Limits...
RNAi-mediated silencing of MLL-AF9 reveals leukemia-associated downstream targets and processes.

Fleischmann KK, Pagel P, Schmid I, Roscher AA - Mol. Cancer (2014)

Bottom Line: The differential gene expression profile was validated for leukemia-association by gene set enrichment analysis of published gene sets from patient studies and MLL-AF9 overexpression studies and revealed 425 differentially expressed genes.Gene ontology analysis was consistent with a more differentiated state of MLL-AF9 depleted cells, with involvement of a wide range of downstream transcriptional regulators and with defined functional processes such as ribosomal biogenesis, chaperone binding, calcium homeostasis and estrogen response.Applying the antagonist SCH39166 against the dopamine receptor DRD5 resulted in reduced leukemic cell characteristics of THP1 cells.

View Article: PubMed Central - HTML - PubMed

Affiliation: Children's Research Center, Division of Pediatric Hematology and Oncology, Dr, von Hauner Children's Hospital, Ludwig-Maximilians-Universität München, Lindwurmstrasse 2a, München 80337, Germany. katrin.fleischmann@med.uni-muenchen.de.

ABSTRACT

Background: The translocation t(9;11)(p22;q23) leading to the leukemogenic fusion gene MLL-AF9 is a frequent translocation in infant acute myeloid leukemia (AML). This study aimed to identify genes and molecular processes downstream of MLL-AF9 (alias MLL-MLLT3) which could assist to develop new targeted therapies for such leukemia with unfavorable prognosis.

Methods: In the AML cell line THP1 which harbors this t(9;11) translocation, endogenous MLL-AF9 was silenced via siRNA while ensuring specificity of the knockdown and its efficiency on functional protein level.

Results: The differential gene expression profile was validated for leukemia-association by gene set enrichment analysis of published gene sets from patient studies and MLL-AF9 overexpression studies and revealed 425 differentially expressed genes. Gene ontology analysis was consistent with a more differentiated state of MLL-AF9 depleted cells, with involvement of a wide range of downstream transcriptional regulators and with defined functional processes such as ribosomal biogenesis, chaperone binding, calcium homeostasis and estrogen response. We prioritized 41 gene products as candidate targets including several novel and potentially druggable effectors of MLL-AF9 (AHR, ATP2B2, DRD5, HIPK2, PARP8, ROR2 and TAS1R3). Applying the antagonist SCH39166 against the dopamine receptor DRD5 resulted in reduced leukemic cell characteristics of THP1 cells.

Conclusion: Besides potential new therapeutic targets, the described transcription profile shaped by MLL-AF9 provides an information source into the molecular processes altered in MLL aberrant leukemia.

Show MeSH

Related in: MedlinePlus

MLL-AF9 knockdown associated enriched functional gene annotations identified via DAVID. Enriched annotation terms (fold enrichment (FE) ≥ 1.5 and p < 0.1) were manually assorted to six higher-order terms according to the major role of the process in the biological setting under investigation. Annotation terms assigned to two higher-order terms are indicated by dotted division lines between these two. Annotation terms which could not be assigned to one of the five specific higher-order terms are depicted under the term “other”. Some annotations were abbreviated as indicated by superscript numbers: 1Antigen processing and presentation of peptide or polysaccharide antigen via MHC class II, 2Regulation of transcription from RNA polymerase II promoter. Columns show proportion of down- (white) and up-regulated (black) genes after MLL-AF9 knockdown in THP1 cells. All differentially expressed genes contained in each functional annotation term are given in Additional file 4 together with the term identifier, FE and p value of the terms.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3924703&req=5

Figure 3: MLL-AF9 knockdown associated enriched functional gene annotations identified via DAVID. Enriched annotation terms (fold enrichment (FE) ≥ 1.5 and p < 0.1) were manually assorted to six higher-order terms according to the major role of the process in the biological setting under investigation. Annotation terms assigned to two higher-order terms are indicated by dotted division lines between these two. Annotation terms which could not be assigned to one of the five specific higher-order terms are depicted under the term “other”. Some annotations were abbreviated as indicated by superscript numbers: 1Antigen processing and presentation of peptide or polysaccharide antigen via MHC class II, 2Regulation of transcription from RNA polymerase II promoter. Columns show proportion of down- (white) and up-regulated (black) genes after MLL-AF9 knockdown in THP1 cells. All differentially expressed genes contained in each functional annotation term are given in Additional file 4 together with the term identifier, FE and p value of the terms.

Mentions: Functional bioinformatic analysis via DAVID resulted in 31 enriched gene ontology annotation terms with potential biological relevance (Figure 3, Additional file 4). These terms were selected out of 312 significantly enriched annotations (Additional file 4) by omitting related and redundant terms and by evaluating their biological relevance as recommended [19]. To structure the results, the enriched annotation terms were manually assorted to functional higher-order terms according to their major role in the biological setting under investigation (Figure 3 and details in Additional file 3: Table S1).


