Large-scale gene network analysis reveals the significance of extracellular matrix pathway and homeobox genes in acute myeloid leukemia: an introduction to the Pigengene package and its applications

Acute myeloid leukemia (AML) is an aggressive bone marrow malignancy, and non-leukemic stromal cells (including mesenchymal stem cells, MSCs) are involved in leukemogenesis and show AML-supporting effects. We investigated how constitutive extracellular mediator release by primary human AML cells alters proteomic profiles of normal bone marrow MSCs. An average of 6814 proteins (range 6493−6918 proteins) were quantified for 41 MSC cultures supplemented with AML-cell conditioned medium, whereas an average of 6715 proteins (range 6703−6722) were quantified for untreated control MSCs. The AML effect on global MSC proteomic profiles varied between patients. Hierarchical clustering analysis identified 10 patients (5/10 secondary AML) showing more extensive AML-effects on the MSC proteome, whereas the other 31 patients clustered together with the untreated control MSCs and showed less extensive AML-induced effects. These two patient subsets differed especially with regard to MSC levels of extracellular matrix and mitochondrial/metabolic regulatory proteins. Less than 10% of MSC proteins were significantly altered by the exposure to AML-conditioned media; 301 proteins could only be quantified after exposure to conditioned medium and 201 additional proteins were significantly altered compared with the levels in control samples (153 increased, 48 decreased). The AML-modulated MSC proteins formed several interacting networks mainly reflecting intracellular organellar structure/trafficking but also extracellular matrix/cytokine signaling, and a single small network reflecting altered DNA replication. Our results suggest that targeting of intracellular trafficking and/or intercellular communication is a possible therapeutic strategy in AML.

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Identification of hub genes associated with adult acute myeloid leukemia progression through weighted gene co-expression network analysis

Aging ◽

10.18632/aging.202493 ◽

2021 ◽

Vol 13 (4) ◽

pp. 5686-5697

Author(s):

Ruiqi Zhu ◽

Wenyi Lin ◽

Liang Tang ◽

Yu Hu

Keyword(s):

Acute Myeloid Leukemia ◽

Network Analysis ◽

Myeloid Leukemia ◽

Hub Genes ◽

Acute Myeloid

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Human acute myeloid leukemia cells bind to bone marrow stroma via a combination of beta-1 and beta-2 integrin mechanisms

Blood ◽

10.1182/blood.v82.10.3125.3125 ◽

1993 ◽

Vol 82 (10) ◽

pp. 3125-3132 ◽

Cited By ~ 65

Author(s):

LJ Bendall ◽

K Kortlepel ◽

DJ Gottlieb

Keyword(s):

Bone Marrow ◽

Extracellular Matrix ◽

Acute Myeloid Leukemia ◽

Cell Adhesion ◽

Myeloid Leukemia ◽

Extracellular Matrix Proteins ◽

Matrix Proteins ◽

Leukemic Cells ◽

Beta 2 ◽

Acute Myeloid

Abstract Acute myeloid leukemia (AML) cells respond to exogenous stimulation from myeloid growth factors that may be secreted by cells of the bone marrow (BM) stroma and retained by glycosaminoglycans in the extracellular matrix. We have analyzed the capacity of malignant cells from patients with AML to maintain close proximity to sites of growth factor production and retention by binding to BM stromal elements, including fibroblasts and extracellular matrix proteins. Leukemic cells from all cases of AML adhered to BM fibroblast (BMF) monolayers (mean +/- standard error [SE] percentage binding, 30.9% +/- 2.5%; n = 23) and to fibronectin and laminin (mean +/- SE percentage binding, 28.0% +/- 4.1% [n = 11] and 21.5% +/- 2.3% [n = 8], respectively). Binding to bovine and human collagen type 1, vitronectin, hyaluronic acid, and albumin was minimal. Analysis of binding mechanisms indicated that very late antigen-4 (VLA-4) and VLA-5 were responsible for AML cell binding to fibronectin. Binding to laminin could be inhibited by antibody to the alpha chain of VLA-6. In contrast, AML cell adhesion to BMF monolayers was not impaired by blocking antibodies to either beta 1 or beta 2 integrins used alone, although the combination of anti-CD11/CD18 and anti-VLA-4 inhibited binding in more than 50% of cases. When anti- VLA-5 was added in these cases, mean +/- SE inhibition of binding of 45.5% +/- 9.1% (P < .001) was observed. Binding of AML cells to extracellular matrix proteins fibronectin and laminin is predominantly beta 1-integrin-dependent, but AML cell adhesion to BMF relies on the simultaneous involvement of beta 1 and beta 2 integrins as well as other currently unrecognized ligands.

