scholarly journals Identification of Prognosis-Related Genes of Acute Myeloid Leukemia

2021 ◽  
pp. 1-12
Author(s):  
Baoan Chen ◽  
Fang Zhou ◽  
Baoan Chen
Keyword(s):  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Proportional Hazards ◽  
Expression Profiles ◽  
Cox Proportional Hazards ◽  
Curve Analysis ◽  
Receptor Interaction ◽  
Roc Curve Analysis ◽  
Study Gene Expression ◽  
Acute Myeloid

Background: Acute myeloid leukemia (AML) is a clinically and genetically heterogeneous hematological malignancy and relapse is the main reason for the poor therapeutic effect and low survival rate. Bioinformatic technology could screen out relative genes that promote the recurrence of AML, providing a theoretical basis for further improving the precision stratification treatment of AML. Methods: In this study, gene expression profiles of Dataset Acute Myeloid Leukemia (OHSU, Nature 2018) and GSE134589 were downloaded from cBioPortal and GEO, respectively. R software and limma packages were used to identify the DEGs and then run GO enrichment, KEGG pathway, and PPI network. CIBERSORTx was used to enumerate tumor-infiltrating immune cells. Prognosis-related genes were selected by univariate and multivariate Cox proportional hazards regression analyses and the expression of them were verified by GEPIA. Kaplan-Meier curve analysis could compare the survival time. ROC curve analysis was performed to predict the value of the selected genes. Results: Functional analysis showed that the up-regulated DEGs were strikingly enriched in Cytokine-cytokine receptor interaction and positive regulation of cytokine production, and the down-regulated DEGs in the regulation of cell-cell adhesion, TNF signaling pathway. CIBERSORTx analysis revealed that the immune response of AML acted as an intricate network and proceeded in a tightly regulated way. Cox analysis showed that ALDH1L2, KLK1, and LRRN2 were correlated with AML prognosis. Conclusion: ALDH1L2, KLK1, and LRRN2 are prognosis-related genes in AML, which may, together with some immune pathways, induce poor prognosis and can be used as potential biomarkers in AML treatment.

scholarly journals Identification of Molecular and Immune Prognostic Classifiers of Acute Myeloid Leukemia

2021 ◽  
Author(s):  
Fang Zhou ◽  
Baoan Chen
Keyword(s):  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Proportional Hazards ◽  
Expression Profiles ◽  
Cox Proportional Hazards ◽  
Curve Analysis ◽  
Receptor Interaction ◽  
Roc Curve Analysis ◽  
Study Gene Expression ◽  
Acute Myeloid

Abstract Background Acute myeloid leukemia (AML) is a clinically and genetically heterogeneous hematological malignancy and relapse is the main reason for the poor therapeutic effect and low survival rate. Bioinformatic technology could screen out relative genes that promote the recurrence of AML, providing a theoretical basis for further improving the precision stratification treatment of AML. Methods In this study, gene expression profiles of Dataset Acute Myeloid Leukemia (OHSU, Nature 2018) and GSE134589 were downloaded from cbioportal and GEO, respectively. R software and limma packages were used to identify the DEGs and then run GO enrichment, KEGG pathway, and PPI network. CIBERSORTx was used to enumerate tumor-infiltrating immune cells. Prognosis-related genes were selected by Univariate and multivariate Cox proportional hazards regression analyses and the expression of them were verified by GEPIA. Kaplan–Meier curve analysis could compare the survival time. ROC curve analysis was performed to predict the value of the selected genes. Results Functional analysis showed that the up-regulated DEGs were strikingly enriched in Cytokine-cytokine receptor interaction and positive regulation of cytokine production, and the down-regulated DEGs in the regulation of cell-cell adhesion, TNF signaling pathway. CIBERSORTx analysis revealed that the immune response of AML acted as an intricate network and proceeded in a tightly regulated way. Cox analysis showed that ALDH1L2, KLK1, and LRRN2 were correlated with AML prognosis. Conclusions ALDH1L2, KLK1, and LRRN2 are prognosis-related genes in AML, which may together with some immune pathways, induce poor prognosis, and can be used as potential biomarkers in AML treatment.

