Examining the Role of a Novel Long Noncoding RNA, linc02454, in Resistance of Glioblastoma to Temozolomide

Project Summary/Abstract
Glioblastoma (GBM), the most common primary brain tumor, has a 15 month patient survival due to inevitable
recurrence of tumor despite standard treatment – temozolomide chemotherapy (TMZ), radiation, and surgery.
It is critical to characterize and target genes modulating GBM chemoresistance. Long noncoding RNAs
(lncRNAs) are a novel class of genetic transcripts comprising 80% of the genome. These lncRNAs induce
profound alterations in transcriptional regulation and phenotype, including chemotherapy response. Because
few GBM lncRNAs have been studied, characterizing new candidates among this abundant and novel class of
genes may significantly improve chemotherapeutic efficacy. To assess lncRNAs involved in GBM
chemotherapy resistance, we identified linc02454 among the most highly upregulated lncRNAs following TMZ
treatment. Knockdown (KD) of linc02454 decreased in vitro GBM cell viability in response to TMZ, while RNA-
seq identified CXC-chemokine receptor type 4 (CXCR4) among the most heavily downregulated genes after
lncRNA KD. CXCR4 is a well-characterized modulator of GBM chemoresistance, currently targeted in multiple
clinical trials. We hypothesize TMZ regulates linc02454 expression and that linc02454 exerts GBM resistance
to TMZ through modulation of CXCR4. In this project, we will evaluate the role of linc02454 on GBM response
to TMZ treatment. In aim 1, we identify if linc02454 relies upon increased CXCR4 expression, assessing
functional interaction via epistasis and CXCR4 rescue, as well as evaluating whether linc02454 directly
regulates CXCR4 via Fluorescence in Situ Hybridization. In aim 2, we will assess how TMZ increases
linc02454. SA2.1 will perform integrative analysis of lncRNA methylation at DNA loci (including linc02454) and
methylation-dependent lncRNA transcription at initial resection/recurrence. SA2.2 will assess chromatin state
of linc02454 before and after TMZ. In aim 3, we will assess if linc02454 repression, when combined with TMZ
+ radiotherapy, improves treatment response, in vitro and in vivo. These aims will examine whether lin02454
meditates GBM response to TMZ via CXCR4 and how linc02454 is regulated by TMZ exposure. We will also
test whether linc02454 is a potential therapeutic target in GBM therapy. If successful, this five-year study will
provide a more thorough understanding of lncRNA biology in the context of TMZ-induced treatment resistance.
With my mentorship group, we have developed a career development plan for tailored training in
transcriptional regulation of GBM lncRNAs. The project will be closely supervised through regular one-on-one
interaction with primary mentor Dr. Yali Dou, an international expert in chromatin and transcriptional regulation
in cancer. NIH-funded co-mentors, Dr. Behnam Badie, a neurosurgeon focusing on GBM biology, and Dr.
William Mack also have extensive experience mentoring neurosurgeon-scientists to independence, and have
functioned as close mentors. Importantly, by completing this work, I will develop expertise in transcriptional
regulation, a critical component in the function of lncRNAs and treatment-induced changes in GBM.

Grant Number: 5K08NS114172-05
NIH Institute/Center: NIH
Principal Investigator: Frank Attenello