Signature In Acute Myeloid Leukemia Research Articles

A novel prognostic model based on pyroptosis signature in AML

Acute myeloid leukemia (AML), a highly heterogeneous myeloid malignancy, remains a challenge in terms of proper risk stratification. In this study, we developed a novel pyroptosis prognostic model based on pyroptosis-related gene pairs, which exhibited excellent prognostic performance across multiple cohorts (N = 1506) and accurately predicted both adult and pediatric AML prognosis. Additionally, we integrated the pyroptosis risk model with other clinical risk factors to construct a highly operational nomogram. Moreover, our findings indicate a significant correlation between elevated pyroptosis risk scores and increased stemness of AML. Using CIBERSORT immune analysis, we found a decreased proportion of resting NK cells and activated mast cells in the high-risk group. Through analyzing the correlation between chemotherapy drug response sensitivity and risk scores, we found that AZD1332 and BPD-0008900 were extremely sensitive in the high-risk group.

The Immune Resistance Signature of Acute Myeloid Leukemia and Current Immunotherapy Strategies.

Acute myeloid leukemia (AML) is a complex hematopoietic clonal disorder with limited curative options beyond stem cell transplantation. The success of transplant is intimately linked with the graft versus leukemia effect from the alloreactive donor immune cells including, T and NK cells. The immune system plays a dynamic role in leukemia survival and resistance. Despite our growing understanding of the immune microenvironment, responses to immune-based therapies differ greatly between patients. Herein, we review the biology of immune evasion mechanisms in AML, discuss the current landscape of immunotherapeutic strategies, and discuss the implications of therapeutic targets. This review focuses on T and NK cell-based therapy, including modified and non-modified NK cells, CAR-T and CAR-NK cells, antibodies, and checkpoint blockades. Understanding the complex interchange between immune tolerance and the emergence of tumor resistance will improve patient outcomes.

Construction and validation of a necroptosis-related prognostic signature in acute myeloid leukemia.

Acute myeloid leukemia (AML), an uncommonly low 5-year survival and high mortality rate, is a potentially catastrophic diagnosed subtype of leukemia. The development of new prognostic markers is urgently needed to guide its treatment. Necroptosis is a newly defined biological process for regulating cell death, and previous studies have confirmed that the abnormality of the physical function can lead to multiple malignancies. Here, we performed necroptosis-related genes (NRGs) to build a predictive model in the Cancer Genome Atlas (TCGA)-AML patients, thus exploring the correlation between the NRG prognosis signature (NRG score) of this model and immune infiltration, pathway activity, clinical features, and immunotherapy. Besides, we computed the statistical measure Spearman rank correlation between the NRG score and the Log IC50 values of therapeutic agents. Subsequently, we divided the TCGA-AML cohort into 2 groups, one with high scores and the other with low scores depending on the model score. AML patients with high NRG scores exhibited a lower estimated overall survival (OS) rate than those with low NRG scores, which was confirmed in the validation set. The prognostic value of the constructed NRG signature to the AML, independent of other variables, was demonstrated by uni- and multivariate stepwise regression analysis. When comparing the infiltrating states of specialized cells associated with immune system from the 2 groups, B cells naive, Plasma cells, and monocytes represented significant differences among various subgroups of samples. Moreover, the 30 hallmark-related pathways related to necroptosis characteristics were remarkably different between the high/low NRG score groups. And patients showed remarkable NRG score distribution in clinical features of bone marrow lymphocyte, category, and FAB classifications. Besides, we found that the BIRB0796, VX680, Vorinostat, and Axitinib positively related with NRG score, whereas CI. 1040, PD. 0325901, Z.L LNle. CHO, and AZD6244 negatively correlated with the NRG score. These drugs may provide a reference for subsequent treatment.

Expression signature of ten small nuclear RNAs serves as novel biomarker for prognosis prediction of acute myeloid leukemia

