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Pan Y, Zeng W, Nie X, Chen H, Xie C, Guo S, Xu D, Chen Y. Immunotherapy-relevance of a candidate prognostic score for Acute Myeloid Leukemia. Heliyon 2024; 10:e32154. [PMID: 38961904 PMCID: PMC11219318 DOI: 10.1016/j.heliyon.2024.e32154] [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: 07/26/2023] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 07/05/2024] Open
Abstract
Background Acute Myeloid Leukemia (AML) exhibits a wide array of phenotypic manifestations, progression patterns, and heterogeneous responses to immunotherapies, suggesting involvement of complex immunobiological mechanisms. This investigation aimed to develop an integrated prognostic model for AML by incorporating cancer driver genes, along with clinical and phenotypic characteristics of the disease, and to assess its implications for immunotherapy responsiveness. Methods Critical oncogenic driver genes linked to survival were identified by screening primary effector and corresponding gene pairs using data from The Cancer Genome Atlas (TCGA), through univariate Cox proportional hazard regression analysis. This was independently verified using dataset GSE37642. Primary effector genes were further refined using LASSO regression. Transcriptomic profiling was quantified using multivariate Cox regression, and the derived prognostic score was subsequently validated. Finally, a multivariate Cox regression model was developed, incorporating the transcriptomic score along with clinical parameters such as age, gender, and French-American-British (FAB) classification subtype. The 'Accurate Prediction Model of AML Overall Survival Score' (APMAO) was developed and subsequently validated. Investigations were conducted into functional pathway enrichment, alterations in the gene mutational landscape, and the extent of immune cell infiltration associated with varying APMAO scores. To further investigate the potential of APMAO scores as a predictive biomarker for responsiveness to cancer immunotherapy, we conducted a series of analyses. These included examining the expression profiles of genes related to immune checkpoints, the interferon-gamma signaling pathway, and m6A regulation. Additionally, we explored the relationship between these gene expression patterns and the Tumor Immune Dysfunction and Exclusion (TIDE) dysfunction scores. Results Through the screening of 95 cancer genes associated with survival and 313 interacting gene pairs, seven genes (ACSL6, MAP3K1, CHIC2, HIP1, PTPN6, TFEB, and DAXX) were identified, leading to the derivation of a transcriptional score. Age and the transcriptional score were significant predictors in Cox regression analysis and were integral to the development of the final APMAO model, which exhibited an AUC greater than 0.75 and was successfully validated. Notable differences were observed in the distribution of the transcriptional score, age, cytogenetic risk categories, and French-American-British (FAB) classification between high and low APMAO groups. Samples with high APMAO scores demonstrated significantly higher mutation rates and pathway enrichments in NFKB, TNF, JAK-STAT, and NOTCH signaling. Additionally, variations in immune cell infiltration and immune checkpoint expression, activation of the interferon-γ pathway, and expression of m6A regulators were noted, including a negative correlation between CD160, m6A expression, and APMAO scores. Conclusion The combined APMAO score integrating transcriptional and clinical parameters demonstrated robust prognostic performance in predicting AML survival outcomes. It was linked to unique phenotypic characteristics, distinctive immune and mutational profiles, and patterns of expression for markers related to immunotherapy sensitivity. These observations suggest the potential for facilitating precision immunotherapy and advocate for its exploration in upcoming clinical trials.
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Affiliation(s)
- Yiyun Pan
- Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu, China
- Ganzhou Cancer Hospital, Gannan Medical University, Ganzhou, 341000, Jiangxi, China
| | - Wen Zeng
- Ganzhou Cancer Hospital, Gannan Medical University, Ganzhou, 341000, Jiangxi, China
| | - Xiaoming Nie
- Ganzhou Cancer Hospital, Gannan Medical University, Ganzhou, 341000, Jiangxi, China
| | - Hailong Chen
- Ganzhou Cancer Hospital, Gannan Medical University, Ganzhou, 341000, Jiangxi, China
| | - Chuanhua Xie
- Ganzhou Cancer Hospital, Gannan Medical University, Ganzhou, 341000, Jiangxi, China
| | - Shouju Guo
- Ganzhou Cancer Hospital, Gannan Medical University, Ganzhou, 341000, Jiangxi, China
| | - Dechang Xu
- Ganzhou Cancer Hospital, Gannan Medical University, Ganzhou, 341000, Jiangxi, China
| | - Yijian Chen
- Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu, China
- The First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi, China
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Yu PC, Hou D, Chang B, Liu N, Xu CH, Chen X, Hu CL, Liu T, Wang X, Zhang Q, Liu P, Jiang Y, Fei MY, Zong LJ, Zhang JY, Liu H, Chen BY, Chen SB, Wang Y, Li ZJ, Li X, Deng CH, Ren YY, Zhao M, Jiang S, Wang R, Jin J, Yang S, Xue K, Shi J, Chang CK, Shen S, Wang Z, He PC, Chen Z, Chen SJ, Sun XJ, Wang L. SMARCA5 reprograms AKR1B1-mediated fructose metabolism to control leukemogenesis. Dev Cell 2024:S1534-5807(24)00296-X. [PMID: 38776924 DOI: 10.1016/j.devcel.2024.04.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 03/13/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
A significant variation in chromatin accessibility is an epigenetic feature of leukemia. The cause of this variation in leukemia, however, remains elusive. Here, we identify SMARCA5, a core ATPase of the imitation switch (ISWI) chromatin remodeling complex, as being responsible for aberrant chromatin accessibility in leukemia cells. We find that SMARCA5 is required to maintain aberrant chromatin accessibility for leukemogenesis and then promotes transcriptional activation of AKR1B1, an aldo/keto reductase, by recruiting transcription co-activator DDX5 and transcription factor SP1. Higher levels of AKR1B1 are associated with a poor prognosis in leukemia patients and promote leukemogenesis by reprogramming fructose metabolism. Moreover, pharmacological inhibition of AKR1B1 has been shown to have significant therapeutic effects in leukemia mice and leukemia patient cells. Thus, our findings link the aberrant chromatin state mediated by SMARCA5 to AKR1B1-mediated endogenous fructose metabolism reprogramming and shed light on the essential role of AKR1B1 in leukemogenesis, which may provide therapeutic strategies for leukemia.
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Affiliation(s)
- Peng-Cheng Yu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Dan Hou
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Binhe Chang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Na Liu
- Department of Hematology, Institute of Hematology, Shanghai Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Chun-Hui Xu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xinchi Chen
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Cheng-Long Hu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ting Liu
- Key Laboratory of Pediatric Hematology & Oncology of the Ministry of Health of China, Department of Hematology & Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xiaoning Wang
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Qunling Zhang
- Department of Medical Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Ping Liu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yilun Jiang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ming-Yue Fei
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Li-Juan Zong
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jia-Ying Zhang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hui Liu
- Key Laboratory of Pediatric Hematology & Oncology of the Ministry of Health of China, Department of Hematology & Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Bing-Yi Chen
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shu-Bei Chen
- School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yong Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zi-Juan Li
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiya Li
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chu-Han Deng
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yi-Yi Ren
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Muying Zhao
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shiyu Jiang
- Department of Medical Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Roujia Wang
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Jiacheng Jin
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Shaoxin Yang
- Department of Hematology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Kai Xue
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jun Shi
- Department of Hematology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Chun-Kang Chang
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Shuhong Shen
- Key Laboratory of Pediatric Hematology & Oncology of the Ministry of Health of China, Department of Hematology & Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Zhikai Wang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei 230027, China
| | - Peng-Cheng He
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Zhu Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Sai-Juan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiao-Jian Sun
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lan Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
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Pan Y, Xie F, Zeng W, Chen H, Chen Z, Xu D, Chen Y. T cell-mediated tumor killing sensitivity gene signature-based prognostic score for acute myeloid leukemia. Discov Oncol 2024; 15:121. [PMID: 38619693 PMCID: PMC11018597 DOI: 10.1007/s12672-024-00962-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/29/2024] [Indexed: 04/16/2024] Open
Abstract
BACKGROUND AND OBJECTIVE Acute myeloid leukemia (AML) is an aggressive, heterogenous hematopoetic malignancies with poor long-term prognosis. T-cell mediated tumor killing plays a key role in tumor immunity. Here, we explored the prognostic performance and functional significance of a T-cell mediated tumor killing sensitivity gene (GSTTK)-based prognostic score (TTKPI). METHODS Publicly available transcriptomic data for AML were obtained from TCGA and NCBI-GEO. GSTTK were identified from the TISIDB database. Signature GSTTK for AML were identified by differential expression analysis, COX proportional hazards and LASSO regression analysis and a comprehensive TTKPI score was constructed. Prognostic performance of the TTKPI was examined using Kaplan-Meier survival analysis, Receiver operating curves, and nomogram analysis. Association of TTKPI with clinical phenotypes, tumor immune cell infiltration patterns, checkpoint expression patterns were analysed. Drug docking was used to identify important candidate drugs based on the TTKPI-component genes. RESULTS From 401 differentially expressed GSTTK in AML, 24 genes were identified as signature genes and used to construct the TTKPI score. High-TTKPI risk score predicted worse survival and good prognostic accuracy with AUC values ranging from 75 to 96%. Higher TTKPI scores were associated with older age and cancer stage, which showed improved prognostic performance when combined with TTKPI. High TTKPI was associated with lower naïve CD4 T cell and follicular helper T cell infiltrates and higher M2 macrophages/monocyte infiltration. Distinct patterns of immune checkpoint expression corresponded with TTKPI score groups. Three agents; DB11791 (Capmatinib), DB12886 (GSK-1521498) and DB14773 (Lifirafenib) were identified as candidates for AML. CONCLUSION A T-cell mediated killing sensitivity gene-based prognostic score TTKPI showed good accuracy in predicting survival in AML. TTKPI corresponded to functional and immunological features of the tumor microenvironment including checkpoint expression patterns and should be investigated for precision medicine approaches.
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Affiliation(s)
- Yiyun Pan
- Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
- Ganzhou Cancer Hospital, Gannan Medical University, No.19, Huayuan Road, Zhanggong Avenue, Ganzhou, Jiangxi, People's Republic of China
| | - FangFang Xie
- Ganzhou People's Hospital, Ganzhou, 341000, Jiangxi, People's Republic of China
| | - Wen Zeng
- Ganzhou Cancer Hospital, Gannan Medical University, No.19, Huayuan Road, Zhanggong Avenue, Ganzhou, Jiangxi, People's Republic of China
| | - Hailong Chen
- Ganzhou Cancer Hospital, Gannan Medical University, No.19, Huayuan Road, Zhanggong Avenue, Ganzhou, Jiangxi, People's Republic of China
| | - Zhengcong Chen
- Ganzhou Cancer Hospital, Gannan Medical University, No.19, Huayuan Road, Zhanggong Avenue, Ganzhou, Jiangxi, People's Republic of China
| | - Dechang Xu
- Ganzhou Cancer Hospital, Gannan Medical University, No.19, Huayuan Road, Zhanggong Avenue, Ganzhou, Jiangxi, People's Republic of China.
| | - Yijian Chen
- Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.
- The First Affiliated Hospital of Gannan Medical University, No.23, Qingnian Road, Zhanggong Avenue, Ganzhou, 8105640, Jiangxi, People's Republic of China.
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4
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Gao L, Wang Y, Gao Q, Chen Y, Zhang Z. Transcriptional control of CCAAT/enhancer binding protein zeta gene in chicken adipose tissue. Poult Sci 2024; 103:103540. [PMID: 38417330 PMCID: PMC10907851 DOI: 10.1016/j.psj.2024.103540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/25/2024] [Accepted: 02/05/2024] [Indexed: 03/01/2024] Open
Abstract
CCAAT/enhancer binding protein zeta (C/EBPZ) was differentially expressed in abdominal adipose tissues of fat and lean broilers and regulated adipogenesis in chicken. The objective of this study was to elucidate the transcriptional regulation of C/EBPZ gene in chicken adipose tissue. A 2,031-base pair (bp) chicken C/EBPZ sequence (2,025 nucleotides upstream to 6 nucleotides downstream from the initiator codon, -2,025/+6) was studied. The sequence exhibited a significant promoter activity (P < 0.05) and had some cis-acting elements, notably, a core promoter was identified in nucleotides -94 to +6. Additionally, DNA pull-down assay showed that proteins interacted with chicken C/EBPZ promoter (-173/+6) in preadipocytes were implicated in transcription, post-transcriptional regulation and translation. In addition, KLF2 facilitated the activities of chicken C/EBPZ promoter (-2,025/+6, -1,409/+6, -793/+6, -485/+6, -173/+6, and -94/+6) in preadipocytes (P < 0.05). The expression levels of KLF2 and C/EBPZ in chicken abdominal adipose tissue were substantially associated (r = 0.5978278, P < 0.0001), and KLF2 increased C/EBPZ expression in vitro (P < 0.05). Additionally, chromatin immunoprecipitation (ChIP)-PCR analysis revealed that KLF2 has the ability to interact with the chicken C/EBPZ promoter regions at least at the positions -1,245/-1,048 and -571/-397. Mutation analysis showed that the CGCAGCGCCCG motif located in the chicken C/EBPZ promoter at positions -45 to -35 is involved in regulating transcription and facilitates trans activation by KLF2. These results provided some information of transcription control of C/EBPZ in chicken adipose tissue.
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Affiliation(s)
- Lingyu Gao
- Department of Histology and Embryology, Shihezi University School of Medicine, Shihezi, Xinjiang, 832000, PR China; Key Medical Laboratory of Stem Cell Transformation and Application, The First People's Hospital of Zhengzhou, Zhengzhou, Henan, 450000, PR China
| | - Yingjun Wang
- Department of Histology and Embryology, Shihezi University School of Medicine, Shihezi, Xinjiang, 832000, PR China
| | - Qin Gao
- Department of Histology and Embryology, Shihezi University School of Medicine, Shihezi, Xinjiang, 832000, PR China
| | - Yuechan Chen
- Department of Reproductive Medicine, The First Affiliated Hospital of Shihezi University, Shihezi, Xinjiang, 832000, PR China
| | - Zhiwei Zhang
- Department of Histology and Embryology, Shihezi University School of Medicine, Shihezi, Xinjiang, 832000, PR China.
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Uechi L, Vasudevan S, Vilenski D, Branciamore S, Frankhouser D, O'Meally D, Meshinchi S, Marcucci G, Kuo YH, Rockne R, Kravchenko-Balasha N. Transcriptome free energy can serve as a dynamic patient-specific biomarker in acute myeloid leukemia. NPJ Syst Biol Appl 2024; 10:32. [PMID: 38527998 DOI: 10.1038/s41540-024-00352-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 02/26/2024] [Indexed: 03/27/2024] Open
Abstract
Acute myeloid leukemia (AML) is prevalent in both adult and pediatric patients. Despite advances in patient categorization, the heterogeneity of AML remains a challenge. Recent studies have explored the use of gene expression data to enhance AML diagnosis and prognosis, however, alternative approaches rooted in physics and chemistry may provide another level of insight into AML transformation. Utilizing publicly available databases, we analyze 884 human and mouse blood and bone marrow samples. We employ a personalized medicine strategy, combining state-transition theory and surprisal analysis, to assess the RNA transcriptome of individual patients. The transcriptome is transformed into physical parameters that represent each sample's steady state and the free energy change (FEC) from that steady state, which is the state with the lowest free energy.We found the transcriptome steady state was invariant across normal and AML samples. FEC, representing active molecular processes, varied significantly between samples and was used to create patient-specific barcodes to characterize the biology of the disease. We discovered that AML samples that were in a transition state had the highest FEC. This disease state may be characterized as the most unstable and hence the most therapeutically targetable since a change in free energy is a thermodynamic requirement for disease progression. We also found that distinct sets of ongoing processes may be at the root of otherwise similar clinical phenotypes, implying that our integrated analysis of transcriptome profiles may facilitate a personalized medicine approach to cure AML and restore a steady state in each patient.
