scholarly journals A deconvolution method and its application in analyzing the cellular fractions in acute myeloid leukemia samples

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Huamei Li ◽  
Amit Sharma ◽  
Wenglong Ming ◽  
Xiao Sun ◽  
Hongde Liu
Keyword(s):  
Gene Expression ◽  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Molecular Mechanisms ◽  
Cell Types ◽  
Bulk Sample ◽  
Marker Genes ◽  
Benchmark Datasets ◽  
Multiple Conditions ◽  
Acute Myeloid

Abstract Background The identification of cell type-specific genes (markers) is an essential step for the deconvolution of the cellular fractions, primarily, from the gene expression data of a bulk sample. However, the genes with significant changes identified by pair-wise comparisons cannot indeed represent the specificity of gene expression across multiple conditions. In addition, the knowledge about the identification of gene expression markers across multiple conditions is still paucity. Results Herein, we developed a hybrid tool, LinDeconSeq, which consists of 1) identifying marker genes using specificity scoring and mutual linearity strategies across any number of cell types, and 2) predicting cellular fractions of bulk samples using weighted robust linear regression with the marker genes identified in the first stage. On multiple publicly available datasets, the marker genes identified by LinDeconSeq demonstrated better accuracy and reproducibility compared to MGFM and RNentropy. Among deconvolution methods, LinDeconSeq showed low average deviations (≤0.0958) and high average Pearson correlations (≥0.8792) between the predicted and actual fractions on the benchmark datasets. Importantly, the cellular fractions predicted by LinDeconSeq appear to be relevant in the diagnosis of acute myeloid leukemia (AML). The distinct cellular fractions in granulocyte-monocyte progenitor (GMP), lymphoid-primed multipotent progenitor (LMPP) and monocytes (MONO) were found to be closely associated with AML compared to the healthy samples. Moreover, the heterogeneity of cellular fractions in AML patients divided these patients into two subgroups, differing in both prognosis and mutation patterns. GMP fraction was the most pronounced between these two subgroups, particularly, in SubgroupA, which was strongly associated with the better AML prognosis and the younger population. Totally, the identification of marker genes by LinDeconSeq represents the improved feature for deconvolution. The data processing strategy with regard to the cellular fractions used in this study also showed potential for the diagnosis and prognosis of diseases. Conclusions Taken together, we developed a freely-available and open-source tool LinDeconSeq (https://github.com/lihuamei/LinDeconSeq), which includes marker identification and deconvolution procedures. LinDeconSeq is comparable to other current methods in terms of accuracy when applied to benchmark datasets and has broad application in clinical outcome and disease-specific molecular mechanisms.

Aggressive Aneuploid Acute Myeloid Leukemia Is Dependent on Alterations of P53, Gain of APC and PLK1 and Loss of RAD50

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 1702-1702
Author(s):  
Giorgia Simonetti ◽  
Antonella Padella ◽  
Marco Manfrini ◽  
Italo Faria do Valle ◽  
Cristina Papayannidis ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Dna Repair ◽  
Acute Myeloid Leukemia ◽  
Copy Number ◽  
Myeloid Leukemia ◽  
Molecular Mechanisms ◽  
Copy Number Loss ◽  
Mutation Load ◽  
Acute Myeloid