This study aimed to screen for small nuclear RNAs (snRNAs) associated with the prognosis of acute myeloid leukemia (AML) by using The Cancer Genome Atlas (TCGA) whole-transcriptome sequencing dataset. A total of 130 AML patients from TCGA cohort with complete prognostic information and transcriptome data were enrolled in the current study. Comprehensive survival and functional enrichment analyses were performed to explore the prognostic value and potential biological functions of prognostic snRNAs in AML patients. In the current study, we screened 72 snRNAs that were notably associated with the clinical outcome of AML and developed an expression signature consist of ten snRNAs, that can be accurately applied to assess the overall survival of AML patients. Functional mechanism analysis revealed that this expression signature may be strongly linked to some classical tumor-associated pathways, such as Notch and Wnt pathways, as well as being closely related to B and T cell receptor pathways. Furthermore, we screened six compounds (chicago sky blue 6 B, 5230742, clorsulon, nefopam, nicardipine, and streptomycin) that may serve as targeted therapeutic drugs for AML using connectivity maps. Tumor immunoassays indicated significant differences in the immune microenvironment of the bone marrow tissue between high-risk and low-risk AML patients. Immune infiltration analysis also revealed significant differences in the abundance of multiple immune cells in the bone marrow of the two groups of AML patients groups. In conclusion, our results revealed a novel prognostic expression signature of AML consisting of ten snRNAs, and we conducted a preliminary exploration of its potential biological functions and tumor immunity.

The m6A modulator-mediated cytarabine sensitivity and immune cell infiltration signature in acute myeloid leukemia.

The study aims to investigate the impact of m6A modulators on drug resistance and the immune microenvironment in acute myeloid leukemia (AML). The emergence of drug resistance is a significant factor that contributes to relapse and refractory AML, leading to a poor prognosis. The AML transcriptome data were retrieved from the TCGA database. The "oncoPredict" R package was utilized to assess the sensitivity of each sample to cytarabine (Ara-C) and classify them into distinct groups. Differential expression analysis was performed to identify m6A modulators differentially expressed between the two groups. Select Random Forest (RF) to build a predictive model. Model performance was evaluated using calibration curve, clinical decision curve, and clinical impact curve. The impacts of METTL3 on Ara-C sensitivity and immune microenvironment in AML were examined using GO, KEGG, CIBERSORT, and GSEA analyses. Seventeen out of 26 m6A modulators exhibited differential expression between the Ara-C-sensitive and resistant groups, with a high degree of correlation. We selected the 5 genes with the highest scores in the RF model to build a reliable and accurate prediction model. METTL3 plays a vital role in m6A modification, and further analysis shows its impact on the sensitivity of AML cells to Ara-C through its interaction with 7 types of immune-infiltrating cells and autophagy. This study utilizes m6A modulators to develop a prediction model for the sensitivity of AML patients to Ara-C, which can assist in treating AML drug resistance by targeting mRNA methylation.

A novel necroptosis-related gene signature in acute myeloid leukemia

ABSTRACTObjective:Necroptosis has been reported to play an important role in different cancers, including leukemia. However, biomarkers of necroptosis-related genes (NRGs) that help predict the prognosis of AML are still lacking. Our research aims to build a novel signature of NRGs that could enhance our understanding of the molecular heterogeneity in leukemia.Method:Gene expression profiles as well as clinical features were downloaded from TCGA and GEO databases. Data analysis were executed using R software version 4.2.1 and GraphPad Prism version 9.0.0.Result:Univariate cox regression and lasso regression were applied to identify survival-specific genes. Four genes including FADD, PLA2G4A, PYCARD and ZBP1 were considered as independent risk factors that affect the prognosis of patients. Risk scores were calculated according to the coefficient of four genes. Then clinical characteristics and risk scores were enrolled to construct a nomogram. CellMiner was also used to screen potential drugs and analyze the correlations between genes and drug sensitivity.Conclusion:In general, we established a signature of four genes related to necroptosis that could be helpful for future risk stratification in patients with AML.

Single-Cell Profiling of CD8+ T Cells in Acute Myeloid Leukemia Reveals a Continuous Spectrum of Differentiation and Clonal Hyperexpansion.

Comprehensive investigation of CD8+ T cells in acute myeloid leukemia (AML) is essential for developing immunotherapeutic strategies beyond immune checkpoint blockade. Herein, we performed single-cell RNA profiling of CD8+ T cells from 3 healthy bone marrow donors and 23 newly diagnosed (NewlyDx) and 8 relapsed/refractory (RelRef) patients with AML. Cells coexpressing canonical exhaustion markers formed a cluster constituting <1% of all CD8+ T cells. We identified two effector CD8+ T-cell subsets characterized by distinct cytokine and metabolic profiles that were differentially enriched in NewlyDx and RelRef patients. We refined a 25-gene CD8-derived signature correlating with therapy resistance, including genes associated with activation, chemoresistance, and terminal differentiation. Pseudotemporal trajectory analysis supported enrichment of a terminally differentiated state in CD8+ T cells with high CD8-derived signature expression at relapse or refractory disease. Higher expression of the 25-gene CD8 AML signature correlated with poorer outcomes in previously untreated patients with AML, suggesting that the bona fide state of CD8+ T cells and their degree of differentiation are clinically relevant. Immune clonotype tracking revealed more phenotypic transitions in CD8 clonotypes in NewlyDx than in RelRef patients. Furthermore, CD8+ T cells from RelRef patients had a higher degree of clonal hyperexpansion associated with terminal differentiation and higher CD8-derived signature expression. Clonotype-derived antigen prediction revealed that most previously unreported clonotypes were patient-specific, suggesting significant heterogeneity in AML immunogenicity. Thus, immunologic reconstitution in AML is likely to be most successful at earlier disease stages when CD8+ T cells are less differentiated and have greater capacity for clonotype transitions.

