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Lu J, Zheng G, Dong A, Chang X, Cao X, Liu M, Shi X, Wang C, Yang Y, Jia X. Prognostic characteristics of immune subtypes associated with acute myeloid leukemia and their identification in cell subsets based on single-cell sequencing analysis. Front Cell Dev Biol 2022; 10:990034. [PMID: 36211454 PMCID: PMC9540204 DOI: 10.3389/fcell.2022.990034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 09/05/2022] [Indexed: 11/19/2022] Open
Abstract
Immune genes play an important role in the development and progression of acute myeloid leukemia (AML). However, the role of immune genes in the prognosis and microenvironment of AML remains unclear. In this study, we analyzed 151 AML patients in the TCGA database for relevant immune cell infiltration. AML patients were divided into high and low immune cell infiltration clusters based on ssGSEA results. Immune-related pathways, AML pathways and glucose metabolism pathways were enriched in the high immune cell infiltration cluster. Then we screened the differential immune genes between the two immune cell infiltration clusters. Nine prognostic immune genes were finally identified in the train set by LASSO-Cox regression. We constructed a model in the train set based on the nine prognostic immune genes and validated the predictive capability in the test set. The areas under the ROC curve of the train set and the test set for ROC at 1, 3, 5 years were 0.807, 0.813, 0.815, and 0.731, 0.745, 0.830, respectively. The areas under ROC curve of external validation set in 1, 3, and 5 years were 0.564, 0.619, and 0.614, respectively. People with high risk scores accompanied by high TMB had been detected with the worst prognosis. Single-cell sequencing analysis revealed the expression of prognostic genes in AML cell subsets and pseudo-time analysis described the differentiation trajectory of cell subsets. In conclusion, our results reveal the characteristics of immune microenvironment and cell subsets of AML, while it still needs to be confirmed in larger samples studies. The prognosis model constructed with nine key immune genes can provide a new method to assess the prognosis of AML patients.
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Affiliation(s)
- Jie Lu
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Guowei Zheng
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Ani Dong
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Xinyu Chang
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Xiting Cao
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Mengying Liu
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Xuezhong Shi
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Chunmei Wang
- Children’s Hospital, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yongli Yang
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Xiaocan Jia
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
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Identification of Protein Biomarker Signatures for Acute Myeloid Leukemia (AML) Using Both Nontargeted and Targeted Approaches. Proteomes 2021; 9:proteomes9040042. [PMID: 34842843 PMCID: PMC8628952 DOI: 10.3390/proteomes9040042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 12/17/2022] Open
Abstract
Acute myeloid leukemia (AML) is characterized by an increasing number of clonal myeloid blast cells which are incapable of differentiating into mature leukocytes. AML risk stratification is based on genetic background, which also serves as a means to identify the optimal treatment of individual patients. However, constant refinements are needed, and the inclusion of significant measurements, based on the various omics approaches that are currently available to researchers/clinicians, have the potential to increase overall accuracy with respect to patient management. Using both nontargeted (label-free mass spectrometry) and targeted (multiplex immunoassays) proteomics, a range of proteins were found to be significantly changed in AML patients with different genetic backgrounds. The inclusion of validated proteomic biomarker panels could be an important factor in the prognostic classification of AML patients. The ability to measure both cellular and secreted analytes, at diagnosis and during the course of treatment, has advantages in identifying transforming biological mechanisms in patients, assisting important clinical management decisions.
