Expression of hypoxia-inducible factor-1α predicts benefit from hypoxia modification in invasive bladder cancer.

BACKGROUND: The addition of carbogen and nicotinamide (CON) to radiotherapy (RT) improves overall survival in invasive bladder cancer. We explored whether expression of the hypoxia marker hypoxia-inducible factor-1α (HIF-1α) alone or in combination with other markers predicted benefit from CON. METHODS: A retrospective study was carried out using material from patients with high-grade invasive bladder carcinoma enrolled in the BCON phase III trial of RT alone or with CON (RT+CON). HIF-1α expression was studied in 137 tumours using tissue microarrays and immunohistochemistry. Data were available from other studies for carbonic anhydrase IX and glucose transporter 1 protein and gene expression and tumour necrosis. RESULTS: Patients with high HIF-1α expression had improved 5-year local relapse-free survival with RT+CON (47%) compared with RT alone (21%; hazard ratio (HR) 0.48, 95% CI 0.26-0.8, P=0.02), no benefit was seen with low HIF-1α expression (HR 0.81, 95% CI 0.43-1.50, P=0.5). Combinations of markers including necrosis also predicted benefit but did not improve on prediction using necrosis alone. CONCLUSIONS: HIF-1α may be used to predict benefit from CON in patients with bladder cancer but does not improve on use of necrosis.

Enhanced stability of microRNA expression facilitates classification of FFPE tumour samples exhibiting near total mRNA degradation.

BACKGROUND: As degradation of formalin-fixed paraffin-embedded (FFPE) samples limits the ability to profile mRNA expression, we explored factors predicting the success of mRNA expression profiling of FFPE material and investigated an approach to overcome the limitation. METHODS: Bladder (n=140, stored 3-8 years) and cervix (n=160, stored 8-23 years) carcinoma FFPE samples were hybridised to Affymetrix Exon 1.0ST arrays. Percentage detection above background (%DABG) measured technical success. Biological signal was assessed by distinguishing cervix squamous cell carcinoma (SCC) and adenocarcinoma (AC) using a gene signature. As miR-205 had been identified as a marker of SCC, precursor mir-205 was measured by Exon array and mature miR-205 by qRT-PCR. Genome-wide microRNA (miRNA) expression (Affymetrix miRNA v2.0 arrays) was compared in eight newer FFPE samples with biological signal and eight older samples without. RESULTS: RNA quality controls (QCs) (e.g., RNA integrity (RIN) number) failed to predict profiling success, but sample age correlated with %DABG in bladder (R=-0.30, P<0.01) and cervix (R=-0.69, P<0.01). Biological signal was lost in older samples and neither a signature nor precursor mir-205 separated samples by histology. miR-205 qRT-PCR discriminated SCC from AC, validated by miRNA profiling (26-fold higher in SCC; P=1.10 × 10(-5)). Genome-wide miRNA (R=0.95) and small nucleolar RNA (R=0.97) expression correlated well in the eight newer vs older FFPE samples and better than mRNA expression (R=0.72). CONCLUSION: Sample age is the best predictor of successful mRNA profiling of FFPE material, and miRNA profiling overcomes the limitation of age and copes well with older samples.

Exon-array profiling unlocks clinically and biologically relevant gene signatures from formalin-fixed paraffin-embedded tumour samples.

BACKGROUND: Degradation and chemical modification of RNA in formalin-fixed paraffin-embedded (FFPE) samples hamper their use in expression profiling studies. This study aimed to show that useful information can be obtained by Exon-array profiling archival FFPE tumour samples. METHODS: Nineteen cervical squamous cell carcinoma (SCC) and 9 adenocarcinoma (AC) FFPE samples (10-16-year-old) were profiled using Affymetrix Exon arrays. The gene signature derived was tested on a fresh-frozen non-small cell lung cancer (NSCLC) series. Exploration of biological networks involved gene set enrichment analysis (GSEA). Differential gene expression was confirmed using Quantigene, a multiplex bead-based alternative to qRT-PCR. RESULTS: In all, 1062 genes were higher in SCC vs AC, and 155 genes higher in AC. The 1217-gene signature correctly separated 58 NSCLC into SCC and AC. A gene network centered on hepatic nuclear factor and GATA6 was identified in AC, suggesting a role in glandular cell differentiation of the cervix. Quantigene analysis of the top 26 differentially expressed genes correctly partitioned cervix samples as SCC or AC. CONCLUSION: FFPE samples can be profiled using Exon arrays to derive gene expression signatures that are sufficiently robust to be applied to independent data sets, identify novel biology and design assays for independent platform validation.

Interventions for squamous cell carcinoma of the conjunctiva in HIV-infected individuals.

BACKGROUND: Squamous cell carcinoma of the conjunctiva is a rare, slow-growing tumour of the eye, normally affecting elderly men around 70 years of age. In Africa, however, the disease is different. The incidence is rising rapidly, affecting young persons (around 35 years off age), and usually affecting women. It is more aggressive, with a mean history of three months at presentation. This pattern is related to the co-existence of the HIV/AIDS pandemic, high HPV exposure, and solar radiation in the region. Various interventions exist, but despite therapy, there is a high recurrence rate (up to 43%) and poor cosmetic results in late disease. This review was conducted to evaluate the interventions for treatment of conjunctival squamous cell carcinoma in HIV-infected individuals. OBJECTIVES: To evaluate the effect of interventions for treating squamous cell carcinoma of the conjunctiva in HIV-infected individuals on local control, recurrence, death, time to recurrence, and adverse events. SEARCH STRATEGY: Using a sensitive search strategy, we attempted to identify all relevant trials, regardless of language or publication status, from the following electronic databases; Medline/PubMed, CENTRAL, AIDSearch, EMBASE, LILACS, African Healthline, Cochrane HIV/AIDS Specialised Register, and the Cochrane Cancer Network Specialised Register. We searched the clinical trial register of the US National Institutes of Health, searched the international conference proceedings of AIDS and AIDS-related cancers, and contacted individual researchers, research organisations, and pharmaceutical companies that manufacture the drugs used as interventions. Searches were done between September 2005 and June 2006. SELECTION CRITERIA: Randomised controlled trials (RCTs) involving HIV-infected individuals with ocular surface squamous neoplasia. DATA COLLECTION AND ANALYSIS: We independently screened the results of the search to select potentially relevant studies and to retrieve the full articles. We independently applied the inclusion criteria to the potentially relevant studies. No studies were identified that fulfilled the selection criteria. MAIN RESULTS: No RCTs of interventions currently used against conjunctival squamous cell carcinoma in HIV-infected individuals were identified. IMPLICATIONS FOR PRACTICE: Current clinical practice in treatment of squamous cell carcinoma of the conjunctiva rests on a weak evidence base of case series and case reports. IMPLICATIONS FOR RESEARCH: Randomised controlled trials for treatment of this disease are needed in settings where it occurs most frequently. Preventive interventions also need to be identified. HIV/AIDS research has not focused on treatment of this tumour.