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Contrasting roles of histone 3 lysine 27 demethylases in acute lymphoblastic leukaemia.

Ntziachristos P, Tsirigos A, Welstead GG, Trimarchi T, Bakogianni S, Xu L, Loizou E, Holmfeldt L, Strikoudis A, King B, Mullenders J, Becksfort J, Nedjic J, Paietta E, Tallman MS, Rowe JM, Tonon G, Satoh T, Kruidenier L, Prinjha R, Akira S, Van Vlierberghe P, Ferrando AA, Jaenisch R, Mullighan CG, Aifantis I - Nature (2014)

Bottom Line: T-cell acute lymphoblastic leukaemia (T-ALL) is a haematological malignancy with a dismal overall prognosis, including a relapse rate of up to 25%, mainly because of the lack of non-cytotoxic targeted therapy options.By contrast, we found that UTX functions as a tumour suppressor and is frequently genetically inactivated in T-ALL.These findings show that two proteins with a similar enzymatic function can have opposing roles in the context of the same disease, paving the way for treating haematopoietic malignancies with a new category of epigenetic inhibitors.

View Article: PubMed Central - PubMed

Affiliation: 1] Howard Hughes Medical Institute and Department of Pathology, NYU School of Medicine, New York, New York 10016, USA [2] NYU Cancer Institute and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York 10016, USA [3].

ABSTRACT
T-cell acute lymphoblastic leukaemia (T-ALL) is a haematological malignancy with a dismal overall prognosis, including a relapse rate of up to 25%, mainly because of the lack of non-cytotoxic targeted therapy options. Drugs that target the function of key epigenetic factors have been approved in the context of haematopoietic disorders, and mutations that affect chromatin modulators in a variety of leukaemias have recently been identified; however, 'epigenetic' drugs are not currently used for T-ALL treatment. Recently, we described that the polycomb repressive complex 2 (PRC2) has a tumour-suppressor role in T-ALL. Here we delineated the role of the histone 3 lysine 27 (H3K27) demethylases JMJD3 and UTX in T-ALL. We show that JMJD3 is essential for the initiation and maintenance of T-ALL, as it controls important oncogenic gene targets by modulating H3K27 methylation. By contrast, we found that UTX functions as a tumour suppressor and is frequently genetically inactivated in T-ALL. Moreover, we demonstrated that the small molecule inhibitor GSKJ4 (ref. 5) affects T-ALL growth, by targeting JMJD3 activity. These findings show that two proteins with a similar enzymatic function can have opposing roles in the context of the same disease, paving the way for treating haematopoietic malignancies with a new category of epigenetic inhibitors.