Characterization of cuproptosis identified immune microenvironment and prognosis in acute myeloid leukemia.

Recent studies have reported that cuproptosis, a novel cell death pathway, strongly correlates with mitochondrial metabolism. In addition, the studies reported that cuproptosis plays a role in the development of several cancers and is regulated by protein lipoylation. During cuproptosis, copper binds to the lipoylated proteins and mediates cancer progression. However, the role of cuproptosis in acute myeloid leukemia (AML) patients is yet to be explored. This study curated seven cuproptosis-related-genes (CRGs): FDX1, DLAT, PDHB, PDHA1, DLD, LIAS, and LIPT1 to determine cuproptosis modification patterns and the CRGs signature in AML. The CIBERSORT and ssGSEA algorithms were utilized to evaluate the infiltration levels of different immune cell subtypes. A cuproptosis score system based on differentially expressed genes (DEGs) was constructed using the least absolute shrinkage and selection operator (LASSO) regression analysis. The developed cuproptosis score system was validated using two immunotherapy datasets, IMvigor210 and GSE78220. Three distinct cuproptosis regulation patterns were identified using the Beat AML cohort. The results demonstrated that the three cuproptosis regulation patterns were correlated with various biological pathways and clinical outcomes. Tumor microenvironment (TME) characterization revealed that the identified cuproptosis regulation patterns were consistent with three immune profiles: immune-desert, immune-inflamed, and immune-excluded. The AML patients were grouped into low- and high-score groups based on the cuproptosis score system abstracted from 486 cuproptosis-related DEGs. Patients with lower cuproptosis scores were characterized by longer survival time and attenuated immune infiltration. It was found that lower cuproptosis scores were strongly correlated with lower somatic mutation frequency. Moreover, patients with lower cuproptosis scores presented more favorable immune responses and dual clinical benefits among external validation cohorts. Cuproptosis phenotypes are significantly correlated with immune microenvironment complexity and variety. Cuprotopsis regulates the response of cancer cells to the immune system. Quantitatively assessing cuproptosis phenotypes in AML improves the understanding and knowledge regarding immune microenvironment characteristics and promotes the development of therapeutic interventions.

The prognostic signature based on glycolysis-immune related genes for acute myeloid leukemia patients

Acute myeloid leukemia (AML) is widely considered an immunoresponsive malignancy. However, potential association between glycolysis-immune related genes and AML patients’ prognosis has been seldom studied. AML-related data was downloaded from TCGA and GEO databases. We grouped patients according to Glycolysis status, Immune Score and combination analysis, basing on which overlapped differentially expressed genes (DEGs) were identified. The Risk Score model was then established. The results showed that totally 142 overlapped genes were probably correlated with glycolysis-immunity in AML patients, among which 6 optimal genes were screened to construct Risk Score. High Risk Score was an independent poor prognostic factor for AML. In conclusion, we established a relatively reliable prognostic signature of AML based on glycolysis-immunity related genes, including METTL7B, HTR7, ITGAX, TNNI2, SIX3 and PURG.

Extracellular Vesicle-Based Liquid Biopsy Shows Clinical Relevance and Reveals Links with Single-Cell Metabolic Signature in Acute Myeloid Leukemia

