Expression profiling of primary non-small cell lung cancer for target identification

Abstract

Using a panel of cDNA microarrays comprising 47 650 transcript elements, we have carried out a dual-channel analysis of gene expression in 39 resected primary human non-small cell lung tumours versus normal lung tissue. Whilst *11 000 elements were scored as differentially expressed at least twofold in at least one sample, 96 transcripts were scored as over-represented fourfold or more in at least seven out of 39 tumours and 30 sequences 16-fold in at least two out of 39 tumours, including 24 transcripts in common. Transcripts (178) were found under-represented fourfold in at least seven out of 39 tumours, 31 of which are underrepresented 16-fold in at least two out of 39 lesions. The relative expression levels of representative genes from these lists were analysed by comparative multiplex RT -PCR and found to be broadly consistent with the microarray data. Two dramatically over-represented genes, previously designated as potential tumour suppressors in breast (maspin) and lung and breast (S100A2) cancers, were analysed more extensively and demonstrate the effectiveness of this approach in identifying potential lung cancer diagnostic or therapeutic targets. Whilst it has been reported that S100A2 is downregulated in NSCLC at an early stage, our microarray, cmRT -PCR, Western and immunohistochemistry data indicate that it is strongly expressed in the majority of tumours.

15-Hydroxyprostaglandin dehydrogenase (15-PGDH) and lung cancer

“…Whether the degrading enzyme, 15-PGDH, plays any role in contributing to the elevated levels of PGE 2 in tumors is not clear. Heighway et al (10) reported that 15-PGDH was under-represented at least 2-fold in 69% of lung tumor in a cDNA microarray study. Ding et al (11) also showed that 100% of lung tumor-tissue pairs exhibited a 2-fold decrease in 15-PGDH expression and 61% exhibited a 10-fold decrease using quantitative RT-PCR analysis.…”

S100A2 is strongly expressed in airway basal cells, preneoplastic bronchial lesions and primary non-small cell lung carcinomas

“…Comparative multiplex (cm) RT -PCR was used to compare levels of test gene transcripts between normal lung and tumour samples, as described previously (Heighway et al, 2002;Smith et al, 2003). Briefly, the test gene transcript was coamplified with a nondifferentially expressed control transcript (APPBP2 -KIAA0228) in the same reaction.…”

“…Levels of S100A2 transcript in tumour samples of this new series were compared to those in matched normal lung, by cmRT -PCR. An endogenous control transcript (ABPPBP2) previously identified as not differentially expressed between normal lung and lung tumours (Heighway et al, 2002) was used as an internal control transcript. Results of this analysis are illustrated in Figure 1.…”

“…There is little doubt (based on our earlier transcript and protein-based analyses: Heighway et al, 2002) that S100A2 is very strongly expressed in the majority of primary NSCLC lesions. In an attempt to explore whether high-level expression is either normal or associated with carcinogenesis, we have carried out a series of immunohistochemical analyses on an independent series of tumour and multiple matched normal and preneoplastic bronchial epithelial sites from a panel of NSCLC patients.…”

“…Dual-channel cDNA microarray analysis of relative expression in 39 primary non-small cell lung carcinomas (NSCLC) compared to matched normal tissue was used to construct ranked lists of the most frequently and dramatically differentially expressed genes (Heighway et al, 2002). One of the sequences so highlighted, S100A2, a gene considered to be a tumour suppressor, was found to be over-represented in tumour samples compared to matched normal lung.…”