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Liu H, Zhang X, Li M, Zhou W, Jiang G, Yin W, Song C. The incidence and prognostic effect of Fms-like tyrosine kinase 3 gene internal tandem and nucleolar phosphoprotein 1 genes in acute myeloid leukaemia: A PRISMA-compliant systematic review and meta-analysis. Medicine (Baltimore) 2020; 99:e23707. [PMID: 33371116 PMCID: PMC7748362 DOI: 10.1097/md.0000000000023707] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 11/17/2020] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Molecular genotyping is an important prognostic role in acute myeloid leukemia (AML) patients. We aimed to design this meta-analysis to discuss the incidence and prognostic effect of nucleolar phosphoprotein 1 (NPM1) and Fms-like tyrosine kinase 3 gene internal tandem (FLT3-ITD) gene in AML patients. METHODS PubMed, Embase, Medline, and Cochrane library were systematically searched due to May 15, 2020. Four combinations of genotypes (FLT3-ITDneg/NPM1mut, FLT3-ITDpos/NPM1mut, FLT3-ITDneg/NPM1wt, FLT3-ITDpos/NPM1wt) were compared in association with the overall survival (OS) and leukemia-free survival (LFS) outcome, which expressed as pooled hazard ratio (HR) and 95% confidence intervals (CIs). RESULTS Twenty-eight studies were included in our study. The incidence of FLT3-ITDneg/NPM1mut, FLT3-ITDpos/NPM1mut, FLT3-ITDneg/NPM1wt, and FLT3-ITDpos/NPM1wt was 16%, 13%, 50%, and 10%, respectively. The patients with FLT3-ITDneg/NPM1mut gene may have the best OS and LFS when comparing with FLT3-ITDpos/NPM1mut (HR = 1.94 and 1.70, P < .01), FLT3-ITDneg/NPM1wt (HR = 1.57 and 2.09, P < .01), and FLT3-ITDpos/NPM1wt (HR = 2.25 and 2.84, P < .001). CONCLUSION AML patients with FLT3-ITDneg/NPM1mut gene type have the best survival outcome than the other 3 gene types, which should be an independent genotyping in AML classification.
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Affiliation(s)
| | | | - Ming Li
- Department of Laboratory Medicine
| | | | | | - Weihua Yin
- Department of Oncology, Yichun City People's Hospital
| | - Chunping Song
- Department of Blood Supply, Blood Station, Yichun City, Jiangxi Province, China
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Casas E, Ma H, Lippolis JD. Expression of Viral microRNAs in Serum and White Blood Cells of Cows Exposed to Bovine Leukemia Virus. Front Vet Sci 2020; 7:536390. [PMID: 33195511 PMCID: PMC7536277 DOI: 10.3389/fvets.2020.536390] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 08/17/2020] [Indexed: 12/16/2022] Open
Abstract
Bovine leukemia virus (BLV) affects the health and productivity of cattle. The virus causes abnormal immune function and immunosuppression. MicroRNAs (miRNAs) are involved in gene expression, having been associated with stress and immune response, tumor growth, and viral infection. The objective of this study was to determine the expression of circulating miRNAs produced by BLV in animals exposed to the virus. Sera from 14 animals were collected to establish IgG reactivity to BLV by ELISA, where seven animals were seropositive and seven were seronegative for BLV exposure. White blood cells (WBC) from each animal were also collected and miRNAs were identified by sequencing from sera and WBC. The seropositive group had higher counts of BLV miRNAs when compared to seronegative group in sera and WBC. Blv-miR-1-3p, blv-miR-B2-5p, blv-miR-B4-3p, and blv-miR-B5-5p were statistically significant (P < 0.00001) in serum with an average of 7 log2 fold difference between seropositive and seronegative groups. Blv-miR-B1-3p, blv-miR-B1-5p, blv-miR-B3, blv-miR-B4-3p, blv-miR-B4-5p, blv-miR-B5-5p were statistically significant (P < 1.08e−9) in WBC with an average of 7 log2 fold difference between the seropositive and the seronegative groups. Blv-miR-B2-3p and blv-miR-B2-5p were also statistically significant in WBC (P < 2.79e-17), with an average of 27 log2 fold difference between the seropositive and the seronegative groups. There were 18 genes identified as being potential targets for blv-miR-B1-5p, and 3 genes for blv-miR-B4-5p. Gene ontology analysis indicated that the target genes are mainly involved in the response to stress and in the immune system process. Several of the identified genes have been associated with leukemia development in humans and cattle. Differential expression of genes targeted by BLV miRNAs should be evaluated to determine their effect in BLV replication.
