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Hu X, Wang Z, Qin Y, Xu J, Xu N, Wang Q, Lin R, Zhao K, Zhou H, Xuan L, Yu S, Liu Q. Allogeneic haematopoietic stem cell transplantation might overcome the poor prognosis of adolescents and adult patients with T-lineage acute lymphoblastic leukaemia and CDKN2 deletion. Bone Marrow Transplant 2024; 59:1146-1153. [PMID: 38769349 DOI: 10.1038/s41409-024-02306-2] [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: 01/25/2024] [Revised: 04/28/2024] [Accepted: 05/02/2024] [Indexed: 05/22/2024]
Abstract
This study delves into the clinical implications of cyclin-dependent kinase inhibitor 2 (CDKN2) deletion in adult T-lineage acute lymphoblastic leukemia (T-ALL). Among 241 patients included in this study, 57 had CDKN2 deletion and 184 had CDKN2 wild-type (WT), and 165 underwent allogeneic hematopoietic stem cell transplantation (allo-HSCT) and 76 did not undergo allo-HSCT. CDKN2 deletion correlated with higher white blood cell count, more high-risk diseases, and complex karyotype. The 5-year overall survival (OS) was 36.8% and 58.2% (P < 0.001), 5-year disease-free survival (DFS) was 47.1% and 59.3% (P = 0.018), and 5-year cumulative incidence of relapse (CIR) was 33.7% and 22.3% (P = 0.019) in patients with CDKN2 deletion and WT, respectively. Multivariate analysis identified CDKN2 deletion as an independent adverse prognostic factor for OS (HR 2.11, P = 0.003). In the CDKN2 deletion subgroup, landmark analysis showed that the 5-year OS was 56.7% and 19% (P = 0.002) for patients who underwent allo-HSCT and those who did not, respectively. And multivariate analysis confirmed the beneficial role of allo-HSCT in OS (HR 0.23, P < 0.001). In conclusion, CDKN2 deletion was associated with a poor prognosis in adult T-ALL, and allo-HSCT might be beneficial for this population.
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Affiliation(s)
- Xiaoshan Hu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Medical Oncology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
- Clinical Medical Research Center of Hematology Diseases of Guangdong Province, Guangzhou, China
| | - Zhixiang Wang
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Clinical Medical Research Center of Hematology Diseases of Guangdong Province, Guangzhou, China
| | - Yuting Qin
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Clinical Medical Research Center of Hematology Diseases of Guangdong Province, Guangzhou, China
| | - Jun Xu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Clinical Medical Research Center of Hematology Diseases of Guangdong Province, Guangzhou, China
| | - Na Xu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Clinical Medical Research Center of Hematology Diseases of Guangdong Province, Guangzhou, China
| | - Qiang Wang
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Clinical Medical Research Center of Hematology Diseases of Guangdong Province, Guangzhou, China
| | - Ren Lin
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Clinical Medical Research Center of Hematology Diseases of Guangdong Province, Guangzhou, China
| | - Ke Zhao
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Clinical Medical Research Center of Hematology Diseases of Guangdong Province, Guangzhou, China
| | - Hongsheng Zhou
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Clinical Medical Research Center of Hematology Diseases of Guangdong Province, Guangzhou, China
| | - Li Xuan
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Clinical Medical Research Center of Hematology Diseases of Guangdong Province, Guangzhou, China
| | - Sijian Yu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
- Clinical Medical Research Center of Hematology Diseases of Guangdong Province, Guangzhou, China.
| | - Qifa Liu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
- Clinical Medical Research Center of Hematology Diseases of Guangdong Province, Guangzhou, China.
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Muacevic A, Adler JR, Arora M, Ali MS, Pandey AK, Benjamin M, Palanichamy JK, Bakhshi S, Qamar I, Chopra A. Copy Number Alterations in CDKN2A/2B and MTAP Genes Are Associated With Low MEF2C Expression in T-cell Acute Lymphoblastic Leukemia. Cureus 2022; 14:e32151. [PMID: 36601176 PMCID: PMC9806946 DOI: 10.7759/cureus.32151] [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] [Accepted: 12/02/2022] [Indexed: 12/07/2022] Open
Abstract
The molecular heterogeneity of T-cell acute lymphoblastic leukemia (T-ALL) makes this disease complex. Early T-cell precursor ALL (ETP-ALL) is a recognized subtype of T-ALL associated with a high probability of induction failure with conventional therapy. Higher expression of myocyte enhancer factor 2C (MEF2C) and the absence of a biallelic deletion (ABD) are the designated markers for the ETP-ALL. Co-deletion of the contiguous genes cyclin-dependent kinase inhibitor 2A/2B (CDKN2A/2B) and the methylthioadenosine phosphorylase (MTAP) cluster, located at 9p21.3, is another common alteration in T-ALL and confers poor response to treatment. We used real-time polymerase chain reaction (PCR) analysis to assess MEF2C mRNA expression and ABD status. Copy number alterations (CNAs) in key genes previously reported to be altered in T-ALL were assessed using multiple ligation probe amplification (MLPA). We observed that CNAs in this co-deletion cluster of CDKN2A/B and MTAP genes exhibited low MEF2C expression while ABD was associated with CNA in the Abelson murine leukemia 1 (ABL1) gene. Assessment of MEF2C expression based on immunophenotype revealed that its association with CDKN2A/2B alteration is present in non-immature immunophenotype. Additionally, ABD was associated with copy number alterations of T-cell acute lymphocytic leukemia protein 1 (TAL1), myeloblastosis (MYB), and LIM domain only 2 (LMO2) genes in immature immunophenotypes. Further, STIL::TAL1 fusion was associated with low expression of MEF2C. These associations may help explain the difficulties in assessing disease heterogeneity and the prognostic importance of 9p21.3 alterations in T-ALL.
