title: Lung cancer transcriptomes refined with laser capture microdissection.
abstract: We evaluated the importance of tumor cell selection for generating gene signatures in non-small cell lung cancer. Tumor and nontumor tissue from macroscopically dissected (Macro) surgical specimens (31 pairs from 32 subjects) was homogenized, extracted, amplified, and hybridized to microarrays. Adjacent scout sections were histologically mapped; sets of approximately 1000 tumor cells and nontumor cells (alveolar or bronchial) were procured by laser capture microdissection (LCM). Within histological strata, LCM and Macro specimens exhibited approximately 67% to 80% nonoverlap in differentially expressed (DE) genes. In a representative subset, LCM uniquely identified 300 DE genes in tumor versus nontumor specimens, largely attributable to cell selection; 382 DE genes were common to Macro, Macro with preamplification, and LCM platforms. RT-qPCR validation in a 33-gene subset was confirmatory (ρ = 0.789 to 0.964, P = 0.0013 to 0.0028). Pathway analysis of LCM data suggested alterations in known cancer pathways (cell growth, death, movement, cycle, and signaling components), among others (eg, immune, inflammatory). A unique nine-gene LCM signature had higher tumor-nontumor discriminatory accuracy (100%) than the corresponding Macro signature (87%). Comparison with Cancer Genome Atlas data sets (based on homogenized Macro tissue) revealed both substantial overlap and important differences from LCM specimen results. Thus, cell selection via LCM enhances expression profiling precision, and confirms both known and under-appreciated lung cancer genes and pathways.
authors.affiliation: Biostatistics Core Division, Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York.
authors.forename: Juan
authors.initials: J
authors.lastname: Lin
authors.affiliation: Division of Pulmonary Medicine, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York.
authors.forename: Gabrielle
authors.initials: G
authors.lastname: Marquardt
authors.affiliation: Division of Pulmonary Medicine, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York.
authors.forename: Nandita
authors.initials: N
authors.lastname: Mullapudi
authors.affiliation: Biostatistics Core Division, Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York.
authors.forename: Tao
authors.initials: T
authors.lastname: Wang
authors.affiliation: Division of Pulmonary Medicine, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York.
authors.forename: Weiguo
authors.initials: W
authors.lastname: Han
authors.affiliation: Division of Pulmonary Medicine, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York.
authors.forename: Miao
authors.initials: M
authors.lastname: Shi
authors.affiliation: Department of Cardiovascular and Thoracic Surgery, Albert Einstein College of Medicine, Bronx, New York.
authors.forename: Steven
authors.initials: S
authors.lastname: Keller
authors.affiliation: Department of Pathology, Albert Einstein College of Medicine, Bronx, New York.
authors.forename: Changcheng
authors.initials: C
authors.lastname: Zhu
authors.affiliation: Department of Pathology, Albert Einstein College of Medicine, Bronx, New York.
authors.forename: Joseph
authors.initials: J
authors.lastname: Locker
authors.affiliation: Division of Pulmonary Medicine, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York. Electronic address: simon.spivack@einstein.yu.edu.
authors.forename: Simon D
authors.initials: SD
authors.lastname: Spivack
mesh_terms: D000368:Aged; D000369:Aged, 80 and over; D002289:Carcinoma, Non-Small-Cell Lung / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D061346:Laser Capture Microdissection; D008175:Lung Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D008297:Male; D008875:Middle Aged; D059467:Transcriptome