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Affiliation(s)
- Lisa Uechi
- Division of Mathematical Oncology and Computational Systems Biology, Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Swetha Vasudevan
- The Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem, 91120, Israel
| | - Daniela Vilenski
- The Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem, 91120, Israel
| | - Sergio Branciamore
- Division of Mathematical Oncology and Computational Systems Biology, Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - David Frankhouser
- Division of Mathematical Oncology and Computational Systems Biology, Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Denis O'Meally
- Department of Diabetes and Cancer Discovery Science, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, D5-112, Seattle, WA, 98109, USA
| | - Guido Marcucci
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - Ya-Huei Kuo
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - Russell Rockne
- Division of Mathematical Oncology and Computational Systems Biology, Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA.
| | - Nataly Kravchenko-Balasha
- The Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem, 91120, Israel.
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Mei X, Huang T, Chen A, Liu W, Jiang L, Zhong S, Shen D, Qiao P, Zhao Q. BmC/EBPZ gene is essential for the larval growth and development of silkworm, Bombyx mori. Front Physiol 2024; 15:1298869. [PMID: 38523808 PMCID: PMC10959570 DOI: 10.3389/fphys.2024.1298869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 02/19/2024] [Indexed: 03/26/2024] Open
Abstract
The genetic male sterile line (GMS) of the silkworm Bombyx mori is a recessive mutant that is naturally mutated from the wild-type 898WB strain. One of the major characteristics of the GMS mutant is its small larvae. Through positional cloning, candidate genes for the GMS mutant were located in a region approximately 800.5 kb long on the 24th linkage group of the silkworm. One of the genes was Bombyx mori CCAAT/enhancer-binding protein zeta (BmC/EBPZ), which is a member of the basic region-leucine zipper transcription factor family. Compared with the wild-type 898WB strain, the GMS mutant features a 9 bp insertion in the 3'end of open reading frame sequence of BmC/EBPZ gene. Moreover, the high expression level of the BmC/EBPZ gene in the testis suggests that the gene is involved in the regulation of reproduction-related genes. Using the CRISPR/Cas9-mediated knockout system, we found that the BmC/EBPZ knockout strains had the same phenotypes as the GMS mutant, that is, the larvae were small. However, the larvae of BmC/EBPZ knockout strains died during the development of the third instar. Therefore, the BmC/EBPZ gene was identified as the major gene responsible for GMS mutation.
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Affiliation(s)
- Xinglin Mei
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Tianchen Huang
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Anli Chen
- Key Sericultural Laboratory of Shaanxi, Ankang University, Ankang, Shaanxi, China
| | - Weibin Liu
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Li Jiang
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Shanshan Zhong
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Dongxu Shen
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu, China
| | - Peitong Qiao
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Qiaoling Zhao
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu, China
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7
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Shimony S, Chen EC. Tri-ing to decipher trisomy AML. Br J Haematol 2024; 204:751-752. [PMID: 38190804 DOI: 10.1111/bjh.19294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 12/27/2023] [Indexed: 01/10/2024]
Abstract
Lam et al. compared trisomy acute myeloid leukaemia (AML) patients (inclusive of single trisomy, double trisomy or tetrasomy cases) with cytogenetically normal AML to uncover distinguishing molecular and prognostic features of trisomy AML. The study contributes to our understanding of trisomy AML, but the heterogeneity of trisomy subtypes remains a barrier to its study. Commentary on: Lam et al. Distinct karyotypic and mutational landscape in trisomy AML. Br J Haematol 2024;204:939-944.
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Affiliation(s)
- Shai Shimony
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Rabin Medical Center and Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Evan C Chen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
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8
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Lam SSY, Tsui SP, Fung CY, Saw NY, Javed A, Ip AHW, Ma ESK, Leung AYH. Distinct karyotypic and mutational landscape in trisomy AML. Br J Haematol 2024; 204:939-944. [PMID: 38054248 DOI: 10.1111/bjh.19249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/07/2023]
Abstract
Trisomy karyotype occurs in 5%-10% of AML. Its mutational landscape and prognostic significance are not well defined. A cohort of 156 trisomy AML patients was analysed, with reference to 615 cytogenetically normal (CN) AML patients. Trisomy AML showed distinct mutational landscape with more prevalent SMC1A, N/KRAS, ASXL1 and BCOR but fewer CEBPAbZIP and NPM1 mutations in patients ≤60, and fewer NPM1 mutations in those >60. NRAS mutations were associated with poor outcome in trisomy AML, whereas DNMT3A and FLT3-ITD mutations had neutral effect. Trisomy AML appeared biologically distinct from CN-AML.
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Affiliation(s)
- Stephen S Y Lam
- Division of Haematology, Department of Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Sze P Tsui
- Division of Haematology, Department of Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Department of Pathology, Queen Mary Hospital, Hong Kong SAR, China
| | - C Y Fung
- Division of Haematology, Department of Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Nicole Y Saw
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Asif Javed
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Alvin H W Ip
- Department of Pathology, Queen Mary Hospital, Hong Kong SAR, China
| | - Edmond S K Ma
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanitorium & Hospital, Hong Kong SAR, China
| | - Anskar Y H Leung
- Division of Haematology, Department of Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- The Jockey Club Centre for Clinical Innovation and Discovery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China
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9
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Poiré X, Labopin M, Polge E, Ganser A, Socié G, Gedde-Dahl T, Forcade E, Finke J, Chalandon Y, Bulabois CE, Yakoub-Agha I, Aljurf M, Kröger N, Blau IW, Nagler A, Esteve J, Mohty M. Allogeneic hematopoietic cell transplantation for acute myeloid leukemia with hyperdiploid complex karyotype. Bone Marrow Transplant 2024; 59:264-269. [PMID: 38092959 DOI: 10.1038/s41409-023-02167-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 10/23/2023] [Accepted: 11/29/2023] [Indexed: 02/09/2024]
Abstract
Allogeneic hematopoietic cell transplantation (allo-HCT) remains the best consolidation strategy for acute myeloid leukemia (AML) with complex karyotype (CK). However, CK is a heterogenous and highly diverse entity. Numerical abnormalities have been associated with a controversial prognosis and AML with only multiple numerical abnormalities known as pure hyperdiploid karyotype (HDK) may have a distinct prognosis after allo-HCT compared to non-pure HDK CK AML. A total of 236 patients were identified within the EBMT registry as having HDK comprising 95 pure (pHDK) and 141 with other cytogenetic abnormalities (HDK+). The 2-year probability of leukemia-free survival (LFS) was 50% for pHDK and 31% for HDK+ (p = 0.003). The 2-year probability of overall survival (OS) was 57% for pHDK and 36% for HDK+ (p = 0.007). The 2-year cumulative incidence of relapse (RI) was 22% for pHDK and 44% for HDK+ (p = 0.001). The 2-year probability of graft-versus-host disease (GvHD)-free and relapse-free survival (GRFS) was 36% for pHDK and 21% for HDK+ (p = 0.01). On multivariate analysis, pHDK remained associated with significantly better LFS, OS and GRFS and lower RI (all p-values <0.004). pHDK AML constitutes probably a distinct cytogenetic entity from HDK+ or other non-hyperdiploid CK AML with better outcomes after allo-HCT.
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Affiliation(s)
- Xavier Poiré
- Section of Hematology, Institut Roi Albert II, Cliniques Universitaires St-Luc, Brussels, Belgium.
| | - Myriam Labopin
- Acute Leukemia Working Party of the EBMT, Paris, France
- Université Pierre et Marie Curie, Paris, France
- INSERM UMR 938, Paris, France
- Service d'Hématologie, Hôpital Saint-Antoine, Paris, France
| | - Emmanuelle Polge
- Acute Leukemia Working Party of the EBMT, Paris, France
- Université Pierre et Marie Curie, Paris, France
- INSERM UMR 938, Paris, France
- Service d'Hématologie, Hôpital Saint-Antoine, Paris, France
| | | | - Gérard Socié
- Department of Hematology, Bone Marrow Transplantation, Hôpital Saint-Louis, Paris, France
| | | | | | - Jürgen Finke
- Universitätsklinikum Freidburg, Department of Medicine, Hematology, Oncology, Freidburg, Germany
| | - Yves Chalandon
- Hôpitaux Universitaires de Genève, Département d'Oncologie, Service d'Hématologie, Genève, Switzerland
| | | | - Ibrahim Yakoub-Agha
- CHU de Lille, Université de Lille, INSERM U1286, Infinite, 5900, Lille, France
| | - Mahmoud Aljurf
- King Faisal Specialist Hospital & Research Center, Section of Adult Haematology/BMT, Riyadh, Saudi Arabia
| | - Nicolaus Kröger
- University Hospital Eppendorf, Bone Marrow Transplantation Centre, Hamburg, Germany
| | - Igor Wolfgang Blau
- Medizinische Klinik m. S. Hämatologie, Onkologie und Tumorimmunologie, Charité Universitätsmedizin, Berlin, Germany
| | - Arnon Nagler
- Chaim Sheba Medical Center, Tel-Hashomer, Israel
| | - Jordi Esteve
- Hematology department, Hospital Clinic, Barcelona, Spain
| | - Mohamad Mohty
- Acute Leukemia Working Party of the EBMT, Paris, France
- Université Pierre et Marie Curie, Paris, France
- INSERM UMR 938, Paris, France
- Service d'Hématologie, Hôpital Saint-Antoine, Paris, France
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10
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Dong L, Wang H, Miao Z, Yu Y, Gai D, Zhang G, Ge L, Shen X. Endoplasmic reticulum stress-related signature predicts prognosis and immune infiltration analysis in acute myeloid leukemia. Hematology 2023; 28:2246268. [PMID: 37589214 DOI: 10.1080/16078454.2023.2246268] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 08/02/2023] [Indexed: 08/18/2023] Open
Abstract
OBJECTIVES To construct an endoplasmic reticulum stress-related prognostic risk score (RS) model to predict prognosis and perform a preliminary analysis of immune infiltration in patients with acute myeloid leukemia (AML). METHODS The whole-genome expression data for AML and endoplasmic reticulum stress (ER stress)-related genes were downloaded from the GEO and GSEA databases, respectively. The samples were divided into death and survival groups, combined with clinical prognosis information. LASSO regression was used to construct a prognostic RS model. The Kaplan-Meier curve method was used to evaluate the association between different risk groups and actual survival prognosis information. A cox regression analysis was used to screen for independent survival prognostic clinical factors and construct a nomogram. CIBERSORT and ssGSEA was used for immune-related analysis. RESULTS Eighteen ER-stress related genes were identified and a comprehensive network was constructed. Further, 5 CC, 8 MF, 17 BP, and 2 KEGG pathways were enriched. Ten optimal DEGs were obtained and a prognostic risk model was constructed. Compared to the low RS group, the OS values of the high RS group were significantly lower. A significant correlation between the different risk groups and the actual prognosis was demonstrated. Ten immune cells with significantly different distributions in different risk groups were screened. KEGG enrichment analysis showed that there were 5 signaling pathways in the high-risk group. CONCLUSIONS The RS model can effectively predict the prognosis and has clinical implications for the prognosis of AML, combined with the correlation between different RS groups and the immune microenvironment.
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Affiliation(s)
- Lu Dong
- Shanxi Medical University, Taiyuan, People's Republic of China
- Heping Hospital Affiliated to Changzhi Medical College, Changzhi, People's Republic of China
| | - Haili Wang
- Heping Hospital Affiliated to Changzhi Medical College, Changzhi, People's Republic of China
| | - Zefeng Miao
- Heping Hospital Affiliated to Changzhi Medical College, Changzhi, People's Republic of China
| | - Yanhui Yu
- Heping Hospital Affiliated to Changzhi Medical College, Changzhi, People's Republic of China
| | - Dongzheng Gai
- Heping Hospital Affiliated to Changzhi Medical College, Changzhi, People's Republic of China
| | - Guoxiang Zhang
- Heping Hospital Affiliated to Changzhi Medical College, Changzhi, People's Republic of China
| | - Li Ge
- Heping Hospital Affiliated to Changzhi Medical College, Changzhi, People's Republic of China
| | - Xuliang Shen
- Shanxi Medical University, Taiyuan, People's Republic of China
- Heping Hospital Affiliated to Changzhi Medical College, Changzhi, People's Republic of China
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11
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Wu S, Jin J, Huang J, Chen G, Chen Y. Comprehensive analysis of the RSK gene family in acute myeloid leukemia determines a prognostic signature for the prediction of clinical prognosis and treatment responses. Hematology 2023; 28:2235833. [PMID: 37462338 DOI: 10.1080/16078454.2023.2235833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 07/08/2023] [Indexed: 07/20/2023] Open
Abstract
OBJECTIVE The prognosis of acute myeloid leukemia (AML) remains poor although the basic and translational research has been highly productive in understanding the genetics and pathopoiesis of AML and a plethora of targeted therapies have been developed. Consequently, it is crucial to deepen the knowledge of molecular pathogenesis underlying AML for the advancement of new treatment options. METHOD A RSK gene family-related signature was constructed to investigate whether RSK gene family members were useful in predicting the prognosis of AML patients. The relationship between the RSK gene family-related signature and the infiltration of immune cells was further assessed using the CIBERSORT algorithm. The 'oncoPredict' package was used to analyze relationships between the RSK gene family-related signature and the sensitivity to drugs or small molecules. RESULTS Patients were classified into two groups using the RSK gene family-related signature following the median risk score. Overall survival (OS) was significantly longer in patients with low-risk scores than that in patients with high-risk scores as showed by both training and validation datasets. Moreover, the signature was helpful in predicting 1-year, 3-year, and 5-year OS in training and validation datasets. In addition, it was identified that low-risk patients exhibited greater sensitivity to 20 drugs or small molecules and that high-risk patients had higher sensitivity to 38 drugs or small molecules. CONCLUSION RSK gene family members, particularly RPS6KA1 and RPS6KA4, may help to predict prognosis for AML patients. Furthermore, RPS6KA1 may serve as a novel drug target for AML.
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Affiliation(s)
- Shasha Wu
- Guizhou Medical University, Guiyang, People's Republic of China
- Department of Pediatrics, The Affiliated Hospital of Guizhou Medical University, Guiyang, People's Republic of China
| | - Jiao Jin
- Department of Pediatrics, The Affiliated Hospital of Guizhou Medical University, Guiyang, People's Republic of China
| | - Jing Huang
- Department of Pediatrics, The Affiliated Hospital of Guizhou Medical University, Guiyang, People's Republic of China
| | - Guifang Chen
- Department of Pediatrics, The Affiliated Hospital of Guizhou Medical University, Guiyang, People's Republic of China
| | - Yan Chen
- Guizhou Medical University, Guiyang, People's Republic of China
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, People's Republic of China
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12
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Angelakis A, Soulioti I, Filippakis M. Diagnosis of acute myeloid leukaemia on microarray gene expression data using categorical gradient boosted trees. Heliyon 2023; 9:e20530. [PMID: 37860531 PMCID: PMC10582309 DOI: 10.1016/j.heliyon.2023.e20530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/21/2023] Open
Abstract
We define an iterative method for dimensionality reduction using categorical gradient boosted trees and Shapley values and created four machine learning models which potentially could be used as diagnostic tests for acute myeloid leukaemia (AML). For the final Catboost model we use a dataset of 2177 individuals using as features 16 probe sets and the age in order to classify if someone has AML or is healthy. The dataset is multicentric and consists of data from 27 organizations, 25 cities, 15 countries and 4 continents. The performance of our last model is specificity: 0.9909, sensitivity: 0.9985, F1-score: 0.9976 and its ROC-AUC: 0.9962 using ten fold cross validation. On an inference dataset the perormance is: specificity: 0.9909, sensitivity: 0.9969, F1-score: 0.9969 and its ROC-AUC: 0.9939. To the best of our knowledge the performance of our model is the best one in the literature, as regards the diagnosis of AML using similar or not data. Moreover, there has not been any bibliographic reference which associates AML or any other type of cancer with the 16 probe sets we used as features in our final model.
