TY - JOUR
T1 - Prevalent homozygous deletions of type i interferon and defensin genes in human cancers associate with immunotherapy resistance
AU - Ye, Zhenqing
AU - Dong, Haidong
AU - Li, Ying
AU - Ma, Tao
AU - Huang, Haojie
AU - Leong, Hon Sing
AU - Eckel-Passow, Jeanette
AU - Kocher, Jean Pierre A.
AU - Liang, Han
AU - Wang, Liguo
N1 - Publisher Copyright:
© 2018 American Association for Cancer Research.
PY - 2018/7/15
Y1 - 2018/7/15
N2 - 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, a-, and b-defensin genes were homozygously deleted in 19 cancer types with high frequencies (7%–31%, median ¼ 12%; interquartile range ¼ 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 ¼ 0.0029, OR ¼ 11.8) and defensin (P ¼ 0.06, OR ¼ 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.
AB - 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, a-, and b-defensin genes were homozygously deleted in 19 cancer types with high frequencies (7%–31%, median ¼ 12%; interquartile range ¼ 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 ¼ 0.0029, OR ¼ 11.8) and defensin (P ¼ 0.06, OR ¼ 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.
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U2 - 10.1158/1078-0432.CCR-17-3008
DO - 10.1158/1078-0432.CCR-17-3008
M3 - Article
C2 - 29618619
AN - SCOPUS:85050155613
SN - 1078-0432
VL - 24
SP - 3299
EP - 3308
JO - Clinical Cancer Research
JF - Clinical Cancer Research
IS - 14
ER -