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Sahoo K, Sundararajan V. Methods in DNA methylation array dataset analysis: A review. Comput Struct Biotechnol J 2024; 23:2304-2325. [PMID: 38845821 PMCID: PMC11153885 DOI: 10.1016/j.csbj.2024.05.015] [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: 12/18/2023] [Revised: 04/25/2024] [Accepted: 05/08/2024] [Indexed: 06/09/2024] Open
Abstract
Understanding the intricate relationships between gene expression levels and epigenetic modifications in a genome is crucial to comprehending the pathogenic mechanisms of many diseases. With the advancement of DNA Methylome Profiling techniques, the emphasis on identifying Differentially Methylated Regions (DMRs/DMGs) has become crucial for biomarker discovery, offering new insights into the etiology of illnesses. This review surveys the current state of computational tools/algorithms for the analysis of microarray-based DNA methylation profiling datasets, focusing on key concepts underlying the diagnostic/prognostic CpG site extraction. It addresses methodological frameworks, algorithms, and pipelines employed by various authors, serving as a roadmap to address challenges and understand changing trends in the methodologies for analyzing array-based DNA methylation profiling datasets derived from diseased genomes. Additionally, it highlights the importance of integrating gene expression and methylation datasets for accurate biomarker identification, explores prognostic prediction models, and discusses molecular subtyping for disease classification. The review also emphasizes the contributions of machine learning, neural networks, and data mining to enhance diagnostic workflow development, thereby improving accuracy, precision, and robustness.
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Affiliation(s)
| | - Vino Sundararajan
- Correspondence to: Department of Bio Sciences, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632 014, Tamil Nadu, India.
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Shi Q, Song G, Song L, Wang Y, Ma J, Zhang L, Yuan E. Unravelling the function of prdm16 in human tumours: A comparative analysis of haematologic and solid tumours. Biomed Pharmacother 2024; 178:117281. [PMID: 39137651 DOI: 10.1016/j.biopha.2024.117281] [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: 04/26/2024] [Revised: 08/03/2024] [Accepted: 08/07/2024] [Indexed: 08/15/2024] Open
Abstract
Extensive research has shown that PR domain 16 (PRDM16) plays a critical role in adipose tissue metabolism, including processes such as browning and thermogenesis of adipocytes, beigeing of adipocytes, and adipogenic differentiation of myoblasts. These functions have been associated with diseases such as obesity and diabetes. Additionally, PRDM16 has been correlated with various other conditions, including migraines, heterochromatin abnormalities, metabolic syndrome, cardiomyopathy, sarcopenia, nonsyndromic cleft lip, and essential hypertension, among others. However, there is currently no systematic or comprehensive conclusion regarding the mechanism of PRDM16 in human tumours, including haematologic and solid tumours. The aim of this review is to provide an overview of the research progress on PRDM16 in haematologic and solid tumours by incorporating recent literature findings. Furthermore, we explore the prospects of PRDM16 in the precise diagnosis and treatment of human haematologic and solid tumours.
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Affiliation(s)
- Qianqian Shi
- Department of Laboratory Medicine, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China; Zhengzhou Key Laboratory for In Vitro Diagnosis of Hypertensive Disorders of Pregnancy, Zhengzhou, Henan 450052, China; Tianjian Laboratory of Advanced Biomedical Sciences, Institute of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou, Henan 450000, China.
| | - Guangyong Song
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Liying Song
- Department of Laboratory Medicine, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China; Zhengzhou Key Laboratory for In Vitro Diagnosis of Hypertensive Disorders of Pregnancy, Zhengzhou, Henan 450052, China
| | - Yu Wang
- Department of Laboratory Medicine, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China; Zhengzhou Key Laboratory for In Vitro Diagnosis of Hypertensive Disorders of Pregnancy, Zhengzhou, Henan 450052, China
| | - Jun Ma
- Department of Laboratory Medicine, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China; Zhengzhou Key Laboratory for In Vitro Diagnosis of Hypertensive Disorders of Pregnancy, Zhengzhou, Henan 450052, China
| | - Linlin Zhang
- Department of Laboratory Medicine, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China; Zhengzhou Key Laboratory for In Vitro Diagnosis of Hypertensive Disorders of Pregnancy, Zhengzhou, Henan 450052, China; Tianjian Laboratory of Advanced Biomedical Sciences, Institute of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou, Henan 450000, China.
| | - Enwu Yuan
- Department of Laboratory Medicine, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China; Zhengzhou Key Laboratory for In Vitro Diagnosis of Hypertensive Disorders of Pregnancy, Zhengzhou, Henan 450052, China; Tianjian Laboratory of Advanced Biomedical Sciences, Institute of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou, Henan 450000, China.
