wide expression and DNA methylation analyses. AZA-induced pathways were analyzed in The Cancer Genome Atlas (TCGA) project by mapping the derived gene signatures in hundreds of lung adeno (LUAD) and squamous cell carcinoma (LUSC) samples. AZA up-regulates genes and pathways related to both innate and adaptive immunity and genes related to immune evasion in a several NSCLC lines. DNA hypermethylation and low expression of IRF7, an interferon transcription factor, tracks with this signature particularly in LUSC. In concert with these events, AZA up-regulates PD-L1 transcripts and protein, a key ligand-mediator of immune tolerance. Analysis of TCGA samples demonstrates that a significant proportion of primary NSCLC have low expression of AZA-induced immune genes, including PD-L1. We hypothesize that epigenetic therapy combined with blockade of immune checkpoints – in particular the PD-1/PD-L1 pathway - may augment response of NSCLC by shifting the balance between immune activation and immune inhibition, particularly in a subset of NSCLC with low expression of these pathways. Our studies define a biomarker strategy for response in a recently initiated trial to examine the potential of epigenetic therapy to sensitize patients with NSCLC to PD-1 immune checkpoint blockade.

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