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Lin D, Wang D, Li P, Deng L, Zhang Z, Zhang Y, Zhang M, Zhang N. Whole-exome sequencing identified recurrent and novel variants in benzene-induced leukemia. BMC Med Genomics 2023; 16:13. [PMID: 36703207 PMCID: PMC9878782 DOI: 10.1186/s12920-023-01442-w] [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: 04/13/2022] [Accepted: 01/23/2023] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Genome-wide sequencing may extensively identify potential pathogenic variants, which helps to understand mechanisms of tumorigenesis, but such study has not been reported in benzene-induced leukemia (BIL). METHODS We recruited 10 BIL patients and conducted the whole-exome sequencing on their peripheral blood samples. The obtained sequencing data were screened for potential pathogenic and novel variants, then the variants-located genes were clustered to identify cancer-related pathways. Shared or recurrent variants among the BIL cases were also identified and evaluated for their potential functional impact. RESULTS We identified 48,802 variants in exons in total, 97.3% of which were single nucleotide variants. After filtering out variants with minor allele frequency ≥ 1%, we obtained 8667 potentially pathogenic variants, of which 174 were shared by all the BIL cases. The identified variants located in genes that could be significantly enriched into certain cancer-related pathways such as PI3K-AKT signaling pathway and Ras signaling pathway. We also identified 1010 novel variants with no record in the Genome Aggregation Database and in dbSNP, and one of them was shared by 90% cases. The recurrent and novel variant caused a missense mutation in SESN3. CONCLUSIONS We examined variations of the whole exome in BIL patients for the first time. The commonly shared variants implied a relation with BIL, and the recurrent and novel variant might be specifically related to BIL. The related variants may help unravel the carcinogenic mechanisms of BIL.
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Affiliation(s)
- Dafeng Lin
- Occupational Health Department, Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Rd., Luohu District, Shenzhen, 518020 China
| | - Dianpeng Wang
- Medical Laboratory, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, 518020 China
| | - Peimao Li
- Medical Laboratory, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, 518020 China
| | - Lihua Deng
- Occupational Diseases Department, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, 518020 China
| | - Zhimin Zhang
- Medical Laboratory, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, 518020 China
| | - Yanfang Zhang
- Medical Laboratory, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, 518020 China
| | - Ming Zhang
- Occupational Health Department, Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Rd., Luohu District, Shenzhen, 518020 China
| | - Naixing Zhang
- Occupational Health Department, Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Rd., Luohu District, Shenzhen, 518020 China
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SON inhibits megakaryocytic differentiation via repressing RUNX1 and the megakaryocytic gene expression program in acute megakaryoblastic leukemia. Cancer Gene Ther 2021; 28:1000-1015. [PMID: 33247227 PMCID: PMC8155101 DOI: 10.1038/s41417-020-00262-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/07/2020] [Accepted: 11/10/2020] [Indexed: 02/07/2023]
Abstract
A high incidence of acute megakaryoblastic leukemia (AMKL) in Down syndrome patients implies that chromosome 21 genes have a pivotal role in AMKL development, but the functional contribution of individual genes remains elusive. Here, we report that SON, a chromosome 21-encoded DNA- and RNA-binding protein, inhibits megakaryocytic differentiation by suppressing RUNX1 and the megakaryocytic gene expression program. As megakaryocytic progenitors differentiate, SON expression is drastically reduced, with mature megakaryocytes having the lowest levels. In contrast, AMKL cells express an aberrantly high level of SON, and knockdown of SON induced the onset of megakaryocytic differentiation in AMKL cell lines. Genome-wide transcriptome analyses revealed that SON knockdown turns on the expression of pro-megakaryocytic genes while reducing erythroid gene expression. Mechanistically, SON represses RUNX1 expression by directly binding to the proximal promoter and two enhancer regions, the known +23 kb enhancer and the novel +139 kb enhancer, at the RUNX1 locus to suppress H3K4 methylation. In addition, SON represses the expression of the AP-1 complex subunits JUN, JUNB, and FOSB which are required for late megakaryocytic gene expression. Our findings define SON as a negative regulator of RUNX1 and megakaryocytic differentiation, implicating SON overexpression in impaired differentiation during AMKL development.