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Gao ZX, He T, Zhang P, Hu X, Ge M, Xu YQ, Wang P, Pan HF. Epigenetic regulation of immune cells in systemic lupus erythematosus: insight from chromatin accessibility. Expert Opin Ther Targets 2024; 28:637-649. [PMID: 38943564 DOI: 10.1080/14728222.2024.2375372] [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: 03/19/2024] [Accepted: 06/28/2024] [Indexed: 07/01/2024]
Abstract
INTRODUCTION Systemic Lupus Erythematosus (SLE) is a multi-dimensional autoimmune disease involving numerous tissues throughout the body. The chromatin accessibility landscapes in immune cells play a pivotal role in governing their activation, function, and differentiation. Aberrant modulation of chromatin accessibility in immune cells is intimately associated with the onset and progression of SLE. AREAS COVERED In this review, we described the chromatin accessibility landscapes in immune cells, summarized the recent evidence of chromatin accessibility related to the pathogenesis of SLE, and discussed the potential of chromatin accessibility as a valuable option to identify novel therapeutic targets for this disease. EXPERT OPINION Dynamic changes in chromatin accessibility are intimately related to the pathogenesis of SLE and have emerged as a new direction for exploring its epigenetic mechanisms. The differently accessible chromatin regions in immune cells often contain binding sites for transcription factors (TFs) and cis-regulatory elements such as enhancers and promoters, which may be potential therapeutic targets for SLE. Larger scale cohort studies and integrating epigenomic, transcriptomic, and metabolomic data can provide deeper insights into SLE chromatin biology in the future.
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Affiliation(s)
- Zhao-Xing Gao
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Tian He
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Peng Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Xiao Hu
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
- Teaching Center for Preventive Medicine, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Man Ge
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Yi-Qing Xu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Peng Wang
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
- Teaching Center for Preventive Medicine, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Hai-Feng Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
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Tong M, Bai Y, Han X, Kong L, Ren L, Zhang L, Li X, Yao J, Yan B. Single-cell profiling transcriptomic reveals cellular heterogeneity and cellular crosstalk in choroidal neovascularization model. Exp Eye Res 2024; 242:109877. [PMID: 38537669 DOI: 10.1016/j.exer.2024.109877] [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: 10/14/2023] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/01/2024]
Abstract
Choroidal neovascularization (CNV) is a hallmark of neovascular age-related macular degeneration (nAMD) and a major contributor to vision loss in nAMD cases. However, the identification of specific cell types associated with nAMD remains challenging. Herein, we performed single-cell sequencing to comprehensively explore the cellular diversity and understand the foundational components of the retinal pigment epithelium (RPE)/choroid complex. We unveiled 10 distinct cell types within the RPE/choroid complex. Notably, we observed significant heterogeneity within endothelial cells (ECs), fibroblasts, and macrophages, underscoring the intricate nature of the cellular composition in the RPE/choroid complex. Within the EC category, four distinct clusters were identified and EC cluster 0 was tightly associated with choroidal neovascularization. We identified five clusters of fibroblasts actively involved in the pathogenesis of nAMD, influencing fibrotic responses, angiogenic effects, and photoreceptor function. Additionally, three clusters of macrophages were identified, suggesting their potential roles in regulating the progression of nAMD through immunomodulation and inflammation regulation. Through CellChat analysis, we constructed a complex cell-cell communication network, revealing the role of EC clusters in interacting with fibroblasts and macrophages in the context of nAMD. These interactions were found to govern angiogenic effects, fibrotic responses, and inflammatory processes. In summary, this study reveals noteworthy cellular heterogeneity in the RPE/choroid complex and provides valuable insights into the pathogenesis of CNV. These findings will open up potential avenues for deep understanding and targeted therapeutic interventions in nAMD.
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Affiliation(s)
- Ming Tong
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Yun Bai
- College of Information Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Xiaoyan Han
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Lingjie Kong
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Ling Ren
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Linyu Zhang
- The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, 210000, China; The Affiliated Eye Hospital, Nanjing Medical University, Nanjing, 210000, China
| | - Xiumiao Li
- The Affiliated Eye Hospital, Nanjing Medical University, Nanjing, 210000, China
| | - Jin Yao
- The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, 210000, China; The Affiliated Eye Hospital, Nanjing Medical University, Nanjing, 210000, China.
| | - Biao Yan
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China.
