Global analysis of translational regulation in cancer stem cells using ribosome profiling

Abstract

Growing evidences suggest that aberrant mRNA translation plays a role in tumorigenesis. For example, oncogenic signaling, such as Ras and Myc, induces translation of specific transcripts that are involved in cancer growth and progression. Because it is important to understand translational control of cancer cells, it has not been fully understood the molecular mechanisms of cancer stem cells (CSCs) which are origins of many types of cancers including breast cancer. CSCs can be isolated by functional marker aldehyde dehydrogenase (ALDH) from various cancer cell lines as well as clinical samples. In the present study, we examined translational control of CSCs using ALDH-positive and -negative cells from breast cancer cell line MCF-7. We first examined protein synthesis by measurement of incorporation of Alexa647-labeled alanine analogue. Rate of incorporated alanine analogue in ALDH-positive cells was higher than that in ALDH-negative cells. To investigate the translational regulation of ALDH-positive cells, we next performed the ribosome profile technique that is a powerful tool for globally monitoring translation by quantifying ribosome-protected mRNA fragment using the deep sequencing. We analyzed translation efficiency that is calculated by normalizing the ribosome-protected mRNA frequency to total transcript abundance and identified upregulation of 1218 transcripts and downregulation of 680 transcripts in ALDH-positive cells, compared to ALDH-negative cells. Similar with previous studies, oncogene Ras was up-regulated, suggesting that ribosome profiling worked well in the ALDH assay. We are now trying to screen the target protein for CSC regulation. Thus, our approach using ribosome profile would provide new insights to drug development for breast cancer.