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Affiliation(s)
- Athanasios Angelakis
- Department of Epidemiology and Data Science, Amsterdam University Medical Centers, Amsterdam Public Health Research Institute, University of Amsterdam Data Science Center, Netherlands
| | - Ioanna Soulioti
- Department of Biology, National and Kapodistrian University of Athens, Greece
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13
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Deregulated Gene Expression Profiles and Regulatory Networks in Adult and Pediatric RUNX1/RUNX1T1-Positive AML Patients. Cancers (Basel) 2023; 15:cancers15061795. [PMID: 36980682 PMCID: PMC10046396 DOI: 10.3390/cancers15061795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous and complex disease concerning molecular aberrations and prognosis. RUNX1/RUNX1T1 is a fusion oncogene that results from the chromosomal translocation t(8;21) and plays a crucial role in AML. However, its impact on the transcriptomic profile of different age groups of AML patients is not completely understood. Here, we investigated the deregulated gene expression (DEG) profiles in adult and pediatric RUNX1/RUNX1T1-positive AML patients, and compared their functions and regulatory networks. We retrospectively analyzed gene expression data from two independent Gene Expression Omnibus (GEO) datasets (GSE37642 and GSE75461) and computed their differentially expressed genes and upstream regulators, using limma, GEO2Enrichr, and X2K. For validation purposes, we used the TCGA-LAML (adult) and TARGET-AML (pediatric) patient cohorts. We also analyzed the protein–protein interaction (PPI) networks, as well as those composed of transcription factors (TF), intermediate proteins, and kinases foreseen to regulate the top deregulated genes in each group. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analyses were further performed for the DEGs in each dataset. We found that the top upregulated genes in (both adult and pediatric) RUNX1/RUNX1T1-positive AML patients are enriched in extracellular matrix organization, the cell projection membrane, filopodium membrane, and supramolecular fiber. Our data corroborate that RUNX1/RUNX1T1 reprograms a large transcriptional network to establish and maintain leukemia via intricate PPI interactions and kinase-driven phosphorylation events.
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14
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He X, Hu J, Yan C, Liu X, Zhao Y, Yang P, Wang J, Li S, Zhang W, Dong G, Zhang W, Jing H. High trophinin-associated protein expression predicts good survival in acute myeloid leukemia with normal cytogenetics. Cancer Biomark 2023; 36:221-230. [PMID: 36938721 DOI: 10.3233/cbm-210042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
BACKGROUND Nearly half of adult acute myeloid leukemia (AML) patients were classified into cytogenetic normal acute myeloid leukemia (CN-AML). The expression level of Trophinin associated protein (TROAP) was proven to be associated with the prognosis of several cancers, but it is still unclear in the prognosis of patients with CN-AML. METHODS We integrated CN-AML patients samples from 4 datasets to analyze the relationship between TROAP expression and the survival of CN-AML. In addition, we investigated 92 AML patients of The Cancer Genome Atlas (TCGA) database to analyze the relationship between TROAP expression and the survival of AML patients received chemotherapy. We investigated the relationship between the expression of TROAP and drug sensitivity in AML cell lines. RESULTS CN-AML patients with high TROAP expression were related to good event-free survival (EFS) and overall survival (OS). In AML patients received chemotherapy, high TROAP expression was associated with good survival prognosis. Additionally, the expression of TROAP gene in leukemia stem cells (LSC) + group was lower. Among multiple drugs, the lower the expression of TROAP, the lower the IC50. CONCLUSION TROAP could serve as an independent predictor of CN-AML patients and could act as a potential biomarker for the prognosis of CN-AML. TROAP expression levels were closely correlated with the drug sensitivity of multiple drugs.
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Affiliation(s)
- Xue He
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Pathology, Capital Medical University, Beijing, China.,Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jing Hu
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing, China.,Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Changjian Yan
- The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China.,Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Xiaoni Liu
- Department of Respiratory Medicine, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
| | - Yali Zhao
- General Practice Medicine, The First People's Hospital of Huzhou, Huzhou, Zhejiang, China
| | - Ping Yang
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing, China
| | - Jing Wang
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing, China
| | - Shaoxiang Li
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Pathology, Capital Medical University, Beijing, China
| | - Wei Zhang
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Pathology, Capital Medical University, Beijing, China
| | - Gehong Dong
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Pathology, Capital Medical University, Beijing, China
| | - Weilong Zhang
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing, China
| | - Hongmei Jing
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing, China
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15
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Destefanis F, Manara V, Santarelli S, Zola S, Brambilla M, Viola G, Maragno P, Signoria I, Viero G, Pasini ME, Penzo M, Bellosta P. Reduction of nucleolar NOC1 leads to the accumulation of pre-rRNAs and induces Xrp1, affecting growth and resulting in cell competition. J Cell Sci 2022; 135:285861. [PMID: 36314272 PMCID: PMC9789402 DOI: 10.1242/jcs.260110] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 10/25/2022] [Indexed: 12/12/2022] Open
Abstract
NOC1 is a nucleolar protein necessary in yeast for both transport and maturation of ribosomal subunits. Here, we show that Drosophila NOC1 (annotated CG7839) is necessary for rRNAs maturation and for a correct animal development. Its ubiquitous downregulation results in a dramatic decrease in polysome level and of protein synthesis. NOC1 expression in multiple organs, such as the prothoracic gland and the fat body, is necessary for their proper functioning. Reduction of NOC1 in epithelial cells from the imaginal discs results in clones that die by apoptosis, an event that is partially rescued in a Minute/+ background, suggesting that reduction of NOC1 induces the cells to become less fit and to acquire a 'loser' state. NOC1 downregulation activates the pro-apoptotic Eiger-JNK pathway and leads to an increase of Xrp1, which results in the upregulation of DILP8, a member of the insulin/relaxin-like family known to coordinate organ growth with animal development. Our data underline NOC1 as an essential gene in ribosome biogenesis and highlight its novel functions in the control of growth and cell competition.
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Affiliation(s)
- Francesca Destefanis
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Valeria Manara
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Stefania Santarelli
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Sheri Zola
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Marco Brambilla
- Department of Biosciences, University of Milano, Via Celoria 25, 20133 Milano, Italy
| | - Giacomo Viola
- Department of Biosciences, University of Milano, Via Celoria 25, 20133 Milano, Italy
| | - Paola Maragno
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Ilaria Signoria
- Institute of Biophysics, CNR, Via Sommarive 18, 38123 Trento, Italy
| | - Gabriella Viero
- Institute of Biophysics, CNR, Via Sommarive 18, 38123 Trento, Italy
| | - Maria Enrica Pasini
- Department of Biosciences, University of Milano, Via Celoria 25, 20133 Milano, Italy
| | - Marianna Penzo
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Via Massarenti 9, 40138 Bologna, Italy,Center for Applied Biomedical Research, University of Bologna, Via Massarenti 9, 40138 Bologna, Italy
| | - Paola Bellosta
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy,Department of Medicine, NYU Langone School of Medicine, 550 First Avenue, New York, 10016 NY, USA,Author for correspondence ()
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16
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Carlet M, Schmelz K, Vergalli J, Herold T, Senft D, Jurinovic V, Hoffmann T, Proba J, Weichert N, Junghanß C, Roth M, Eschenburg G, Barz M, Henze G, Eckert C, Eggert A, Zuber J, Hundsdoerfer P, Jeremias I. X-linked inhibitor of apoptosis protein represents a promising therapeutic target for relapsed/refractory ALL. EMBO Mol Med 2022; 15:e14557. [PMID: 36416169 PMCID: PMC9832863 DOI: 10.15252/emmm.202114557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 10/23/2022] [Accepted: 10/28/2022] [Indexed: 11/25/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) represents the most frequent malignancy in children, and relapse/refractory (r/r) disease is difficult to treat, both in children and adults. In search for novel treatment options against r/r ALL, we studied inhibitor of apoptosis proteins (IAP) and Smac mimetics (SM). SM-sensitized r/r ALL cells towards conventional chemotherapy, even upon resistance against SM alone. The combination of SM and chemotherapy-induced cell death via caspases and PARP, but independent from cIAP-1/2, RIPK1, TNFα or NF-κB. Instead, XIAP was identified to mediate SM effects. Molecular manipulation of XIAP in vivo using microRNA-30 flanked shRNA expression in cell lines and patient-derived xenograft (PDX) models of r/r ALL mimicked SM effects and intermediate XIAP knockdown-sensitized r/r ALL cells towards chemotherapy-induced apoptosis. Interestingly, upon strong XIAP knockdown, PDX r/r ALL cells were outcompeted in vivo, even in the absence of chemotherapy. Our results indicate a yet unknown essential function of XIAP in r/r ALL and reveal XIAP as a promising therapeutic target for r/r ALL.
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Affiliation(s)
- Michela Carlet
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum MünchenGerman Center for Environmental Health (HMGU)MunichGermany,Department of Biotechnology and Food EngineeringMCI, The Entrepreneur SchoolInnsbruckAustria
| | - Karin Schmelz
- Department of Pediatric Oncology/HematologyCharité‐UniversitätsmedizinBerlinGermany,German Cancer Consortium (DKTK)BerlinGermany
| | - Jenny Vergalli
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum MünchenGerman Center for Environmental Health (HMGU)MunichGermany
| | - Tobias Herold
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum MünchenGerman Center for Environmental Health (HMGU)MunichGermany,Laboratory for Leukemia Diagnostics, Department of Medicine IIIUniversity Hospital, LMU MunichMunichGermany,German Cancer Consortium (DKTK), Partnering Site MunichMunichGermany
| | - Daniela Senft
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum MünchenGerman Center for Environmental Health (HMGU)MunichGermany
| | - Vindi Jurinovic
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum MünchenGerman Center for Environmental Health (HMGU)MunichGermany,Laboratory for Leukemia Diagnostics, Department of Medicine IIIUniversity Hospital, LMU MunichMunichGermany,Department of Pediatrics, Dr. von Hauner Children's HospitalUniversity Hospital, LMUMunichGermany
| | - Thomas Hoffmann
- Research Institute of Molecular Pathology (IMP)ViennaAustria
| | - Jutta Proba
- Department of Pediatric Oncology/HematologyCharité‐UniversitätsmedizinBerlinGermany
| | - Nina Weichert
- Department of Pediatric Oncology/HematologyCharité‐UniversitätsmedizinBerlinGermany
| | - Christian Junghanß
- Department of Medicine, Clinic III – Hematology, Oncology, Palliative MedicineRostock University Medical CenterRostockGermany
| | - Mareike Roth
- Research Institute of Molecular Pathology (IMP)ViennaAustria
| | - Georg Eschenburg
- Department of Pediatric SurgeryUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | - Malwine Barz
- University Children's Hospital ZurichZurichSwitzerland
| | - Günter Henze
- Department of Pediatric Oncology/HematologyCharité‐UniversitätsmedizinBerlinGermany
| | - Cornelia Eckert
- Department of Pediatric Oncology/HematologyCharité‐UniversitätsmedizinBerlinGermany
| | - Angelika Eggert
- Department of Pediatric Oncology/HematologyCharité‐UniversitätsmedizinBerlinGermany
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP)ViennaAustria
| | - Patrick Hundsdoerfer
- Department of Pediatric Oncology/HematologyCharité‐UniversitätsmedizinBerlinGermany,Berlin Institute of HealthBerlinGermany,Department of PediatricsHelios Klinikum Berlin‐BuchBerlinGermany
| | - Irmela Jeremias
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum MünchenGerman Center for Environmental Health (HMGU)MunichGermany,German Cancer Consortium (DKTK), Partnering Site MunichMunichGermany,Department of Pediatrics, Dr. von Hauner Children's HospitalUniversity Hospital, LMUMunichGermany
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17
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Islam SA, Díaz-Gay M, Wu Y, Barnes M, Vangara R, Bergstrom EN, He Y, Vella M, Wang J, Teague JW, Clapham P, Moody S, Senkin S, Li YR, Riva L, Zhang T, Gruber AJ, Steele CD, Otlu B, Khandekar A, Abbasi A, Humphreys L, Syulyukina N, Brady SW, Alexandrov BS, Pillay N, Zhang J, Adams DJ, Martincorena I, Wedge DC, Landi MT, Brennan P, Stratton MR, Rozen SG, Alexandrov LB. Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor. CELL GENOMICS 2022; 2:None. [PMID: 36388765 PMCID: PMC9646490 DOI: 10.1016/j.xgen.2022.100179] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 04/10/2022] [Accepted: 08/31/2022] [Indexed: 12/09/2022]
Abstract
Mutational signature analysis is commonly performed in cancer genomic studies. Here, we present SigProfilerExtractor, an automated tool for de novo extraction of mutational signatures, and benchmark it against another 13 bioinformatics tools by using 34 scenarios encompassing 2,500 simulated signatures found in 60,000 synthetic genomes and 20,000 synthetic exomes. For simulations with 5% noise, reflecting high-quality datasets, SigProfilerExtractor outperforms other approaches by elucidating between 20% and 50% more true-positive signatures while yielding 5-fold less false-positive signatures. Applying SigProfilerExtractor to 4,643 whole-genome- and 19,184 whole-exome-sequenced cancers reveals four novel signatures. Two of the signatures are confirmed in independent cohorts, and one of these signatures is associated with tobacco smoking. In summary, this report provides a reference tool for analysis of mutational signatures, a comprehensive benchmarking of bioinformatics tools for extracting signatures, and several novel mutational signatures, including one putatively attributed to direct tobacco smoking mutagenesis in bladder tissues.
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Affiliation(s)
- S.M. Ashiqul Islam
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Yang Wu
- Centre for Computational Biology and Programme in Cancer & Stem Cell Biology, Duke NUS Medical School, Singapore 169857, Singapore
| | - Mark Barnes
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Raviteja Vangara
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Erik N. Bergstrom
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Yudou He
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Mike Vella
- NVIDIA Corporation, 2788 San Tomas Expressway, Santa Clara, CA 95051, USA
| | - Jingwei Wang
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Jon W. Teague
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Peter Clapham
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Sarah Moody
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Sergey Senkin
- Genetic Epidemiology Group, International Agency for Research on Cancer, Cedex 08, 69372 Lyon, France
| | - Yun Rose Li
- Departments of Radiation Oncology and Cancer Genetics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Laura Riva
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Andreas J. Gruber
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
- Manchester Cancer Research Centre, The University of Manchester, Manchester M20 4GJ, UK
- Department of Biology, University of Konstanz, Universitaetsstrasse 10, D-78464 Konstanz, Germany
| | - Christopher D. Steele
- Research Department of Pathology, Cancer Institute, University College London, London WC1E 6BT, UK
| | - Burçak Otlu
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Azhar Khandekar
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Ammal Abbasi
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Laura Humphreys
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | | | - Samuel W. Brady
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Boian S. Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Nischalan Pillay
- Research Department of Pathology, Cancer Institute, University College London, London WC1E 6BT, UK
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex HA7 4LP, UK
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - David J. Adams
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Iñigo Martincorena
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - David C. Wedge
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
- Manchester Cancer Research Centre, The University of Manchester, Manchester M20 4GJ, UK
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Paul Brennan
- Genetic Epidemiology Group, International Agency for Research on Cancer, Cedex 08, 69372 Lyon, France
| | - Michael R. Stratton
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Steven G. Rozen
- Centre for Computational Biology and Programme in Cancer & Stem Cell Biology, Duke NUS Medical School, Singapore 169857, Singapore
| | - Ludmil B. Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
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18
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A novel heptasomy 21 associated with complete loss of heterozygosity and loss of function RUNX1 mutation in acute myeloid leukemia. Cancer Genet 2022; 266-267:69-73. [DOI: 10.1016/j.cancergen.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 06/07/2022] [Accepted: 07/01/2022] [Indexed: 11/17/2022]
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19
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Han C, Zheng J, Li F, Guo W, Cai C. Novel Prognostic Signature for Acute Myeloid Leukemia: Bioinformatics Analysis of Combined CNV-Driven and Ferroptosis-Related Genes. Front Genet 2022; 13:849437. [PMID: 35559049 PMCID: PMC9086455 DOI: 10.3389/fgene.2022.849437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/22/2022] [Indexed: 12/19/2022] Open
Abstract
Background: Acute myeloid leukemia (AML), which has a difficult prognosis, is the most common hematologic malignancy. The role of copy number variations (CNVs) and ferroptosis in the tumor process is becoming increasingly prominent. We aimed to identify specific CNV-driven ferroptosis-related genes (FRGs) and establish a prognostic model for AML. Methods: The combined analysis of CNV differential data and differentially expressed genes (DEGs) data from The Cancer Genome Atlas (TCGA) database was performed to identify key CNV-driven FRGs for AML. A risk model was constructed based on univariate and multivariate Cox regression analysis. The Gene Expression Omnibus (GEO) dataset was used to validate the model. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted to clarify the functional roles of DEGs and CNV-driven FRGs. Results: We identified a total of 6828 AML-related DEGs, which were shown to be significantly associated with cell cycle and immune response processes. After a comprehensive analysis of CNVs and corresponding DEGs and FRGs, six CNV-driven FRGs were identified, and functional enrichment analysis indicated that they were involved in oxidative stress, cell death, and inflammatory response processes. Finally, we screened 2 CNV-driven FRGs (DNAJB6 and HSPB1) to develop a prognostic risk model. The overall survival (OS) of patients in the high-risk group was significantly shorter in both the TCGA and GEO (all p < 0.05) datasets compared to the low-risk group. Conclusion: A novel signature based on CNV-driven FRGs was established to predict the survival of AML patients and displayed good performance. Our results may provide potential targets and new research ideas for the treatment and early detection of AML.