RNAi-mediated silencing of MLL-AF9 reveals leukemia-associated downstream targets and processes.

Fleischmann KK, Pagel P, Schmid I, Roscher AA - Mol. Cancer (2014)

MLL-AF9 knockdown associated enriched functional gene annotations identified via DAVID. Enriched annotation terms (fold enrichment (FE) ≥ 1.5 and p < 0.1) were manually assorted to six higher-order terms according to the major role of the process in the biological setting under investigation. Annotation terms assigned to two higher-order terms are indicated by dotted division lines between these two. Annotation terms which could not be assigned to one of the five specific higher-order terms are depicted under the term “other”. Some annotations were abbreviated as indicated by superscript numbers: 1Antigen processing and presentation of peptide or polysaccharide antigen via MHC class II, 2Regulation of transcription from RNA polymerase II promoter. Columns show proportion of down- (white) and up-regulated (black) genes after MLL-AF9 knockdown in THP1 cells. All differentially expressed genes contained in each functional annotation term are given in Additional file 4 together with the term identifier, FE and p value of the terms.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3924703&req=5

Figure 3: MLL-AF9 knockdown associated enriched functional gene annotations identified via DAVID. Enriched annotation terms (fold enrichment (FE) ≥ 1.5 and p < 0.1) were manually assorted to six higher-order terms according to the major role of the process in the biological setting under investigation. Annotation terms assigned to two higher-order terms are indicated by dotted division lines between these two. Annotation terms which could not be assigned to one of the five specific higher-order terms are depicted under the term “other”. Some annotations were abbreviated as indicated by superscript numbers: 1Antigen processing and presentation of peptide or polysaccharide antigen via MHC class II, 2Regulation of transcription from RNA polymerase II promoter. Columns show proportion of down- (white) and up-regulated (black) genes after MLL-AF9 knockdown in THP1 cells. All differentially expressed genes contained in each functional annotation term are given in Additional file 4 together with the term identifier, FE and p value of the terms.
Mentions: Functional bioinformatic analysis via DAVID resulted in 31 enriched gene ontology annotation terms with potential biological relevance (Figure 3, Additional file 4). These terms were selected out of 312 significantly enriched annotations (Additional file 4) by omitting related and redundant terms and by evaluating their biological relevance as recommended [19]. To structure the results, the enriched annotation terms were manually assorted to functional higher-order terms according to their major role in the biological setting under investigation (Figure 3 and details in Additional file 3: Table S1).

Bottom Line: The differential gene expression profile was validated for leukemia-association by gene set enrichment analysis of published gene sets from patient studies and MLL-AF9 overexpression studies and revealed 425 differentially expressed genes.Gene ontology analysis was consistent with a more differentiated state of MLL-AF9 depleted cells, with involvement of a wide range of downstream transcriptional regulators and with defined functional processes such as ribosomal biogenesis, chaperone binding, calcium homeostasis and estrogen response.Applying the antagonist SCH39166 against the dopamine receptor DRD5 resulted in reduced leukemic cell characteristics of THP1 cells.

View Article: PubMed Central - HTML - PubMed

Affiliation: Children's Research Center, Division of Pediatric Hematology and Oncology, Dr, von Hauner Children's Hospital, Ludwig-Maximilians-Universität München, Lindwurmstrasse 2a, München 80337, Germany. katrin.fleischmann@med.uni-muenchen.de.

ABSTRACT

Background: The translocation t(9;11)(p22;q23) leading to the leukemogenic fusion gene MLL-AF9 is a frequent translocation in infant acute myeloid leukemia (AML). This study aimed to identify genes and molecular processes downstream of MLL-AF9 (alias MLL-MLLT3) which could assist to develop new targeted therapies for such leukemia with unfavorable prognosis.

Methods: In the AML cell line THP1 which harbors this t(9;11) translocation, endogenous MLL-AF9 was silenced via siRNA while ensuring specificity of the knockdown and its efficiency on functional protein level.

Results: The differential gene expression profile was validated for leukemia-association by gene set enrichment analysis of published gene sets from patient studies and MLL-AF9 overexpression studies and revealed 425 differentially expressed genes. Gene ontology analysis was consistent with a more differentiated state of MLL-AF9 depleted cells, with involvement of a wide range of downstream transcriptional regulators and with defined functional processes such as ribosomal biogenesis, chaperone binding, calcium homeostasis and estrogen response. We prioritized 41 gene products as candidate targets including several novel and potentially druggable effectors of MLL-AF9 (AHR, ATP2B2, DRD5, HIPK2, PARP8, ROR2 and TAS1R3). Applying the antagonist SCH39166 against the dopamine receptor DRD5 resulted in reduced leukemic cell characteristics of THP1 cells.

Conclusion: Besides potential new therapeutic targets, the described transcription profile shaped by MLL-AF9 provides an information source into the molecular processes altered in MLL aberrant leukemia.

Show MeSH
Related in: MedlinePlus