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JMJD3 binds to genes with important oncogenic function and is vital for T-ALL growtha, JMJD3-but not UTX-genetic inactivation impairs the expression of important oncogenic genes. NOTCH1, MYC and MAZ, as well as JMJD3 expression levels are shown. shUTX shows a significant up-regulation of JMJD3 compared to shRenilla (control) cells. The average of three studies is shown. b, Significant expression changes of NRARP transcript upon JMJD3 knockdown. c, ChIP for H3K27me3 on NRARP locus. d, e, Binding of JMJD3 on NOTCH1 (d) and MAZ (e) promoter upon shJMJD3 and shRenilla (control). The average of three studies is shown. f, Numbers of up- and down-regulated genes are shown for shJMJD3 and shUTX compared to shRenilla. g, Scatterplot showing the expression levels of important genes in shJMJD3 and shUTX in CUTLL1 T-ALL cells. Emphasis is given to NOTCH1 pathway and apoptosis-related genes. This is a scatterplot representation of expression analysis comparing three independent studies for shJMJD3 and two for shUTX.h, i, Scatterplots showing the expression levels of important genes on shJMJD3 and shRenilla (h) and shUTX (i) in CCRF-CEM T-ALL cells. CEM exhibit increased NOTCH1 levels through mutations in the heterodimerization (HD) domain of NOTCH1 and in the NOTCH1-associated ligase FBXW7. Emphasis is given to NOTCH1 pathway and apoptosis-related genes. This is a scatterplot representation of expression analysis comparing two studies for shJMJD3, two for shUTX and two for shRenilla.
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Figure 7: JMJD3 binds to genes with important oncogenic function and is vital for T-ALL growtha, JMJD3-but not UTX-genetic inactivation impairs the expression of important oncogenic genes. NOTCH1, MYC and MAZ, as well as JMJD3 expression levels are shown. shUTX shows a significant up-regulation of JMJD3 compared to shRenilla (control) cells. The average of three studies is shown. b, Significant expression changes of NRARP transcript upon JMJD3 knockdown. c, ChIP for H3K27me3 on NRARP locus. d, e, Binding of JMJD3 on NOTCH1 (d) and MAZ (e) promoter upon shJMJD3 and shRenilla (control). The average of three studies is shown. f, Numbers of up- and down-regulated genes are shown for shJMJD3 and shUTX compared to shRenilla. g, Scatterplot showing the expression levels of important genes in shJMJD3 and shUTX in CUTLL1 T-ALL cells. Emphasis is given to NOTCH1 pathway and apoptosis-related genes. This is a scatterplot representation of expression analysis comparing three independent studies for shJMJD3 and two for shUTX.h, i, Scatterplots showing the expression levels of important genes on shJMJD3 and shRenilla (h) and shUTX (i) in CCRF-CEM T-ALL cells. CEM exhibit increased NOTCH1 levels through mutations in the heterodimerization (HD) domain of NOTCH1 and in the NOTCH1-associated ligase FBXW7. Emphasis is given to NOTCH1 pathway and apoptosis-related genes. This is a scatterplot representation of expression analysis comparing two studies for shJMJD3, two for shUTX and two for shRenilla.

Mentions: To clarify the role of JMJD3 and UTX in the maintenance of leukemia, we performed genomic knockdown of JMJD3 in human T-ALL using two different short hairpin RNAs (shRNAs, Fig. 2a, b and Extended Data Fig 2d). Treatment with shJMJD3 but not shUTX affected the viability of leukemic cells, as shown by loss of representation studies and apoptosis assays, in contrast to myeloid leukemia lines used as controls (Fig. 2cExtended Data Fig. 2e, f). Expression of NOTCH1 targets was negatively affected by shJMJD3, accompanied by loss of JMJD3 and gain of H3K27me3 on their promoters (Extended Data Fig. 3 a–e). Genome-wide expression analysis showed that more transcripts were significantly down-regulated than upregulated (749 protein-coding genes vs 297, Fig. 2d top panel and Extended Data Fig. 3f), in agreement with the JMJD3 role as a transcriptional activator. The down-regulated genes were found significantly enriched in genes that gained H3K27me3 on their promoters (Fig. 2d, bottom panel, P=1.015673e-07). shUTX downand up-regulated gene signatures were reversed in terms of gene numbers (46 down-regulated and 189 upregulated protein-coding genes, when compared to both shRenilla and shJMJD3). Intriguingly, JMJD3 expression itself is significantly upregulated upon UTX silencing (Extended Data 3a). Well-characterized NOTCH1 targets, as well as genes of the NFkB pathway were downregulated as part of the JMJD3 signature (Fig. 2d top and Extended Data Fig. 3g). These findings were confirmed using additional T-ALL lines with high levels of oncogenic NOTCH1 activity21 (Extended Data Fig. 3h, i). Subcutaneous (subq) or intravenous (i.v.) xenograft models of T-ALL cell lines (CUTLL1, CEM and P12) treated with either of the two shRNAs against JMJD3 (shJMJD3a and b) and transplanted into immuno-compromised mice (Rag2−/−γc−/−) showed a significant growth disadvantage (Fig. 2e and Extended Data Fig. 4a–f). Interestingly, silencing of UTX leads to enhanced proliferation in many cases, suggesting a possible tumor suppressor function in vivo (Extended Data Figure 4g).