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5
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Zhang LQ, Liang YC, Wang JX, Zhang J, La T, Li QZ. Unlocking the potential: A novel prognostic index signature for acute myeloid leukemia. Comput Biol Med 2024; 173:108396. [PMID: 38574529 DOI: 10.1016/j.compbiomed.2024.108396] [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: 01/29/2024] [Revised: 03/12/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
Acute myeloid leukemia (AML) is an aggressive malignancy characterized by challenges in treatment, including drug resistance and frequent relapse. Recent research highlights the crucial roles of tumor microenvironment (TME) in assisting tumor cell immune escape and promoting tumor aggressiveness. This study delves into the interplay between AML and TME. Through the exploration of potential driver genes, we constructed an AML prognostic index (AMLPI). Cross-platform data and multi-dimensional internal and external validations confirmed that the AMLPI outperforms existing models in terms of areas under the receiver operating characteristic curves, concordance index values, and net benefits. High AMLPIs in AML patients were indicative of unfavorable prognostic outcomes. Immune analyses revealed that the high-AMLPI samples exhibit higher expression of HLA-family genes and immune checkpoint genes (including PD1 and CTLA4), along with lower T cell infiltration and higher macrophage infiltration. Genetic variation analyses revealed that the high-AMLPI samples associate with adverse variation events, including TP53 mutations, secondary NPM1 co-mutations, and copy number deletions. Biological interpretation indicated that ALDH2 and SPATS2L contribute significantly to AML patient survival, and their abnormal expression correlates with DNA methylation at cg12142865 and cg11912272. Drug response analyses revealed that different AMLPI samples tend to have different clinical selections, with low-AMLPI samples being more likely to benefit from immunotherapy. Finally, to facilitate broader access to our findings, a user-friendly and publicly accessible webserver was established and available at http://bioinfor.imu.edu.cn/amlpi. This server provides tools including TME-related AML driver genes mining, AMLPI construction, multi-dimensional validations, AML patients risk assessment, and figures drawing.
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MESH Headings
- Humans
- Prognosis
- Nucleophosmin
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/therapy
- DNA Methylation
- Tumor Microenvironment
- Aldehyde Dehydrogenase, Mitochondrial/genetics
- Aldehyde Dehydrogenase, Mitochondrial/metabolism
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Affiliation(s)
- Lu-Qiang Zhang
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China.
| | - Yu-Chao Liang
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010070, China.
| | - Jun-Xuan Wang
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China.
| | - Jing Zhang
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China.
| | - Ta La
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China.
| | - Qian-Zhong Li
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China; The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010070, China.
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6
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Li J, Gao J, Liu A, Liu W, Xiong H, Liang C, Fang Y, Dai Y, Shao J, Yu H, Wang L, Wang L, Yang L, Yan M, Zhai X, Shi X, Tian X, Ju X, Chen Y, Wang J, Zhang L, Liang H, Chen S, Zhang J, Cao H, Jin J, Hu Q, Wang J, Wang Y, Zhou M, Han Y, Zhang R, Zhao W, Wang X, Lin L, Zhang R, Gao C, Xu L, Zhang Y, Fan J, Wu Y, Lin W, Yu J, Qi P, Huang P, Peng X, Peng Y, Wang T, Zheng H. Homoharringtonine-Based Induction Regimen Improved the Remission Rate and Survival Rate in Chinese Childhood AML: A Report From the CCLG-AML 2015 Protocol Study. J Clin Oncol 2023; 41:4881-4892. [PMID: 37531592 PMCID: PMC10617822 DOI: 10.1200/jco.22.02836] [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: 12/21/2022] [Revised: 05/26/2023] [Accepted: 06/14/2023] [Indexed: 08/04/2023] Open
Abstract
PURPOSE Homoharringtonine (HHT) is commonly used for the treatment of Chinese adult AML, and all-trans retinoic acid (ATRA) has been verified in acute promyelocytic leukemia (APL). However, the efficacy and safety of HHT-based induction therapy have not been confirmed for childhood AML, and ATRA-based treatment has not been evaluated among patients with non-APL AML. PATIENTS AND METHODS This open-label, multicenter, randomized Chinese Children's Leukemia Group-AML 2015 study was performed across 35 centers in China. Patients with newly diagnosed childhood AML were first randomly assigned to receive an HHT-based (H arm) or etoposide-based (E arm) induction regimen and then randomly allocated to receive cytarabine-based (AC arm) or ATRA-based (AT arm) maintenance therapy. The primary end points were the complete remission (CR) rate after induction