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Fan X, Zeng Y, Song W, Li J, Ai S, Yang D, Mao X, Yang M. The role of Sestrins in the regulation of the aging process. Mech Ageing Dev 2020; 188:111251. [DOI: 10.1016/j.mad.2020.111251] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 04/06/2020] [Accepted: 04/15/2020] [Indexed: 12/14/2022]
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4
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Wang LX, Zhu XM, Yao YM. Sestrin2: Its Potential Role and Regulatory Mechanism in Host Immune Response in Diseases. Front Immunol 2019; 10:2797. [PMID: 31867002 PMCID: PMC6904332 DOI: 10.3389/fimmu.2019.02797] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 11/14/2019] [Indexed: 12/12/2022] Open
Abstract
Sestrin2 (SESN2), a highly evolutionarily conserved protein, is critically involved in cellular responses to various stresses. SESN2 has a protective effect on physiological and pathological states mainly via regulating oxidative stress, endoplasmic reticulum stress, autophagy, metabolism, and inflammation. In recent years, breakthrough investigations with regard to the regulation and signaling mechanisms of SESN2 have markedly deepened our understanding of its potential role as well as its significance in host response. However, the functions of SESN2 in the immune system and inflammation remain elusive. It has been documented that many immune cells positively express SESN2 and, in turn, that SESN2 might modulate cellular activities. This review incorporates recent progress and aims to provide novel insight into the protective role and regulatory pathway of SESN2, which acts as a potential biomarker and therapeutic target in the context of various diseases.
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Affiliation(s)
- Li-Xue Wang
- Trauma Research Center, Fourth Medical Center of the Chinese PLA General Hospital, Beijing, China
| | - Xiao-Mei Zhu
- Trauma Research Center, Fourth Medical Center of the Chinese PLA General Hospital, Beijing, China
| | - Yong-Ming Yao
- Trauma Research Center, Fourth Medical Center of the Chinese PLA General Hospital, Beijing, China.,State Key Laboratory of Kidney Disease, The Chinese PLA General Hospital, Beijing, China
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5
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Wang F, Li Z, Wang G, Tian X, Zhou J, Yu W, Fan Z, Dong L, Lu J, Xu J, Zhang W, Liang A. Integrated transcriptomic and epigenetic data analysis identifiesaberrant expression of genes in acute myeloid leukemia with MLL‑AF9 translocation. Mol Med Rep 2019; 21:883-893. [PMID: 31789407 PMCID: PMC6947934 DOI: 10.3892/mmr.2019.10849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 12/14/2018] [Indexed: 11/06/2022] Open
Abstract
Rearrangement of the mixed lineage leukemia (MLL; also known as lysine methyltransferase 2A) gene is a recurrent genomic aberration in acute myeloid leukemia (AML). MLLT3, super elongation complex subunit (AF9) is one of the most common MLL fusion partners in AML. The present study aimed to explore the aberrant expression of genes associated with the MLL-AF9 translocation and identified potential new targets for the therapy of AML with MLL-AF9 translocation. The transcriptomic and epigenetic datasets were downloaded from National Center of Biotechnology Information Gene Expression Omnibus (GEO) database. Differentially expressed genes were obtained from two independent datasets (GSE68643 and GSE73457). Gene Ontology biological process and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis was performed using the Database for Annotation, Visualization and Integrated Discovery. MLL-AF9-associated chromatin immunoprecipitation sequencing (ChIP-Seq) data was analyzed and identified binding sites for MLL-AF9 and wild type MLL (MLL WT). The ChIP-Seq of histone modification data was downloaded from the GEO database, including histone 3 lysine 4 trimethylation (H3K4me3), histone 3 lysine 79 dimethylation (H3K79me2) and histone 3 lysine 27 acetylation (H3K27ac), was used for comparing histone modification marks between the MLL-AF9 leukemia cells and normal hematopoietic cells at MLL-AF9 and MLL WT binding sites. The differentially expressed genes with the same trend in H3K79me2, H3K27ac and H3K4me3 alteration were identified as potential MLL-AF9 direct target genes. Upon validation using RNA-Seq data from the Therapeutically Applicable Research to Generate Effective Treatments AML project, eight potential direct target genes of MLL-AF9 were identified and further confirmed in MLL-AF9 mouse model using reverse transcription-quantitative polymerase chain reaction. These genes may have a critical role in AML with MLL-AF9 translocation.
