Genome-Wide Circular RNA Expression Patterns Reflect Resistance to Immunomodulatory Drugs in Multiple Myeloma Cells.

Theresa Jakobsen,Kirsten Grønbæk,Konstantinos Dimopoulos,Jørgen Kjems,Mette Dahl,Lasse Sommer Kristensen

doi:10.3390/cancers13030365

Abstract

Simple SummaryMultiple myeloma (MM) constitutes the second most common hematological malignancy and is caused by aberrant plasma cell proliferation in the bone marrow. While recent improvements in the treatment of MM has been observed using immunomodulatory drugs (IMiDs), patients often relapse due to acquired drug resistance and no cure for the disease is currently available. In this report, we profile circular RNA (circRNA) expression patterns in cultured MM cells being sensitive to IMiDs and their resistant counterparts. CircRNAs constitute a large class of non-coding RNA molecules with emerging roles in cancer development and progression, but have not previously been explored in this context. We found that global circRNA expression patterns reflect IMiD sensitivity, but the most downregulated circRNA in IMiD resistant MM cells did not seem to be a direct driver of IMiD resistance. Future studies should investigate other circRNA candidates identified here in the context of IMiD resistance.Immunomodulatory drugs (IMiDs), such as lenalidomide and pomalidomide, may induce significant remissions in multiple myeloma (MM) patients, but relapses are frequently observed and the underlying molecular mechanisms for this are not completely understood. Circular RNAs (circRNAs) constitute an emerging class of non-coding RNAs with important roles in cancer. Here, we profiled genome-wide expression patterns of circRNAs in IMiD-sensitive MM cells and their resistant counterparts as well as in IMiD-resistant cells treated with specific epigenetic drugs alone or in combination. We found that genome-wide circRNA expression patterns reflect IMiD sensitivity and ciRS-7 (also known as CDR1as) was the most downregulated circRNA upon acquired resistance. The depletion of ciRS-7 correlated with increased methylation levels of the promoter CpG island of its host gene, LINC00632. Expression of LINC00632 and ciRS-7 was partly restored by treatment with a combination of an EZH2 inhibitor (EPZ-6438) and a DNA methyl transferase inhibitor (5-azacytidine), which also restores the IMiD sensitivity of the cells. However, knockdown of ciRS-7 did not affect IMiD sensitivity and we found that ciRS-7 also becomes epigenetically silenced after prolonged cell culture without drug-exposure. In conclusion, we found that genome-wide circRNA expression patterns reflect IMiD sensitivity in an in vitro model of acquired resistance.

Highlights

Multiple myeloma (MM) is a malignancy of terminally differentiated monoclonal plasma cells that accumulate in the bone marrow
We further investigated the most downregulated circRNA in both lenalidomide- and pomalidomide-resistant cells, circular RNA sponging miR-7 (ciRS-7), and found that it became epigenetically silenced in resistant cells and partially restored upon treatment with specific epi-drugs
We were able to show that the T3 transcript, as well as ciRS-7, could be re-activated upon treatment with epi-drugs, including a DNMT inhibitor, providing additional evidence that ciRS-7 is epigenetically regulated through methylation of this CpG island

Summary

Introduction

Multiple myeloma (MM) is a malignancy of terminally differentiated monoclonal plasma cells that accumulate in the bone marrow. It is the second most common hematological malignancy and accounts for nearly 2% of all cancer cases in the United States [1], and the incidence of MM is globally increasing due to an ageing population [2]. Introduced treatments, including proteasome inhibitors, epigenetic drugs (epi-drugs), monoclonal antibodies and immunomodulatory drugs (IMiDs), have significantly prolonged the survival expectancy of MM patients [3]. When bound by IMiDs, the complex changes its affinity for many of its targets, including the transcription factors, Ikaros (encoded by IKZF1) and Aiolos (encoded by IKZF3), which upon ubiquitination are degraded by the proteasome [7,8,9]

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