Abstract Chromosome number alterations, aneuploidy, is a hallmark of cancer. It occurs in about 15% of acute myeloid leukemia (AML) cases, is generally preserved throughout disease progression (Bochtler et al. Leukemia 2015) and correlates with adverse prognosis (Breems et al. JCO 2008, Papaemmanuil et al. NEJM 2016). This evidence highlights the need of understanding the molecular mechanisms that promote and sustain aneuploidy in AML, in order to define novel potential therapeutic targets. In the NGS-PTL project we profiled the genomic landscape of 536 hematological samples by whole exome sequencing (WES, Illumina). Among them, we analyzed 88 and 68 samples from aneuploid (A-) FLT3-wildtype AML (isolated trisomy and monosomy, complex and monosomal karyotype) and euploid (E-) AML (normal and complex karyotype, <3 abnormalities), respectively (100 bp, paired-end). Variants were called by MuTect and Varscan 2.0. WES output was integrated with genotype data (CytoScan HD Array, Affymetrix and Nexus Copy Number analysis) and gene expression profiling (HTA 2.0 and TAC 3.0, Affymetrix). A-AML showed an increased genomic instability, as confirmed by a higher mutation load compared with E-AML (median number of variants: 22 (range: 2-95) and 11 (range: 3-45), respectively, p<.001), which was associated with increased patients' age (median age of 62 for A-AML and 55 for E-AML, p<.05). The increased age and mutation load correlated with a mutational signature with prominence of C>A substitutions, compared with the C>T transition-related signature, which is prevalent in AML. A-AML was associated with mutations and/or heterozygous deletion of TP53 (p<.001), which co-occurred with copy number loss of both the tumor suppressor APC and the DNA repair gene RAD50 in 93% of cases (p<.001). Moreover, A-AML was enriched for a gene expression signature of p53-deficiency, independently of TP53 structural defects (p<.05, GSEA). Mutations and deregulated expression of genes involved in cell cycle contributed to the A-AML phenotype, with 68% A-AML vs. 32% E-AML patients (p<.01) carrying at least one genomic lesion affecting the process. The alterations targeted the following pathways: DNA repair (i.e. reduced RAD50 expression, p<.001), cell cycle checkpoints (i.e. mutated CHK2), regulation of PLK1 activity at G2/M transition (i.e. mutation and 2-fold upregulation of PLK1, p<.01), mitotic metaphase and anaphase (i.e. increased CDC20 level, p<.001) and separation of sister chromatids (i.e. mutated BUB1B, ESPL1, CENPO). Of note, a 3-gene signature composed of PLK1, CDC20 and RAD50, was able to discriminate 73% of patients between the A- and E-AML cohorts. This signature was confirmed at protein level. In parallel, E-AML showed a preferential dependency on epigenetic mechanisms, with recurrent genomic lesions of ASXL1/2, BCOR/L1, EZH2 and MLL, enrichment of FLT3 alterations and mutations activating RAS signal transduction (p<.05). Of note, a HOX-related signature characterized by overexpression of the HOX family members HOXA7, HOXB3 and MEIS1 identified E-AML. We show here for the first time the molecular mechanisms promoting and maintaining aneuploidy in AML. Our results indicate that p53 deficiency, either caused by somatic mutations, copy number loss, impaired DNA damage response and enhanced PLK1 signaling synergize with APCgain, RAD50 structural or functional loss and forced progression through mitosis, to override cell cycle and mitotic checkpoints and allow the formation of daughter cells with an aberrant chromosome number. These mechanisms cooperate with recurrent mutations of genes involved in protein ubiquitination and proteasome-mediated protein catabolic process in A-AML, indicative of the attempt of aneuploid cells to override the proteotoxic stress due to the unbalanced protein load generated by the aneuploid condition. This evidence provides the rationale for exploiting proteasome inhibition (Velcade), p53 reactivation (MDM2/4 inhibitor) and targeting of the cell cycle (CHK1/2 inhibitor) downstream to p53 (WEE1 inhibitor) as strategies for novel combination therapies against aggressive aneuploid AML, which are under clinical investigation in our Institution and may serve as a model for aneuploid tumors. GS and AP: equal contribution. Supported by: FP7 NGS-PTL project, ELN, AIL, AIRC, PRIN, progetto Regione-Università 2010-12 (L. Bolondi). Disclosures Haferlach: MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Martinelli:Ariad: Consultancy, Speakers Bureau; MSD: Consultancy; Celgene: Consultancy, Speakers Bureau; Roche: Consultancy, Speakers Bureau; Genentech: Consultancy; Novartis: Speakers Bureau; BMS: Speakers Bureau; Pfizer: Consultancy, Speakers Bureau; Amgen: Consultancy, Speakers Bureau.