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Affiliation(s)
- Fangce Wang
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai 200092, P.R. China
| | - Zheng Li
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai 200092, P.R. China
| | - Guangming Wang
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai 200092, P.R. China
| | - Xiaoxue Tian
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai 200092, P.R. China
| | - Jie Zhou
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai 200092, P.R. China
| | - Wenlei Yu
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai 200092, P.R. China
| | - Zhuoyi Fan
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai 200092, P.R. China
| | - Lin Dong
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai 200092, P.R. China
| | - Jinyuan Lu
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai 200092, P.R. China
| | - Jun Xu
- Medical Center for Stem Cell Engineering and Transformation, East Hospital, Tongji University School of Medicine, Shanghai 200120, P.R. China
| | - Wenjun Zhang
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai 200092, P.R. China
| | - Aibin Liang
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai 200092, P.R. China
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Sánchez-Álvarez M, Strippoli R, Donadelli M, Bazhin AV, Cordani M. Sestrins as a Therapeutic Bridge between ROS and Autophagy in Cancer. Cancers (Basel) 2019; 11:cancers11101415. [PMID: 31546746 PMCID: PMC6827145 DOI: 10.3390/cancers11101415] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/15/2019] [Accepted: 09/19/2019] [Indexed: 02/07/2023] Open
Abstract
The regulation of Reactive Oxygen Species (ROS) levels and the contribution therein from networks regulating cell metabolism, such as autophagy and the mTOR-dependent nutrient-sensing pathway, constitute major targets for selective therapeutic intervention against several types of tumors, due to their extensive rewiring in cancer cells as compared to healthy cells. Here, we discuss the sestrin family of proteins—homeostatic transducers of oxidative stress, and drivers of antioxidant and metabolic adaptation—as emerging targets for pharmacological intervention. These adaptive regulators lie at the intersection of those two priority nodes of interest in antitumor intervention—ROS control and the regulation of cell metabolism and autophagy—therefore, they hold the potential not only for the development of completely novel compounds, but also for leveraging on synergistic strategies with current options for tumor therapy and classification/stadiation to achieve personalized medicine.
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Affiliation(s)
- Miguel Sánchez-Álvarez
- Mechanoadaptation & Caveolae Biology Lab, Cell and Developmental Biology Area, Centro Nacional de Investigaciones Cardiovasculares (CNIC). Madrid 28029, Spain.
| | - Raffaele Strippoli
- Department of Molecular Medicine, Sapienza University of Rome, Rome 00161, Italy.
- Gene Expression Laboratory, National Institute for Infectious Diseases "Lazzaro Spallanzani" IRCCS, Rome 00161, Italy.
| | - Massimo Donadelli
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Verona 37134, Italy.
| | - Alexandr V Bazhin
- Department of General, Visceral and Transplantation Surgery, Ludwig-Maximilians University, Munich 81377, Germany.
- German Cancer Consortium (DKTK), Partner Site Munich, Munich 80366, Germany.
| | - Marco Cordani
- IMDEA Nanociencia, C/Faraday 9, Ciudad Universitaria de Cantoblanco, Madrid 28049, Spain..
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Dawidowska M, Jaksik R, Drobna M, Szarzyńska-Zawadzka B, Kosmalska M, Sędek Ł, Machowska L, Lalik A, Lejman M, Ussowicz M, Kałwak K, Kowalczyk JR, Szczepański T, Witt M. Comprehensive Investigation of miRNome Identifies Novel Candidate miRNA-mRNA Interactions Implicated in T-Cell Acute Lymphoblastic Leukemia. Neoplasia 2019; 21:294-310. [PMID: 30763910 PMCID: PMC6372882 DOI: 10.1016/j.neo.2019.01.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/15/2019] [Accepted: 01/17/2019] [Indexed: 02/08/2023] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy originating from T-cell precursors. The genetic landscape of T-ALL has been largely characterized by next-generation sequencing. Yet, the transcriptome of miRNAs (miRNome) of T-ALL has been less extensively studied. Using small RNA sequencing, we characterized the miRNome of 34 pediatric T-ALL samples, including the expression of isomiRs and the identification of candidate novel miRNAs (not previously annotated in miRBase). For the first time, we show that immunophenotypic subtypes of T-ALL present different miRNA expression profiles. To extend miRNome characteristics in T-ALL (to 82 T-ALL cases), we combined our small RNA-seq results with data available in Gene Expression Omnibus. We report on miRNAs most abundantly expressed in pediatric T-ALL and miRNAs differentially expressed in T-ALL versus normal mature T-lymphocytes and thymocytes, representing candidate oncogenic and tumor suppressor miRNAs. Using eight target prediction algorithms and pathway enrichment analysis, we identified differentially expressed miRNAs and their predicted targets implicated in processes (defined in Gene Ontology and Kyoto Encyclopedia of Genes and Genomes) of potential importance in pathogenesis of T-ALL, including interleukin-6-mediated signaling, mTOR signaling, and regulation of apoptosis. We finally focused on hsa-mir-106a-363 cluster and functionally validated direct interactions of hsa-miR-20b-5p and hsa-miR-363-3p with 3' untranslated regions of their predicted targets (PTEN, SOS1, LATS2), overrepresented in regulation of apoptosis. hsa-mir-106a-363 is a paralogue of prototypic oncogenic hsa-mir-17-92 cluster with yet unestablished role in the pathogenesis of T-ALL. Our study provides a firm basis and data resource for functional analyses on the role of miRNA-mRNA interactions in T-ALL.
