Patients were recruited from three hospitals: Istituto Nazionale Tumori, Istituto Europeo di Oncologia (both in Milan, Italy) and Royal Brompton Hospital (London, UK). Study protocols for recruitment were approved by the ethics committees of the three hospitals. Each subject gave informed consent to the use of their biological samples for research purposes. All patients underwent lung lobectomy and the excised specimens were pathologically examined and stored frozen. In addition, from each patient, a small section of normal lung parenchyma distant from the macroscopic lung cancer tissue was removed at surgery and stored frozen. All the tumors were clinically staged, with a prevalence of stage I patients (54%); 19% of patients were non-smokers (Tables –). Within 5–10 min after removal, the tissue was put in plastic tubes and then frozen at −80 C.
Characteristics of 100 lung cancer patients assayed for HPV DNA in normal lung tissue and in the cancer tissue
Results of HPV DNA testing on lung cancer and adjacent normal lung tissue specimens and characteristics of smoking habit in 100 lung cancer patients, by tumor histology
Genomic DNA was extracted from both tumoral and adjacent non-tumoral lung tissue using the DNeasy Blood & Tissue Kit (Qiagen, Valencia, CA, USA); it was quantified using Picogreen dsDNA Quantitation Kit (Invitrogen, Carlsbad, CA, USA).
For the detection of HPV infection, we used the Clinical Array Technology (CLART) HPV 2 kit (Genomica, Madrid, Spain), which combines highly specific and highly sensitive PCR with the technology of low-density arrays. The method is based on the PCR amplification of a 450-bp fragment within the highly conserved L1 region of the viral genome followed by hybridization with specific probes for each HPV type. This method allows detection of minimal quantities of viral DNA of up to 35 of the most clinically relevant HPV types, including 20 types considered high risk (16, 18, 26, 31, 33, 35, 39, 45, 51, 52, 53, 56, 58, 59, 66, 68, 70, 73, 82 and 85) and 15 types classified as low risk (6, 11, 40, 42, 43, 44, 54, 61, 62, 71, 72, 81, 83, 84 and 89) for cervical cancer.
The whole procedure was performed in two physically separated areas: the pre-PCR area, where samples were prepared and DNA was extracted, and the post-PCR area, where products were amplified and then visualized, and strict procedures were developed to avoid specimen contamination. For each HPV test, a pair of primers permitting the amplification of a fragment of the human CFTR gene was used as a genomic DNA control; this was essential for confirming a negative result, since it indicated the presence of DNA from the patient even if HPV was not found. Also, a pair of primers for the amplification of a modified plasmid was used as a PCR control; this was essential to distinguish between an inhibited amplification reaction and a sample that contained no DNA.
We have used previously analyzed cervical cytobrush specimens that were selected as either negative or positive controls. Negative controls derived from patients with negative histological and cytological findings, and resulted HPV negative; positive controls derived from patients with positive histological and cytological findings and found positive for either HPV-6 or HPV-16 genotype (Figure ).
Figure 1 Array analysis of the presence of HPV DNA in negative (A) and HPV-16 positive (B) controls derived from cervical cytobrush specimens. For each sample, a pair of primers amplify a fragment of human gene CFTR that is detected in the array as a positive (more ...)