scholarly journals The Prognostic Significance of PDE7B in Cytogenetically Normal Acute Myeloid Leukemia

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Ling Cao ◽  
Weilong Zhang ◽  
Xiaoni Liu ◽  
Ping Yang ◽  
Jing Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Proportional Hazards ◽  
Expression Profiles ◽  
Prognostic Significance ◽  
Gene Expression Profiles ◽  
Cox Proportional Hazards ◽  
The Cancer Genome Atlas ◽  
Acute Myeloid

AbstractAcute myeloid leukemia (AML) is a malignant hematological disease in which nearly half have normal cytogenetics. We have tried to find some significant molecular markers for this part of the cytogenetic normal AML, which hopes to provide a benefit for the diagnosis, molecular typing and prognosis prediction of AML patients. In the present study, we calculated and compared the gene expression profiles of cytogenetically normal acute myeloid leukemia (CN-AML) patients in database of The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) and dataset Vizome (a total of 632 CN-AML samples), and we have demonstrated a correlation between PDE7B gene and CN-AML. Then we proceeded to a survival analysis and prognostic risk analysis between the expression levels of PDE7B gene and CN-AML patients. The result showed that the event-free survival (EFS) and overall survival (OS) were significantly shorter in CN-AML patients with high PDE7B levels in each dataset. And we detected a significantly higher expression level of PDE7B in the leukemia stem cell (LSC) positive group. The Cox proportional hazards regression model showed that PDE7B is an independent risk predictor for CN-AML. All results indicate that PDE7B is an unfavorable prognostic factor for CN-AML.

MiR-340 Expression As a Prognostic Marker to Guide Clinical Decision-Making in Acute Myeloid Leukemia

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 2728-2728
Author(s):  
Tingting Shao ◽  
Yuan Feng ◽  
Ninghan Zhang ◽  
Rong Wang ◽  
Ting Pan ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Proportional Hazards ◽  
Cox Proportional Hazards ◽  
Hematopoietic Stem ◽  
Proportional Hazards Models ◽  
Chemotherapy Group ◽  
Cox Proportional Hazards Models ◽  
Hoxa Genes ◽  
Acute Myeloid