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Affiliation(s)
- Chunjiao Han
- Clinical School of Paediatrics, Tianjin Medical University, Tianjin, China
| | - Jiafeng Zheng
- Department of Pulmonology, Tianjin Children's Hospital/Tianjin University Children's Hospital, Tianjin, China
| | - Fangfang Li
- Department of Rheumatology and Immunology, Tianjin Children's Hospital/Tianjin University Children's Hospital, Tianjin, China
| | - Wei Guo
- Clinical School of Paediatrics, Tianjin Medical University, Tianjin, China.,Department of Pulmonology, Tianjin Children's Hospital/Tianjin University Children's Hospital, Tianjin, China
| | - Chunquan Cai
- Department of Institute of Pediatrics, Tianjin Children's Hospital/Tianjin University Children's Hospital, Tianjin, China
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20
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Zhang L, Ke W, Hu P, Li Z, Geng W, Guo Y, Song B, Jiang H, Zhang X, Wan C. N6-Methyladenosine-Related lncRNAs Are Novel Prognostic Markers and Predict the Immune Landscape in Acute Myeloid Leukemia. Front Genet 2022; 13:804614. [PMID: 35615374 PMCID: PMC9125310 DOI: 10.3389/fgene.2022.804614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 04/06/2022] [Indexed: 12/16/2022] Open
Abstract
Background: Acute myelocytic leukemia (AML) is one of the hematopoietic cancers with an unfavorable prognosis. However, the prognostic value of N 6-methyladenosine-associated long non-coding RNAs (lncRNAs) in AML remains elusive. Materials and Methods: The transcriptomic data of m6A-related lncRNAs were collected from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) database. AML samples were classified into various subgroups according to the expression of m6A-related lncRNAs. The differences in terms of biological function, tumor immune microenvironment, copy number variation (CNV), and drug sensitivity in AML between distinct subgroups were investigated. Moreover, an m6A-related lncRNA prognostic model was established to evaluate the prognosis of AML patients. Results: Nine prognosis-related m6A-associated lncRNAs were selected to construct a prognosis model. The accuracy of the model was further determined by the Kaplan–Meier analysis and time-dependent receiver operating characteristic (ROC) curve. Then, AML samples were classified into high- and low-risk groups according to the median value of risk scores. Gene set enrichment analysis (GSEA) demonstrated that samples with higher risks were featured with aberrant immune-related biological processes and signaling pathways. Notably, the high-risk group was significantly correlated with an increased ImmuneScore and StromalScore, and distinct immune cell infiltration. In addition, we discovered that the high-risk group harbored higher IC50 values of multiple chemotherapeutics and small-molecule anticancer drugs, especially TW.37 and MG.132. In addition, a nomogram was depicted to assess the overall survival (OS) of AML patients. The model based on the median value of risk scores revealed reliable accuracy in predicting the prognosis and survival status. Conclusion: The present research has originated a prognostic risk model for AML according to the expression of prognostic m6A-related lncRNAs. Notably, the signature might also serve as a novel biomarker that could guide clinical applications, for example, selecting AML patients who could benefit from immunotherapy.
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Affiliation(s)
- Lulu Zhang
- Department of Hematology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
- *Correspondence: Lulu Zhang,
| | - Wen Ke
- Department of Osteology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Pin Hu
- Department of Hematology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Zhangzhi Li
- Department of Hematology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Wei Geng
- Department of Hematology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Yigang Guo
- Department of Hematology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Bin Song
- Department of Hematology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Hua Jiang
- Department of Hematology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Xia Zhang
- Department of Hematology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Chucheng Wan
- Department of Hematology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
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21
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Jiang Y, Wu SY, Chen YL, Zhang ZM, Tao YF, Xie Y, Liao XM, Li XL, Li G, Wu D, Wang HR, Zuo R, Cao HB, Pan JJ, Yu JJ, Jia SQ, Zhang Z, Chu XR, Zhang YP, Feng CX, Wang JW, Hu SY, Li ZH, Pan J, Fang F, Lu J. CEBPG promotes acute myeloid leukemia progression by enhancing EIF4EBP1. Cancer Cell Int 2021; 21:598. [PMID: 34743716 PMCID: PMC8574011 DOI: 10.1186/s12935-021-02305-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/27/2021] [Indexed: 12/18/2022] Open
Abstract
Background Acute myeloid leukemia (AML) is a myeloid neoplasm accounts for 7.6% of hematopoietic malignancies. AML is a complex disease, and understanding its pathophysiology is contributing to the improvement in the treatment and prognosis of AML. In this study, we assessed the expression profile and molecular functions of CCAAT enhancer binding protein gamma (CEBPG), a gene implicated in myeloid differentiation and AML progression. Methods shRNA mediated gene interference was used to down-regulate the expression of CEBPG in AML cell lines, and knockdown efficiency was detected by RT-qPCR and western blotting. The effect of knockdown on the growth of AML cell lines was evaluated by CCK-8. Western blotting was used to detect PARP cleavage, and flow cytometry were used to determine the effect of knockdown on apoptosis of AML cells. Genes and pathways affected by knockdown of CEBPG were identified by gene expression analysis using RNA-seq. One of the genes affected by knockdown of CEBPG was Eukaryotic translation initiation factor 4E binding protein 1 (EIF4EBP1), a known repressor of translation. Knockdown of EIF4EBP1 was used to assess its potential role in AML progression downstream of CEBPG. Results We explored the ChIP-Seq data of AML cell lines and non-AML hematopoietic cells, and found CEBPG was activated through its distal enhancer in AML cell lines. Using the public transcriptomic dataset, the Cancer Cell Line Encyclopedia (CCLE) and western blotting, we also found CEBPG was overexpressed in AML. Moreover, we observed that CEBPG promotes AML cell proliferation by activating EIF4EBP1, thus contributing to the progression of AML. These findings indicate that CEBPG could act as a potential therapeutic target for AML patients. Conclusion In summary, we systematically explored the molecular characteristics of CEBPG in AML and identified CEBPG as a potential therapeutic target for AML patients. Our findings provide novel insights into the pathophysiology of AML and indicate a key role for CEBPG in promoting AML progression. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02305-z.
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Affiliation(s)
- You Jiang
- Department of Hematology, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, Jiangsu, China
| | - Shui-Yan Wu
- Department of Hematology, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, Jiangsu, China.,Intensive Care Unit, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Yan-Ling Chen
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China.,School of Basic Medicine and Biological Sciences, Soochow University, Suzhou, 215003, China
| | - Zi-Mu Zhang
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Yan-Fang Tao
- Department of Hematology, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, Jiangsu, China.,Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Yi Xie
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Xin-Mei Liao
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Xiao-Lu Li
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Gen Li
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Di Wu
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Hai-Rong Wang
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Ran Zuo
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Hai-Bo Cao
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Jing-Jing Pan
- Department of Hematology, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, Jiangsu, China.,Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Juan-Juan Yu
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Si-Qi Jia
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China.,School of Basic Medicine and Biological Sciences, Soochow University, Suzhou, 215003, China
| | - Zheng Zhang
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Xin-Ran Chu
- Department of Hematology, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, Jiangsu, China
| | - Yong-Ping Zhang
- Department of Hematology, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, Jiangsu, China
| | - Chen-Xi Feng
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Jian-Wei Wang
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Shao-Yan Hu
- Department of Hematology, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, Jiangsu, China.,Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Zhi-Heng Li
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Jian Pan
- Department of Hematology, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, Jiangsu, China. .,Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China.
| | - Fang Fang
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China.
| | - Jun Lu
- Department of Hematology, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, Jiangsu, China.
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22
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de Oliveira Lisboa M, Brofman PRS, Schmid-Braz AT, Rangel-Pozzo A, Mai S. Chromosomal Instability in Acute Myeloid Leukemia. Cancers (Basel) 2021; 13:cancers13112655. [PMID: 34071283 PMCID: PMC8198625 DOI: 10.3390/cancers13112655] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/23/2021] [Accepted: 05/26/2021] [Indexed: 12/20/2022] Open
Abstract
Chromosomal instability (CIN), the increasing rate in which cells acquire new chromosomal alterations, is one of the hallmarks of cancer. Many studies highlighted CIN as an important mechanism in the origin, progression, and relapse of acute myeloid leukemia (AML). The ambivalent feature of CIN as a cancer-promoting or cancer-suppressing mechanism might explain the prognostic variability. The latter, however, is described in very few studies. This review highlights the important CIN mechanisms in AML, showing that CIN signatures can occur largely in all the three major AML types (de novo AML, secondary-AML, and therapy-related-AML). CIN features in AML could also be age-related and reflect the heterogeneity of the disease. Although most of these abnormalities show an adverse prognostic value, they also offer a strong new perspective on personalized therapy approaches, which goes beyond assessing CIN in vitro in patient tumor samples to predict prognosis. Current and emerging AML therapies are exploring CIN to improve AML treatment, which includes blocking CIN or increasing CIN beyond the limit threshold to induce cell death. We argue that the characterization of CIN features, not included yet in the routine diagnostic of AML patients, might provide a better stratification of patients and be extended to a more personalized therapeutic approach.
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Affiliation(s)
- Mateus de Oliveira Lisboa
- Core for Cell Technology, School of Medicine, Pontifícia Universidade Católica do Paraná—PUCPR, Curitiba 80215-901, Paraná, Brazil; (M.d.O.L.); (P.R.S.B.)
| | - Paulo Roberto Slud Brofman
- Core for Cell Technology, School of Medicine, Pontifícia Universidade Católica do Paraná—PUCPR, Curitiba 80215-901, Paraná, Brazil; (M.d.O.L.); (P.R.S.B.)
| | - Ana Teresa Schmid-Braz
- Hospital das Clínicas, Universidade Federal do Paraná, Curitiba 80060-240, Paraná, Brazil;
| | - Aline Rangel-Pozzo
- Department of Physiology and Pathophysiology, University of Manitoba, Cell Biology, CancerCare Manitoba Research Institute, Winnipeg, MB R3C 2B7, Canada
- Correspondence: (A.R.-P.); (S.M.); Tel.: +1-(204)787-4125 (S.M.)
| | - Sabine Mai
- Department of Physiology and Pathophysiology, University of Manitoba, Cell Biology, CancerCare Manitoba Research Institute, Winnipeg, MB R3C 2B7, Canada
- Correspondence: (A.R.-P.); (S.M.); Tel.: +1-(204)787-4125 (S.M.)
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23
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Samimi H, Mehta I, Docking TR, Zainulabadeen A, Karsan A, Zare H. DNA methylation analysis improves the prognostication of acute myeloid leukemia. EJHAEM 2021; 2:211-218. [PMID: 34308417 PMCID: PMC8294109 DOI: 10.1002/jha2.187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/24/2021] [Accepted: 03/04/2021] [Indexed: 12/12/2022]
Abstract
Integration of orthogonal data could provide new opportunities to pinpoint the underlying molecular mechanisms of hematologic disorders. Using a novel gene network approach, we integrated DNA methylation data from The Cancer Genome Atlas (n = 194 cases) with the corresponding gene expression profile. Our integrated gene network analysis classified AML patients into low-, intermediate-, and high-risk groups. The identified high-risk group had significantly shorter overall survival compared to the low-risk group (p-value ≤10-11). Specifically, our approach identified a particular subgroup of nine high-risk AML cases that died within 2 years after diagnosis. These high-risk cases otherwise would be incorrectly classified as intermediate-risk solely based on cytogenetics, mutation profiles, and common molecular characteristics of AML. We confirmed the prognostic value of our integrative gene network approach using two independent datasets, as well as through comparison with European LeukemiaNet and LSC17 criteria. Our approach could be useful in the prognostication of a subset of borderline AML cases. These cases would not be classified into appropriate risk groups by other approaches that use gene expression, but not DNA methylation data. Our findings highlight the significance of epigenomic data, and they indicate integrating DNA methylation data with gene coexpression networks can have a synergistic effect.
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Affiliation(s)
- Hanie Samimi
- Department of Computer ScienceTexas State UniversitySan MarcosTexasUSA
| | - Isha Mehta
- Department of Cell Systems & AnatomyThe University of Texas Health Science CenterSan AntonioTexasUSA
| | - Thomas Roderick Docking
- Canada's Michael Smith Genome Sciences CentreBritish Columbia Cancer Research CentreVancouverBritish ColumbiaCanada
| | | | - Aly Karsan
- Canada's Michael Smith Genome Sciences CentreBritish Columbia Cancer Research CentreVancouverBritish ColumbiaCanada
| | - Habil Zare
- Department of Cell Systems & AnatomyThe University of Texas Health Science CenterSan AntonioTexasUSA
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative DiseasesUniversity of Texas Health Sciences CenterSan AntonioTexasUSA
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24
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Wang Y, Cai YY, Herold T, Nie RC, Zhang Y, Gale RP, Metzeler KH, Zeng Y, Wang SQ, Pan XY, Yang TH, Wu YB, Zhang Q, Wuxiao ZJ, Du X, Liang ZW, Su YZ, Xu JB, Wang YQ, Liu ZL, Wu JW, Zhang X, Wu BY, Xiao RZ, Wang SB, Li JY, Chi PD, Zhang QY, Chen SL, Qin ZY, Zhang XM, Zhong N, Hiddemann W, Liu QF, Zhang B, Liang Y. An Immune Risk Score Predicts Survival of Patients with Acute Myeloid Leukemia Receiving Chemotherapy. Clin Cancer Res 2021; 27:255-266. [PMID: 33262139 DOI: 10.1158/1078-0432.ccr-20-3417] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/06/2020] [Accepted: 10/22/2020] [Indexed: 02/05/2023]
Abstract
PURPOSE Prediction models for acute myeloid leukemia (AML) are useful, but have considerable inaccuracy and imprecision. No current model includes covariates related to immune cells in the AML microenvironment. Here, an immune risk score was explored to predict the survival of patients with AML. EXPERIMENTAL DESIGN We evaluated the predictive accuracy of several in silico algorithms for immune composition in AML based on a reference of multi-parameter flow cytometry. CIBERSORTx was chosen to enumerate immune cells from public datasets and develop an immune risk score for survival in a training cohort using least absolute shrinkage and selection operator Cox regression model. RESULTS Six flow cytometry-validated immune cell features were informative. The model had high predictive accuracy in the training and four external validation cohorts. Subjects in the training cohort with low scores had prolonged survival compared with subjects with high scores, with 5-year survival rates of 46% versus 19% (P < 0.001). Parallel survival rates in validation cohorts-1, -2, -3, and -4 were 46% versus 6% (P < 0.001), 44% versus 18% (P = 0.041), 44% versus 24% (P = 0.004), and 62% versus 32% (P < 0.001). Gene set enrichment analysis indicated significant enrichment of immune relation pathways in the low-score cohort. In multivariable analyses, high-risk score independently predicted shorter survival with HRs of 1.45 (P = 0.005), 2.12 (P = 0.004), 2.02 (P = 0.034), 1.66 (P = 0.019), and 1.59 (P = 0.001) in the training and validation cohorts, respectively. CONCLUSIONS Our immune risk score complements current AML prediction models.
