BCALM (AC099524.1) is a human B lymphocyte-specific lncRNA that modulates B cell receptor-mediated calcium signaling

• Published in: The Journal of immunology (1950) 2020-06, Vol.205 (3), p.595-607
• Main Authors: Pyfrom, Sarah C., Quinn, Chaz C., Dorando, Hannah K., Luo, Hong, Payton, Jacqueline E.
• Format: Article
• Language: English
• ISSN: 0022-1767; 1550-6606
• DOI: 10.4049/jimmunol.2000088

Of the thousands of long non-coding RNAs (lncRNA) identified in lymphocytes, very few have defined functions. Here we report the discovery and functional elucidation of a human B-cell specific lncRNA with high levels of expression in three types of B-cell cancer and normal B cells. The AC099524.1 gene is upstream of the gene encoding the B-cell specific phospholipase C gamma 2 ( PLCG2 ), a B-cell specific enzyme that stimulates intracellular Ca 2+ signaling in response to B cell receptor (BCR) activation. AC099524.1 (BCALM) transcripts are localized in the cytoplasm and, as expected, CRISPR/Cas9 knockout (KO) of AC099524.1 did not affect PLCG2 mRNA or protein expression. LncRNA interactome, RNA immunoprecipitation (RIP), and co-IP studies identified BCALM-interacting proteins in B cells, including phospholipase D 1 (PLD1), and kinase adaptor proteins AKAP9 (AKAP450) and AKAP13 (AKAP-Lbc). These two AKAP proteins form signaling complexes containing protein kinases A and C (PKA & PKC), which phosphorylate and activate PLD1 to produce phosphatidic acid (PA). BCR stimulation of BCALM-deficient B cells resulted in decreased PLD1 phosphorylation and increased intracellular Ca + flux relative to wild-type cells. These results suggest that BCALM promotes negative feedback that down-modulates BCR-mediated Ca + signaling by promoting phosphorylation of PLD1 by AKAP-associated kinases, enhancing production of PA. PA activates SHP-1, which negatively regulates BCR signaling. We propose the name BCALM for B - C ell A ssociated L ncRNA M odulator of BCR-mediated Ca + signaling. Our findings suggest a new paradigm for lncRNA-mediated modulation of lymphocyte activation and signaling, with implications for B-cell immune response and BCR-dependent cancers.