PF583 COMPREHENSIVE ANALYSIS OF THE COMPLEXITY AND HETEROGENEITY OF THE LNCRNAS TRANSCRIPTOME IN MULTIPLE MYELOMA
Authors: Carrasco‐Leon A. , Ezponda T. , Meydan C. , Valcárcel L.V. , Ordoñez R. , Kulis M. , Garate L. , Miranda E. , Segura V. , Guruceaga E. , Vilas‐Zornoza A. , Alignani D. , Castro‐Labrador L. , Pascual M. , Amundarain A. , El‐Omri H. , Taha R. Y , Calasanz M.J. , Planes F.J. , Mason C. , Miguel J. San , Subero J.I. Martin , Melnick A. , Prosper F. , Agirre X. 
Published: June 2019

Background:

Deregulation of long non‐coding RNAs (lncRNAs) is emerging as a common hallmark of different human tumors and their investigation may uncover novel biomarkers and oncogenic mechanisms. In multiple myeloma (MM), the alteration of some lncRNAs has been detected, suggesting that they can play an important role, but the complete transcriptome of the lncRNAs in this disease is not yet known.

Aims:

In the present work, our objective was to characterize the complete transcriptome of the lncRNAs in the MM, to determine their functional involvement in the myelomagenesis and in the clinical outcome of the patients.

Methods:

We performed the paired‐end strand‐specific RNA sequencing (ssRNA‐seq) in 38 purified plasma cell (PC) samples from MM patients and in 3 bone marrow PCs (BMPCs) of healthy donors. We also performed the same ssRNA‐seq in distinct B cell subpopulations (Naïve, Cetroblast, Centrocyte, Memory and Tonsilar PCs). To study the heterogeneity of lncRNAs expression, we compared each MM patient with BMPCs and studied their expression dynamism along human humoral immune response and MM patients. We also determined the epigenetic deregulation of those dynamic lncRNAs by analyzing the chromatin states of their promoter regions. The functional implication of one lncRNA, LINC‐SMILO (Specific Myeloma INtergenic LOng non‐coding RNA), was analyzed in MM cell lines by its knockdown using shRNAs, analyzing the cell phenotype using MTS (cell proliferation) and annexin V (death) assays. Finally, using the data from CoMMpass, we studied the biomarker potential of lncRNAs expressed specifically in MM through analyzing the overall survival of MM patients.

Results:

We identified 40.511 novel lncRNAs that were expressed in MM patients, showing a much more heterogeneous expression than the coding genes. After the comparative analysis between each MM patient and BMPCs, we detected 16.668 lncRNAs deregulated (11,067 were overexpressed and 5,601 downregulated) in more than 40% of patients. Analysis of the transcriptional dynamisms through the distinct B cell subpopulations showed 1.465 lncRNAs exclusive expression in MM, from which 31 showed de novo epigenomic activation. To determine the functional role of such altered lncRNAs in the biology of MM cells we focused on the study of LINC‐SMILO, epigenetically de novo activated and specifically expressed in MM cells. Knockdown of LINC‐SMILO in 3 different MM cell lines (MM.1S, MM.1R and KMS‐11) resulted in reduced proliferation and induction of apoptosis by activation of ERVs and modulation of IFN pathway, indicating that this lncRNA is essential for the survival of MM cells. Finally, we showed that overexpression of the lncRNA PDLIM1P4 together with amp1q and del17p genetic alterations, divides MM patients in three prognostic risk groups.

Summary/Conclusion:

In summary, our study shows the complexity of the lncRNA transcriptome in MM, and suggests that some of these lncRNAs may be a potential prognostic markers or key therapeutic targets for the treatment of this disease.