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Affiliation(s)
- Yun Wang
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P.R. China
| | - Yan-Yu Cai
- Department of VIP Region, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P.R. China
| | - Tobias Herold
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Run-Cong Nie
- Department of Gastric Surgery, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P.R. China
| | - Yu Zhang
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Robert Peter Gale
- Haematology Research Centre, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Klaus H Metzeler
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Yun Zeng
- Department of Hematology, the First Affiliated Hospital of Kunming Medical University, Yunnan Hematology Research Center, Kunming, Yunnan, P.R. China
| | - Shun-Qing Wang
- Department of Hematology, Guangzhou First People's Hospital, School of Medicine South China University of Technology, Guangzhou, Guangdong, P.R. China
| | - Xue-Yi Pan
- Department of Hematology, the First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, Guangdong, P.R. China
| | - Tong-Hua Yang
- Department of Hematology, the First People's Hospital of Yunnan Province, Kunming, Yunnan, P.R. China
| | - Yuan-Bin Wu
- Department of Hematology, Guangdong Hospital of Traditional Chinese Medicine, Guangzhou, Guangdong, P.R. China
| | - Qing Zhang
- Department of Hematology, the Second People's Hospital of Guangdong Province, Guangzhou, Guangdong, P.R. China
| | - Zhi-Jun Wuxiao
- Department of Hematologic Oncology, the First Affiliated Hospital, Hainan Medical College, Haikou, Hainan, P.R. China
| | - Xin Du
- Department of Hematology, Shenzhen Second People's Hospital, Shenzhen, Guangdong, P.R. China
| | - Zhi-Wei Liang
- Department of Hematology, Kaiping Central Hospital, Kaiping, Guangdong, P.R. China
| | - Yong-Zhong Su
- Department of Hematology, the First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, P.R. China
| | - Jing-Bo Xu
- Department of Hematology, the Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, P.R. China
| | - Yong-Qing Wang
- Department of Hematology, Fuyang Hospital of Anhui Medical University, Fuyang, Anhui, P.R. China
| | - Ze-Lin Liu
- Department of Hematology, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital), Shenzhen, Guangdong, P.R. China
| | - Jian-Wei Wu
- Department of Hematology, Jinan University Affiliated Jiangmen Hospital of Traditional Chinese Medicine, Jiangmen, Guangdong, P.R. China
| | - Xiong Zhang
- Department of Hematology, Maoming People's Hospital, Maoming, Guangdong, P.R. China
| | - Bing-Yi Wu
- Department of Hematology, Shunde Hospital of Southern Medical University, Shunde, Guangdong, P.R. China
| | - Ruo-Zhi Xiao
- Department of Hematology, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - San-Bin Wang
- Department of Hematology, the 920 Hospital of PLA Joint Logistics Support Force, Kunming, Yunnan, P.R. China
| | - Jin-Yuan Li
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P.R. China
| | - Pei-Dong Chi
- Department of Clinical Laboratory, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P.R. China
| | - Qian-Yi Zhang
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P.R. China
| | - Si-Liang Chen
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P.R. China
| | - Zhe-Yuan Qin
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P.R. China
| | - Xin-Mei Zhang
- Becton Dickinson Medical Devices (Shanghai) Co., Ltd, Guangzhou, Guangdong, P.R. China
| | - Na Zhong
- Becton Dickinson Medical Devices (Shanghai) Co., Ltd, Guangzhou, Guangdong, P.R. China
| | - Wolfgang Hiddemann
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Qi-Fa Liu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R. China.
| | - Bei Zhang
- Department of VIP Region, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P.R. China.
| | - Yang Liang
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P.R. China.
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25
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Wang C, Li M, Li L, Shen X, Liu Y, Wang S. Strongylocentrotus nudos Egg Polysaccharide induces autophagy and apoptosis in leukaemia cells by regulating mitochondrial function. J Cell Mol Med 2020; 25:272-283. [PMID: 33289295 PMCID: PMC7810953 DOI: 10.1111/jcmm.15995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 09/22/2020] [Accepted: 09/29/2020] [Indexed: 12/26/2022] Open
Abstract
In this study, we investigated the ability of the Polysaccharide from the Eggs of Strongylocentrotus nudus (SEP) to regulate cellular autophagy and apoptosis in leukaemia cells. Human acute myeloid leukaemia (AML) cells (HL60) and murine AML cells (L1210) treated with SEP were used to assess viability using Cell Counting Kit‐8, cytotoxicity by measuring lactate dehydrogenase release, the generation of reactive oxygen species (ROS) by DCFH‐DA staining. In addition, we utilized a mouse model of leukaemia in which L1210 cells were injected into DBA/2 mice by sub‐axillary injection. Treatment with SEP decreased cell viability, increased in cytotoxicity and increased the release of ROS in a dose‐dependent manner. SEP treatment was also associated with the activation of pro‐apoptotic proteins cleaved caspase‐3, cleaved caspase‐9 and cleaved poly (ADP‐ribose) polymerase (PARP). Activation of the apoptotic pathway led to the release of cytochrome C (CytoC) into the cytosol of the cell resulting in decreased membrane potential. The effect of SEP treatment was depended on the activation of the nuclear factor kappa‐B (NF‐κB) signalling pathway as SEP treatment led to an increase in NF‐κB phosphorylation, and inhibition of NF‐κB signalling using PDTC blocked SEP‐mediated activation of apoptosis. Treatment with SEP also prolonged survival time in our leukaemia mouse model and was associated with diminished tumour volume, increased leucocyte and lymphocyte proliferation, promoted pro‐inflammatory factor release in serum and enhanced immune function. Taken together, these data suggest that SEP inhibits the progression of leukaemia by initiating mitochondrial dysfunction, autophagy, and apoptosis via the NF‐κB signalling pathway.
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Affiliation(s)
- Chong Wang
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Mengya Li
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lingling Li
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaohui Shen
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanfang Liu
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shujuan Wang
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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26
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Hamline MY, Corcoran CM, Wamstad JA, Miletich I, Feng J, Lohr JL, Hemberger M, Sharpe PT, Gearhart MD, Bardwell VJ. OFCD syndrome and extraembryonic defects are revealed by conditional mutation of the Polycomb-group repressive complex 1.1 (PRC1.1) gene BCOR. Dev Biol 2020; 468:110-132. [PMID: 32692983 PMCID: PMC9583620 DOI: 10.1016/j.ydbio.2020.06.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/16/2020] [Accepted: 06/26/2020] [Indexed: 12/15/2022]
Abstract
BCOR is a critical regulator of human development. Heterozygous mutations of BCOR in females cause the X-linked developmental disorder Oculofaciocardiodental syndrome (OFCD), and hemizygous mutations of BCOR in males cause gestational lethality. BCOR associates with Polycomb group proteins to form one subfamily of the diverse Polycomb repressive complex 1 (PRC1) complexes, designated PRC1.1. Currently there is limited understanding of differing developmental roles of the various PRC1 complexes. We therefore generated a conditional exon 9-10 knockout Bcor allele and a transgenic conditional Bcor expression allele and used these to define multiple roles of Bcor, and by implication PRC1.1, in mouse development. Females heterozygous for Bcor exhibiting mosaic expression due to the X-linkage of the gene showed reduced postnatal viability and had OFCD-like defects. By contrast, Bcor hemizygosity in the entire male embryo resulted in embryonic lethality by E9.5. We further dissected the roles of Bcor, focusing on some of the tissues affected in OFCD through use of cell type specific Cre alleles. Mutation of Bcor in neural crest cells caused cleft palate, shortening of the mandible and tympanic bone, ectopic salivary glands and abnormal tongue musculature. We found that defects in the mandibular region, rather than in the palate itself, led to palatal clefting. Mutation of Bcor in hindlimb progenitor cells of the lateral mesoderm resulted in 2/3 syndactyly. Mutation of Bcor in Isl1-expressing lineages that contribute to the heart caused defects including persistent truncus arteriosus, ventricular septal defect and fetal lethality. Mutation of Bcor in extraembryonic lineages resulted in placental defects and midgestation lethality. Ubiquitous over expression of transgenic Bcor isoform A during development resulted in embryonic defects and midgestation lethality. The defects we have found in Bcor mutants provide insights into the etiology of the OFCD syndrome and how BCOR-containing PRC1 complexes function in development.
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Affiliation(s)
- Michelle Y Hamline
- The Molecular, Cellular, Developmental Biology and Genetics Graduate Program, University of Minnesota, Minneapolis, MN, 55455, USA; University of Minnesota Medical Scientist Training Program, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Connie M Corcoran
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Joseph A Wamstad
- The Molecular, Cellular, Developmental Biology and Genetics Graduate Program, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Isabelle Miletich
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, SE1 9RT, UK
| | - Jifan Feng
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, SE1 9RT, UK
| | - Jamie L Lohr
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Myriam Hemberger
- Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Paul T Sharpe
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, SE1 9RT, UK; Medical Research Council Centre for Transplantation, King's College London, London, SE1 9RT, UK
| | - Micah D Gearhart
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA; Developmental Biology Center, University of Minnesota, Minneapolis, MN, 55455, USA.
| | - Vivian J Bardwell
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA; Developmental Biology Center, University of Minnesota, Minneapolis, MN, 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA.
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27
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Yang Y, Li T, Geng Y, Li J. [RUNX1 gene mutations are associated with adverse prognosis of patients with acute myeloidleukemia]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2020; 40:1601-1606. [PMID: 33243739 DOI: 10.12122/j.issn.1673-4254.2020.11.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To explore the rate and distribution of Runt- related transcription factor 1 (RUNX1) gene mutations in patients with acute myeloid leukemia (AML) and the correlation of these mutations with the clinical characteristics and survival outcomes of the patients. METHODS The genomic DNA extracted from the bone marrow of 158 patients with newly diagnosed AML for PCR amplification of RUNX1 gene and sequence analysis to identify the mutations. The mutations of ASXL1, DNMT3A, TET2, FLT3, CEBPA, NPM1, IDH2, NRAS and c-KIT genes were also examined to analyze their association with RUNX1 gene mutations. RESULTS Among the 158 AML patients, 19 (12.0%) were found to have RUNX1 mutations in A166G (9 cases), A142T (6 cases) and A162L (4 cases). RUNX1 mutations were more frequent in elderly patients (P < 0.01) and in cases of AML subtypes M4 and M5, and were associated with more frequent CD36 and CD7 expression as compared with the wild type. RUNX1 mutations were more likely to occur in patients with normal karyotype or karyotypes associated with moderate prognostic risks, but the difference was not significant (P > 0.05). The patients with RUNX1 mutations had significantly lower complete remission (CR) rate and overall survival (OS) rate than those without the mutations (P < 0.05). RUNX1 mutations were not associated with gender, white blood cell count upon diagnosis, hemoglobin level, platelet count, bone marrow blast cell ratio or lactate dehydrogenase level (P > 0.05). CONCLUSIONS RUNX1 gene mutations are associated with an adverse prognosis of patients with AML.
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Affiliation(s)
- Yanli Yang
- Department of Hematology, First Affiliated Hospital of Bengbu Medical College, Bengbu 233000, China
| | - Tiantian Li
- Department of Hematology, First Affiliated Hospital of Bengbu Medical College, Bengbu 233000, China
| | - Yinghua Geng
- Department of Hematology, First Affiliated Hospital of Bengbu Medical College, Bengbu 233000, China
| | - Jun Li
- Department of Hematology, First Affiliated Hospital of Bengbu Medical College, Bengbu 233000, China
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28
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Sportoletti P, Sorcini D, Guzman AG, Reyes JM, Stella A, Marra A, Sartori S, Brunetti L, Rossi R, Papa BD, Adamo FM, Pianigiani G, Betti C, Scialdone A, Guarente V, Spinozzi G, Tini V, Martelli MP, Goodell MA, Falini B. Bcor deficiency perturbs erythro-megakaryopoiesis and cooperates with Dnmt3a loss in acute erythroid leukemia onset in mice. Leukemia 2020; 35:1949-1963. [PMID: 33159179 PMCID: PMC8257496 DOI: 10.1038/s41375-020-01075-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/19/2020] [Accepted: 10/20/2020] [Indexed: 12/18/2022]
Abstract
Recurrent loss-of-function mutations of BCL6 co-repressor (BCOR) gene are found in about 4% of AML patients with normal karyotype and are associated with DNMT3a mutations and poor prognosis. Therefore, new anti-leukemia treatments and mouse models are needed for this combinatorial AML genotype. For this purpose, we first generated a Bcor-/- knockout mouse model characterized by impaired erythroid development (macrocytosis and anemia) and enhanced thrombopoiesis, which are both features of myelodysplasia/myeloproliferative neoplasms. We then created and characterized double Bcor-/-/Dnmt3a-/- knockout mice. Interestingly, these animals developed a fully penetrant acute erythroid leukemia (AEL) characterized by leukocytosis secondary to the expansion of blasts expressing c-Kit+ and the erythroid marker Ter119, macrocytic anemia and progressive reduction of the thrombocytosis associated with loss of Bcor alone. Transcriptomic analysis of double knockout bone marrow progenitors revealed that aberrant erythroid skewing was induced by epigenetic changes affecting specific transcriptional factors (GATA1-2) and cell-cycle regulators (Mdm2, Tp53). These findings prompted us to investigate the efficacy of demethylating agents in AEL, with significant impact on progressive leukemic burden and mice overall survival. Information gained from our model expands the knowledge on the biology of AEL and may help designing new rational treatments for patients suffering from this high-risk leukemia.
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Affiliation(s)
- Paolo Sportoletti
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy.
| | - Daniele Sorcini
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Anna G Guzman
- Stem Cell and Regenerative Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Center for Cell and Gene Therapy, Texas Children's Hospital and Houston Methodist Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jaime M Reyes
- Stem Cell and Regenerative Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Center for Cell and Gene Therapy, Texas Children's Hospital and Houston Methodist Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Arianna Stella
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Andrea Marra
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Sara Sartori
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Lorenzo Brunetti
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Roberta Rossi
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Beatrice Del Papa
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Francesco Maria Adamo
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Giulia Pianigiani
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Camilla Betti
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Annarita Scialdone
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Valerio Guarente
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Giulio Spinozzi
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Valentina Tini
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Maria Paola Martelli
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Margaret A Goodell
- Stem Cell and Regenerative Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Center for Cell and Gene Therapy, Texas Children's Hospital and Houston Methodist Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Brunangelo Falini
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy.