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Integrin α7 and Extracellular Matrix Laminin 211 Interaction Promotes Proliferation of Acute Myeloid Leukemia Cells and Is Associated with Granulocytic Sarcoma

Cancers ◽

10.3390/cancers12020363 ◽

2020 ◽

Vol 12 (2) ◽

pp. 363 ◽

Cited By ~ 2

Author(s):

Nobuhiko Kobayashi ◽

Tsukasa Oda ◽

Makiko Takizawa ◽

Takuma Ishizaki ◽

Norifumi Tsukamoto ◽

...

Keyword(s):

Bone Marrow ◽

Extracellular Matrix ◽

Cell Proliferation ◽

Acute Myeloid Leukemia ◽

Myeloid Leukemia ◽

Granulocytic Sarcoma ◽

Underlying Mechanism ◽

Erk Phosphorylation ◽

Acute Myeloid Leukemia Cells ◽

Acute Myeloid

Acute myeloid leukemia (AML) with granulocytic sarcoma (GS) is characterized by poor prognosis; however, its underlying mechanism is unclear. Bone marrow samples from 64 AML patients (9 with GS and 55 without GS) together with AML cell lines PL21, THP1, HL60, Kasumi-1, and KG-1 were used to elucidate the pathology of AML with GS. RNA-Seq analyses were performed on samples from seven AML patients with or without GS. Gene set enrichment analyses revealed significantly upregulated candidates on the cell surface of the GS group. Expression of the adhesion integrin α7 (ITGA7) was significantly higher in the GS group, as seen by RT-qPCR (p = 0.00188) and immunohistochemistry of bone marrow formalin-fixed, paraffin-embedded (FFPE) specimens. Flow cytometry revealed enhanced proliferation of PL21 and THP1 cells containing surface ITGA7 in the presence of laminin 211 and stimulated ERK phosphorylation; this effect was abrogated following ITGA7 knockdown or ERK inhibition. Overall, high ITGA7 expression was associated with poor patient survival (p = 0.0477). In summary, ITGA7 is highly expressed in AML with GS, and its ligand (laminin 211) stimulates cell proliferation through ERK signaling. This is the first study demonstrating the role of integrin α7 and extracellular matrix interactions in AML cell proliferation and extramedullary disease development.

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Aberrant expression of NKL homeobox genes HMX2 and HMX3 interferes with cell differentiation in acute myeloid leukemia

PLoS ONE ◽

10.1371/journal.pone.0240120 ◽

2020 ◽

Vol 15 (10) ◽

pp. e0240120

Author(s):

Stefan Nagel ◽

Claudia Pommerenke ◽

Corinna Meyer ◽

Roderick A. F. MacLeod ◽

Hans G. Drexler

Keyword(s):

Acute Myeloid Leukemia ◽

Cell Differentiation ◽

Myeloid Leukemia ◽

Homeobox Genes ◽

Aberrant Expression ◽

Acute Myeloid

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RNAi-Based Functional Genomics Screening of the Human Kinome Identifies Major Growth Regulating Kinases in Acute Myeloid Leukemia Cells

Blood ◽

10.1182/blood.v112.11.2951.2951 ◽

2008 ◽

Vol 112 (11) ◽

pp. 2951-2951

Author(s):

Raoul Tibes ◽

Ashish Choudhary ◽

Amanda Henrichs ◽

Sadia Guled ◽

Irma Monzon ◽

...

Keyword(s):