therapy, and the secondary end points were the overall survival (OS) and event-free survival (EFS) at 3 years. RESULTS We enrolled 1,258 patients, of whom 1,253 were included in the intent-to-treat analysis. The overall CR rate was significantly higher in the H arm than in the E arm (79.9% v 73.9%, P = .014). According to the intention-to-treat analysis, the 3-year OS was 69.2% (95% CI, 65.1 to 72.9) in the H arm and 62.8% (95% CI, 58.7 to 66.6) in the E arm (P = .025); the 3-year EFS was 61.1% (95% CI, 56.8 to 65.0) in the H arm and 53.4% (95% CI, 49.2 to 57.3) in the E arm (P = .022). Among the per-protocol population, who received maintenance therapy, the 3-year EFS did not differ significantly across the four arms (H + AT arm: 70.7%, 95% CI, 61.1 to 78.3; H + AC arm: 74.8%, 95% CI, 67.0 to 81.0, P = .933; E + AC arm: 72.9%, 95% CI, 65.1 to 79.2, P = .789; E + AT arm: 66.2%, 95% CI, 56.8 to 74.0, P = .336). CONCLUSION HHT is an alternative combination regimen for childhood AML. The effects of ATRA-based maintenance are comparable with those of cytarabine-based maintenance therapy.
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Affiliation(s)
- Jing Li
- Hematology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology Oncology, Beijing, China
- National Key Clinical Discipline of Pediatric Hematology, National Key Discipline of Pediatrics (Capital Medical University), Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Ju Gao
- West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Chronobiology (Sichuan University), National Health Commission of China, Chengdu, China
| | | | - Wei Liu
- Children's Hospital of Henan Province, Zhengzhou, China
| | - Hao Xiong
- Wuhan Children's Hospital, Wuhan, China
| | - Changda Liang
- Jiangxi Provincial Children's Hospital, Nanchang, China
| | - Yongjun Fang
- Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Yunpeng Dai
- Shandong First Medical University Affiliated Shandong Provincial Hospital, Jinan, China
| | - Jingbo Shao
- Shanghai Children's Hospital, Shanghai, China
| | - Hui Yu
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lingzhen Wang
- Affiliated Hospital of Qingdao University, Qingdao, China
| | - Li Wang
- Children's Hospital of Hebei Province, Shijiazhuang, China
| | - Liangchun Yang
- Department of Pediatrics, Xiangya Hospital Central South University, Changsha, China
| | - Mei Yan
- The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Xiaowen Zhai
- Children's Hospital of Fudan University, Shanghai, China
| | - Xiaodong Shi
- Capital Institute of Pediatrics' Children's Hospital, Beijing, China
| | - Xin Tian
- Kunming Children's Hospital, Kunming, China
| | - Xiuli Ju
- Qilu Hospital of Shandong University, Jinan, China
| | - Yan Chen
- Children's Hospital of Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Jing Wang
- Children's Hospital of Shanxi Province, Taiyuan, China
| | - Leping Zhang
- Peking University People's Hospital, Beijing, China
| | - Hui Liang
- Women and Children's Hospital, Qingdao University, Qingdao, China
| | - Sen Chen
- Tianjin Children's Hospital, Tianjin, China
| | | | - Haixia Cao
- Qinghai Women's and Children's Hospital, Xining, China
| | - Jiao Jin
- The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Qun Hu
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Junlan Wang
- Northwest Women's and Children's Hospital, Xian, China
| | | | - Min Zhou
- Chengdu Women's and Children's Central Hospital, Chengdu, China
| | - Yueqin Han
- Children's Hospital of Liaocheng, Liaocheng, China
| | - Rong Zhang
- Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China
| | - Weihong Zhao
- First Hospital, Peking University, Beijing, China
| | | | - Limin Lin
- Second Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Ruidong Zhang
- Hematology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology Oncology, Beijing, China
- National Key Clinical Discipline of Pediatric Hematology, National Key Discipline of Pediatrics (Capital Medical University), Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Chao Gao
- Beijing Key Laboratory of Pediatric Hematology Oncology, Beijing, China
- National Key Clinical Discipline of Pediatric Hematology, National Key Discipline of Pediatrics (Capital Medical University), Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
- Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- Laboratory of Hematologic Diseases, Beijing Pediatric Research Institute, Beijing, China
| | - Liting Xu
- Children's Hospital of Zhejiang University School of Medicine, the Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, Hangzhou, China
| | - Yuanyuan Zhang
- Hematology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology Oncology, Beijing, China
- National Key Clinical Discipline of Pediatric Hematology, National Key Discipline of Pediatrics (Capital Medical University), Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Jia Fan
- Hematology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology Oncology, Beijing, China
