Using bioinformatics approaches to investigate driver genes and identify BCL7A as a prognostic gene in colorectal cancer.

Colorectal cancer (CRC) results from the uncontrolled growth of cells in the colon, rectum, or appendix. The 5-year relative survival rate for patients with CRC is 65% and is correlated with the stage at diagnosis (being 91% for stage I at diagnosis versus 12% for stage IV). This study aimed to identify CRC driver genes to assist in the design of a cancer panel to detect gene mutations during clinical early-stage screening and identify genes for use in prognostic assessments and the evaluation of appropriate treatment options. First, we utilized bioinformatics approaches to analyze 354 paired sequencing profiles from The Cancer Genome Atlas (TCGA) to identify CRC driver genes and analyzed the sequencing profiles of 38 patients with >5 years of follow-up data to search for prognostic genes. The results revealed eight driver genes and ten prognostic genes. Next, the presence of the identified gene mutations was verified using tissue and blood samples from Taiwanese CRC patients. The results showed that the set identified gene mutations provide high coverage for driver gene screening, and APC, TP53, PIK3CA, and FAT4 could be detected in blood as ctDNA test targets. We further found that BCL7A gene mutation was correlated with prognosis in CRC (log-rank p-value = 0.02), and that mutations of BCL7A could be identified in ctDNA samples. These findings may be of value in clinical early cancer detection, disease monitoring, drug development, and treatment efforts in the future.

YM500v2: a small RNA sequencing (smRNA-seq) database for human cancer miRNome research.

We previously presented YM500, which is an integrated database for miRNA quantification, isomiR identification, arm switching discovery and novel miRNA prediction from 468 human smRNA-seq datasets. Here in this updated YM500v2 database (http://ngs.ym.edu.tw/ym500/), we focus on the cancer miRNome to make the database more disease-orientated. New miRNA-related algorithms developed after YM500 were included in YM500v2, and, more significantly, more than 8000 cancer-related smRNA-seq datasets (including those of primary tumors, paired normal tissues, PBMC, recurrent tumors, and metastatic tumors) were incorporated into YM500v2. Novel miRNAs (miRNAs not included in the miRBase R21) were not only predicted by three independent algorithms but also cleaned by a new in silico filtration strategy and validated by wetlab data such as Cross-Linked ImmunoPrecipitation sequencing (CLIP-seq) to reduce the false-positive rate. A new function 'Meta-analysis' is additionally provided for allowing users to identify real-time differentially expressed miRNAs and arm-switching events according to customer-defined sample groups and dozens of clinical criteria tidying up by proficient clinicians. Cancer miRNAs identified hold the potential for both basic research and biotech applications.

Preoperative chemoradiotherapy with oxaliplatin and tegafur-uracil in locally advanced rectal cancer: pathologic complete response rate and preliminary results of overall and disease-free survival in a single institute in Taiwan.

BACKGROUND: We conducted a Phase II study of biweekly oxaliplatin plus oral tegafur-uracil in the preoperative chemoradiotherapy (CRT) for locally advanced resectable mid-to-lower rectal cancer in our hospital, to evaluate the feasibility of this drug combination in tumor pathologic response, acute toxicity, local control, disease-free survival (DFS), overall survival (OS), and time to distant metastasis in an Asian cohort. METHODS: Twenty patients with histopathologically confirmed rectal cancer (Stage II-III) were enrolled in the study. Radiotherapy of 50 Gy was delivered in 25 fractions of 2 Gy, one fraction/day, five fractions/week, for 5 weeks. Oxaliplatin 55 mg/m(2) was administered intravenously for 60 minutes on Day 1 every 2 weeks, and tegafur-uracil 350 mg/m(2) was given orally everyday during the whole radiotherapy course, including holidays. Surgery was scheduled 6 weeks after completion of the preoperative chemoradiotherapy. The primary endpoint was to determine the pathologic complete response (pCR) rate after this neoadjuvant chemoradiotherapy. The secondary endpoint was to determine the treatment-related toxicity profile, local control, DFS, OS, and time to metastasis. RESULTS: All patients underwent a complete course of preoperative chemoradiotherapy. There was no local recurrence during the study period. The complete resection rate was 20/20 (100%) and the close resection margin rate was 3/20 (15%). The pCR rate was 8/20 (40%). During chemoradiotherapy, the most frequent toxicity was diarrhea 9/20 (45% of patients, grade 2 in 3/20, 15%). There were no grade 3 or higher hematologic or non-hematologic events or treatment-related deaths. The 3-year OS and DFS rates were 94.1% and 78.6%, respectively. CONCLUSION: Preoperative chemoradiotherapy with oxaliplatin and tegafur-uracil was well-tolerated and achieved an excellent pCR in our patients with locally advanced mid-to-lower rectal cancer.