Purpose. To determine the feasibility of RNA collection in a multi-institutio nal cooperative group setting to be utilized for micro-array gene expression an alysis, and to describe the methodology. Methods. RTOG C0128, a phase I-II, pro tocol was designed to look at the safety and efficacy of external beam radiation therapy to 45 Gy with concomitant 5-FU and cisplatin chemotherapy, brachythera py to deliver 85 Gy to point A, and Celecoxib at 400 mg twice daily for 1 year. Patients had the option of participating in a tissue collection portion of the p rotocol to be utilized for micro-array gene expression analysis before treatmen t and at the time of the first implant. RNA quality was determined by two parame ters: the absorbance ratio at 260 nm/280 nm, and by the ratio of the integrated peak of 28S RNA to 18S RNA after gel electrophoresis. Results. From August 2001 to March 2004, 84 patients were accrued to the trial, and tissue was obtained pr ior to initiation of therapy on 34 patients (40%). FIGO stages for the patients who provided tissue were IB (23%), II (57%), and IIIA-IVA (20%). Additional ly, biopsies were obtained at the time of the first implant from 22 of the accru ed patients making paired samples available on 26%for RNA extraction and micro -array gene expression analysis. The mean ±SEM amount of tissue obtained pretr eatment was 97±13 mg compared with 51±8 mg for tissue obtained at the time of the first implant (P = 0.009). The mean total RNA extracted from the samples pri or to treatment was 119 ±19 μg versus 35 ±6 μg at the time of the first proc edure (P = 0.001). The RNA quality was assessed via the absorbance ratio at 260 nm divided by 280 nm. The mean values pretreatment and at first implant were 1.8 7 ±0.07 versus 1.66 ±0.11, respectively (P = 0.002); however, the integrated p eak of 28S RNA to 18S RNA after gel electrophoresis was not significantly differ ent (P = 0.26). Conclusions. RNA extraction for gene expression analysis can be successfully performed in the multi-institutional cooperative group setting. Fr esh tissue samples were obtainZed on 40%of accrued patients prior to treatment. The amount of biopsy material and the quantity of RNA extracted were greater pr ior to treatment compared with the first implant. The quality of RNA was superio r prior to treatment as measured by the ratio of absorbance at 260 nm/280 nm. Th ese results indicate that gene expression analysis is feasible in the cooperativ e group setting utilizing amplification techniques for the RNA. Hopefully, this will allow for improvement in prognosis, therapeutic development, and correlatio n with acute and late toxicities in patients with cancer.
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