Genome-wide analyses identify KLF4 as an important negative regulator in T-cell acute lymphoblastic leukemia through directly inhibiting T-cell associated genes

Abstract

BackgroundKruppel-like factor 4 (KLF4) induces tumorigenesis or suppresses tumor growth in a tissue-dependent manner. However, the roles of KLF4 in hematological malignancies and the mechanisms of action are not fully understood.MethodsInducible KLF4-overexpression Jurkat cell line combined with mouse models bearing cell-derived xenografts and primary T-cell acute lymphoblastic leukemia (T-ALL) cells from four patients were used to assess the functional role of KLF4 in T-ALL cells in vitro and in vivo. A genome-wide RNA-seq analysis was conducted to identify genes regulated by KLF4 in T-ALL cells. Chromatin immunoprecipitation (ChIP) PCR was used to determine direct binding sites of KLF4 in T-ALL cells.ResultsHere we reveal that KLF4 induced apoptosis through the BCL2/BCLXL pathway in human T-ALL cell lines and primary T-ALL specimens. In consistence, mice engrafted with KLF4-overexpressing T-ALL cells exhibited prolonged survival. Interestingly, the KLF4-induced apoptosis in T-ALL cells was compromised in xenografts but the invasion capacity of KLF4-expressing T-ALL cells to hosts was dramatically dampened. We found that KLF4 overexpression inhibited T cell-associated genes including NOTCH1, BCL11B, GATA3, and TCF7. Further mechanistic studies revealed that KLF4 directly bound to the promoters of NOTCH1, BCL2, and CXCR4 and suppressed their expression. Additionally, KLF4 induced SUMOylation and degradation of BCL11B.ConclusionsThese results suggest that KLF4 as a major transcription factor that suppresses the expression of T-cell associated genes, thus inhibiting T-ALL progression.Electronic supplementary materialThe online version of this article (doi:10.1186/s12943-014-0285-x) contains supplementary material, which is available to authorized users.

Protein Kinase C-Mediated Phosphorylation of BCL11B at Serine 2 Negatively Regulates Its Interaction with NuRD Complexes during CD4+ T-Cell Activation

“…6E). Another Ser/Thr phosphatase inhibitor, calyculin A, is also a SUMOylation inhibitor as initially shown for PML (30) and later for BCL11B (21,31). Upon activation and calyculin A treatment of Jurkat cells, we observed an electromobility shift for the major BCL11B proteins, whereas the slowest migrating BCL11B-SUMO band totally disappeared (Fig.…”

“…7D). ChIP analyses demonstrated the direct binding of KLF4 on the BCL11B promoter and on CXCR4, a bona fide KLF4 direct target gene (31) (Fig. 7E) after 5 h of activation when BCL11B and CXCR4 expression are severely repressed (Fig.…”

“…Okadaic acid and calyculin A were dissolved in dimethyl sulfoxide (DMSO) and used at a final concentration of 1 M and 50 nM, respectively. Calyculin A also inhibits arsenicinduced PML (promyelocytic leukemia protein) SUMOylation (30) and BCL11B SUMOylation (21,31). The SUMOylation inhibitors 2-D08 [2=,3=,4=-trihydroxy-flavone, 2-(2,3,4-trihydroxyphenyl)-4H-1-benzopyran-4-one], which is specific and blocks SUMO (small ubiquitinlike modifier) transfer from the Ubc9-thioester complex to the substrates (32), and anacardic acid, which blocks SUMOylation without affecting ubiquitination (33), were both obtained from Sigma and used at a final concentration of 50 M (34).…”

Deregulated KLF4 Expression in Myeloid Leukemias Alters Cell Proliferation and Differentiation through MicroRNA and Gene Targets

“…On the other hand, in Jurkat T-cell leukemia cells, we observed a greater impact on miR-150 expression with KLF2 silencing. A role for KLF4 as a tumor suppressor in B-cell non-Hodgkin lymphoma and T-ALL has been described (14,15); however, in lymphoid malignancies, KLF2 may be equally important. Recent reports indicate that a loss of function of KLF2 contributes to splenic marginal-zone lymphoma (53,54).…”

“…In normal hematopoiesis, KLF2 and KLF4 regulate myeloid differentiation and KLF4 expression induces CDKN1A (p21), which contributes to cell cycle arrest (9)(10)(11)(12)(13). In T-cell acute lymphoblastic leukemia (T-ALL) (14) and B-cell lymphomas, KLF4 has been described as a tumor suppressor regulating proliferation, apoptosis, and differentiation (15). A recent study showed that the homeobox transcription factor CDX2 represses KLF4 in myeloid leukemia cells (16).…”