Contrasting roles of histone 3 lysine 27 demethylases in acute lymphoblastic leukaemia.

Ntziachristos P, Tsirigos A, Welstead GG, Trimarchi T, Bakogianni S, Xu L, Loizou E, Holmfeldt L, Strikoudis A, King B, Mullenders J, Becksfort J, Nedjic J, Paietta E, Tallman MS, Rowe JM, Tonon G, Satoh T, Kruidenier L, Prinjha R, Akira S, Van Vlierberghe P, Ferrando AA, Jaenisch R, Mullighan CG, Aifantis I - Nature (2014)

JMJD3 binds to genes with important oncogenic function and is vital for T-ALL growtha, JMJD3-but not UTX-genetic inactivation impairs the expression of important oncogenic genes. NOTCH1, MYC and MAZ, as well as JMJD3 expression levels are shown. shUTX shows a significant up-regulation of JMJD3 compared to shRenilla (control) cells. The average of three studies is shown. b, Significant expression changes of NRARP transcript upon JMJD3 knockdown. c, ChIP for H3K27me3 on NRARP locus. d, e, Binding of JMJD3 on NOTCH1 (d) and MAZ (e) promoter upon shJMJD3 and shRenilla (control). The average of three studies is shown. f, Numbers of up- and down-regulated genes are shown for shJMJD3 and shUTX compared to shRenilla. g, Scatterplot showing the expression levels of important genes in shJMJD3 and shUTX in CUTLL1 T-ALL cells. Emphasis is given to NOTCH1 pathway and apoptosis-related genes. This is a scatterplot representation of expression analysis comparing three independent studies for shJMJD3 and two for shUTX.h, i, Scatterplots showing the expression levels of important genes on shJMJD3 and shRenilla (h) and shUTX (i) in CCRF-CEM T-ALL cells. CEM exhibit increased NOTCH1 levels through mutations in the heterodimerization (HD) domain of NOTCH1 and in the NOTCH1-associated ligase FBXW7. Emphasis is given to NOTCH1 pathway and apoptosis-related genes. This is a scatterplot representation of expression analysis comparing two studies for shJMJD3, two for shUTX and two for shRenilla.
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Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4209203&req=5

