Long Non-Coding RNAs (lncRNAs) Function in Tumorigenesis and Cancer Therapy Response

Long non-coding RNAs (lncRNAs) have been discovered for decades, and numerous scientists have contributed significant efforts to studying this type of RNA in various diseases. Gradually, lncRNA-related research started to focus on the cancer biology area. Two essential questions researchers are trying to address are: a. What are the functions of specific lncRNAs in different cancer types, or in other words, what are the mechanisms of different lncRNAs? b. How can these lncRNAs influence anti-cancer drug treatment in patients, and how can they be identified as novel critical lncRNAs based on the therapy? In this thesis, we explored the function and mechanism of three types of lncRNAs (in three chapters) based on three different anti-cancer treatments. Furthermore, we have identified novel lncRNAs as potential biomarkers for cancer patients using a high-throughput screening method in Chapters 2 and 3. In Chapter 1, we found EPIC1 (epigenetically-induced lncRNA 1) is a Myc-binding lncRNA, which has been previously demonstrated to be overexpressed in multiple cancer types. In a pathway analysis including 4962 cancer patients, we observed that lncRNA EPIC1 expression was positively correlated with the AKT-mTORC1 signaling pathway in more than 10 cancer types, including breast and ovarian cancers. In MCF-7 (breast), OVCAR4 (ovarian), and A2780cis (ovarian) cell lines, EPIC1 knockdown and overexpression, respectively, inhibited and activated phosphorylated AKT and the downstream phosphorylation levels of 4EBP1 and S6K. Moreover, EPIC1 overexpression in breast and ovarian cancer cells led to rapamycin (mTOR inhibitor) resistance in breast and ovarian cancer (Y. Wang, Zhang, Wang, Guo, & Yang, 2020). In Chapter 2, we performed a CRISPR activation screening (a high-throughput screening method) of 9744 lncRNAs in melanoma cells cocultured with human CD8+ T cells. We identified 16 lncRNAs potentially regulating tumor immune response. Further integrative analysis using tumor immunogenomics data revealed that IL10RB-DT and LINC01198 are significantly correlated with tumor immune response and survival in melanoma and breast cancer. Specifically, IL10RB-DT suppresses CD8+ T cells activation via inhibiting IFN-γ–JAK–STAT1 signaling and antigen presentation in melanoma and breast cancer cells. On the other hand, LINC01198’s up-regulation sensitizes the killing of tumor cells by CD8+ T cells. Mechanistically, LINC01198 interacts and activates NF-κB component p65 to trigger the type I and type II interferon responses in melanoma and breast cancer cells. Our study systematically characterized novel lncRNAs involved in tumor immune response (Y. Wang et al., 2022). In Chapter 3, we conducted a gain-of-function characterization of oncogenic lncRNAs by using a two-stage CRISPR-SAM activation (CRISPRa) screening. Further integration of lncRNA expression across 10,327 tumors and 815 cancer lines with functional validation pinpointed potential oncogenic lncRNAs that promote cancer cell proliferation in vivo and in vitro. In a parallel effort to screen lncRNA targets for FDA-approved CDK4/6 inhibitors (CDK4/6i), we observed a strong negative correlation between lncRNAs’ regulation of cell proliferation and CDK4/6i response. We have revealed that tumor overexpressing three novel oncogenic lncRNAs are sensitive to CDK4/6i treatment. Mechanistically, these lncRNAs drive tumors to a fast proliferative but less stemness phenotype, potentially through ERα-MYC axis, leading to aggressive tumor growth and making them sensitive to CDK4/6i therapies. Our study provides a novel understanding of the molecular events that contribute to cancer proliferation and CDK4/6i response, which helps to develop effective therapies and biomarkers for cancer patients.