Background: Acute myeloid leukemia (AML) is an aggressive hematological disease. Allogeneic hematopoietic stem cell transplantation (Allo-HSCT) and chemotherapy are major treatment regimens for AML. However, prognostic markers cannot guide the decision for a specific treatment, as they are related with a various prognosis regardless of the given treatment. HOXA (homeobox A) genes cluster could promote tumor survival, proliferation, invasion, and increase the resistance of AML. The aim of this study was to screen potential miRNAs (microRNAs) that would target HOXA genes, and evaluate the utility of miRNAs in AML, help patients choose a better treatment between chemotherapy and allo-HCST. Methods: Clinical data and RNA-Seq expression data of selected cases were provided by The Cancer Genome Atlas (TCGA). Genome-wide screening was performed to identify miRNA in a heterogeneous AML population. Univariable Cox proportional hazards models and Multivariable Cox proportional hazards models were employed to identify whether OS and EFS would be affected by other variables. Results: In this study, totally 162 AML patients were recruited. All patients were firstly divided into the chemotherapy and allo-HSCT groups. Subsequently, according to median values of miR-340, patients were divided into miR-340high and miR-340low expressers, respectively. In chemotherapy group, no difference was found in clinical characteristics, such as the median age, FAB subtypes, karyotypes and genes mutation between miR-340high and miR-340low expressers. However, miR-340low expressers often accompanied with high first relapse rate or death rate in one year than high expressers (P=0.012; 82.2% vs 55.6%). To identify the independent prognostic role of miR-340 in chemotherapy group patients, Univariable and Multivariable Cox proportional hazards models were performed. We found that miR-340lowpatients showed shorter OS (P=0.0005; 5-year OS, 35.6% vs. 5.4%) and EFS (P=0.0005) compared with high expressers. In multivariable analysis, miR-340low patients showed reduced OS (P=0.004; HR: 2.07) and EFS (P=0.01; HR: 1.909) after adjusting other co-variates, such as age, WBC count and several genes mutation in chemotherapy group. Therefore, low miR-340 amounts could be an independent adverse bio-marker in AML patients undergoing chemotherapy. However, in the allo-HSCT group, miR-340 expression level was not associated with outcome in AML patients. To further explore the potential of allo-HSCT in overcoming the adverse characteristics of low miR-340 amounts, the whole 162 patients were regrouped into miR-340low and miR-340high groups. Then patients were divided into chemotherapy and allo-HSCT subgroups. Subgroup analysis revealed that miR-340low patients had significantly longer OS (P<0.0001; HR: 0.316; 95%CI: 0.167-0.459) and EFS (P=0.002; HR: 0.391; 95%CI: 0.231-0.622) in allo-HSCT subgroup than in chemotherapy subgroup (Figure 1). However, in cases highly expressing miR-340, no difference in survival events was detected between the two treatment subgroups. These findings indicated, allo-HSCT may overcome the adverse prognostic effects of low mir-340 expression. Therefore, for low miR-340 cases, early allo-HSCT may be a better option. To explore underlying biological functions of miR-340, we examined gene expression signatures related to the miR-340 expression in AML patients. We observed 135 genes expression levels that associated with miR-340 expression, with 61 and 74 showing positive and negative correlations, respectively. Gene Ontology showed that these genes involved in cellular and developmental processes, transcription regulation, immune system process, cell apoptosis and proliferation, myeloid cell differentiation and hematopoietic organ development. Furthermore, miR-340 expression was negatively correlated with HOXA and HOXB cluster levels. Strikingly, HOXA10, HOXB2, MEIS1 and PRDM16 were predicted miR-340 targets according to in silico analysis. The results hint a prospective regulatory mechanism that links miR-340 to HOXA genes associated with AML. Conclusions: Our data indicate that decreased miR-340 expression predicts an adverse prognosis and allo-HSCT may overcome the potential adverse characteristics of low miR-340 expression. Therefore, lower miR-340 cases should be strongly considered for early allo-HSCT. Disclosures No relevant conflicts of interest to declare.

Outcome after Relapse of Childhood Acute Myeloid Leukemia: The St. Jude Experience.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 273-273
Author(s):  
Jeffrey Rubnitz ◽  
Bassem Razzouk ◽  
Shelly Lensing ◽  
Stanley Pounds ◽  
Ching-Hon Pui ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Proportional Hazards ◽  
Cox Proportional Hazards ◽  
Cell Transplant ◽  
Hematopoietic Stem ◽  
Significant Difference ◽  
First Remission ◽  
Acute Myeloid

