Whole-exome sequencing and immune profiling of early-stage lung adenocarcinoma with fully annotated clinical follow-up.
Lung adenocarcinomas (LUADs) lead to the majority of deaths attributable to lung cancer. We performed whole-exome sequencing (WES) and immune profiling analyses of a unique set of clinically annotated early-stage LUADs to better understand the pathogenesis of this disease and identify clinically relevant molecular markers.



We performed WES of 108 paired stage I-III LUADs and normal lung tissues using the Illumina HiSeq 2000 platform. Ten immune markers (PD-L1, PD-1, CD3, CD4, CD8, CD45ro, CD57, CD68, FOXP3 and Granzyme B) were profiled by imaging-based immunohistochemistry (IHC) in a subset of LUADs (n = 92). Associations among mutations, immune markers and clinicopathological variables were analyzed using ANOVA and Fisher's exact test. Cox proportional hazards regression models were used for multivariate analysis of clinical outcome.



LUADs in this cohort exhibited an average of 243 coding mutations. We identified 28 genes with significant enrichment for mutation. SETD2-mutated LUADs exhibited relatively poor recurrence- free survival (RFS) and mutations in STK11 and ATM were associated with poor RFS among KRAS-mutant tumors. EGFR, KEAP1 and PIK3CA mutations were predictive of poor response to adjuvant therapy. Immune marker analysis revealed that LUADs in smokers and with relatively high mutation burdens exhibited increased levels of immune markers. Analysis of immunophenotypes revealed that LUADs with STK11 mutations exhibited relatively low levels of infiltrating CD4+/CD8+ T-cells indicative of a muted immune response. Tumoral PD-L1 was significantly elevated in TP53 mutant LUADs whereas PIK3CA mutant LUADs exhibited markedly down-regulated PD-L1 expression. LUADs with TP53 or KEAP1 mutations displayed relatively increased CD57 and Granzyme B levels indicative of augmented natural killer (NK) cell infiltration.



Our study highlights molecular and immune phenotypes that warrant further analysis for their roles in clinical outcomes and personalized immune-based therapy of LUAD.
Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon.
H
H
Kadara
Department of Genetics, Howard Hughes Medical Institute, Maryland, USA.|Department of Biomedical Sciences, Seoul National University, Seoul, Republic of Korea.
M
M
Choi
Department of Biostatistics and Computational Biology, Indiana University Melvin and Bren Simon Cancer Center , Indianapolis , Indiana , USA.
J
J
Zhang
Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston.
E R
ER
Parra
Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston.
J
J
Rodriguez-Canales
Department of Ecology and Evolutionary Biology, Yale University, New Haven.
S G
SG
Gaffney
Department of Ecology and Evolutionary Biology, Yale University, New Haven.
Z
Z
Zhao
Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA.
C
C
Behrens
Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston.
J
J
Fujimoto
Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston.
C
C
Chow
Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea.
Y
Y
Yoo
N
N
Kalhor
C
C
Moran
Yale Comprehensive Cancer Center, Yale School of Medicine, Yale University, New Haven.
D
D
Rimm
Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston.
S
S
Swisher
Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA.
D L
DL
Gibbons
Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA.
J
J
Heymach
Yale Comprehensive Cancer Center, Yale School of Medicine, Yale University, New Haven.
E
E
Kaftan
Department of Ecology and Evolutionary Biology, Yale University, New Haven.
J P
JP
Townsend
Yale Comprehensive Cancer Center, Yale School of Medicine, Yale University, New Haven.
T J
TJ
Lynch
Yale Comprehensive Cancer Center, Yale School of Medicine, Yale University, New Haven.
J
J
Schlessinger
Department of Biostatistics and Computational Biology, Indiana University Melvin and Bren Simon Cancer Center , Indianapolis , Indiana , USA.
J
J
Lee
Department of Genetics, Howard Hughes Medical Institute, Maryland, USA.|Yale Center for Genome Analysis, Yale School of Medicine, Yale University, New Haven, USA.
R P
RP
Lifton
Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston.
I I
II
Wistuba
Yale Comprehensive Cancer Center, Yale School of Medicine, Yale University, New Haven.
R S
RS
Herbst
D000230:Adenocarcinoma / Q000235:genetics* / Q000276:immunology* / Q000401:mortality; D000077192:Adenocarcinoma of Lung; D014408:Biomarkers, Tumor / Q000032:analysis; D004252:DNA Mutational Analysis; D018572:Disease-Free Survival; D059472:Exome; D005260:Female; D005500:Follow-Up Studies; D055106:Genome-Wide Association Study; D006801:Humans; D007150:Immunohistochemistry; D053208:Kaplan-Meier Estimate; D008175:Lung Neoplasms / Q000235:genetics* / Q000276:immunology* / Q000401:mortality; D008297:Male; D009154:Mutation; D009367:Neoplasm Staging; D011379:Prognosis; D016016:Proportional Hazards Models
D014408:Biomarkers, Tumor
immune profiles; lung adenocarcinoma; whole-exome sequencing
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