Format

Send to

Choose Destination
Sci Rep. 2019 Apr 15;9(1):6032. doi: 10.1038/s41598-019-42184-z.

Unveiling novel targets of paclitaxel resistance by single molecule long-read RNA sequencing in breast cancer.

Lian B1,2, Hu X3,4, Shao ZM5,6.

Author information

1
Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, 200032, China.
2
Department of Oncology, Shanghai Medical College, Fudan University, 138 Yixueyuan Rd, Shanghai, 200032, China.
3
Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, 200032, China. xinhu@fudan.edu.cn.
4
Department of Oncology, Shanghai Medical College, Fudan University, 138 Yixueyuan Rd, Shanghai, 200032, China. xinhu@fudan.edu.cn.
5
Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, 200032, China. zhi_ming_shao@163.com.
6
Department of Oncology, Shanghai Medical College, Fudan University, 138 Yixueyuan Rd, Shanghai, 200032, China. zhi_ming_shao@163.com.

Abstract

RNA sequencing has become one of the most common technology to study transcriptomes in cancer, whereas its length limits its application on alternative splicing (AS) events and novel isoforms. Firstly, we applied single molecule long-read RNA sequencing (Iso-seq) and de novo assembly with short-read RNA sequencing (RNA-seq) in both wild type (231-WT) and paclitaxel resistant type (231-PTX) of human breast cancer cell MDA-MBA-231. The two sequencing technology provide both the accurate transcript sequences and the deep transcript coverage. Then we combined shor-read and long-read RNA-seq to analyze alternative events and novel isoforms. Last but not the least, we selected BAK1 as our candidate target to verify our analysis. Our results implied that improved characterization of cancer genomic function may require the application of the single molecule long-read RNA sequencing to get the deeper and more precise view to transcriptional level. Our results imply that improved characterization of cancer genomic function may require the application of the single molecule long-read RNA sequencing to get the deeper and more precise view to transcriptional level.

Supplemental Content

Full text links

Icon for Nature Publishing Group Icon for PubMed Central
Loading ...
Support Center