- National Key Clinical Discipline of Pediatric Hematology, National Key Discipline of Pediatrics (Capital Medical University), Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Ying Wu
- Hematology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology Oncology, Beijing, China
- National Key Clinical Discipline of Pediatric Hematology, National Key Discipline of Pediatrics (Capital Medical University), Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Wei Lin
- Hematology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology Oncology, Beijing, China
- National Key Clinical Discipline of Pediatric Hematology, National Key Discipline of Pediatrics (Capital Medical University), Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Jiaole Yu
- Hematology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology Oncology, Beijing, China
- National Key Clinical Discipline of Pediatric Hematology, National Key Discipline of Pediatrics (Capital Medical University), Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Peijing Qi
- Hematology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology Oncology, Beijing, China
- National Key Clinical Discipline of Pediatric Hematology, National Key Discipline of Pediatrics (Capital Medical University), Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Pengli Huang
- Hematology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology Oncology, Beijing, China
- National Key Clinical Discipline of Pediatric Hematology, National Key Discipline of Pediatrics (Capital Medical University), Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Xiaoxia Peng
- Center for Clinical Epidemiology and Evidence-Based Medicine, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Yaguang Peng
- Center for Clinical Epidemiology and Evidence-Based Medicine, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Tianyou Wang
- Hematology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology Oncology, Beijing, China
- National Key Clinical Discipline of Pediatric Hematology, National Key Discipline of Pediatrics (Capital Medical University), Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Huyong Zheng
- Hematology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology Oncology, Beijing, China
- National Key Clinical Discipline of Pediatric Hematology, National Key Discipline of Pediatrics (Capital Medical University), Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
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7
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Zhu H, Xu Y, Xia J, Guo X, Fang Y, Fan J, Li F, Wu J, Zheng G, Liu Y. Identification and analysis of methylation signature genes and association with immune infiltration in pediatric acute myeloid leukemia. J Cancer Res Clin Oncol 2023; 149:14965-14982. [PMID: 37606761 DOI: 10.1007/s00432-023-05284-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 08/11/2023] [Indexed: 08/23/2023]
Abstract
BACKGROUND Acute myeloid leukemia (AML) is a common leukemia with low cure rate and poor prognosis among pediatric patients. The regulation of AML immune microenvironment and methylation remains to be explored. Pediatric and adult AML patients differ significantly in epigenetic factors, and the efficiency of treatment modalities varies between the two groups of patients. METHODS We collected mRNA, miRNA and DNA methylation data from pediatric AML patients across multiple databases. Differentially expression genes were identified, and a gene-miRNA regulatory network was constructed. Prognostic risk models were established by integrating LASSO and Cox regression, and a nomogram was generated. Based on this model, we investigated tumor-infiltrating immune cells and cell communication, analyzing the biological functions and pathways associated with prognostic factors. Furthermore, the relationships between all prognostic factors and gene modules were explored, and the impact of these factors on treatment modalities was determined. RESULTS We developed an efficient prognostic risk model and identified HOXA9, SORT1, SH3BP5, mir-224 and mir-335 as biomarkers. We validated these findings in an external dataset and observed a correlation between age and risk in pediatric patients. AML samples with lower risk scores have a better prognosis and higher expression of immune-upregulated biomarkers, and have lower immune scores. Furthermore, we detected discrepancies in immune cell infiltration and interactions between high- and low-risk group samples, which affected the efficacy of immunotherapy. We evaluated all prognostic factors and predicted the effect of immunotherapy and medicine. CONCLUSION This study comprehensively investigated the role of methylation signature genes in pediatric AML at the level of genomes and transcriptomes. The research aims to enhance the risk stratification, prognosis evaluation and assessment of treatment effectiveness of AML patients. This study also highlight the uniqueness of pediatric AML and foster the development of new immunotherapy and targeted therapy strategies.