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Clinico-pathologic characteristics and outcomes of the World Health Organization (WHO) provisional entity de novo acute myeloid leukemia with mutated RUNX1. Mod Pathol 2020; 33:1678-1689. [PMID: 32238878 DOI: 10.1038/s41379-020-0531-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/13/2020] [Accepted: 03/13/2020] [Indexed: 02/03/2023]
Abstract
We studied the characteristics of the provisional category de novo acute myeloid leukemia (AML) with mutated RUNX1 (AML-RUNX1mut) proposed by the World Health Organization (WHO). Until now, most published studies have combined de novo and secondary AML-RUNX1mut. We compared the clinicopathologic characteristics and outcomes of WHO-defined de novo AML-RUNX1mut with de novo AML without RUNX1 alterations (AML-RUNX1wt). We performed sequential NGS to assess RUNX1 mutation stability over disease course. We identified 46 de novo AML-RUNX1mut patients [32 (70%) men, 14 (30%) women; median age, 66.5 years] with 54 RUNX1 mutations [median VAF, 32% (2-97%)]. Point mutations clustered within the runt-homology-domain and frame-shift mutations within the transactivation domain. Compared with AML-RUNX1wt, AML-RUNX1mut showed male predominance (p = 0.02), higher frequency of SRSF2 (p = 0.02), and ASXL1 (p = 0.0004) mutations and normal karyotype (p = 0.01), and absent NPM1 mutations (p = 0.0002). De novo AML-RUNX1mut showed no significant difference in overall survival (OS) compared with AML-RUNX1wt (median: 26 vs. 32 months) (p = 0.71). AML-RUNX1mut with clonal RUNX1 mutation (≥20% VAF) had shorter OS than subclonal <20% VAF (23 months vs. undefined; p = 0.04). However, the difference was not significant when compared with AML-RUNX1wt (23 vs. 32 months; p = 0.23). No significant OS difference was noted between de novo AML-RUNX1mut and AML-NOS-RUNX1wt. By sequential multigene mutation profiling, RUNX1 mutation disappeared at relapse in one of ten patients. Overall, the findings support separate categorization of this entity. However, there is no significant outcome difference compared with AML-RUNX1wt.
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30
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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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31
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Bewersdorf JP, Shallis RM, Diadamo A, Gowda L, Podoltsev NA, Siddon A, Zeidan AM. Isolated trisomy 11 in patients with acute myeloid leukemia - is the prognosis not as grim as previously thought? Leuk Lymphoma 2020; 61:2254-2257. [PMID: 32338096 DOI: 10.1080/10428194.2020.1755858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Jan Philipp Bewersdorf
- Department of Internal Medicine, Section of Hematology, Yale School of Medicine, New Haven, CT, USA
| | - Rory M Shallis
- Department of Internal Medicine, Section of Hematology, Yale School of Medicine, New Haven, CT, USA
| | - Autumn Diadamo
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Lohith Gowda
- Department of Internal Medicine, Section of Hematology, Yale School of Medicine, New Haven, CT, USA
| | - Nikolai A Podoltsev
- Department of Internal Medicine, Section of Hematology, Yale School of Medicine, New Haven, CT, USA
| | - Alexa Siddon
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA.,Department of Pathology, Section of Hematopathology, Yale School of Medicine, New Haven, CT, USA
| | - Amer M Zeidan
- Department of Internal Medicine, Section of Hematology, Yale School of Medicine, New Haven, CT, USA.,Cancer Outcomes, Public Policy, and Effectiveness Research (COPPER) Center, Yale University, New Haven, CT, USA
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32
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Pourrajab F, Zare-Khormizi MR, Hashemi AS, Hekmatimoghaddam S. Genetic Characterization and Risk Stratification of Acute Myeloid Leukemia. Cancer Manag Res 2020; 12:2231-2253. [PMID: 32273762 PMCID: PMC7104087 DOI: 10.2147/cmar.s242479] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 02/22/2020] [Indexed: 12/24/2022] Open
Abstract
The most common acute leukemia in adults is acute myeloid leukemia (AML). The pathophysiology of the disease associates with cytogenetic abnormalities, gene mutations and aberrant gene expressions. At the molecular level, the disease manifests as changes in both epigenetic and genetic signatures. At the clinical level, two aspects of AML should be taken into account. First, the molecular changes occurring in the disease are important prognostic and predictive markers of AML. Second, use of novel therapies targeting these molecular changes. Currently, cytogenetic abnormalities and molecular alterations are the common biomarkers for the prognosis and choice of treatment for AML. Finding a panel of multiple biomarkers is a crucial diagnostic step for patient classification and serves as a prerequisite for individualized treatment strategies. Furthermore, the most important way of identifying relevant targets for new treatment approaches is defining specific patterns or a spectrum of driver gene mutations occurring in AML. Then, an algorithm can be established by the use of several biomarkers, to be used for personalized medicine. This review deals with molecular alterations, risk stratification, and relevant therapeutic decision-making in AML.
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Affiliation(s)
- Fatemeh Pourrajab
- Department of Biochemistry and Molecular Biology, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.,Nutrition and Food Security Research Centre, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | | | - Azam Sadat Hashemi
- Hematology & Oncology Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Seyedhossein Hekmatimoghaddam
- Hematology & Oncology Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.,Department of Advanced Medical Sciences and Technologies, School of Paramedicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
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Abstract
Introduction: Trisomy 8 is one of the most common cytogenetic alterations in acute myeloid leukemia (AML), with a frequency between 10% and 15%.Areas covered: The authors summarize the latest research regarding biological, translational and clinical aspects of trisomy 8 in AML.Expert opinion: Trisomy 8 can be found together with other karyotypes, although it also occurs as a sole aberration. The last decade's research has brought attention to molecular genetic alterations as strong contributors of leukemogenesis. AML with trisomy 8 seems to be associated with mutations in DNA methylation genes, spliceosome complex genes, and myeloid transcription factor genes, and these alterations probably have stronger implication for leukemic pathogenesis, treatment and hence prognosis, than the existence of trisomy 8 itself. Especially mutations in the RUNX1 and ASXL1 genes occur in high frequencies, and search for such mutations should be mandatory part of the diagnostic workup. AML with trisomy 8 is classified as intermediate-risk AML after recent European Leukemia Net (ELN) classification, and hence allogenic hematopoietic stem cell transplantation (Allo-HSCT) should be consider as consolidation therapy for this patient group.Trisomy 8 is frequently occurring in AML, although future molecular genetic workup should be performed, to optimize the diagnosis and treatment of these patients.
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Affiliation(s)
- Anette Lodvir Hemsing
- Division for Hematology, Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Randi Hovland
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.,Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Galina Tsykunova
- Division for Hematology, Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Håkon Reikvam
- Division for Hematology, Department of Medicine, Haukeland University Hospital, Bergen, Norway.,Institute of Clinical Science, University of Bergen, Bergen, Norway
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34
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Clinical and molecular characterization of patients with acute myeloid leukemia and sole trisomies of chromosomes 4, 8, 11, 13 or 21. Leukemia 2019; 34:358-368. [PMID: 31462731 DOI: 10.1038/s41375-019-0560-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 07/01/2019] [Accepted: 07/15/2019] [Indexed: 12/13/2022]
Abstract
Sole trisomies of chromosomes 4, 8, 11, 13 and 21 account for 89-95% of all sole trisomies in adult AML patients. We analyzed clinical and molecular characteristics of 138 de novo AML patients with sole +4, +8, +11, +13 or +21, and compared them with AML patients with those trisomies occurring in addition to other chromosome abnormalities (non-sole trisomy) and with cytogenetically normal AML (CN-AML) patients. Mutations in methylation-related genes were most commonly observed within each sole trisomy group (+4, 55%; +8, 58%; +11, 71%; +13, 71%; +21, 75% of patients). Patients with sole trisomies, excluding +4, also had frequent mutations in spliceosome genes (+8, 43%; +11, 65%; +13, 65%; +21, 45% of patients). In contrast, +4 patients frequently had mutations in transcription factor genes (44%) and NPM1 (36%). While 48% of patients with sole trisomies harbored mutations in a spliceosome gene, spliceosome mutations were observed in only 24% of non-sole trisomy (n = 131, P < 0.001) and 19% of CN-AML patients (n = 716, P < 0.001). Our data suggest that mutations affecting methylation-related genes are a molecular hallmark of sole trisomies. Mutations in spliceosome genes were also commonly observed in many sole trisomy patients and represent a novel finding in this cytogenetic subgroup.
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35
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Multi-study reanalysis of 2,213 acute myeloid leukemia patients reveals age- and sex-dependent gene expression signatures. Sci Rep 2019; 9:12413. [PMID: 31455838 PMCID: PMC6712049 DOI: 10.1038/s41598-019-48872-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 08/14/2019] [Indexed: 11/19/2022] Open
Abstract
In 2019 it is estimated that more than 21,000 new acute myeloid leukemia (AML) patients will be diagnosed in the United States, and nearly 11,000 are expected to die from the disease. AML is primarily diagnosed among the elderly (median 68 years old at diagnosis). Prognoses have significantly improved for younger patients, but as much as 70% of patients over 60 years old will die within a year of diagnosis. In this study, we conducted a reanalysis of 2,213 acute myeloid leukemia patients compared to 548 healthy individuals, using curated publicly available microarray gene expression data. We carried out an analysis of normalized batch corrected data, using a linear model that included considerations for disease, age, sex, and tissue. We identified 974 differentially expressed probe sets and 4 significant pathways associated with AML. Additionally, we identified 375 age- and 70 sex-related probe set expression signatures relevant to AML. Finally, we trained a k nearest neighbors model to classify AML and healthy subjects with 90.9% accuracy. Our findings provide a new reanalysis of public datasets, that enabled the identification of new gene sets relevant to AML that can potentially be used in future experiments and possible stratified disease diagnostics.
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36
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Angenendt L, Bormann E, Pabst C, Alla V, Görlich D, Braun L, Dohlich K, Schwöppe C, Bohlander SK, Arteaga MF, Wethmar K, Hartmann W, Angenendt A, Kessler T, Mesters RM, Stelljes M, Rothenberg-Thurley M, Spiekermann K, Hébert J, Sauvageau G, Valk PJM, Löwenberg B, Serve H, Müller-Tidow C, Lenz G, Wörmann BJ, Sauerland MC, Hiddemann W, Berdel WE, Krug U, Metzeler KH, Mikesch JH, Herold T, Schliemann C. The neuropeptide receptor calcitonin receptor-like (CALCRL) is a potential therapeutic target in acute myeloid leukemia. Leukemia 2019; 33:2830-2841. [PMID: 31182782 DOI: 10.1038/s41375-019-0505-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/12/2019] [Accepted: 04/18/2019] [Indexed: 11/09/2022]
Abstract
Calcitonin receptor-like (CALCRL) is a G-protein-coupled neuropeptide receptor involved in the regulation of blood pressure, angiogenesis, cell proliferation, and apoptosis, and is currently emerging as a novel target for the treatment of migraine. This study characterizes the role of CALCRL in acute myeloid leukemia (AML). We analyzed CALCRL expression in collectively more than 1500 well-characterized AML patients from five international cohorts (AMLCG, HOVON, TCGA, Leucegene, and UKM) and evaluated associations with survival. In the AMLCG analytic cohort, increasing transcript levels of CALCRL were associated with decreasing complete remission rates (71.5%, 53.7%, 49.6% for low, intermediate, high CALCRL expression), 5-year overall (43.1%, 26.2%, 7.1%), and event-free survival (29.9%, 15.8%, 4.7%) (all P < 0.001). CALCRL levels remained associated with all endpoints on multivariable regression analyses. The prognostic impact was confirmed in all validation sets. Genes highly expressed in CALCRLhigh AML were significantly enriched in leukemic stem cell signatures and CALCRL levels were positively linked to the engraftment capacity of primary patient samples in immunocompromised mice. CRISPR-Cas9-mediated knockout of CALCRL significantly impaired colony formation in human myeloid leukemia cell lines. Overall, our study demonstrates that CALCRL predicts outcome beyond existing risk factors and is a potential therapeutic target in AML.
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Affiliation(s)
- Linus Angenendt
- Department of Medicine A, University Hospital Münster, Münster, Germany.
| | - Eike Bormann
- Institute of Biostatistics and Clinical Research, University of Münster, Münster, Germany
| | - Caroline Pabst
- Department of Medicine V, University Hospital Heidelberg, Heidelberg, Germany
| | - Vijay Alla
- Department of Medicine A, University Hospital Münster, Münster, Germany
| | - Dennis Görlich
- Institute of Biostatistics and Clinical Research, University of Münster, Münster, Germany
| | - Leonie Braun
- Department of Medicine A, University Hospital Münster, Münster, Germany
| | - Kim Dohlich
- Department of Medicine A, University Hospital Münster, Münster, Germany
| | | | - Stefan K Bohlander
- Leukaemia & Blood Cancer Research Unit, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | | | - Klaus Wethmar
- Department of Medicine A, University Hospital Münster, Münster, Germany
| | - Wolfgang Hartmann
- Gerhard-Domagk-Institute of Pathology, University Hospital Münster, Münster, Germany
| | - Adrian Angenendt
- Department of Biophysics, Faculty of Medicine, Centre for Integrative Physiology and Molecular Medicine (CIPMM), Saarland University, Homburg, Germany
| | - Torsten Kessler
- Department of Medicine A, University Hospital Münster, Münster, Germany
| | - Rolf M Mesters
- Department of Medicine A, University Hospital Münster, Münster, Germany
| | - Matthias Stelljes
- Department of Medicine A, University Hospital Münster, Münster, Germany
| | | | - Karsten Spiekermann
- Department of Medicine III, University Hospital Grosshadern, LMU Munich, Munich, Germany
| | - Josée Hébert
- The Leucegene Project at Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada.,Division of Hematology-Oncology, Maisonneuve-Rosemont Hospital, Montreal, QC, Canada.,Quebec Leukemia Cell Bank, Maisonneuve-Rosemont Hospital, Montreal, QC, Canada.,Department of Medicine, University of Montreal, Montreal, QC, Canada
| | - Guy Sauvageau
- The Leucegene Project at Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada.,Division of Hematology-Oncology, Maisonneuve-Rosemont Hospital, Montreal, QC, Canada.,Quebec Leukemia Cell Bank, Maisonneuve-Rosemont Hospital, Montreal, QC, Canada.,Department of Medicine, University of Montreal, Montreal, QC, Canada
| | - Peter J M Valk
- Department of Hematology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Bob Löwenberg
- Department of Hematology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Hubert Serve
- Department of Hematology and Oncology, University Hospital Frankfurt, Frankfurt, Germany
| | | | - Georg Lenz
- Department of Medicine A, University Hospital Münster, Münster, Germany
| | - Bernhard J Wörmann
- Department of Hematology, Oncology and Tumor Immunology, Charité University Medicine, Campus Virchow, Berlin, Germany
| | - M Christina Sauerland
- Institute of Biostatistics and Clinical Research, University of Münster, Münster, Germany
| | - Wolfgang Hiddemann
- Department of Medicine III, University Hospital Grosshadern, LMU Munich, Munich, Germany
| | - Wolfgang E Berdel
- Department of Medicine A, University Hospital Münster, Münster, Germany
| | - Utz Krug
- Department of Medicine 3, Klinikum Leverkusen, Leverkusen, Germany
| | - Klaus H Metzeler
- Department of Medicine III, University Hospital Grosshadern, LMU Munich, Munich, Germany
| | | | - Tobias Herold
- Department of Medicine III, University Hospital Grosshadern, LMU Munich, Munich, Germany. .,Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Center for Environmental Health (HMGU), Munich, Germany.
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Abstract
BCOR is a gene that encodes for an epigenetic regulator involved in the specification of cell differentiation and body structure development and takes part in the noncanonical polycomb repressive complex 1. This review provides a comprehensive summary of BCOR’s involvement in oncology, illustrating that various BCOR aberrations, such as the internal tandem duplications of the PCGF Ub-like fold discriminator domain and different gene fusions (mainly BCOR–CCNB3, BCOR–MAML3 and ZC3H7B–BCOR), represent driver elements of various sarcomas such as clear cell sarcoma of the kidney, primitive mesenchymal myxoid tumor of infancy, small round blue cell sarcoma, endometrial stromal sarcoma and histologically heterogeneous CNS neoplasms group with similar genomic methylation patterns known as CNS-HGNET-BCOR. Furthermore, other BCOR alterations (often loss of function mutations) recur in a large variety of mesenchymal, epithelial, neural and hematological tumors, suggesting a central role in cancer evolution.
