| 1. |
- Cozzi, Elisabetta, et al.
(author)
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Identification of long non-coding RNAs involved in leukemogenesis and venetoclax response in acute myeloid leukemia through functional CRISPR-dCas9 interference screens
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Other publication (other academic/artistic)abstract
- Acute myeloid leukemia (AML) is a malignant hematologic disease with poor prognosis. Increased understanding of disease biology is therefore needed to improve outcome for patients. While the protein-coding genome is well characterized in AML, knowledge about the involvement of non-coding genes is very limited in AML. Here, it was sought to investigate how long non-coding RNAs (lncRNAs) could contribute to disease biology and treatment resistance in AML. Three high-throughput lncRNA-CRISPR-interference screens were performed in MOLM-13 cells, knocking down about 8000 lncRNA expressed in hematopoietic cells. Effects on cell proliferation, cell differentiation and response to the anti-leukemic Bcl-2-inhibitor venetoclax were investigated upon lncRNA repression. LncRNAs most likely to positively or negatively regulate these processes were identified and top lncRNA candidates investigated with respect to expression in AML and healthy CD34+ cells and clinical AML correlations. Four lncRNAs involved in AML cell proliferation were identified (lncRNAs MIR17HG, CATG00000056335, CATG00000095269, CATG00000002239), two lncRNAs involved in differentiation (lncRNAs RP11-444A22.1, CATG00000058672) and seven lncRNAs implicated in venetoclax response. Among those, enhanced expression of proliferation-promoting lncRNA MIR17HG significantly correlated with poor outcome in AML patients (p= 0.03; p= 0.016). Further, lncRNA RP11-444A2 was identified as a predicted negative regulator of cell differentiation and was found to correlate with poor outcome (p=0.014). Further, lncRNA AC009299.3, predicted in venetoclax sensitivity, was found to be associated with poor outcome (p<0.0001), adverse risk (p=0.0014) and increased age (p=0.0045) in AML patients. Together, this study identified 14 lncRNAs proposed to be implicated in key leukemogenic events, highlighting their potential for elucidating AML biology, prognosis or treatment-response prediction and/or therapeutic use.
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| 2. |
- Miliara, Sophia, et al.
(author)
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The biological and prognostic role of long non-coding RNA NEAT1 in acute myeloid leukemia
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Other publication (other academic/artistic)abstract
- Nuclear paraspeckle assembly transcript 1 (NEAT1) is a long non-coding RNA localized in the cell nucleus that has been associated to promote several malignant solid tumors. Its role in acute myeloid leukemia (AML) remains largely elusive. Therefore, the aim of this study was to define the role of NEAT1 in AML compared to normal hematopoiesis. During normal hematopoiesis, it was identified that NEAT1 expression was low in early progenitors but increased in more differentiated cells, especially in monocytes. NEAT1 expression was increased in AML as a whole compared to normal bone marrow (NBM). It was specifically high in AML with inv(16) and t(8;21), while it was lower in patients with t(15;17). Further, NEAT1 expression correlated positively with ASXL1, KRAS and NRAS mutations and negatively with TP53 mutant AML. Higher NEAT expression was associated to better overall survival in AML, independent of other known risk factors. Antisense oligo-mediated knockdown of NEAT1 in AML cells significantly increased expression of the monocytic marker CD14 while granulocytic markers did not change. Genes affected by NEAT1-knockdown using CAGE-sequencing were significantly enriched for genes involved in glucose metabolism. By investigating genome-wide RNA and DNA interactions using RADICL-sequencing, it was revealed that NEAT1 binds to the loci of key hematopoietic regulator RUNX2 as well as the chromatin regulators KMT2A, KMT5B and CHD7. The results suggest that lncRNA NEAT1 has a potential role in hematopoietic and AML cell differentiation and could be a potential new biomarker in AML.
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| 3. |
- Mujahed, Huthayfa, et al.
(author)
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AML displays increased CTCF occupancy associated with aberrant gene expression and transcription factor binding
- 2020
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In: Blood. - : American Society of Hematology. - 0006-4971 .- 1528-0020. ; 136:3, s. 339-352
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Journal article (peer-reviewed)abstract
- CCTC-binding factor (CTCF) is a key regulator of gene expression through organization of the chromatin structure. Still, it is unclear how CTCF binding is perturbed in leukemia or in cancer in general. We studied CTCF binding by chromatin immunoprecipitation sequencing in cells from patients with acute myeloid leukemia (AML) and in normal bone marrow (NBM) in the context of gene expression, DNA methylation, and azacitidine exposure. CTCF binding was increased in AML compared with NBM. Aberrant CTCF binding was enriched for motifs for key myeloid transcription factors such as CEBPA, PU.1, and RUNX1. AML with TET2 mutations was characterized by a particularly strong gain of CTCF binding, highly enriched for gain in promoter regions, while AML in general was enriched for changes at enhancers. There was a strong anticorrelation between CTCF binding and DNA methylation. Gain of CTCF occupancy was associated with increased gene expression; however, the genomic location (promoter vs distal regions) and enrichment of motifs (for repressing vs activating cofactors) were decisive for the gene expression pattern. Knockdown of CTCF in K562 cells caused loss of CTCF binding and transcriptional repression of genes with changed CTCF binding in AML, as well as loss of RUNX1 binding at RUNX1/CTCF-binding sites. In addition, CTCF knockdown caused increased differentiation. Azacitidine exposure caused major changes in CTCF occupancy in AML patient cells, partly by restoring a CTCF-binding pattern similar to NBM. We conclude that AML displays an aberrant increase in CTCF occupancy that targets key genes for AML development and impacts gene expression.
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