scholarly journals IGF1R-IRS1/2 Pharmacological Inhibitors Act By Distinct Cellular and Molecular Mechanisms and Reveals Vulnerabilities for Treatment of Acute Myeloid Leukemia

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 1869-1869
Author(s):  
Juan L Coelho-Silva ◽  
Diego A Pereira-Martins ◽  
Virginia Campos Silvestrini ◽  
João Agostinho Machado-Neto ◽  
Eduardo M Rego ◽  
...  
Keyword(s):  
Gene Expression ◽  
Acute Myeloid Leukemia ◽  
Tyrosine Kinase ◽  
Myeloid Leukemia ◽  
Molecular Mechanisms ◽  
Experimental Conditions ◽  
Proteomic Data ◽  
Cellular Energetics ◽  
Molecular Functions ◽  
Acute Myeloid

Abstract Background: Preclinical rationale for targeting the insulin-like growth factor 1 (IGF1R)-Insulin Receptor Substrates 1 and 2 (IRS1/2) signaling in acute myeloid leukemia (AML), particularly in cells harboring the FLT3-ITD mutation, has been recently provided [Blood (2018) 132 Supp: 1512 and [Blood (2019) 134 Supp: 2689]. However, little is known about the non-canonical molecular mechanisms regulated by IGF1R-IRS1/2 signaling and pharmacological inhibition of this pathway in AML. Aims: To depict distinctive non-explicit molecular effects of linsitinib (IGF1R tyrosine kinase inhibitor) and NT157 (IGF1R-IRS1/2 allosteric inhibitor) treatment in FLT3-ITD-mutated AML cells. Material and methods: The MOLM-13 (homozygous) and MV4-11 (heterozygous) FLT3-ITD-mutated AML cell lines were treated with linsitinib (10 µM) or NT157 (1 µM) for 24 hours and used for label-free proteomic quantification analysis (n=3). Raw MS/MS data were processed using the SORCERER system and proteins were identified with built-in Andromeda search engine based on the human Uniprot proteome database. False discovery rate cutoffs were set to 1% on peptide, protein, and site decoy level, only allowing high quality identification to pass. Expression values were normalized across experimental conditions by quantile normalization based on the Limma-Voom pipeline, and then systematically compared similarities and differences in protein expression across experimental conditions by applying the Benjamin-Hochberg correction for multiple comparisons. To depict pathways associated to IGF1R, IRS1 and IRS2 gene expression related to processes identified by the proteomic data, we performed a gene-set enrichment analysis (GSEA) using the curated genesets for oncogenic events and molecular functions (MSigDB, Broad Institute) from RNA-seq data of the Cancer Genome Atlas AML cohort (n=173). Results: Considering a ≥ 2-fold change difference in both directions, linsitinib treatment downregulated 6 and 18 and upregulated 13 and 116 proteins in MOLM-13 and MV4-11 cells, respectively. Likewise, NT157 downregulated 12 and 126 and upregulated 204 and 297 proteins. When compared directly, linsitinib reduced expression of 11 and 35 and increased expression of 110 and 70 proteins in MOLM-13 and MV4-11 cells, respectively. Gene ontology identified that linsitinib resulted in upregulation of 7 molecular functions, while the NT157 ensued the upregulation of 18 and downregulation of 17 molecular functions pathways in a consistently manner between all comparisons. Of note, linsitinib activates post-transcriptional regulatory mechanisms, RNA metabolism (RNA binding P=1.15E-12; RNA processing P=8.64E-7) and reduced the protein and macromolecule metabolism (cellular protein metabolism P=3.86E-6). NT157 affected several of mitochondrial functions (increasing proton transmembrane transport activity P=1.55E-12, reducing oxidoreductase activity P=9.11E-10, and oxidative phosphorylation P=5.19E-8). Altogether, these data highlighted that NT157 profounder cytotoxic effect is a result of reprogramming of cellular energetics metabolism, and that linsitinib altered transcription and translation processes, probably as a result of autophagy, a mechanism originally described by our group [Blood (2017) 130 Supp: 3966]. GSEA analysis revealed that high IGF1R expression is positively enriched with RPS14 signature (Normalized Enriched Score [NES]=2.23; FDR-q&lt;0.001), a ribosomal protein related to pathophysiology of myeloid neoplasms related to chromosome 5q deletion. Both IRS1 and IRS2 transcriptional signatures were associated with cellular growth signaling, such as AKT (NES=1.86; FDR-q= 0.006) and MYC (NES=1.67; FDR-q= 0.005), mitochondrial function [mitochondrial gene expression (NES=1.71; FDR-q= 0.001)]. Conclusion: Our proteomic data shed light on new and non-explicit mechanisms related to IGF1R-IRS1/2 inhibitors. Linsitinib modulates molecular processes related to RNA transcription and translation, while NT157 profoundly affect the cellular energetics, and, at least in part, explain the differential pre-clinical efficiency. Moreover, allosteric pharmacological inhibition of IGF1R-IRS1/2 pathway seems a more promising strategy than the tyrosine kinase inhibition, especially for AML subgroup more dependent of mitochondrial metabolism, such as AML with FLT3 mutation. Disclosures No relevant conflicts of interest to declare.