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Affiliation(s)
- Huawei Zhu
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, 124221, China
| | - Yanbo Xu
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, 124221, China
| | - Jun Xia
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, 124221, China
| | - Xu Guo
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, 124221, China
| | - Yujie Fang
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, 124221, China
| | - Jingzhi Fan
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, 124221, China
| | - Fangjun Li
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, 124221, China
| | - Jinhong Wu
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, 124221, China
| | - Guoliang Zheng
- Liaoning Cancer Hospital, China Medical University, Shenyang, 110042, China.
| | - Yubo Liu
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, 124221, China.
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Chianese U, Papulino C, Megchelenbrink W, Tambaro FP, Ciardiello F, Benedetti R, Altucci L. Epigenomic machinery regulating pediatric AML: clonal expansion mechanisms, therapies, and future perspectives. Semin Cancer Biol 2023; 92:84-101. [PMID: 37003397 DOI: 10.1016/j.semcancer.2023.03.009] [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: 12/15/2022] [Revised: 03/07/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023]
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease with a genetic, epigenetic, and transcriptional etiology mainly presenting somatic and germline abnormalities. AML incidence rises with age but can also occur during childhood. Pediatric AML (pAML) accounts for 15-20% of all pediatric leukemias and differs considerably from adult AML. Next-generation sequencing technologies have enabled the research community to "paint" the genomic and epigenomic landscape in order to identify pathology-associated mutations and other prognostic biomarkers in pAML. Although current treatments have improved the prognosis for pAML, chemoresistance, recurrence, and refractory disease remain major challenges. In particular, pAML relapse is commonly caused by leukemia stem cells that resist therapy. Marked patient-to-patient heterogeneity is likely the primary reason why the same treatment is successful for some patients but, at best, only partially effective for others. Accumulating evidence indicates that patient-specific clonal composition impinges significantly on cellular processes, such as gene regulation and metabolism. Although our understanding of metabolism in pAML is still in its infancy, greater insights into these processes and their (epigenetic) modulation may pave the way toward novel treatment options. In this review, we summarize current knowledge on the function of genetic and epigenetic (mis)regulation in pAML, including metabolic features observed in the disease. Specifically, we describe how (epi)genetic machinery can affect chromatin status during hematopoiesis, leading to an altered metabolic profile, and focus on the potential value of targeting epigenetic abnormalities in precision and combination therapy for pAML. We also discuss the possibility of using alternative epidrug-based therapeutic approaches that are already in clinical practice, either alone as adjuvant treatments and/or in combination with other drugs.
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Affiliation(s)
- Ugo Chianese
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy.
| | - Chiara Papulino
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy.
| | - Wout Megchelenbrink
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy; Princess Máxima Center, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands.
| | - Francesco Paolo Tambaro
- Bone Marrow Transplant Unit, Pediatric Oncology Department AORN Santobono Pausilipon, 80129, Naples Italy.
| | - Fortunato Ciardiello
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy.
| | - Rosaria Benedetti
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy.
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy; Biogem Institute of Molecular and Genetic Biology, 83031 Ariano Irpino, Italy; IEOS, Institute for Endocrinology and Oncology "Gaetano Salvatore" (IEOS), 80131 Naples, Italy.
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9
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Shiba N. Comprehensive molecular understanding of pediatric acute myeloid leukemia. Int J Hematol 2023; 117:173-181. [PMID: 36653696 DOI: 10.1007/s12185-023-03533-x] [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: 10/31/2022] [Revised: 12/28/2022] [Accepted: 01/05/2023] [Indexed: 01/19/2023]
Abstract
Pediatric acute myeloid leukemia (AML) is a heterogeneous disease with various genetic abnormalities. Recent advances in genetic analysis have enabled the identification of causative genes in > 90% of pediatric AML cases. Fusion genes such as RUNX1::RUNX1T1, CBFB::MYH11, and KMT2A::MLLT3 are frequently detected in > 70% of pediatric AML cases, whereas FLT3-internal tandem duplication, CEBPA-bZip, and NPM1 mutations are detected in approximately 5-15% of cases, respectively. Conversely, mutations in DNMT3A, TET2, and IDH, which are common in adults, are extremely rare in pediatric AML. The genetic characteristics of pediatric AML are slightly different from those of adult AML. For accurate risk stratification and treatment intensity, genome analysis should be performed in a simple, fast, and inexpensive manner and the results should be returned to patients in real time. As with acute lymphoblastic leukemia, the presence or absence of minimal residual disease is an important factor in determining the success of treatment against AML, and it is important to predict prognosis and formulate treatment strategies considering the genetic abnormalities. For the development and clinical application of new molecularly targeted therapies based on identified genetic abnormalities, it is necessary to explore when and in which combinations drugs will be most effective.