Abstract We reviewed the records of 408 patients who were less than 21 years old at the time of diagnosis of acute myeloid leukemia (excluding patients with Down syndrome or acute promyelocytic leukemia) treated on five consecutive institution protocols from 1980–2002 to investigate prognostic factors for attainment of second complete remission (CR2) and overall survival (OS) after first relapse. Of the 320 (78%) patients who achieved CR, 158 patients suffered hematologic relapses at a median of 11.9 months (range, 2.9–119.9 months) from the time of diagnosis. Forty-one patients relapsed on therapy and 117 relapsed after the completion of all planned therapy. For patients who relapsed off therapy, 38 were diagnosed with relapse because of symptoms suggestive of recurrent leukemia and 78 were diagnosed at the time of a routine follow up (information not available for one patient). After relapse, 20 patients received palliative care, 82 received chemotherapy alone, 36 received chemotherapy followed by hematopoietic stem cell transplant (SCT), and 20 proceeded directly to SCT. Eighty-five (54%) patients attained CR2. In univariate analyses, factors associated with the achievement of CR2 include initial therapy (chemotherapy alone, 56%; autologous SCT, 71%; allogeneic SCT, 20%; p=0.008) and time from the diagnosis of AML to relapse (≤ 1 year, 44%; &gt; 1 year, 65%; p=0.010). Logistic regression analysis demonstrated that patients with male gender (odds ratio [OR], 2.46; 95% confidence interval [CI], 1.14–5.28; p=0.021) and greater time from diagnosis to relapse (OR, 1.05; CI, 1.01–1.09; p=0.016) were more likely to achieve CR2, whereas patients with M7 morphology (OR, 0.11; CI, 0.01–1.04; p=0.054) and allogeneic SCT in first remission (OR, 0.17; CI, 0.03–0.85; p=0.031) were less likely to achieve CR2. At the time of last follow up, 19 patients were alive, 115 died of progressive disease, and 24 died of regimen-related toxicity. The 2-year OS estimate ± SE for the entire cohort of 158 patients was 15.8% ± 2.8%. For patients who relapsed off therapy, there was no significant difference in outcome between those whose relapse was diagnosed at the time of a routine follow up and those diagnosed because of symptoms. Cox proportional-hazards regression modeling indicated that M7 morphology (hazard ratio [HR], 3.06; CI, 1.44–6.51; p=0.004) and allogeneic SCT in first remission (HR, 2.17; CI, 1.22–3.87; p=0.008) were associated with significantly worse OS after relapse. In fact, there were no survivors in these two groups of patients. In contrast, age 1–10 years (HR, 0.53; CI, 0.36–0.77; p=0.001), M2 morphology (HR, 0.57; CI, 0.39–0.85; p=0.006), allogeneic SCT after relapse (HR, 0.34; CI, 0.22–0.53; p&lt;0.001), and greater time from diagnosis to relapse (HR, 0.97; CI, 0.95–0.99; p=0.003) had significantly favorable effects on OS. However, outcome was poor even among patients who underwent allogeneic SCT after relapse (2-year OS, 34.5% ± 6.1%) and among patients who relapsed greater than one year from diagnosis (2-year OS, 19.2% ± 4.3%), suggesting that novel therapies are warranted for all patients with relapsed AML.

scholarly journals Computational deconvolution of gene expression in leukemic cell hierarchies

2019 ◽  
Author(s):  
Linnea Jäarvstråt ◽  
Ram Ajore ◽  
Anna-Karin Wihlborg ◽  
Urban Gullberg ◽  
Björn Nilsson
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Expression Profiles ◽  
Leukemic Cell ◽  
Computational Method ◽  
Specific Gene ◽  
Study Gene Expression ◽  
Acute Myeloid

AbstractLeukemias and some solid tumors are organized as cell hierarchies, sustained by cancer stem cells. We developed a computational method to study gene expression cancer cell hierarchies. Unlike traditional approaches based on physical cell sorting, our method extracts cell type-specific gene expression signals from gene expression profiles of unsorted tumor cells by deconvolution. We apply our method in the context of acute myeloid leukemia, and recover markers for acute myeloid leukemia stem cells (AML-LSC).

scholarly journals The characteristics of circRNA as competing endogenous RNA in pathogenesis of acute myeloid leukemia

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Siyuan Zhang
Keyword(s):  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Expression Profiles ◽  
Gene Expression Omnibus ◽  
The Novel ◽  
Competing Endogenous Rna ◽  
Regulatory Modules ◽  
Cerna Network ◽  
Regulatory Module ◽  
Acute Myeloid