scholarly journals Prognostic value of CIP2A gene expression in adult Egyptian acute myeloid leukemia patients

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Roxan E. Shafik ◽  
Azza M. Ibrahim ◽  
Fadwa Said ◽  
Naglaa M. Hassan ◽  
Hanan E. Shafik ◽  
...  
Keyword(s):  
Gene Expression ◽  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Prognostic Value ◽  
Acute Myeloid

scholarly journals Single-cell map of diverse immune phenotypes in the acute myeloid leukemia microenvironment

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Rongqun Guo ◽  
Mengdie Lü ◽  
Fujiao Cao ◽  
Guanghua Wu ◽  
Fengcai Gao ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Single Cell ◽  
Myeloid Leukemia ◽  
Immune Cell ◽  
Immune Surveillance ◽  
Cell Types ◽  
Developmental Trajectory ◽  
Significant Difference ◽  
Cell Phenotypes ◽  
Acute Myeloid

Abstract Background Knowledge of immune cell phenotypes, function, and developmental trajectory in acute myeloid leukemia (AML) microenvironment is essential for understanding mechanisms of evading immune surveillance and immunotherapy response of targeting special microenvironment components. Methods Using a single-cell RNA sequencing (scRNA-seq) dataset, we analyzed the immune cell phenotypes, function, and developmental trajectory of bone marrow (BM) samples from 16 AML patients and 4 healthy donors, but not AML blasts. Results We observed a significant difference between normal and AML BM immune cells. Here, we defined the diversity of dendritic cells (DC) and macrophages in different AML patients. We also identified several unique immune cell types including T helper cell 17 (TH17)-like intermediate population, cytotoxic CD4+ T subset, T cell: erythrocyte complexes, activated regulatory T cells (Treg), and CD8+ memory-like subset. Emerging AML cells remodels the BM immune microenvironment powerfully, leads to immunosuppression by accumulating exhausted/dysfunctional immune effectors, expending immune-activated types, and promoting the formation of suppressive subsets. Conclusion Our results provide a comprehensive AML BM immune cell census, which can help to select pinpoint targeted drug and predict efficacy of immunotherapy.

Poster: AML-320: A Prospective Evaluation of WT1 Gene Expression in Primary Acute Myeloid Leukemia: Bench to Bedside

2021 ◽  
Vol 21 ◽  
pp. S217
Author(s):  
Ishan Gupta ◽  
Harsh Goel ◽  
Pranay Tanwar ◽  
Dimpy Gupta ◽  
Anita Chopra ◽  
...  
Keyword(s):  
Gene Expression ◽  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Wt1 Gene ◽  
Prospective Evaluation ◽  
Acute Myeloid
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