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Affiliation(s)
- Norio Shiba
- Department of Pediatrics, Yokohama City University Graduate School of Medicine, 3-9, Fukuura, Kanazawa-Ku, Yokohama, 236-0004, Japan.
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Hua J, Ma C, Wang CH, Wang Y, Feng S, Xiao T, Zhu C. Abnormal GRHL2 Methylation Confers Malignant Progression to Acute Leukemia. Appl Bionics Biomech 2022; 2022:9708829. [PMID: 35855840 PMCID: PMC9288345 DOI: 10.1155/2022/9708829] [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: 05/28/2022] [Revised: 06/16/2022] [Accepted: 06/24/2022] [Indexed: 11/17/2022] Open
Abstract
Purpose Abnormal methylation of Grainyhead-like 2 (GRHL2) is associated with a substantial role in the malignant phenotype of tumor patients. Our present research is aimed at studying the abnormal expression of GRHL2 and the association of methylation in patients with acute leukemia and its relationship with prognosis. Materials and Methods We used quantitative real-time polymerase chain reaction (qRT-PCR) for detecting the aberrant expression level of GRHL2 in 60 patients with acute leukemia and 60 normal controls. We analyzed the significant correlation between the expression level of GRHL2 with clinicopathological features and patients' prognosis in acute leukemia using the corresponding statistical methods. Secondly, we employed qRT-PCR and Western blotting to detect the mRNA and protein levels of GRHL2 in leukemia cell lines. Next, we used methylation-specific polymerase chain reaction (MSP) technology for detecting the methylation of GRHL2 in clinical samples with acute leukemia and cell lines. Then we investigated the demethylating effect of arsenic trioxide and 5-azacitidine on the mRNA and protein expression levels of GRHL2 in cell lines of acute leukemia. Finally, we studied the effects of arsenide trioxide and 5-azacitidine on the proliferation of leukemia cells and the TGF-β signaling pathway. Results We found a lower level of GRHL2 expression not only in acute leukemia patients but also in cell lines when compared with normal controls. At the same time, the expression level of GRHL2 in patients with acute leukemia was significantly correlated with leukocyte count, platelet count, and cytogenetic risk grouping. In addition, the lower GRHL2 expression group showed a significantly lower overall survival rate in acute leukemia patients than that of patients with a higher GRHL2 expression group. Univariate and multivariate analyses revealed that the expression of GRHL2 is an independent risk factor in acute leukemia patients. The methylation level of the GRHL2 promoter region in acute leukemia patients and cell lines was significantly higher than the normal control group, and we found the elevated mRNA and protein levels of GRHL2 in acute leukemia cell lines after the use of the demethylation drug arsenic trioxide and 5-azacitidine. At the same time, arsenide trioxide and 5-azacitidine are associated with the inhibition of cellular proliferation of acute leukemia cells and also promote the elevated expression of TGF-β signaling pathway-linked proteins, including TGF-β, Smad2, Smad3, and Smad4. Conclusion Increased expression and methylation level of GRHL2 are closely associated with the prognosis and malignant phenotype of acute leukemia patients and play an irreplaceable role in the occurrence and development of patients with acute leukemia.
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Affiliation(s)
- Jing Hua
- Department of Hematology, Shandong Provincial Qianfoshan Hospital, Shandong University, China
| | - Congcong Ma
- Department of Hematology, Liaocheng People's Hospital, Shandong University, China
| | - Chao Hui Wang
- Department of Hematology, Qingdao Haici Medical Group, China
| | - Yan Wang
- Department of Hematology, Shandong Provincial Qianfoshan Hospital, Shandong University, China
| | - Saran Feng
- Department of Hematology, Shandong Provincial Qianfoshan Hospital, Shandong University, China
| | - Taiwu Xiao
- Department of Hematology, Liaocheng People's Hospital, Shandong University, China
| | - ChuanSheng Zhu
- Department of Hematology, Shandong Provincial Qianfoshan Hospital, Shandong University, China
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