The long non-coding RNAlnc-HLX-2-7is oncogenic in group 3 medulloblastomas
Authors: Katsushima Keisuke , Lee Bongyong , Kunhiraman Haritha , Zhong Cuncong , Murath Rabi , Ying Jun , Liu Ben , Garancher Alexandra , Gonzalez-Gomez Ignacio , Monforte Hector L. , Stapleton Stacie , Vibhakar Rajeev , Bettegowda Chetan , Wechsler-Reya Robert J. , Jallo George , Raabe Eric , Eberhart Charles G. , Perera Ranjan J. 
Published: June 2020

Background

Medulloblastoma (MB) is an aggressive brain tumor that predominantly affects children. Recent high-throughput sequencing studies suggest that the non-coding RNA genome, in particular long non-coding RNAs (lncRNAs), contributes to MB sub-grouping. Here we report the identification of a novel lncRNA,lnc-HLX-2-7, as a potential molecular marker and therapeutic target in group 3 MBs.

Methods

Publicly available RNA sequencing (RNA-seq) data from 175 MB patients were interrogated to identify lncRNAs that differentiate between MB subgroups. After characterizing a subset of differentially expressed lncRNAsin vitroandin vivo, the group 3-enriched lncRNAlnc-HLX2-7was deleted by CRISPR/Cas9 in the MB cell line D425 Med. Intracranially injected tumors were further characterized by bulk and single-cell RNA-sequencing.

Results

lnc-HLX-2-7is highly upregulated in group 3 MB cell lines, patient-derived xenografts, and primary MBs compared to other MB sub-groups as assessed by qRT-PCR, RNA-seq, and RNA fluorescencein situhybridization (FISH). Depletion oflnc-HLX-2-7with antisense oligonucleotides or CRISPR/Cas9 significantly reduced cell proliferation and 3D colony formation and induced apoptosis.lnc-HLX-2-7-deletedD425 Med cells injected into mouse cerebella produced smaller tumors than those derived from parental cells. Pathway analysis revealed thatlnc-HLX2-7modulated oxidative phosphorylation, mitochondrial dysfunction, and sirtuin signaling pathways. TheMYConcogene regulatedlnc-HLX-2-7, and the small molecule BET-bromodomain (BRD4) inhibitor JQ1 reducedlnc-HLX2-7expression.

Conclusions

lnc-HLX-2-7is oncogenic in MB and represents a promising novel molecular marker and a potential therapeutic target in group 3 MBs in children.

Key points

lnc-HLX-2-7is highly upregulated in group 3 medulloblastomas compared to other sub-groups.

In vitroandin vivostudies strongly support an oncogenic role forlnc-HLX2-7in group 3 medulloblastoma.

lnc-HLX-2-7may be a novel biomarker and a potential therapeutic target in group 3 medulloblastoma.

Importance of the study

Group 3 medulloblastomas are associated with poor clinical outcomes, are difficult to subtype clinically, and their biology is poorly understood. In an effort to address these problems, we identified a group 3-specific long non-coding RNA,lnc-HLX-2-7, in anin silicoanalysis of 175 medulloblastomas and confirmed its expression in group 3 medulloblastoma cell lines, patient-derived xenografts, and FFPE samples. CRISPR/Cas9 deletion and antisense oligonucleotide knockdown oflnc-HLX-2-7significantly reduced cell growth and 3D colony formation and induced apoptosis. Deletion oflnc-HLX-2-7in cells injected into mouse cerebellums reduced tumor growth compared to parental cells, and RNA sequencing of these tumors revealedlnc-HLX-2-7-associated modulation of cell viability and cell death signaling pathways. The oncogeneMYCregulateslnc-HLX-2-7, and its expression can be controlled by the BET-bromodomain (BRD4) inhibitor JQ1.lnc-HLX-2-7is a candidate biomarker and a potential therapeutic target in group 3 medulloblastomas in children.