Identification of Long Non-Coding RNAs Regulated By the TAL1 Complex in T-Cell Acute Lymphoblastic Leukemia

T-cell acute lymphoblastic leukemia (T-ALL) is a malignant disorder of thymic T-cell precursors and one of the most prevalent oncogenes in T-ALL is the transcription factor TAL1/SCL. We previously reported that in T-ALL cells, TAL1 and several hematopoietic transcription factors (GATA3, RUNX1 and MYB) coordinately regulate expressions of downstream target genes. These four factors also co-occupy their own regulatory elements and positively regulate each other, thus forming an interconnected auto-regulatory loop and at the same time also coordinately regulate the expression of downstream target genes in T-ALL cells. We have recently identified several protein-coding genes and microRNAs such as GIMAPs, TRIB2 and miR-223 which are directly activated by the TAL1 complex and contribute to T-ALL pathogenesis.

However, the long non-coding RNAs (lncRNAs) regulated by these factors are entirely unknown. Here, we established a novel bioinformatics pipeline and analyzed RNA-seq datasets with deep coverage to identify lncRNAs in TAL1-positive and TAL1-negative T-ALL cell lines. We were able to identify over 2000 putative lncRNAs including lnc-FAM160A1-6and lnc-DUSP6-2 which have been previously reported to be expressed in T-ALL cells. We also analyzed lncRNAs that are regulated by TAL1 in T-ALL cells after knockdown of each member of the TAL1 complex in T-ALL cells. Our analysis identified approximately 60 lncRNA loci that are directly activated by TAL1, including previously-unannotated lncRNAs. Many of those lncRNAs were coordinately regulated by GATA3, RUNX1 and MYB. Interestingly, some of them were not expressed in normal human thymocytes, suggesting that those transcripts are aberrantly activated by TAL1 in T-ALL cells. We further validated our pipeline by carrying out functional studies on identified lncRNAs. Our results indicate that one of the lncRNAs is required for the survival of T-ALL cells and carries out its function by mediating the expression of its neighboring protein-coding gene.

Taken together, our study is the first of its kind to provide a list of lncRNAs that are deregulated in TAL1-positive T-ALL cells. Our functional studies also suggest that some of these aberrantly activated lncRNAs might be involved in leukemogenesis in T-ALL.