IDH mutant gliomas escape natural killer cell immune surveillance by downregulation of NKG2D ligand expression.
Diffuse gliomas are poorly immunogenic, fatal brain tumors. The basis for insufficient antitumor immunity in diffuse gliomas is unknown. Gain-of-function mutations in isocitrate dehydrogenases (IDH1 and IDH2) promote diffuse glioma formation through epigenetic reprogramming of a number of genes, including immune-related genes. Here, we identify epigenetic dysregulation of natural killer (NK) cell ligand genes as significant contributors to immune escape in glioma.



We analyzed the database of The Cancer Genome Atlas for immune gene expression patterns in IDH mutant or wild-type gliomas and identified differentially expressed immune genes. NKG2D ligand expression levels and NK cell-mediated lysis were measured in IDH mutant and wild-type patient-derived glioma stem cells and genetically engineered astrocytes. Finally, we assessed the impact of hypomethylating agent 5-aza-2'deoxycytodine (decitabine) as a potential NK cell sensitizing agent in IDH mutant cells.



IDH mutant glioma stemlike cell lines exhibited significantly lower expression of NKG2D ligands compared with IDH wild-type cells. Consistent with these findings, IDH mutant glioma cells and astrocytes are resistant to NK cell-mediated lysis. Decitabine increases NKG2D ligand expression and restores NK-mediated lysis of IDH mutant cells in an NKG2D-dependent manner.



