MicroRNA expression in epithelial and stromal compartments of stage I human non-small cell lung cancer tumors

To identify tumor compartment-specific microRNA expression in stage I non-small cell lung cancer in humans, surgically resected and formalin-fixed tumor tissues were used in laser capture microdissection to isolate tumor epithelia and stroma. Total RNA extracted from the microdissectates was analyzed for microRNA expression using the 7th generation miRCURY™ locked nucleic acid microarray platform (Exiqon®, Vedbaek, Denmark). 69 pairs of RNA from epithelia or stroma microdissected from tumors of 68 patients were obtained. Not all samples yielded microarray data of good quality (thus, excluded here). The tumor component (E=epithelia, S=stroma), individuality of patients, the histology (AC=adenocarcinoma, BAC=bronchioloalveolar carcinoma, AS=adenosquamous carcinoma, SCC=squamous cell carcinoma) and pathologic stage of tumors, patients' age (at surgey, in years), gender (M=male), race, history of smoking at time of surgery, status of recurrence of cancer during post-surgery follow-up (N=no recurrence; at least 36 months to denote non-recurrence), time in months to recurrence (or death if time to recurrence is unknown), and time in months to death or censorship are noted for the samples. Six RNA samples were assayed in duplicate (thus, 6 sets of technical duplicates: samples 1 & 7, 2 & 27, 3 & 59, 4 & 91, 5 & 127, and 6 & 143). One tumor (patient ID 62) was microdissected twice; thus, samples 127 & 143, and 128 & 144 can be considered as pairs of biological duplicates. The reference RNA, a human 'universal reference total RNA,' was obtained by Exiqon® from Ambion® (catalog# AM6000; Austin, TX), and was used in the reference channel (channel 2) of all microarrays. Microdissections and RNA extractions were performed over a period of about 18 months. All RNA samples were analyzed by microarrays within a period of about a month, with samples 1-6 analyzed first, in a batch separate from the other samples. Data from a total of 136 microarrays obtained using 130 unique RNA samples from 68 tumors of 68 patients is used here.