Background. Acute myeloid leukemia (AML) is an aggressive disease that shows dysregulated cell metabolism and a high relapse rate. To date, less invasive tools are urgently needed to explore disease dynamics in AML. In this regard, Extracellular Vesicles (EV) from plasma represent a promising tool for liquid biopsy. Also, the material extracted from blood (including circulating leukemic stem cells, LSC) can be used for clinical purposes revealing clinically relevant (metabolic) vulnerabilities. Along with EV profiling in AML patients, we explored the clinically relevant (metabolic) signature carried by CD34+ cells in circulation. Methods. Peripheral blood (PB) was collected from AML patients at diagnosis (n=70) and healthy donors (HD, n=20). EVs were purified from platelet-poor plasma by size exclusion chromatography and ultrafiltration. Quantitative lipidomic profiling was performed by Liquid Chromatography coupled with High-Resolution Mass Spectrometry (LC/HRMS). Single Cell ENergetic metabolism by Profiling Translation inhibition (SCENITH) has been performed in fresh whole blood. Results. We profiled the surface protein of isolated circulating EVs by AML patients at diagnosis. Compared to EV from HD, leukemic EV from newly diagnosed AML patients were mainly enriched in cancer stem cell marker, CD44. Intriguingly, the area under the curve (AUC) confirmed a reliable performance for employing this marker on EVs to discriminate EVs from AML patients. Among other 36 markers explored, CD4 (immune marker), CD105 (mesenchymal stromal cell marker), CD14 (monocyte marker), and CD133-1 (stem cell marker) were highly expressed only in leukemic EVs. In particular, CD11c as the well-known dendritic marker was solely expressed in EVs from some AML patients and totally absent in healthy EVs. By contrast, in circulating leukemic EVs, we observed depletion in markers such as CD62P, CD41b, and CD41a suggesting an impaired function in leukemic megakaryocytes and platelets. From the clinic point of view, according to European LeukemiaNet (ELN) 2017 risk classification, we observed that CD9, CD29, CD31, and CD42a were enriched in the favorable AML group in comparison with adverse/intermediate-risk AML patients. Notably, non-survivor AML patients showed a significant reduction in the expression of EV markers including CD11c, CD69, and ROR-1. Then, to further highlight crucial characteristics in EV composition, we performed an untargeted lipidomic analysis on circulating EVs. Fatty acids (FA) and Diacylglycerols (DG) were significantly overexpressed in leukemic EVs compared to healthy EVs. Leukemic EVs were depleted in Cholesteryl ester (CE) suggesting an increase in membrane stiffness. Interestingly, the lipid CE18:2 was found high in adverse-risk AML patients encouraging further studies on EV lipidomic profiles for better AML stratification. An in-depth investigation of the metabolic dependencies of leukemia (stem) cells from blood might be crucial for detecting novel metabolic vulnerabilities in AML patients. Thus, we applied the innovative SCENITH approach in fresh blood from AML patients at diagnosis. We found that circulating AML CD34+ cells were highly dependent on glucose oxidation and less prone to use fatty acids and amino acids as sources for ATP production when glucose oxidation was inhibited. Also, AML CD34+ cells in circulation reported a higher glycolytic capacity compared to mitochondrial dependence. Towards a clinically relevant implication, SCENITH analysis showed that mitochondrial dependence was solely increased in adverse and intermediate-risk AML patients compared to favorable AML patients. Interestingly, the percentage of mitochondrial dependence in AML CD34+ was positively correlated to the expression of CD24 (cancer stem marker) observed on leukemic EVs suggesting a novel potential link between EV profiling and energy metabolism for leukemia. Conclusion. Overall, these results demonstrate that an abnormal signature characterizes the phenotype of circulating EVs in AML patients. Indeed, the depletion of selected EV markers could be associated with high-risk AML disease and supports their prognostic relevance. This work might reveal novel metabolic vulnerabilities in the AML scenario by exploiting both EV-based liquid biopsy and single-cell metabolic phenotyping.

Repressive β-Catenin-Ikaros Complexes Are Essential to Prevent Clonal Evolution of Human Lymphopoiesis