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Affiliation(s)
- Annalisa Astolfi
- 'Giorgio Prodi' Cancer Research Center, University of Bologna, 40138 Bologna, Italy
| | - Michele Fiore
- Pediatric Oncology & Hematology Unit 'Lalla Seràgnoli', S Orsola-Malpighi Hospital, 40138 Bologna, Italy
| | - Fraia Melchionda
- Pediatric Oncology & Hematology Unit 'Lalla Seràgnoli', S Orsola-Malpighi Hospital, 40138 Bologna, Italy
| | - Valentina Indio
- 'Giorgio Prodi' Cancer Research Center, University of Bologna, 40138 Bologna, Italy
| | - Salvatore N Bertuccio
- Pediatric Oncology & Hematology Unit 'Lalla Seràgnoli', S Orsola-Malpighi Hospital, 40138 Bologna, Italy
| | - Andrea Pession
- Pediatric Oncology & Hematology Unit 'Lalla Seràgnoli', S Orsola-Malpighi Hospital, 40138 Bologna, Italy.,Department of Medical & Surgical Sciences, University of Bologna, S Orsola-Malpighi Hospital, 40138 Bologna, Italy
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38
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Klau S, Martin-Magniette ML, Boulesteix AL, Hoffmann S. Sampling uncertainty versus method uncertainty: A general framework with applications to omics biomarker selection. Biom J 2019; 62:670-687. [PMID: 31099917 DOI: 10.1002/bimj.201800309] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 04/12/2019] [Accepted: 04/23/2019] [Indexed: 12/19/2022]
Abstract
Uncertainty is a crucial issue in statistics which can be considered from different points of view. One type of uncertainty, typically referred to as sampling uncertainty, arises through the variability of results obtained when the same analysis strategy is applied to different samples. Another type of uncertainty arises through the variability of results obtained when using the same sample but different analysis strategies addressing the same research question. We denote this latter type of uncertainty as method uncertainty. It results from all the choices to be made for an analysis, for example, decisions related to data preparation, method choice, or model selection. In medical sciences, a large part of omics research is focused on the identification of molecular biomarkers, which can either be performed through ranking or by selection from among a large number of candidates. In this paper, we introduce a general resampling-based framework to quantify and compare sampling and method uncertainty. For illustration, we apply this framework to different scenarios related to the selection and ranking of omics biomarkers in the context of acute myeloid leukemia: variable selection in multivariable regression using different types of omics markers, the ranking of biomarkers according to their predictive performance, and the identification of differentially expressed genes from RNA-seq data. For all three scenarios, our findings suggest highly unstable results when the same analysis strategy is applied to two independent samples, indicating high sampling uncertainty and a comparatively smaller, but non-negligible method uncertainty, which strongly depends on the methods being compared.
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Affiliation(s)
- Simon Klau
- Institute for Medical Information Processing, Biometry and Epidemiology (IBE), Munich, Germany
| | - Marie-Laure Martin-Magniette
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Orsay, France.,Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Orsay, France.,UMR MIA-Paris, AgroParisTech, INRA, Université Paris-Saclay, Paris, France
| | - Anne-Laure Boulesteix
- Institute for Medical Information Processing, Biometry and Epidemiology (IBE), Munich, Germany
| | - Sabine Hoffmann
- Institute for Medical Information Processing, Biometry and Epidemiology (IBE), Munich, Germany
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Ianniello Z, Paiardini A, Fatica A. N 6-Methyladenosine (m 6A): A Promising New Molecular Target in Acute Myeloid Leukemia. Front Oncol 2019; 9:251. [PMID: 31024852 PMCID: PMC6465620 DOI: 10.3389/fonc.2019.00251] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 03/19/2019] [Indexed: 12/25/2022] Open
Abstract
Recent studies have uncovered an important role for RNA modifications in gene expression regulation, which led to the birth of the epitranscriptomics field. It is now acknowledged that RNA modifiers play a crucial role in the control of differentiation of stem and progenitor cells and that changes in their levels are a relevant feature of different types of cancer. To date, among more than 160 different RNA chemical modifications, the more relevant in cancer biology is the reversible and dynamic N6-methylation of adenosine, yielding N6-methyladenosine (m6A). m6A is the more abundant internal modification in mRNA, regulating the expression of the latter at different levels, from maturation to translation. Here, we will describe the emerging role of m6A modification in acute myeloid leukemia (AML), which, among first, has demonstrated how mis-regulation of the m6A modifying system can contribute to the development and progression of cancer. Moreover, we will discuss how AML is paving the way to the development of new therapeutic options based on the inhibition of m6A deposition.
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Affiliation(s)
- Zaira Ianniello
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, Rome, Italy
| | - Alessandro Paiardini
- Department of Biochemical Sciences "A. Rossi Fanelli," Sapienza University of Rome, Rome, Italy
| | - Alessandro Fatica
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, Rome, Italy
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40
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Vosberg S, Hartmann L, Metzeler KH, Konstandin NP, Schneider S, Varadharajan A, Hauser A, Krebs S, Blum H, Bohlander SK, Hiddemann W, Tischer J, Spiekermann K, Greif PA. Relapse of acute myeloid leukemia after allogeneic stem cell transplantation is associated with gain of WT1 alterations and high mutation load. Haematologica 2018; 103:e581-e584. [PMID: 29954937 PMCID: PMC6269290 DOI: 10.3324/haematol.2018.193102] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Sebastian Vosberg
- Experimental Leukemia and Lymphoma Research, Department of Medicine III, University Hospital, LMU Munich, Germany
- German Cancer Consortium (DKTK), partner site Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Germany
| | - Luise Hartmann
- Experimental Leukemia and Lymphoma Research, Department of Medicine III, University Hospital, LMU Munich, Germany
- German Cancer Consortium (DKTK), partner site Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Germany
| | - Klaus H Metzeler
- Experimental Leukemia and Lymphoma Research, Department of Medicine III, University Hospital, LMU Munich, Germany
- German Cancer Consortium (DKTK), partner site Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Germany
| | - Nikola P Konstandin
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Germany
| | - Stephanie Schneider
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Germany
- Institute of Human Genetics, University Hospital, LMU Munich, Germany
| | - Ashok Varadharajan
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Germany
| | - Andreas Hauser
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Germany
| | - Stefan K Bohlander
- Leukaemia and Blood Cancer Research Unit, Department of Molecular Medicine and Pathology, The University of Auckland, New Zealand
| | - Wolfgang Hiddemann
- Experimental Leukemia and Lymphoma Research, Department of Medicine III, University Hospital, LMU Munich, Germany
- German Cancer Consortium (DKTK), partner site Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Germany
| | - Johanna Tischer
- Hematopoietic Stem Cell Transplantation, Department of Medicine III, University Hospital, LMU Munich, Germany
| | - Karsten Spiekermann
- Experimental Leukemia and Lymphoma Research, Department of Medicine III, University Hospital, LMU Munich, Germany
- German Cancer Consortium (DKTK), partner site Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Germany
| | - Philipp A Greif
- Experimental Leukemia and Lymphoma Research, Department of Medicine III, University Hospital, LMU Munich, Germany
- German Cancer Consortium (DKTK), partner site Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Germany
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41
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Simonetti G, Padella A, do Valle IF, Fontana MC, Fonzi E, Bruno S, Baldazzi C, Guadagnuolo V, Manfrini M, Ferrari A, Paolini S, Papayannidis C, Marconi G, Franchini E, Zuffa E, Laginestra MA, Zanotti F, Astolfi A, Iacobucci I, Bernardi S, Sazzini M, Ficarra E, Hernandez JM, Vandenberghe P, Cools J, Bullinger L, Ottaviani E, Testoni N, Cavo M, Haferlach T, Castellani G, Remondini D, Martinelli G. Aneuploid acute myeloid leukemia exhibits a signature of genomic alterations in the cell cycle and protein degradation machinery. Cancer 2018; 125:712-725. [PMID: 30480765 PMCID: PMC6587451 DOI: 10.1002/cncr.31837] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/08/2018] [Accepted: 06/26/2018] [Indexed: 12/19/2022]
Abstract
Background Aneuploidy occurs in more than 20% of acute myeloid leukemia (AML) cases and correlates with an adverse prognosis. Methods To understand the molecular bases of aneuploid acute myeloid leukemia (A‐AML), this study examined the genomic profile in 42 A‐AML cases and 35 euploid acute myeloid leukemia (E‐AML) cases. Results A‐AML was characterized by increased genomic complexity based on exonic variants (an average of 26 somatic mutations per sample vs 15 for E‐AML). The integration of exome, copy number, and gene expression data revealed alterations in genes involved in DNA repair (eg, SLX4IP, RINT1, HINT1, and ATR) and the cell cycle (eg, MCM2, MCM4, MCM5, MCM7, MCM8, MCM10, UBE2C, USP37, CK2, CK3, CK4, BUB1B, NUSAP1, and E2F) in A‐AML, which was associated with a 3‐gene signature defined by PLK1 and CDC20 upregulation and RAD50 downregulation and with structural or functional silencing of the p53 transcriptional program. Moreover, A‐AML was enriched for alterations in the protein ubiquitination and degradation pathway (eg, increased levels of UHRF1 and UBE2C and decreased UBA3 expression), response to reactive oxygen species, energy metabolism, and biosynthetic processes, which may help in facing the unbalanced protein load. E‐AML was associated with BCOR/BCORL1 mutations and HOX gene overexpression. Conclusions These findings indicate that aneuploidy‐related and leukemia‐specific alterations cooperate to tolerate an abnormal chromosome number in AML, and they point to the mitotic and protein degradation machineries as potential therapeutic targets. Aneuploid acute myeloid leukemia (A‐AML) is associated with genomic and transcriptional alterations in the cell cycle and protein degradation pathways. The upregulation of PLK1 and CDC20 and the downregulation of RAD50 and of a p53‐related signature are hallmarks of A‐AML.
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Affiliation(s)
- Giorgia Simonetti
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Antonella Padella
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Italo Farìa do Valle
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy.,CAPES Foundation, Ministry of Education of Brazil, Brasília, Brazil
| | - Maria Chiara Fontana
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Eugenio Fonzi
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Samantha Bruno
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Carmen Baldazzi
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Viviana Guadagnuolo
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Marco Manfrini
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Anna Ferrari
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Stefania Paolini
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Cristina Papayannidis
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Giovanni Marconi
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Eugenia Franchini
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Elisa Zuffa
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Maria Antonella Laginestra
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Federica Zanotti
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Annalisa Astolfi
- Giorgio Prodi Cancer Research Center, University of Bologna, Bologna, Italy
| | - Ilaria Iacobucci
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Simona Bernardi
- Unit of Blood Diseases and Stem Cell Transplantation, University of Brescia, Brescia, Italy
| | - Marco Sazzini
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | | | - Jesus Maria Hernandez
- Fundación de Investigación del Cáncer de la Universidad de Salamanca, Salamanca, Spain
| | | | - Jan Cools
- Katholieke Universiteit Leuven, Leuven, Belgium
| | | | - Emanuela Ottaviani
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Nicoletta Testoni
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Michele Cavo
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | | | - Gastone Castellani
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - Daniel Remondini
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - Giovanni Martinelli
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
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42
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Priority-Lasso: a simple hierarchical approach to the prediction of clinical outcome using multi-omics data. BMC Bioinformatics 2018; 19:322. [PMID: 30208855 PMCID: PMC6134797 DOI: 10.1186/s12859-018-2344-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 08/29/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The inclusion of high-dimensional omics data in prediction models has become a well-studied topic in the last decades. Although most of these methods do not account for possibly different types of variables in the set of covariates available in the same dataset, there are many such scenarios where the variables can be structured in blocks of different types, e.g., clinical, transcriptomic, and methylation data. To date, there exist a few computationally intensive approaches that make use of block structures of this kind. RESULTS In this paper we present priority-Lasso, an intuitive and practical analysis strategy for building prediction models based on Lasso that takes such block structures into account. It requires the definition of a priority order of blocks of data. Lasso models are calculated successively for every block and the fitted values of every step are included as an offset in the fit of the next step. We apply priority-Lasso in different settings on an acute myeloid leukemia (AML) dataset consisting of clinical variables, cytogenetics, gene mutations and expression variables, and compare its performance on an independent validation dataset to the performance of standard Lasso models. CONCLUSION The results show that priority-Lasso is able to keep pace with Lasso in terms of prediction accuracy. Variables of blocks with higher priorities are favored over variables of blocks with lower priority, which results in easily usable and transportable models for clinical practice.
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43
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N6-Methyladenosine Role in Acute Myeloid Leukaemia. Int J Mol Sci 2018; 19:ijms19082345. [PMID: 30096915 PMCID: PMC6121471 DOI: 10.3390/ijms19082345] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 08/07/2018] [Accepted: 08/08/2018] [Indexed: 12/15/2022] Open
Abstract
We are currently assisting in the explosion of epitranscriptomics, which studies the functional role of chemical modifications into RNA molecules. Among more than 100 RNA modifications, the N6-methyladenosine (m6A), in particular, has attracted the interest of researchers all around the world. m6A is the most abundant internal chemical modification in mRNA, and it can control any aspect of mRNA post-transcriptional regulation. m6A is installed by “writers”, removed by “erasers”, and recognized by “readers”; thus, it can be compared to the reversible and dynamic epigenetic modifications in histones and DNA. Given its fundamental role in determining the way mRNAs are expressed, it comes as no surprise that alterations to m6A modifications have a deep impact in cell differentiation, normal development and human diseases. Here, we review the proteins involved in m6A modification in mammals, m6A role in gene expression and its contribution to cancer development. In particular, we will focus on acute myeloid leukaemia (AML), which provides an initial indication of how alteration in m6A modification can disrupt normal cellular differentiation and lead to cancer.
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44
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Mediation analysis reveals common mechanisms of RUNX1 point mutations and RUNX1/RUNX1T1 fusions influencing survival of patients with acute myeloid leukemia. Sci Rep 2018; 8:11293. [PMID: 30050054 PMCID: PMC6062501 DOI: 10.1038/s41598-018-29593-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 07/11/2018] [Indexed: 12/17/2022] Open
Abstract
Alterations of RUNX1 in acute myeloid leukemia (AML) are associated with either a more favorable outcome in the case of the RUNX1/RUNX1T1 fusion or unfavorable prognosis in the case of point mutations. In this project we aimed to identify genes responsible for the observed differences in outcome that are common to both RUNX1 alterations. Analyzing four AML gene expression data sets (n = 1514), a total of 80 patients with RUNX1/RUNX1T1 and 156 patients with point mutations in RUNX1 were compared. Using the statistical tool of mediation analysis we identified the genes CD109, HOPX, and KIAA0125 as candidates for mediator genes. In an analysis of an independent validation cohort, KIAA0125 again showed a significant influence with respect to the impact of the RUNX1/RUNX1T1 fusion. While there were no significant results for the other two genes in this smaller validation cohort, the observed relations linked with mediation effects (i.e., those between alterations, gene expression and survival) were almost without exception as strong as in the main analysis. Our analysis demonstrates that mediation analysis is a powerful tool in the identification of regulative networks in AML subgroups and could be further used to characterize the influence of genetic alterations.
