The lncRNA KTN1-AS1 co-regulates a variety of Myc-target genes and enhances proliferation of Burkitt lymphoma cells

Abstract

Long noncoding RNAs (lncRNAs) are involved in many normal and oncogenic pathways through a diverse repertoire of transcriptional and posttranscriptional regulatory mechanisms. LncRNAs that are under tight regulation of well-known oncogenic transcription factors such as c-Myc (Myc) are likely to be functionally involved in their disease-promoting mechanisms. Myc is a major driver of many subsets of B cell lymphoma and to date remains an undruggable target. We identified three Myc-induced and four Myc-repressed lncRNAs by use of multiple in vitro models of Myc-driven Burkitt lymphoma and detailed analysis of Myc binding profiles. We show that the top Myc-induced lncRNA KTN1-AS1 is strongly upregulated in different types of B cell lymphoma compared to their normal counterparts. We used CRISPR-mediated genome editing to confirm that the direct induction of KTN1-AS1 by Myc is dependent on the presence of a Myc E-box-binding motif. Knockdown of KTN1-AS1 revealed a strong negative effect on the growth of three BL cell lines. Global gene expression analysis upon KTN1-AS1 depletion shows a strong enrichment of key genes in the cholesterol biosynthesis pathway as well as co-regulation of many Myc-target genes, including a moderate negative effect on the levels of Myc itself. Our study suggests a critical role for KTN1-AS1 in supporting BL cell growth by mediating co-regulation of a variety of Myc-target genes and co-activating key genes involved in cholesterol biosynthesis. Therefore, KTN1-AS1 may represent a putative novel therapeutic target in lymphoma.

TMEM244 Is a Long Non-Coding RNA Necessary for CTCL Cell Growth

“…Cytoplasmic, nuclear, and chromatin RNA were isolated using an adaptation of the CD4+ T-cell nuclei extraction by Danko et al [ 28 , 29 ]. RNA from the isolated fractions was reverse transcribed and used for qRT- PCR as described above.…”

Inhibition of SUMOylation enhances DNA hypomethylating drug efficacy to reduce outgrowth of hematopoietic malignancies

“…P493-6 Burkitt lymphoma cells (Obtained from Prof. Van den Berg, UMCG, Groningen [41]) with doxycycline (0.1 µg/mL) inducible MYC knockdown were cultured in RPMI medium (Gibco™) supplemented with 5% P/S and 10% FBS in a humidified incubator at 37 °C and 5% CO 2 .…”

CRISPR/Cas9 screen for genome‐wide interrogation of essential MYC‐bound E‐boxes in cancer cells

“…We designed a sgRNA (single‐guide RNA) library for a genome‐wide disruption of MYC binding sites and conducted a high‐throughput screen in four MYC‐dependent cell lines: K562 (chronic myelogenous leukemia, CML), ST486 (Burkitt lymphoma, BL), HepG2 (hepatoblastoma), and MCF7 (breast cancer). Those cell lines overexpress MYC and strongly depend on its high levels [ 28 , 29 , 30 , 31 ]. To allow identification of the relevant nearby genes regulated by the E‐boxes, in parallel, we utilized the Brunello library for genome‐wide knockout of protein‐coding genes.…”