Introduction β-catenin signaling represents a central driver of proliferation and survival in multiple epithelial, neuronal, and mesenchymal lineages, but is dispensable for hematopoietic development. Illegitimate activation of Wnt/β-catenin signaling induce development arrest at progenitor stages and underlies development of myeloid dysplastic syndrome (MDS). Moreover, β-catenin is required for emergence and self-renewal of leukemia stem cells (LSC), which are responsible for initiation and relapse of acute myeloid leukemia (AML). Experimental approach and results Our global interactome and gene editing experiments revealed that β-catenin engages lymphoid-specific Ikaros zinc finger (IKZF) factors to repress MYC and restrict lymphoid cell proliferation. Therefore, we reasoned that genetic deletion of β-catenin in human hematopoietic stem/progenitor cells (HSPC) could selectively benefit lymphoid development, which could be useful under lymphopenic conditions, immunosenescence and myeloid skewing in elderly. To this end, we introduced Crispr/Cas9 mediated deletion of β-catenin in CD34+ HSPCs from human cord blood and injected them into immune-deficient recipients for assessing multi-lineage reconstitution of human hematopoiesis. Compared to the controls, mice that received β-catenin-deleted progenitor cells showed increased human chimerism in the peripheral blood at 10 and 15 weeks after transplantation. Comparing absolute cell numbers, β-catenin-deficient progenitors gave rise to markedly increased human B-cell and T-cell production in the bone marrow and spleen, while myeloid populations were largely unchanged. Mice receiving β-catenin deficient cells contained significantly more human thymocytes compared to the control mice. These findings suggest that genetic deletion of β-catenin does not adversely impact human hematopoiesis and instead relieves lymphoid-intrinsic repression of B- and T-lymphopoiesis by β-catenin:IKZF complexes. Therefore, we hypothesized that deletion of β-catenin in pre-leukemic cells from MDS patients would favor generation of normal lymphocytes and prevent transformation into AML. To test this hypothesis, we deleted β-catenin in CD34+ HSPCs derived from bone marrow of MDS patients and injected them into immune-deficient recipients. 16 weeks after transplantation, we detected human B cells only in the blood of the recipients that received β-catenin deficient HSPCs but the mice that were injected with control cells only had myeloid cells in their blood. Interestingly, β-catenin deletion increased lymphoid cell generation by 5-and 2-fold in the bone marrow and spleen, respectively. Pseudo-bulk analysis of single-cell RNA sequencing of MDS-derived bone marrow cells revealed that upon β-catenin deletion, genes that define leukemic stem cell signature in AML (LSC17) such as CD34, SOCS2, EMP1 etc. were repressed. Strikingly, β-catenin deleted bone marrow progenitors from MDS patients could migrate to the thymus and give rise to de-novo thymopoeisis, while none of the mice that received control cells could generate human thymocytes. Although β-catenin deletion improved human lymphopoiesis from pre-leukemic HSPCs, we observed evolution into T-ALL and CD8+ TCR γδ T-cell lymphoma in two cases studied. In the first case human thymocytes generated from HSPCs with 5q- deletion, were arrested at CD4CD8 double positive stage (CD7+ CD3-), resembling a subgroup of T-cell acute lymphoblastic leukemia (T-ALL) with 5q- deletions. In the second case, deleting β-catenin in HSPCs carrying EZH2G660V mutation led to clonal expansion of CD8+ γδ-T cells in spleen of the mice. Conclusion In summary, deletion of β-catenin in human HSPCs improved lymphoid output in humanized mice. However, in the absence of β-catenin-IKZF mediated tumor-suppression, HSPCs carrying 5q- deletion and EZH2G660V mutation evolved into T-ALL and γδ-T cell lymphoma, respectively. These results suggest, although targeting Wnt/β-catenin pathway may be a promising strategy to treat MDS and AML and improve lymphopoiesis, interference with β-catenin-IKZF mediated restraint of lymphoid expansion may unleash pathological lymphocytes and lead to development of lymphoid malignancies. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

A novel 10-gene ferroptosis-related prognostic signature in acute myeloid leukemia.

Acute myeloid leukemia (AML) is one of the most common hematopoietic malignancies and exhibits a high rate of relapse and unfavorable outcomes. Ferroptosis, a relatively recently described type of cell death, has been reported to be involved in cancer development. However, the prognostic value of ferroptosis-related genes (FRGs) in AML remains unclear. In this study, we found 54 differentially expressed ferroptosis-related genes (DEFRGs) between AML and normal marrow tissues. 18 of 54 DEFRGs were correlated with overall survival (OS) (P<0.05). Using the least absolute shrinkage and selection operator (LASSO) Cox regression analysis, we selected 10 DEFRGs that were associated with OS to build a prognostic signature. Data from AML patients from the International Cancer Genome Consortium (ICGC) cohort as well as the First Affiliated Hospital of Wenzhou Medical University (FAHWMU) cohort were used for validation. Notably, the prognostic survival analyses of this signature passed with a significant margin, and the riskscore was identified as an independent prognostic marker using Cox regression analyses. Then we used a machine learning method (SHAP) to judge the importance of each feature in this 10-gene signature. Riskscore was shown to have the highest correlation with this 10-gene signature compared with each gene in this signature. Further studies showed that AML was significantly associated with immune cell infiltration. In addition, drug-sensitive analysis showed that 8 drugs may be beneficial for treatment of AML. Finally, the expressions of 10 genes in this signature were verified by real-time quantitative polymerase chain reaction. In conclusion, our study establishes a novel 10-gene prognostic risk signature based on ferroptosis-related genes for AML patients and FRGs may be novel therapeutic targets for AML.

