Dataset Information

Tandem mass tag (TMT) quantitative proteomics of human acute myeloid leukaemia (AML)

ABSTRACT: The branched-chain amino acid (BCAA) pathway and high levels of BCAA transaminase 1 (BCAT1) have recently been associated with aggressiveness in several cancer entities. However, the mechanistic role of BCAT1 in this process remains largely uncertain. Here, by performing high-resolution proteomic analysis of human acute myeloid leukaemia (AML) stem-cell and non-stem-cell populations, we find the BCAA pathway enriched and BCAT1 protein and transcripts overexpressed in leukaemia stem cells. We show that BCAT1, which transfers α-amino groups from BCAAs to α-ketoglutarate (αKG), is a critical regulator of intracellular αKG homeostasis. Further to its role in the tricarboxylic acid cycle, αKG is an essential cofactor for αKG-dependent dioxygenases such as Egl-9 family hypoxia inducible factor 1 (EGLN1) and the ten-eleven translocation (TET) family of DNA demethylases. Knockdown of BCAT1 in leukaemia cells caused accumulation of αKG, leading to EGLN1-mediated HIF1α protein degradation. This resulted in a growth and survival defect and abrogated leukaemia-initiating potential. By contrast, overexpression of BCAT1 in leukaemia cells decreased intracellular αKG levels and caused DNA hypermethylation through altered TET activity. AML with high levels of BCAT1 (BCAT1high) displayed a DNA hypermethylation phenotype similar to cases carrying a mutant isocitrate dehydrogenase (IDHmut), in which TET2 is inhibited by the oncometabolite 2-hydroxyglutarate11,12. High levels of BCAT1 strongly correlate with shorter overall survival in IDHWTTET2WT, but not IDHmut or TET2mutAML. Gene sets characteristic for IDHmut AML13 were enriched in samples from patients with an IDHWTTET2WTBCAT1high status. BCAT1highAML showed robust enrichment for leukaemia stem-cell signatures14,15, and paired sample analysis showed a significant increase in BCAT1 levels upon disease relapse. In summary, by limiting intracellular αKG, BCAT1 links BCAA catabolism to HIF1α stability and regulation of the epigenomic landscape, mimicking the effects of IDH mutations. Our results suggest the BCAA–BCAT1–αKG pathway as a therapeutic target to compromise leukaemia stem-cell function in patients with IDHWTTET2WT AML.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Bone Marrow

DISEASE(S): Acute Leukemia

SUBMITTER: Jenny Hansson

LAB HEAD: Jenny Hansson

PROVIDER: PXD008307 | Pride | 2020-02-21

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	130312_JH_AML_HD20_with_annotation.msf	Msf
	130624_JH_AML_DD08_17.raw	Raw
	130624_JH_AML_DD08_18.raw	Raw
	130624_JH_AML_DD08_19.raw	Raw
	130624_JH_AML_DD08_20.raw	Raw

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Publications

BCAT1 restricts αKG levels in AML stem cells leading to IDHmut-like DNA hypermethylation.

Raffel Simon S Falcone Mattia M Kneisel Niclas N Hansson Jenny J Wang Wei W Lutz Christoph C Bullinger Lars L Poschet Gernot G Nonnenmacher Yannic Y Barnert Andrea A Bahr Carsten C Zeisberger Petra P Przybylla Adriana A Sohn Markus M Tönjes Martje M Erez Ayelet A Adler Lital L Jensen Patrizia P Scholl Claudia C Fröhling Stefan S Cocciardi Sibylle S Wuchter Patrick P Thiede Christian C Flörcken Anne A Westermann Jörg J Ehninger Gerhard G Lichter Peter P Hiller Karsten K Hell Rüdiger R Herrmann Carl C Ho Anthony D AD Krijgsveld Jeroen J Radlwimmer Bernhard B Trumpp Andreas A

Nature 20171108 7680

The branched-chain amino acid (BCAA) pathway and high levels of BCAA transaminase 1 (BCAT1) have recently been associated with aggressiveness in several cancer entities. However, the mechanistic role of BCAT1 in this process remains largely uncertain. Here, by performing high-resolution proteomic analysis of human acute myeloid leukaemia (AML) stem-cell and non-stem-cell populations, we find the BCAA pathway enriched and BCAT1 protein and transcripts overexpressed in leukaemia stem cells. We sho ...[more]

PMID: 29144447

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Project description:Acute myeloid leukaemia (AML) is an aggressive haematological malignancy characterised by the clonal proliferation of myeloid progenitor cells in the bone marrow and peripheral blood. Dysregulation of the Wnt/β-catenin pathway has been implicated in the establishment and maintenance of leukaemic stem cells in AML, where higher expression of β-catenin promotes clonogenic capacity, drug resistance and inferior survival. The finding that low levels of Wnt signalling are necessary to maintain normal haematopoiesis makes β-catenin an attractive therapeutic target, however drug design has been hampered by a poor understanding of its molecular interactions in leukaemia cells. To address this, we previously characterised the β-catenin interactome in myeloid cells and identified a plethora of novel interacting proteins. One such validated interactor was Target of EGR1 (TOE1), a 510-amino acid member of the Asp-Glu-Asp-Asp (DEDD) family of deadenylases with previously uncharacterised function in haematopoietic cells. The β-catenin:TOE1 interaction was detected in the nuclear and cytosolic compartments of myeloid cell lines and primary AML samples, and β-catenin knockdown via short hairpin RNA (shRNA) was found to promote the cytosolic stabilisation of TOE1. Furthermore, TOE1 levels were found to be overexpressed in primary AML blasts versus normal cord-blood derived CD34+ haematopoietic stem and progenitor cells (HSPCs), suggesting that TOE1 levels may be dysregulated in leukaemia. TOE1 depletion using shRNA abrogated Wnt signalling capacity (TCF/LEF activity) through suppression of the Wnt transcription factor lymphoid enhancing factor 1 (LEF-1), likely via post-transcriptional mechanisms. TOE1 shRNA further suppressed the proliferation and survival of myeloid leukaemia cell lines (HEL and OCI-AML2) and primary human CD34+ HSPC, however this could not be fully explained through LEF-1 alone, since OCI-AML2 do not express LEF-1. Therefore, to explore a more unifying mechanism mediating the growth promoting phenotype of TOE1 we performed tandem mass tag (TMT)-labelling coupled to mass spectrometry analysis in TOE1 deficient HEL and OCI-AML2 cells. From this analysis we identified validated p21 (RAC1) activated kinase 2 (PAK2) as a consistently downregulated target across both cell lines, and demonstrated PAK2 knockdown alone was sufficient to reduce the proliferation (but not survival) of AML cell lines. Finally, expression of ectopic PAK2 was able to partially rescue the suppressed proliferation mediated by TOE1 depletion in myeloid cell lines, and primary human CD34+ HSPC. In summary, these data reveal TOE1 as novel interacting partner for β-catenin in haematological cells capable of modulating Wnt signalling output via LEF-1, and as a novel mediator of growth and survival in human HSPC and AML cells partly through PAK2 regulation.