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Affiliation(s)
- Eduardo Casas
- National Animal Disease Center, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Ames, IA, United States
| | - Hao Ma
- National Animal Disease Center, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Ames, IA, United States
| | - John D Lippolis
- National Animal Disease Center, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Ames, IA, United States
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Liu X, Liu P, Chernock RD, Kuhs KA, Lewis JS, Luo J, Gay HA, Thorstad WL, Wang X. A prognostic gene expression signature for oropharyngeal squamous cell carcinoma. EBioMedicine 2020; 61:102805. [PMID: 33038770 PMCID: PMC7648117 DOI: 10.1016/j.ebiom.2020.102805] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/04/2020] [Accepted: 05/05/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Robust prognostic stratification of patients with oropharyngeal squamous cell carcinoma (OPSCC) is important for developing individualized treatment plans. This study was conducted to develop and validate a clinically feasible prognostic classifier based on transcriptome-wide gene expression profiles. METHODS Tumor tissues were collected from 208 OPSCC patients treated at Washington University in St. Louis and 130 OPSCC patients treated at Vanderbilt University, used for model training and validation, respectively. OPSCC patients (n = 70) from the TCGA cohort were also included for independent validation. Based on RNA-seq profiling data, Cox proportional hazards regression analysis was performed to identify genes associated with disease outcomes. Then, Lasso-penalized multivariate survival models were constructed to identify biomarker genes for developing a prognostic gene signature. FINDINGS A 60-gene signature was identified by RNA-seq profiling analysis. Computed risk score of the gene signature was significantly predictive of 5-year overall survival of the training cohort (Hazard ratio (HR) 28·32, P = 4·3E-41). Subgroup analysis stratified by HPV status revealed that the signature was prognostic in HPV-positive OPSCC patients (HR 30·55, P = 7·0E-37) and was independent of clinical features. Importantly, the gene signature was validated in two independent patient cohorts, including the TCGA cohort (HR 3·94, P = 0·0018) and the Vanderbilt cohort (HR 8·50, P = 5·7E-09) for overall survival. INTERPRETATION The prognostic gene signature is a robust tool for risk stratification of OPSCC patients. The signature remains prognostic among HPV-positive OPSCC patients. FUNDING National Institutes of Health.
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Affiliation(s)
- Xinyi Liu
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Ping Liu
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rebecca D. Chernock
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Krystle A.Lang Kuhs
- Department of Otolaryngology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - James S. Lewis
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jingqin Luo
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Hiram A. Gay
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Wade L. Thorstad
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Xiaowei Wang
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA.
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Clinical presentation and differential splicing of SRSF2, U2AF1 and SF3B1 mutations in patients with acute myeloid leukemia. Leukemia 2020; 34:2621-2634. [PMID: 32358566 DOI: 10.1038/s41375-020-0839-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 04/06/2020] [Accepted: 04/14/2020] [Indexed: 12/30/2022]
Abstract
Previous studies demonstrated that splicing factor mutations are recurrent events in hematopoietic malignancies with both clinical and functional implications. However, their aberrant splicing patterns in acute myeloid leukemia remain largely unexplored. In this study, we characterized mutations in SRSF2, U2AF1, and SF3B1, the most commonly mutated splicing factors. In our clinical analysis of 2678 patients, splicing factor mutations showed inferior relapse-free and overall survival, however, these mutations did not represent independent prognostic markers. RNA-sequencing of 246 and independent validation in 177 patients revealed an isoform expression profile which is highly characteristic for each individual mutation, with several isoforms showing a strong dysregulation. By establishing a custom differential splice junction usage pipeline, we accurately detected aberrant splicing in splicing factor mutated samples. A large proportion of differentially used junctions were novel, including several junctions in leukemia-associated genes. In SRSF2(P95H) mutants, we further explored the possibility of a cascading effect through the dysregulation of the splicing pathway. Furthermore, we observed a validated impact on overall survival for two junctions overused in SRSF2(P95H) mutants. We conclude that splicing factor mutations do not represent independent prognostic markers. However, they do have genome-wide consequences on gene splicing leading to dysregulated isoform expression of several genes.
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