A distinct lipid metabolism signature of acute myeloid leukemia with prognostic value.

BackgroundAcute myeloid leukemia (AML) is a highly aggressive hematological malignancy characterized by extensive genetic abnormalities that might affect the prognosis and provide potential drug targets for treatment. Reprogramming of lipid metabolism plays important roles in tumorigenesis and progression and has been newly recognized a new hallmark of malignancy, and some related molecules in the signal pathways could be prognostic biomarkers and potential therapeutic targets for cancer treatment. However, the clinical value of lipid metabolism reprogramming in AML has not been systematically explored. In this study, we aim to explore the clinical value of lipid metabolism reprogramming and develop a prognostic risk signature for AML.MethodsWe implemented univariate Cox regression analysis to identify the prognosis-related lipid metabolism genes, and then performed LASSO analysis to develop the risk signature with six lipid metabolism-related genes (LDLRAP1, PNPLA6, DGKA, PLA2G4A, CBR1, and EBP). The risk scores of samples were calculated and divided into low- and high-risk groups by the median risk score.ResultsSurvival analysis showed the high-risk group hold the significantly poorer outcomes than the low-risk group. The signature was validated in the GEO datasets and displayed a robust prognostic value in the stratification analysis. Multivariate analysis revealed the signature was an independent prognostic factor for AML patients and could serve as a potential prognostic biomarker in clinical evaluation. Furthermore, the risk signature was also found to be closely related to immune landscape and immunotherapy response in AML.ConclusionsOverall, we conducted a comprehensive analysis of lipid metabolism in AML and constructed a risk signature with six genes related to lipid metabolism for the malignancy, prognosis, and immune landscape of AML, and our study might contribute to better understanding in the use of metabolites and metabolic pathways as the potential prognostic biomarkers and therapeutic targets for AML.

Identification of the Integrated Prognostic Signature Associated with Immuno-relevant Genes and Long Non-coding RNAs in Acute Myeloid Leukemia

Background Like other cancers, considerable effort has been made in acute myeloid leukemia (AML) to identify prognostic genes and long noncoding RNAs (lncRNAs) with their potential clinical applications. However, to date, no integrated prognostic model has been developed that combines both gene expression and lncRNAs as a singular approach in AML. Method Comprehensive bioinformatic approaches (Weighted gene co-expression network analysis, Univariate Cox regression analyses, Pearson correlation, LASSO-Cox regression, Wilcoxon test) were used to construct the signature and to define high- and low-risk groups in AML datasets. ESTIMATE and CIBERSORT algorithms were applied to investigate the potential impact of infiltrating immune cells based on the obtained signature in tumor microenvironment. In addition, gene ontology (GO) and KEGG enrichment were applied to explore the potential function of the signature. Results Herein, we focused on immune-related genes (IRGs) and immune-related long noncoding RNAs (IRlncRNAs) and constructed an integrated prognostic immunorelevant signature in AML. The obtained signature exhibit five IRGs (DAXX, PSMB8, CSRP1, RAC2 and PTPN6) and one IRlncRNA (AC080037.2) and is strictly associated with age and FAB (French–American–British classification). Importantly, the high-risk AML group (defined by the signature) correlated positively with three types of scores (immune score, stroma score, and ESTIMATE score). We also identified a few immune cells (resting mast cells and monocytes) potentially involved in the correlation between signature and survival of AML patients. The prognostic ability of the obtained signature was tested in the training cohort and then validated in both test and total cohorts. The pathway enrichment analysis confirmed the possible immune- related role of the signature. Conclusion We constructed an integrated prognostic signature comprising five immune-related protein-coding genes (IRPCG) (DAXX, PSMB8, CSRP1, RAC2, and PTPN6) and one immune-related lncRNA (AC080037.2) that may serve as potential biomarkers for predicting survival and further stratifying AML patients.

Comprehensive Analysis of a Ferroptosis Pattern and Associated Prognostic Signature in Acute Myeloid Leukemia.