IDH mutant glioma cells acquire resistance to NK cells through epigenetic silencing of NKG2D ligands ULBP1 and ULBP3. Decitabine-mediated hypomethylation restores ULBP1 and ULBP3 expression in IDH mutant glioma cells and may provide a clinically useful method to sensitize IDH mutant gliomas to NK cell-mediated immune surveillance in patients with IDH mutated diffuse gliomas.
University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania (X.Z., W.J.K.); Department of Neurological Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (A.P., A.R., C.D., P.S., Y.C., J.E., P.G., N.A.); Department of Neurological Surgery, University of California San Francisco, San Francisco, California (G.K., H.O.); Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania (Y.P.); Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois (J.C); Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York (T.C); Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (M.L.); Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania (A.P.).
Xiaoran
X
Zhang
University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania (X.Z., W.J.K.); Department of Neurological Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (A.P., A.R., C.D., P.S., Y.C., J.E., P.G., N.A.); Department of Neurological Surgery, University of California San Francisco, San Francisco, California (G.K., H.O.); Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania (Y.P.); Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois (J.C); Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York (T.C); Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (M.L.); Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania (A.P.).
Aparana
A
Rao
University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania (X.Z., W.J.K.); Department of Neurological Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (A.P., A.R., C.D., P.S., Y.C., J.E., P.G., N.A.); Department of Neurological Surgery, University of California San Francisco, San Francisco, California (G.K., H.O.); Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania (Y.P.); Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois (J.C); Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York (T.C); Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (M.L.); Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania (A.P.).
Paola
P
Sette
University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania (X.Z., W.J.K.); Department of Neurological Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (A.P., A.R., C.D., P.S., Y.C., J.E., P.G., N.A.); Department of Neurological Surgery, University of California San Francisco, San Francisco, California (G.K., H.O.); Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania (Y.P.); Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois (J.C); Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York (T.C); Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (M.L.); Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania (A.P.).
Christopher
C
Deibert
University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania (X.Z., W.J.K.); Department of Neurological Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (A.P., A.R., C.D., P.S., Y.C., J.E., P.G., N.A.); Department of Neurological Surgery, University of California San Francisco, San Francisco, California (G.K., H.O.); Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania (Y.P.); Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois (J.C); Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York (T.C); Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (M.L.); Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania (A.P.).
Alexander
A
Pomerantz
University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania (X.Z., W.J.K.); Department of Neurological Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (A.P., A.R., C.D., P.S., Y.C., J.E., P.G., N.A.); Department of Neurological Surgery, University of California San Francisco, San Francisco, California (G.K., H.O.); Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania (Y.P.); Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois (J.C); Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York (T.C); Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (M.L.); Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania (A.P.).
Wi Jin
WJ
Kim
University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania (X.Z., W.J.K.); Department of Neurological Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (A.P., A.R., C.D., P.S., Y.C., J.E., P.G., N.A.); Department of Neurological Surgery, University of California San Francisco, San Francisco, California (G.K., H.O.); Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania (Y.P.); Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois (J.C); Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York (T.C); Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (M.L.); Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania (A.P.).
Gary
G
Kohanbash
University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania (X.Z., W.J.K.); Department of Neurological Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (A.P., A.R., C.D., P.S., Y.C., J.E., P.G., N.A.); Department of Neurological Surgery, University of California San Francisco, San Francisco, California (G.K., H.O.); Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania (Y.P.); Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois (J.C); Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York (T.C); Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (M.L.); Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania (A.P.).
Yigang
Y
Chang
University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania (X.Z., W.J.K.); Department of Neurological Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (A.P., A.R., C.D., P.S., Y.C., J.E., P.G., N.A.); Department of Neurological Surgery, University of California San Francisco, San Francisco, California (G.K., H.O.); Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania (Y.P.); Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois (J.C); Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York (T.C); Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (M.L.); Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania (A.P.).
Yongseok
Y
Park
University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania (X.Z., W.J.K.); Department of Neurological Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (A.P., A.R., C.D., P.S., Y.C., J.E., P.G., N.A.); Department of Neurological Surgery, University of California San Francisco, San Francisco, California (G.K., H.O.); Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania (Y.P.); Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois (J.C); Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York (T.C); Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (M.L.); Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania (A.P.).
Johnathan
J
Engh
University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania (X.Z., W.J.K.); Department of Neurological Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (A.P., A.R., C.D., P.S., Y.C., J.E., P.G., N.A.); Department of Neurological Surgery, University of California San Francisco, San Francisco, California (G.K., H.O.); Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania (Y.P.); Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois (J.C); Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York (T.C); Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (M.L.); Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania (A.P.).
Jaehyuk
J
Choi
University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania (X.Z., W.J.K.); Department of Neurological Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (A.P., A.R., C.D., P.S., Y.C., J.E., P.G., N.A.); Department of Neurological Surgery, University of California San Francisco, San Francisco, California (G.K., H.O.); Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania (Y.P.); Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois (J.C); Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York (T.C); Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (M.L.); Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania (A.P.).
Timothy
T
Chan
University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania (X.Z., W.J.K.); Department of Neurological Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (A.P., A.R., C.D., P.S., Y.C., J.E., P.G., N.A.); Department of Neurological Surgery, University of California San Francisco, San Francisco, California (G.K., H.O.); Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania (Y.P.); Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois (J.C); Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York (T.C); Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (M.L.); Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania (A.P.).
Hideho
H
Okada
University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania (X.Z., W.J.K.); Department of Neurological Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (A.P., A.R., C.D., P.S., Y.C., J.E., P.G., N.A.); Department of Neurological Surgery, University of California San Francisco, San Francisco, California (G.K., H.O.); Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania (Y.P.); Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois (J.C); Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York (T.C); Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (M.L.); Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania (A.P.).
Michael
M
Lotze
University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania (X.Z., W.J.K.); Department of Neurological Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (A.P., A.R., C.D., P.S., Y.C., J.E., P.G., N.A.); Department of Neurological Surgery, University of California San Francisco, San Francisco, California (G.K., H.O.); Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania (Y.P.); Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois (J.C); Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York (T.C); Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (M.L.); Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania (A.P.).
Paola
P
Grandi
University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania (X.Z., W.J.K.); Department of Neurological Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (A.P., A.R., C.D., P.S., Y.C., J.E., P.G., N.A.); Department of Neurological Surgery, University of California San Francisco, San Francisco, California (G.K., H.O.); Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania (Y.P.); Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois (J.C); Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York (T.C); Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (M.L.); Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania (A.P.) amankulornm@upmc.edu.
Nduka
N
Amankulor
D000970:Antineoplastic Agents / Q000494:pharmacology; D001374:Azacitidine / Q000031:analogs & derivatives / Q000494:pharmacology; D001932:Brain Neoplasms / Q000235:genetics / Q000276:immunology / Q000473:pathology*; D019175:DNA Methylation; D000077209:Decitabine; D015536:Down-Regulation; D058851:GPI-Linked Proteins / Q000096:biosynthesis; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics*; D005910:Glioma / Q000235:genetics / Q000276:immunology / Q000473:pathology*; D006801:Humans; D007157:Immunologic Surveillance; D036341:Intercellular Signaling Peptides and Proteins / Q000096:biosynthesis*; D007521:Isocitrate Dehydrogenase / Q000235:genetics*; D007694:Killer Cells, Natural / Q000276:immunology; D009154:Mutation; D060888:Real-Time Polymerase Chain Reaction; D059467:Transcriptome; D019139:Tumor Escape / Q000187:drug effects / Q000235:genetics*
D000970:Antineoplastic Agents; D058851:GPI-Linked Proteins; D036341:Intercellular Signaling Peptides and Proteins; C423230:ULBP2 protein, human; D000077209:Decitabine; D007521:Isocitrate Dehydrogenase; D001374:Azacitidine
IDH mutation; NKG2D ligands; Natural Killer cells; glioma; immune escape; immunotherapy