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Prevalent Homozygous Deletions of Type I Interferon and Defensin Genes in Human Cancers Associate with Immunotherapy Resistance.

  • Ye, Zhenqing1
  • Dong, Haidong2, 3
  • Li, Ying1
  • Ma, Tao1, 4
  • Huang, Haojie4
  • Leong, Hon Sing4
  • Eckel-Passow, Jeanette1
  • Kocher, Jean-Pierre A1
  • Liang, Han5
  • Wang, Liguo6, 4
  • 1 Division of Biomedical Statistics and Informatics, Department of Health Sciences, Mayo Clinic, Rochester, Minnesota.
  • 2 Department of Immunology, College of Medicine, Mayo Clinic, Rochester, Minnesota.
  • 3 Department of Urology, Mayo Clinic, Rochester, Minnesota.
  • 4 Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota.
  • 5 Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
  • 6 Division of Biomedical Statistics and Informatics, Department of Health Sciences, Mayo Clinic, Rochester, Minnesota. [email protected]
Published Article
Clinical Cancer Research
American Association for Cancer Research (AACR)
Publication Date
Jul 15, 2018
DOI: 10.1158/1078-0432.CCR-17-3008
PMID: 29618619


Purpose: Homozygous deletions play important roles in carcinogenesis. The genome-wide screening for homozygously deleted genes in many different cancer types with a large number of patient specimens representing the tumor heterogeneity has not been done.Experimental Design: We performed integrative analyses of the copy-number profiles of 10,759 patients across 31 cancer types from The Cancer Genome Atlas project.Results: We found that the type-I interferon, α-, and β-defensin genes were homozygously deleted in 19 cancer types with high frequencies (7%-31%, median = 12%; interquartile range = 10%-16.5%). Patients with homozygous deletion of interferons exhibited significantly shortened overall or disease-free survival time in a number of cancer types, whereas patients with homozygous deletion of defensins did not significantly associate with worse overall or disease-free survival. Gene expression analyses suggested that homozygous deletion of interferon and defensin genes could activate genes involved in oncogenic and cell-cycle pathways but repress other genes involved in immune response pathways, suggesting their roles in promoting tumorigenesis and helping cancer cells evade immune surveillance. Further analysis of the whole exomes of 109 patients with melanoma demonstrated that the homozygous deletion of interferon (P = 0.0029, OR = 11.8) and defensin (P = 0.06, OR = 2.79) genes are significantly associated with resistance to anti-CTLA4 immunotherapy.Conclusions: Our analysis reveals that the homozygous deletion of interferon and defensin genes is prevalent in human cancers, and importantly this feature can be used as a novel prognostic biomarker for immunotherapy resistance. Clin Cancer Res; 24(14); 3299-308. ©2018 AACR. ©2018 American Association for Cancer Research.

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