Ferroptosis is a widespread form of programmed cell death. The environment of cancer cells makes them vulnerable to ferroptosis, including AML cells, yet the specific association between ferroptosis and AML outcome is little known. In this study, we utilized ferroptosis-related genes to distinguish two subtypes in TCGA cohort, which were subsequently validated in independent AML cohorts. The subtypes were linked with tumor-related immunological abnormalities, mutation landscape and pathway dysregulation, and clinical outcome. Further, we developed a 13-gene prognostic model for AML from DEG analysis in the two subtypes. A risk score was calculated for each patient, and then the overall group was stratified into high- and low-risk groups; the higher risk score correlated with short survival. The model was validated in both independent AML cohorts and pan-cancer cohorts, which demonstrated robustness and extended the usage of the model. A nomogram was constructed that integrated risk score, FLT3-ITD, TP53, and RUNX1 mutations, and age. This model had the additional value of discriminating the sensitivity of several chemotherapeutic drugs and ferroptosis inducers in the two risk groups, which increased the translational value of this model as a potential tool in clinical management. Through integrated analysis of ferroptosis pattern and its related model, our work shed new light on the relationship between ferroptosis and AML, which may facilitate clinical application and therapeutics.

Integrative genomic analysis of a novel small nucleolar RNAs prognostic signature in patients with acute myelocytic leukemia.

This study mainly used The Cancer Genome Atlas (TCGA) RNA sequencing dataset to screen prognostic snoRNAs of acute myeloid leukemia (AML), and used for the construction of prognostic snoRNAs signature for AML. A total of 130 AML patients with RNA sequencing dataset were used for prognostic snoRNAs screenning. SnoRNAs co-expressed genes and differentially expressed genes (DEGs) were used for functional annotation, as well as gene set enrichment analysis (GSEA). Connectivity Map (CMap) also used for potential targeted drugs screening. Through genome-wide screening, we identified 30 snoRNAs that were significantly associated with the prognosis of AML. Then we used the step function to screen a prognostic signature composed of 14 snoRNAs (SNORD72, SNORD38, U3, SNORA73B, SNORD79, SNORA73, SNORD12B, SNORA74, SNORD116-12, SNORA65, SNORA14, snoU13, SNORA75, SNORA31), which can significantly divide AML patients into high- and low-risk groups. Through GSEA, snoRNAs co-expressed genes and DEGs functional enrichment analysis, we screened a large number of potential functional mechanisms of this prognostic signature in AML, such as phosphatidylinositol 3-kinase-Akt, Wnt, epithelial to mesenchymal transition, T cell receptors, NF-kappa B, mTOR and other classic cancer-related signaling pathways. In the subsequent targeted drug screening using CMap, we also identified six drugs that can be used for AML targeted therapy, they were alimemazine, MG-262, fluoxetine, quipazine, naltrexone and oxybenzone. In conclusion, our current study was constructed an AML prognostic signature based on the 14 prognostic snoRNAs, which may serve as a novel prognostic biomarker for AML.

TGF-β1 potentiates Vγ9Vδ2 T cell adoptive immunotherapy of cancer

SummaryDespite its role in cancer surveillance, adoptive immunotherapy using γδ T cells has achieved limited efficacy. To enhance trafficking to bone marrow, circulating Vγ9Vδ2 T cells are expanded in serum-free medium containing TGF-β1 and IL-2 (γδ[T2] cells) or medium containing IL-2 alone (γδ[2] cells, as the control). Unexpectedly, the yield and viability of γδ[T2] cells are also increased by TGF-β1, when compared to γδ[2] controls. γδ[T2] cells are less differentiated and yet display increased cytolytic activity, cytokine release, and antitumor activity in several leukemic and solid tumor models. Efficacy is further enhanced by cancer cell sensitization using aminobisphosphonates or Ara-C. A number of contributory effects of TGF-β are described, including prostaglandin E2 receptor downmodulation, TGF-β insensitivity, and upregulated integrin activity. Biological relevance is supported by the identification of a favorable γδ[T2] signature in acute myeloid leukemia (AML). Given their enhanced therapeutic activity and compatibility with allogeneic use, γδ[T2] cells warrant evaluation in cancer immunotherapy.

Adrenomedullin Expression Characterizes Leukemia Stem Cells and Associates With an Inflammatory Signature in Acute Myeloid Leukemia.