Figure 7: JMJD3 binds to genes with important oncogenic function and is vital for T-ALL growtha, JMJD3-but not UTX-genetic inactivation impairs the expression of important oncogenic genes. NOTCH1, MYC and MAZ, as well as JMJD3 expression levels are shown. shUTX shows a significant up-regulation of JMJD3 compared to shRenilla (control) cells. The average of three studies is shown. b, Significant expression changes of NRARP transcript upon JMJD3 knockdown. c, ChIP for H3K27me3 on NRARP locus. d, e, Binding of JMJD3 on NOTCH1 (d) and MAZ (e) promoter upon shJMJD3 and shRenilla (control). The average of three studies is shown. f, Numbers of up- and down-regulated genes are shown for shJMJD3 and shUTX compared to shRenilla. g, Scatterplot showing the expression levels of important genes in shJMJD3 and shUTX in CUTLL1 T-ALL cells. Emphasis is given to NOTCH1 pathway and apoptosis-related genes. This is a scatterplot representation of expression analysis comparing three independent studies for shJMJD3 and two for shUTX.h, i, Scatterplots showing the expression levels of important genes on shJMJD3 and shRenilla (h) and shUTX (i) in CCRF-CEM T-ALL cells. CEM exhibit increased NOTCH1 levels through mutations in the heterodimerization (HD) domain of NOTCH1 and in the NOTCH1-associated ligase FBXW7. Emphasis is given to NOTCH1 pathway and apoptosis-related genes. This is a scatterplot representation of expression analysis comparing two studies for shJMJD3, two for shUTX and two for shRenilla.
Mentions: To clarify the role of JMJD3 and UTX in the maintenance of leukemia, we performed genomic knockdown of JMJD3 in human T-ALL using two different short hairpin RNAs (shRNAs, Fig. 2a, b and Extended Data Fig 2d). Treatment with shJMJD3 but not shUTX affected the viability of leukemic cells, as shown by loss of representation studies and apoptosis assays, in contrast to myeloid leukemia lines used as controls (Fig. 2cExtended Data Fig. 2e, f). Expression of NOTCH1 targets was negatively affected by shJMJD3, accompanied by loss of JMJD3 and gain of H3K27me3 on their promoters (Extended Data Fig. 3 a–e). Genome-wide expression analysis showed that more transcripts were significantly down-regulated than upregulated (749 protein-coding genes vs 297, Fig. 2d top panel and Extended Data Fig. 3f), in agreement with the JMJD3 role as a transcriptional activator. The down-regulated genes were found significantly enriched in genes that gained H3K27me3 on their promoters (Fig. 2d, bottom panel, P=1.015673e-07). shUTX downand up-regulated gene signatures were reversed in terms of gene numbers (46 down-regulated and 189 upregulated protein-coding genes, when compared to both shRenilla and shJMJD3). Intriguingly, JMJD3 expression itself is significantly upregulated upon UTX silencing (Extended Data 3a). Well-characterized NOTCH1 targets, as well as genes of the NFkB pathway were downregulated as part of the JMJD3 signature (Fig. 2d top and Extended Data Fig. 3g). These findings were confirmed using additional T-ALL lines with high levels of oncogenic NOTCH1 activity21 (Extended Data Fig. 3h, i). Subcutaneous (subq) or intravenous (i.v.) xenograft models of T-ALL cell lines (CUTLL1, CEM and P12) treated with either of the two shRNAs against JMJD3 (shJMJD3a and b) and transplanted into immuno-compromised mice (Rag2−/−γc−/−) showed a significant growth disadvantage (Fig. 2e and Extended Data Fig. 4a–f). Interestingly, silencing of UTX leads to enhanced proliferation in many cases, suggesting a possible tumor suppressor function in vivo (Extended Data Figure 4g).

Bottom Line: T-cell acute lymphoblastic leukaemia (T-ALL) is a haematological malignancy with a dismal overall prognosis, including a relapse rate of up to 25%, mainly because of the lack of non-cytotoxic targeted therapy options.By contrast, we found that UTX functions as a tumour suppressor and is frequently genetically inactivated in T-ALL.These findings show that two proteins with a similar enzymatic function can have opposing roles in the context of the same disease, paving the way for treating haematopoietic malignancies with a new category of epigenetic inhibitors.

View Article: PubMed Central - PubMed

Affiliation: 1] Howard Hughes Medical Institute and Department of Pathology, NYU School of Medicine, New York, New York 10016, USA [2] NYU Cancer Institute and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York 10016, USA [3].

ABSTRACT
T-cell acute lymphoblastic leukaemia (T-ALL) is a haematological malignancy with a dismal overall prognosis, including a relapse rate of up to 25%, mainly because of the lack of non-cytotoxic targeted therapy options. Drugs that target the function of key epigenetic factors have been approved in the context of haematopoietic disorders, and mutations that affect chromatin modulators in a variety of leukaemias have recently been identified; however, 'epigenetic' drugs are not currently used for T-ALL treatment. Recently, we described that the polycomb repressive complex 2 (PRC2) has a tumour-suppressor role in T-ALL. Here we delineated the role of the histone 3 lysine 27 (H3K27) demethylases JMJD3 and UTX in T-ALL. We show that JMJD3 is essential for the initiation and maintenance of T-ALL, as it controls important oncogenic gene targets by modulating H3K27 methylation. By contrast, we found that UTX functions as a tumour suppressor and is frequently genetically inactivated in T-ALL. Moreover, we demonstrated that the small molecule inhibitor GSKJ4 (ref. 5) affects T-ALL growth, by targeting JMJD3 activity. These findings show that two proteins with a similar enzymatic function can have opposing roles in the context of the same disease, paving the way for treating haematopoietic malignancies with a new category of epigenetic inhibitors.

Show MeSH
Related in: MedlinePlus