Cell Cycle ◽

Cell Proliferation ◽

Acute Myeloid Leukemia ◽

Gene Silencing ◽

Functional Genomics ◽

Cell Lines ◽

Myeloid Leukemia ◽

Large Scale ◽

Cell Cycle Checkpoint ◽

Acute Myeloid

Abstract In order to improve treatment strategies for Acute Myeloid Leukemia (AML), we adapted a functional genomics approach using RNAi screening to identify molecular targets that are vital to the growth of AML. Herein we report the first large-scale kinome gene silencing screen in AML. A high throughput RNAi screen was developed for the efficient siRNA transfection of AML cell lines. Eight commercially available cationic lipid-based transfection reagents were tested for their ability to transfect several AML cell lines with siRNA. These extensive transfection optimization experiments identified two AML cells lines TF-1 and ML4 with up to 95–100 and 70–75% transfection efficiency respectively. Two independent replicate kinome screens were performed on both cell lines using a siRNA library targeting 572 kinase genes with 2 siRNA/gene. At 96 hours post transfection, cell proliferation was assessed and the B-score method was used to background correct and analyze the screening data. Several siRNA to specific kinases were identified that significantly inhibit cell proliferation of up to ~40–88%. Hits were defined at two thresholds: siRNA having a B-score of <−2 providing a statistically significance of p<0.05 (confidence of > 95%) and a cutoff B-score of <−1.5 providing greater than 87% confidence for each siRNA hit. Two different kinases (2 siRNA/gene/screen) were identified as major growth regulating kinases in TF1 cells with all 4 siRNA/gene having a B-score <−2. For two additional kinases, 3/4 siRNA for each gene had a Bscore <−2. Expanding the cutoff to a B-score <−1.5 three further kinases were targeted by at least 3/4 siRNA/gene. Similar analysis using the same criteria for ML4 cells identified one kinase targeted by 3/4 siRNA at a B-score <−2, seven kinases with 2/4 siRNA <−2 and two kinases with 3/4 siRNA/gene at a B-score of <−1.5. Common hits for both cell lines with at least 6/8 siRNA per gene from 4 screens performing at a B-score <−2 identified two kinases, one of them PLK1. Applying a B-score threshold of <−1.5, we identified five kinases for which at least 5/8 siRNA/gene from 4 screens met these criteria. Kinases/genes will be presented at the meeting.Confirmation of gene silencing and validation of growth response is currently underway for a subset of genes. Among the strongest hits are siRNA targeting PLK1, as well as siRNA targeting three other kinase-genes involved in regulating cell cycle progression and checkpoints and gene ontology (GO) analysis showed enrichment in cell cycle and cell cycle-checkpoint processes. Inhibitors against PLK1 and other kinase hits identified in the screen are in (pre)-clinical development and if confirmed, our experiments provide a strong rational to test these in AML. The application of RNAi based screening is useful in the identification of genes important in AML proliferation, which could serve as targets for therapeutic intervention and guide AML drug development. Furthermore, results from these types of functional genomics approaches hold promise to be rapidly translated into clinical application.

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Altered Regulation of Imprinted Non-Coding RNA Genes in Acute Myeloid Leukemia,

Blood ◽

10.1182/blood.v118.21.3456.3456 ◽

2011 ◽

Vol 118 (21) ◽

pp. 3456-3456 ◽

Cited By ~ 1

Author(s):

Ming-Yu Yang ◽

Jan-Gowth Chang ◽

Pai-Mei Lin ◽

Jui-Feng Hsu ◽

Cheng-Han Wu ◽

...

Keyword(s):