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Affiliation(s)
- Małgorzata Dawidowska
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479 Poznań, Poland.
| | - Roman Jaksik
- Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland.
| | - Monika Drobna
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479 Poznań, Poland.
| | - Bronisława Szarzyńska-Zawadzka
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479 Poznań, Poland; Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479 Poznań, Poland.
| | - Maria Kosmalska
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479 Poznań, Poland.
| | - Łukasz Sędek
- Department of Microbiology and Immunology, Medical University of Silesia in Katowice, Jordana 19, 41-808 Zabrze, Poland.
| | - Ludomiła Machowska
- Clinic of Pediatric Oncology Hematology and Transplantology, Poznań University of Medical Sciences, Szpitalna 27/33, 60-572 Poznań, Poland.
| | - Anna Lalik
- Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland.
| | - Monika Lejman
- Laboratory of Genetic Diagnostics, Medical University of Lublin, Children's University Hospital, Gębali 6, 20-093 Lublin, Poland.
| | - Marek Ussowicz
- Department of Pediatric Bone Marrow Transplantation, Oncology, and Hematology, Wroclaw Medical University, Borowska 213, 50-556 Wroclaw, Poland.
| | - Krzysztof Kałwak
- Department of Pediatric Bone Marrow Transplantation, Oncology, and Hematology, Wroclaw Medical University, Borowska 213, 50-556 Wroclaw, Poland.
| | - Jerzy R Kowalczyk
- Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, Gębali 6, 20-093 Lublin, Poland.
| | - Tomasz Szczepański
- Department of Pediatric Hematology and Oncology, Zabrze, Medical University of Silesia in Katowice, 3 Maja 13-15, 41-800 Zabrze, Poland.
| | - Michał Witt
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479 Poznań, Poland.
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Dinner S, Platanias LC. Targeting the mTOR Pathway in Leukemia. J Cell Biochem 2016; 117:1745-52. [PMID: 27018341 DOI: 10.1002/jcb.25559] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 03/24/2016] [Indexed: 12/16/2022]
Abstract
Optimal function of multiple intracellular signaling pathways is essential for normal regulation of cellular transcription, translation, growth, proliferation, and survival. Dysregulation or aberrant activation of such cascades can lead to inappropriate cell survival and abnormal cell proliferation in leukemia. Successful treatment of chronic myeloid leukemia (CML) with tyrosine kinase inhibitors targeting the BCR-ABL fusion gene is a prime example of effectively inhibiting intracellular signaling cascades. However, even in these patients resistance can develop via emergence of mutations or feedback activation of other pathways that cause refractory disease. Constitutive activation of the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (Akt)/mammalian target of rapamycin (mTOR) signaling pathway has been observed in different types of leukemia, including CML, acute myeloid leukemia, and acute lymphoblastic leukemia. Abnormal mTOR activity may contribute to chemotherapy resistance, while it may also be effectively targeted via molecular means and/or development of specific pharmacological inhibitors. This review discusses the role of PI3K/Akt/mTOR dysre-gulation in leukemia and summarizes the emergence of preliminary data for the development of novel therapeutic approaches. J. Cell. Biochem. 117: 1745-1752, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Shira Dinner
- Division of Hematology-Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, 60611
| | - Leonidas C Platanias
- Division of Hematology-Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, 60611.,Department of Medicine, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois, 60612
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López Villar E, Wu D, Cho WC, Madero L, Wang X. Proteomics-based discovery of biomarkers for paediatric acute lymphoblastic leukaemia: challenges and opportunities. J Cell Mol Med 2014; 18:1239-46. [PMID: 24912534 PMCID: PMC4124009 DOI: 10.1111/jcmm.12319] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 04/04/2014] [Indexed: 01/06/2023] Open
Abstract
There are important breakthroughs in the treatment of paediatric acute lymphoblastic leukaemia (ALL) since 1950, by which the prognosis of the child majority suffered from ALL has been improved. However, there are urgent needs to have disease-specific biomarkers to monitor the therapeutic efficacy and predict the patient prognosis. The present study overviewed proteomics-based research on paediatric ALL to discuss important advances to combat cancer cells and search novel and real protein biomarkers of resistance or sensitivity to drugs which target the signalling networks. We highlighted the importance and significance of a proper phospho-quantitative design and strategy for paediatric ALL between relapse and remission, when human body fluids from cerebrospinal, peripheral blood, or bone-marrow were applied. The present article also assessed the schedule for the analysis of body fluids from patients at different states, importance of proteomics-based tools to discover ALL-specific and sensitive biomarkers, to stimulate paediatric ALL research via proteomics to ‘build’ the reference map of the signalling networks from leukemic cells at relapse, and to monitor significant clinical therapies for ALL-relapse.
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