Abstract Background As one of the novel molecules, circRNA has been identified closely involved in the pathogenesis of many diseases. However, the function of circRNA in acute myeloid leukemia (AML) still remains unknown. Methods In the current study, the RNA expression profiles were obtained from Gene Expression Omnibus (GEO) datasets. The differentially expressed RNAs were identified using R software and the competing endogenous RNA (ceRNA) network was constructed using Cytoscape. Functional and pathway enrichment analyses were performed to identify the candidate circRNA-mediated aberrant signaling pathways. The hub genes were identified by MCODE and CytoHubba plugins of Cytoscape, and then a subnetwork regulatory module was established. Results A total of 27 circRNA-miRNA pairs and 208 miRNA-mRNA pairs, including 12 circRNAs, 24 miRNAs and 112 mRNAs were included in the ceRNA network. Subsequently, a subnetwork, including 4 circRNAs, 5 miRNAs and 6 mRNAs, was established based on related circRNA-miRNA-mRNA regulatory modules. Conclusions In summary, this work analyzes the characteristics of circRNA as competing endogenous RNA in AML pathogenesis, which would provide hints for developing novel prognostic, diagnostic and therapeutic strategy for AML.

Patient-specific microRNA expression profiles as a marker for minimal residual disease in acute myeloid leukemia

Hematology ◽  
2013 ◽  
Vol 19 (1) ◽  
pp. 18-21 ◽  
Author(s):  
Velizar Shivarov ◽  
Angel Stoimenov ◽  
Branimir Spassov ◽  
Svetlana Angelova ◽  
Monika Niagolov ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Minimal Residual Disease ◽  
Myeloid Leukemia ◽  
Residual Disease ◽  
Expression Profiles ◽  
Microrna Expression ◽  
Patient Specific ◽  
Minimal Residual ◽  
Acute Myeloid

scholarly journals Invasive Fungal Disease in Patients with Newly Diagnosed Acute Myeloid Leukemia

2021 ◽  
Vol 7 (9) ◽  
pp. 761
Author(s):  
Anastasia I. Wasylyshyn ◽  
Kathleen A. Linder ◽  
Carol A. Kauffman ◽  
Blair J. Richards ◽  
Stephen M. Maurer ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Induction Chemotherapy ◽  
Myeloid Leukemia ◽  
Proportional Hazards ◽  
Invasive Fungal Disease ◽  
Fungal Disease ◽  
Antifungal Prophylaxis ◽  
Cell Transplant ◽  
Newly Diagnosed ◽  
Acute Myeloid

This single-center retrospective study of invasive fungal disease (IFD) enrolled 251 adult patients undergoing induction chemotherapy for newly diagnosed acute myeloid leukemia (AML) from 2014–2019. Patients had primary AML (n = 148, 59%); antecedent myelodysplastic syndrome (n = 76, 30%), or secondary AML (n = 27, 11%). Seventy-five patients (30%) received an allogeneic hematopoietic cell transplant within the first year after induction chemotherapy. Proven/probable IFD occurred in 17 patients (7%). Twelve of the 17 (71%) were mold infections, including aspergillosis (n = 6), fusariosis (n = 3), and mucomycosis (n = 3). Eight breakthrough IFD (B-IFD), seven of which were due to molds, occurred in patients taking antifungal prophylaxis. Patients with proven/probable IFD had a significantly greater number of cumulative neutropenic days than those without an IFD, HR = 1.038 (95% CI 1.018–1.059), p = 0.0001. By cause-specific proportional hazards regression, the risk for IFD increased by 3.8% for each day of neutropenia per 100 days of follow up. Relapsed/refractory AML significantly increased the risk for IFD, HR = 7.562 (2.585–22.123), p = 0.0002, and Kaplan-Meier analysis showed significantly higher mortality at 1 year in patients who developed a proven/probable IFD, p = 0.02. IFD remains an important problem among patients with AML despite the use of antifungal prophylaxis, and development of IFD is associated with increased mortality in these patients.

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