Gene Expression ◽

Acute Myeloid Leukemia ◽

Myeloid Leukemia ◽

Large Scale ◽

Conflicts Of Interest ◽

Imprinted Genes ◽

Healthy Individuals ◽

Regulatory Functions ◽

Acute Myeloid

Abstract Abstract 3456 Studies in large-scale genome sequencing have shown that only 2% of the mammalian genome encodes mRNAs, but the most part is transcribed as long and short non-coding RNAs (ncRNAs). The ncRNAs with gene regulatory functions are starting to be seen as a common feature of mammalian gene regulation. Genomic imprinting is a form of epigenetic regulation and imprinted genes are silenced in a parental-specific manner. Imprinted genes tend to occur in clusters and ncRNAs have been found at all well-characterized imprinted clusters. Although the exact mechanism how imprinted ncRNA regulates gene expression remains largely unknown, it is general accepted that imprinted ncRNAs binds to chromatin modifying complexes, such as PRC2, TRX, and G9a, and generates specific silencing of genomic loci both in cis and trans. Imprinting is associated with many human diseases or syndromes (e.g. Prader-Willi, Angelman, Beckwith-Wiedemann, Retts, and Silver-Russell syndromes) and various cancers (e.g. breast, prostate, and colorectal cancers), but its role in leukemogenesis remain elusive. In this present study, a panel of 24 human imprinted ncRNAs genes, including ampd3, cpa4, snuf, rasgrf1, slc22a3, lgf2, treb3c, gabrb3, c15orf2, sfmbt2, rtl1, copg2, h19, l3mbtl, ppp1r9a, tspan32, lnpp5f, impact, nr3251, nr3252, znf215, prim2, peg3as and znf264, has been mined using Bioinformatics approach. We investigated the expression of these imprinted ncRNA genes using real-time quantitative RT-PCR in 67 newly-diagnosed acute myeloid leukemia patients with normal karyotypes (AML-NK), 22 AML patients with abnormal karyotypes (AML-AK), and 39 healthy individuals. In AML-NK patients, the expression of lgf2, h19, slc22a3, copg2, and impact were significantly upregulated than in healthy individuals (p < 0.0001). In AML-AK patients, besides lgf2, h19 and impact genes, ampd3 and gabrb3 were also significantly upregulated than in healthy individuals (p < 0.0001). Expression of igf2 was almost undetectable in healthy individuals but drastically increased in all AML patients. Both lgf2 and h19 were significantly increased in both AML-NK and AML-AK patients. From our preliminary results, it is reasonable to hypothesize that loss imprinting of lgf2/h19 is critical for the leukemogenesis of AML and under NK or AK conditions different additional ncRNAs are activated and affect different imprinted gene expression and thus leading to different clinical outcomes. Based on our findings, we will further perform methylation analysis of promoter CpG sites in AML patients to investigate if hypomethylation is responsible for the upregulation of these imprinted ncRNAs. We will also carry out in vitro functional analysis to elucidate the functions and mechanisms of these imprinted ncRNAs in AML tumorigenesis. Updated results of these analysis will be presented at the meeting. Disclosures: No relevant conflicts of interest to declare.

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Understanding the extracellular matrix in acute myeloid leukemia

Haematologica ◽

10.3324/haematol.2017.174847 ◽

2017 ◽

Vol 102 (11) ◽

pp. 1807-1809 ◽

Cited By ~ 4

Author(s):

Valerio Izzi ◽

Ritva Heljasvaara ◽

Taina Pihlajaniemi

Keyword(s):

Extracellular Matrix ◽

Acute Myeloid Leukemia ◽

Myeloid Leukemia ◽

Acute Myeloid

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Large-scale generation of autologous dendritic cells for immunotherapy in patients with acute myeloid leukemia

Transfusion ◽

10.1111/j.1537-2995.2007.01328.x ◽

2007 ◽

Vol 47 (9) ◽

pp. 1588-1594 ◽

Cited By ~ 8

Author(s):

Anita Schmitt ◽

Peter Reinhardt ◽

Iwona Hus ◽

Jacek Tabarkiewicz ◽

Jacek Roliñski ◽

...

Keyword(s):

Acute Myeloid Leukemia ◽

Dendritic Cells ◽

Myeloid Leukemia ◽

Large Scale ◽

Acute Myeloid

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Large-Scale Identification of Disease Genes Involved in Acute Myeloid Leukemia

Journal of Virology ◽

10.1128/jvi.78.4.1971-1980.2004 ◽

2004 ◽

Vol 78 (4) ◽

pp. 1971-1980 ◽

Cited By ~ 27

Author(s):

Stefan J. Erkeland ◽

Marijke Valkhof ◽

Claudia Heijmans-Antonissen ◽

Antoinette van Hoven-Beijen ◽

Ruud Delwel ◽

...

Keyword(s):

Acute Myeloid Leukemia ◽

Myeloid Leukemia ◽

Large Scale ◽

Leukemia Virus ◽

Point Mutations ◽

Insertion Mutagenesis ◽

Disease Genes ◽

Integration Sites ◽

Virus Integration ◽

Acute Myeloid

ABSTRACT Acute myeloid leukemia (AML) is a heterogeneous group of diseases in which chromosomal aberrations, small insertions or deletions, or point mutations in certain genes have profound consequences for prognosis. However, the majority of AML patients present without currently known genetic defects. Retroviral insertion mutagenesis in mice has become a powerful tool for identifying new disease genes involved in the pathogenesis of leukemia and lymphoma. Here we have used the Graffi-1.4 strain of murine leukemia virus, which causes predominantly AML, in a screen to identify novel genes involved in the pathogenesis of this disease. We report 79 candidate disease genes in common integration sites (CISs) and 15 genes whose family members previously were found to be affected in other studies. The majority of the identified sequences (60%) were not found in lymphomas and monocytic leukemias in previous screens, suggesting a specific involvement in AML. Although most of the virus integrations occurred in or near the 5′ or 3′ ends of the genes, suggesting deregulation of gene expression as a consequence of virus integration, 18 CISs were located exclusively within the genes, conceivably causing gene disruption.

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