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45
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Screening for susceptibility genes in hereditary non-polyposis colorectal cancer. Oncol Lett 2018; 15:9413-9419. [PMID: 29844832 DOI: 10.3892/ol.2018.8504] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 09/22/2017] [Indexed: 01/29/2023] Open
Abstract
In the present study, hereditary non-polyposis colorectal cancer (HNPCC) susceptibility genes were screened for using whole exome sequencing in 3 HNPCC patients from 1 family and using single nucleotide polymorphism (SNP) genotyping assays in 96 other colorectal cancer and control samples. Peripheral blood was obtained from 3 HNPCC patients from 1 family; the proband and the proband's brother and cousin. High-throughput sequencing was performed using whole exome capture technology. Sequences were aligned against the HAPMAP, dbSNP130 and 1,000 Genome Project databases. Reported common variations and synonymous mutations were filtered out. Non-synonymous single nucleotide variants in the 3 HNPCC patients were integrated and the candidate genes were identified. Finally, SNP genotyping was performed for the genes in 96 peripheral blood samples. In total, 60.4 Gb of data was retrieved from the 3 HNPCC patients using whole exome capture technology. Subsequently, according to certain screening criteria, 15 candidate genes were identified. Among the 96 samples that had been SNP genotyped, 92 were successfully genotyped for 15 gene loci, while genotyping for HTRA1 failed in 4 sporadic colorectal cancer patient samples. In 12 control subjects and 81 sporadic colorectal cancer patients, genotypes at 13 loci were wild-type, namely DDX20, ZFYVE26, PIK3R3, SLC26A8, ZEB2, TP53INP1, SLC11A1, LRBA, CEBPZ, ETAA1, SEMA3G, IFRD2 and FAT1. The CEP290 genotype was mutant in 1 sporadic colorectal cancer patient and was wild-type in all other subjects. A total of 5 of the 12 control subjects and 30 of the 81 sporadic colorectal cancer patients had a mutant HTRA1 genotype. In all 3 HNPCC patients, the same mutant genotypes were identified at all 15 gene loci. Overall, 13 potential susceptibility genes for HNPCC were identified, namely DDX20, ZFYVE26, PIK3R3, SLC26A8, ZEB2, TP53INP1, SLC11A1, LRBA, CEBPZ, ETAA1, SEMA3G, IFRD2 and FAT1.
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46
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Thurtle DP, Huck MB, Zeller KA, Jewett T. Adenocarcinoma and polyposis of the colon in a 20-year-old patient with Trisomy 13: a case report. J Med Case Rep 2018; 12:56. [PMID: 29501064 PMCID: PMC5835326 DOI: 10.1186/s13256-018-1600-8] [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: 09/13/2017] [Accepted: 01/31/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Trisomy 13 is one of the most common autosomal trisomies, and although increasing in number, patients surviving past the neonatal period remain rare. The natural history and expected complications in these patients as they age remains unknown. Despite the rarity of this condition, unusual malignancies have been reported in the medical literature for decades. It is clear that providers should suspect unusual malignancies in these patients, particularly as they age. CASE PRESENTATION We report a 20-year-old Caucasian woman with Trisomy 13 who presented with colonic volvulus, found to have colonic polyposis and adenocarcinoma of the colon. Genetics of pathology specimens revealed 47(XX) + 13 without other mutations. She underwent prophylactic completion colectomy due to presumed risk of colorectal cancers given underlying adenomatous polyposis. She has recovered well without evidence of recurrence. CONCLUSIONS The presence of colonic polyposis and colorectal cancer without family history or known mutations for polyposis syndrome suggests an intrinsic predisposition toward colorectal cancer in this patient with Trisomy 13. Recent research into colorectal cancer oncogenes supports that aneuploidy or increased copy number of certain genes on chromosome 13 may increase the risk of malignant transformation. This is an important correlation for researchers studying these topics and clinicians caring for patients with Trisomy 13 as they age.
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Affiliation(s)
- Danielle P Thurtle
- Wake Forest School of Medicine, Medical Center Blvd, Winston Salem, NC, 27157, USA.
| | - Michael B Huck
- Lehigh Valley Health Network, 1200 S Cedar Crest Blvd, Allentown, PA, 18103, USA
| | - Kristen A Zeller
- Wake Forest School of Medicine, Medical Center Blvd, Winston Salem, NC, 27157, USA
| | - Tamison Jewett
- Wake Forest School of Medicine, Medical Center Blvd, Winston Salem, NC, 27157, USA
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47
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Kakosaiou K, Panitsas F, Daraki A, Pagoni M, Apostolou P, Ioannidou A, Vlachadami I, Marinakis T, Giatra C, Vasilatou D, Sambani C, Pappa V, Manola KN. ASXL1 mutations in AML are associated with specific clinical and cytogenetic characteristics. Leuk Lymphoma 2018; 59:2439-2446. [PMID: 29411666 DOI: 10.1080/10428194.2018.1433298] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Mutations of ASXL1 are early events in acute myeloid leukemia (AML) leukemogenesis and have been associated with unfavorable prognosis. In this study, we investigated the type and frequency of ASXL1 mutations in a large cohort of patients with de novo or secondary AML (s-AML) and looked for correlations with cytogenetic findings and disease features. ASXL1 mutations were associated with older age, s-AML and higher peripheral leukocytosis. We observed more frequent co-occurrence of ASXL1 mutations with trisomy 8 and chromosome 11 aberrations but a negative correlation with myelodysplastic syndromes (MDS)-related cytogenetic abnormalities, especially -5/del(5q) and -7/del(7q). ASXL1 mutations were also found in other genetically defined AML subgroups such as those with t(9;22), inv(3)/t(3;3), t(8;21) or t(15;17); however, none of our inv(16) cases carried ASXL1 mutations. We detected two previously unreported ASXL1 mutations, p.IIe593Val and p.Cys688Tyr. Our findings suggest that ASXL1 mutations tend to cluster with specific clinical and cytogenetic profiles of AML patients.
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Affiliation(s)
- Katerina Kakosaiou
- a Laboratory of Health Physics, Radiobiology & Cytogenetics , NCSR "Demokritos" , Athens , Greece
| | - Fotios Panitsas
- b Hematology-Lymphoma Department - BMT Unit , Evangelismos Hospital , Athens , Greece
| | - Aggeliki Daraki
- a Laboratory of Health Physics, Radiobiology & Cytogenetics , NCSR "Demokritos" , Athens , Greece
| | - Maria Pagoni
- b Hematology-Lymphoma Department - BMT Unit , Evangelismos Hospital , Athens , Greece
| | | | - Agapi Ioannidou
- a Laboratory of Health Physics, Radiobiology & Cytogenetics , NCSR "Demokritos" , Athens , Greece
| | - Ioanna Vlachadami
- d Department of Pathophysiology , 'Laiko' Hospital, University of Athens , Athens , Greece
| | - Theodoros Marinakis
- e Department of Haematology , "Georgios Gennimatas" General Hospital , Athens , Greece
| | - Chara Giatra
- b Hematology-Lymphoma Department - BMT Unit , Evangelismos Hospital , Athens , Greece
| | | | - Constantina Sambani
- a Laboratory of Health Physics, Radiobiology & Cytogenetics , NCSR "Demokritos" , Athens , Greece
| | - Vassiliki Pappa
- f Hematology Unit , University General Hospital "Attikon" , Athens , Greece
| | - Kalliopi N Manola
- a Laboratory of Health Physics, Radiobiology & Cytogenetics , NCSR "Demokritos" , Athens , Greece
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48
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Greif PA, Hartmann L, Vosberg S, Stief SM, Mattes R, Hellmann I, Metzeler KH, Herold T, Bamopoulos SA, Kerbs P, Jurinovic V, Schumacher D, Pastore F, Bräundl K, Zellmeier E, Ksienzyk B, Konstandin NP, Schneider S, Graf A, Krebs S, Blum H, Neumann M, Baldus CD, Bohlander SK, Wolf S, Görlich D, Berdel WE, Wörmann BJ, Hiddemann W, Spiekermann K. Evolution of Cytogenetically Normal Acute Myeloid Leukemia During Therapy and Relapse: An Exome Sequencing Study of 50 Patients. Clin Cancer Res 2018; 24:1716-1726. [PMID: 29330206 DOI: 10.1158/1078-0432.ccr-17-2344] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 12/03/2017] [Accepted: 01/08/2018] [Indexed: 11/16/2022]
Abstract
Purpose: To study mechanisms of therapy resistance and disease progression, we analyzed the evolution of cytogenetically normal acute myeloid leukemia (CN-AML) based on somatic alterations.Experimental Design: We performed exome sequencing of matched diagnosis, remission, and relapse samples from 50 CN-AML patients treated with intensive chemotherapy. Mutation patterns were correlated with clinical parameters.Results: Evolutionary patterns correlated with clinical outcome. Gain of mutations was associated with late relapse. Alterations of epigenetic regulators were frequently gained at relapse with recurring alterations of KDM6A constituting a mechanism of cytarabine resistance. Low KDM6A expression correlated with adverse clinical outcome, particularly in male patients. At complete remission, persistent mutations representing preleukemic lesions were observed in 48% of patients. The persistence of DNMT3A mutations correlated with shorter time to relapse.Conclusions: Chemotherapy resistance might be acquired through gain of mutations. Insights into the evolution during therapy and disease progression lay the foundation for tailored approaches to treat or prevent relapse of CN-AML. Clin Cancer Res; 24(7); 1716-26. ©2018 AACR.
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Affiliation(s)
- Philipp A Greif
- Department of Medicine III, University Hospital, LMU Munich, München, Germany. .,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Luise Hartmann
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sebastian Vosberg
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sophie M Stief
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Raphael Mattes
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ines Hellmann
- Anthropology and Human Genomics, Department Biology II, LMU Munich, Martinsried, Germany
| | - Klaus H Metzeler
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tobias Herold
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Paul Kerbs
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Vindi Jurinovic
- Institute for Medical Information Procesing, Biometry and Epidemiology (IBE), LMU Munich, München, Germany
| | - Daniela Schumacher
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Friederike Pastore
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kathrin Bräundl
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Evelyn Zellmeier
- Department of Medicine III, University Hospital, LMU Munich, München, Germany
| | - Bianka Ksienzyk
- Department of Medicine III, University Hospital, LMU Munich, München, Germany
| | - Nikola P Konstandin
- Department of Medicine III, University Hospital, LMU Munich, München, Germany
| | - Stephanie Schneider
- Department of Medicine III, University Hospital, LMU Munich, München, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, München, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, München, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, München, Germany
| | - Martin Neumann
- German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Divison of Hematology and Oncology, Charité Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, and Campus Virchow, Berlin, Germany
| | - Claudia D Baldus
- German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Divison of Hematology and Oncology, Charité Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, and Campus Virchow, Berlin, Germany
| | - Stefan K Bohlander
- Leukaemia and Blood Cancer Research Unit, Department of Molecular Medicine and Pathology, The University of Auckland, Auckland, New Zealand
| | - Stephan Wolf
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dennis Görlich
- Institute of Biostatistics and Clinical Research, University of Münster, Münster, Germany
| | - Wolfgang E Berdel
- Department of Medicine A -Hematology, Oncology and Pneumology, University of Münster, Münster, Germany
| | - Bernhard J Wörmann
- Divison of Hematology and Oncology, Charité Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, and Campus Virchow, Berlin, Germany
| | - Wolfgang Hiddemann
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Karsten Spiekermann
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
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49
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Herold T, Jurinovic V, Batcha AMN, Bamopoulos SA, Rothenberg-Thurley M, Ksienzyk B, Hartmann L, Greif PA, Phillippou-Massier J, Krebs S, Blum H, Amler S, Schneider S, Konstandin N, Sauerland MC, Görlich D, Berdel WE, Wörmann BJ, Tischer J, Subklewe M, Bohlander SK, Braess J, Hiddemann W, Metzeler KH, Mansmann U, Spiekermann K. A 29-gene and cytogenetic score for the prediction of resistance to induction treatment in acute myeloid leukemia. Haematologica 2017; 103:456-465. [PMID: 29242298 PMCID: PMC5830382 DOI: 10.3324/haematol.2017.178442] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 12/07/2017] [Indexed: 01/15/2023] Open
Abstract
Primary therapy resistance is a major problem in acute myeloid leukemia treatment. We set out to develop a powerful and robust predictor for therapy resistance for intensively treated adult patients. We used two large gene expression data sets (n=856) to develop a predictor of therapy resistance, which was validated in an independent cohort analyzed by RNA sequencing (n=250). In addition to gene expression markers, standard clinical and laboratory variables as well as the mutation status of 68 genes were considered during construction of the model. The final predictor (PS29MRC) consisted of 29 gene expression markers and a cytogenetic risk classification. A continuous predictor is calculated as a weighted linear sum of the individual variables. In addition, a cut off was defined to divide patients into a high-risk and a low-risk group for resistant disease. PS29MRC was highly significant in the validation set, both as a continuous score (OR=2.39, P=8.63·10−9, AUC=0.76) and as a dichotomous classifier (OR=8.03, P=4.29·10−9); accuracy was 77%. In multivariable models, only TP53 mutation, age and PS29MRC (continuous: OR=1.75, P=0.0011; dichotomous: OR=4.44, P=0.00021) were left as significant variables. PS29MRC dominated all models when compared with currently used predictors, and also predicted overall survival independently of established markers. When integrated into the European LeukemiaNet (ELN) 2017 genetic risk stratification, four groups (median survival of 8, 18, 41 months, and not reached) could be defined (P=4.01·10−10). PS29MRC will make it possible to design trials which stratify induction treatment according to the probability of response, and refines the ELN 2017 classification.
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Affiliation(s)
- Tobias Herold
- Department of Internal Medicine III, University of Munich, Germany .,German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Vindi Jurinovic
- Institute for Medical Informatics, Biometry and Epidemiology, University of Munich, Germany
| | - Aarif M N Batcha
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute for Medical Informatics, Biometry and Epidemiology, University of Munich, Germany
| | | | | | - Bianka Ksienzyk
- Department of Internal Medicine III, University of Munich, Germany
| | - Luise Hartmann
- Department of Internal Medicine III, University of Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Philipp A Greif
- Department of Internal Medicine III, University of Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Stefan Krebs
- Institute of Biostatistics and Clinical Research, University of Münster, Germany
| | - Helmut Blum
- Institute of Biostatistics and Clinical Research, University of Münster, Germany
| | - Susanne Amler
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | | | | | - Dennis Görlich
- Institute of Biostatistics and Clinical Research, University of Munich, Germany
| | - Wolfgang E Berdel
- Department of Medicine, Hematology and Oncology, University of Münster, Germany
| | | | - Johanna Tischer
- Department of Internal Medicine III, University of Munich, Germany
| | - Marion Subklewe
- Department of Internal Medicine III, University of Munich, Germany
| | - Stefan K Bohlander
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Jan Braess
- Department of Oncology and Hematology, Hospital Barmherzige Brüder, Regensburg, Germany
| | - Wolfgang Hiddemann
- Department of Internal Medicine III, University of Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Klaus H Metzeler
- Department of Internal Medicine III, University of Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ulrich Mansmann
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute for Medical Informatics, Biometry and Epidemiology, University of Munich, Germany
| | - Karsten Spiekermann
- Department of Internal Medicine III, University of Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
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50
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Satgé D, Nishi M, Sirvent N, Vekemans M, Chenard MP, Barnes A. A tumor profile in Patau syndrome (trisomy 13). Am J Med Genet A 2017; 173:2088-2096. [DOI: 10.1002/ajmg.a.38294] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 04/24/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Daniel Satgé
- Oncodéfi and University Institute for Clinical Research, Epidemiology and Biostatistics Department (EA 2415); Montpellier France
| | - Motoi Nishi
- Department of Fundamental Health Sciences; Health Sciences University of Hokkaido; Tobetsu Japan
| | - Nicolas Sirvent
- Pediatric Oncology; CHU Arnaud de Villeneuve; Montpellier France
| | - Michel Vekemans
- Department of Genetics; Hôpital Necker Enfants Malades, and Institut Imagine; Université Paris Descartes; Paris France
| | | | - Ann Barnes
- Support Organization for Trisomy 18, 13 and Related Disorders − Surgery Registry (SOFT-SR) Rochester; Rochester New York
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