Adrenomedullin (ADM) is a hypotensive and vasodilator peptide belonging to the calcitonin gene-related peptide family. It is secreted in vitro by endothelial cells and vascular smooth muscle cells, and is significantly upregulated by a number of stimuli. Moreover, ADM participates in the regulation of hematopoietic compartment, solid tumors and leukemias, such as acute myeloid leukemia (AML). To better characterize ADM involvement in AML pathogenesis, we investigated its expression during human hematopoiesis and in leukemic subsets, based on a morphological, cytogenetic and molecular characterization and in T cells from AML patients. In hematopoietic stem/progenitor cells and T lymphocytes from healthy subjects, ADM transcript was barely detectable. It was expressed at low levels by megakaryocytes and erythroblasts, while higher levels were measured in neutrophils, monocytes and plasma cells. Moreover, cells populating the hematopoietic niche, including mesenchymal stem cells, showed to express ADM. ADM was overexpressed in AML cells versus normal CD34+ cells and in the subset of leukemia compared with hematopoietic stem cells. In parallel, we detected a significant variation of ADM expression among cytogenetic subgroups, measuring the highest levels in inv(16)/t(16;16) or complex karyotype AML. According to the mutational status of AML-related genes, the analysis showed a lower expression of ADM in FLT3-ITD, NPM1-mutated AML and FLT3-ITD/NPM1-mutated cases compared with wild-type ones. Moreover, ADM expression had a negative impact on overall survival within the favorable risk class, while showing a potential positive impact within the subgroup receiving a not-intensive treatment. The expression of 135 genes involved in leukemogenesis, regulation of cell proliferation, ferroptosis, protection from apoptosis, HIF-1α signaling, JAK-STAT pathway, immune and inflammatory responses was correlated with ADM levels in the bone marrow cells of at least two AML cohorts. Moreover, ADM was upregulated in CD4+ T and CD8+ T cells from AML patients compared with healthy controls and some ADM co-expressed genes participate in a signature of immune tolerance that characterizes CD4+ T cells from leukemic patients. Overall, our study shows that ADM expression in AML associates with a stem cell phenotype, inflammatory signatures and genes related to immunosuppression, all factors that contribute to therapy resistance and disease relapse.

TGF-β1 Potentiates Adoptive Immunotherapy of Hematological and Solid Tumors Using ex vivo Expanded γδ T-Cells

Despite their role in cancer surveillance, adoptive immunotherapy using γδ T-cells has achieved limited efficacy. To enhance trafficking to bone marrow, circulating γδ T-cells were expanded in serum-free medium containing TGF-β1 and IL-2 (γδ[T2] cells).Unexpectedly, the yield and viability of γδ[T2] cells were also increased by TGF-β1,when compared to γδ[2] controls (IL-2 alone). γδ[T2] cells were less differentiated and yet displayed increased cytolytic activity, cytokine release and anti-tumor activity in several leukemic and solid tumor models. Efficacy was further enhanced by cancer cell sensitization using amino bisphosphonates or cytarabine, or by CAR re-programming. A number of contributory effects of TGF-β1 were identified, including prostaglandinE2 receptor downmodulation, upregulation of CD103 and enhanced IL-9 production by γδ[T2] cells. Biological relevance is supported by the identification of a favorable γδ[T2] signature in acute myeloid leukemia. Given their enhanced therapeutic activity and compatibility with allogeneic use, γδ[T2] cells warrant evaluation in cancer immunotherapy.

NBIA: a network-based integrative analysis framework \u2013 applied to pathway analysis

With the explosion of high-throughput data, effective integrative analyses are needed to decipher the knowledge accumulated in biological databases. Existing meta-analysis approaches in systems biology often focus on hypothesis testing and neglect real expression changes, i.e. effect sizes, across independent studies. In addition, most integrative tools completely ignore the topological order of gene regulatory networks that hold key characteristics in understanding biological processes. Here we introduce a novel meta-analysis framework, Network-Based Integrative Analysis (NBIA), that transforms the challenging meta-analysis problem into a set of standard pathway analysis problems that have been solved efficiently. NBIA utilizes techniques from classical and modern meta-analysis, as well as a network-based analysis, in order to identify patterns of genes and networks that are consistently impacted across multiple studies. We assess the performance of NBIA by comparing it with nine meta-analysis approaches: Impact Analysis, GSA, and GSEA combined with classical meta-analysis methods (Fisher’s and the additive method), plus the three MetaPath approaches that employ multiple datasets. The 10 approaches have been tested on 1,737 samples from 27 expression datasets related to Alzheimer’s disease, acute myeloid leukemia (AML), and influenza. For all of the three diseases, NBIA consistently identifies biological pathways relevant to the underlying diseases while the other 9 methods fail to capture the key phenomena. The identified AML signature is also validated on a completely independent cohort of 167 AML patients. In this independent cohort, the proposed signature identifies two groups of patients that have significantly different survival profiles (Cox p-value 2 × 10−6). The NBIA framework will be included in the next release of BLMA Bioconductor package (http://bioconductor.org/packages/release/bioc/html/BLMA.html).