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EGCG Prevents the Transcriptional Reprogramming of an Inflammatory and Immune-Suppressive Molecular Signature in Macrophage-like Differentiated Human HL60 Promyelocytic Leukemia Cells. Cancers (Basel) 2022; 14:cancers14205065. [PMID: 36291849 PMCID: PMC9599716 DOI: 10.3390/cancers14205065] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/07/2022] [Accepted: 10/13/2022] [Indexed: 11/18/2022] Open
Abstract
Simple Summary Scientists are increasingly harnessing the power of the immune system to prevent cancer. While macrophages are a major component of the tumor microenvironment where they orchestrate various aspects of immunity, dysregulated immune and inflammatory responses will play a key role in cancer initiation and progression. Depending on their activation status, macrophages can have a dual impact on tumorigenesis by either antagonising cytotoxic immune cells or enhancing antitumor responses. Increased infiltration of tumor-associated macrophages has long been associated with poor patient prognosis in most solid cancers, highlighting their value as potential diagnostic and prognostic biomarkers in cancer. A variety of macrophage-centered approaches to cancer therapy have been investigated, including strategies to prevent tumor-promoting activities. In this study, we highlight the chemopreventive properties of EGCG derived from green tea that underpin its ability to re-program macrophage molecular signature and function. Abstract Background: The promyelocytic leukemia cell differentiation process enables recapitulation of the polarized M1 or M2 macrophage-like phenotype with inflammatory and immune-suppressive properties. While evidence supports the anti-inflammatory effect of dietary-derived epigallocatechin-3-gallate (EGCG), its impact on the onset of immune phenotype molecular signature remains unclear. Methods: Human HL60 promyelocytic cells grown in suspension were differentiated into CD11bHigh/CD14Low adherent macrophages with phorbol 12-myristate 13-acetate (PMA). Gelatin zymography was used to assess the levels of matrix metalloproteinase (MMP)-9, and total RNA was isolated for RNAseq and RT-qPCR assessment of differentially expressed gene levels involved in inflammation and immunity. Protein lysates were used to assess the phosphorylation status of signaling intermediates involved in macrophage-like cell differentiation. Results: Cell adhesion and induction of MMP-9 were indicative of HL60 cell differentiation into a macrophage-like phenotype. The extracellular signal-regulated kinase (ERK), glycogen synthase kinase (GSK)-3, p90 ribosomal S6 kinases (RSK), and cAMP-response-element-binding protein (CREB) were all phosphorylated, and EGCG reduced such phosphorylation status. Increases in inflammation and immunity genes included, among others, CCL22, CSF1, CSF2, IL1B, and TNF, which inductions were prevented by EGCG. This was corroborated by unbiased transcriptomic analysis which further highlighted the capacity of EGCG to downregulate the hematopoietic stem cell regulator CBFA2T3. Conclusion: EGCG inhibits inflammatory signaling crosstalk and prevents the onset of an immune phenotype in macrophage-like differentiated cells.
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Use of Publication Dynamics to Distinguish Cancer Genes and Bystander Genes. Genes (Basel) 2022; 13:genes13071105. [PMID: 35885888 PMCID: PMC9315931 DOI: 10.3390/genes13071105] [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: 05/25/2022] [Revised: 06/13/2022] [Accepted: 06/17/2022] [Indexed: 02/01/2023] Open
Abstract
de Magalhães has shown recently that most human genes have several papers in PubMed mentioning cancer, leading the author to suggest that every gene is associated with cancer, a conclusion that contradicts the widely held view that cancer is driven by a limited number of cancer genes, whereas the majority of genes are just bystanders in carcinogenesis. We have analyzed PubMed to decide whether publication metrics supports the distinction of bystander genes and cancer genes. The dynamics of publications on known cancer genes followed a similar pattern: seminal discoveries triggered a burst of cancer-related publications that validated and expanded the discovery, resulting in a rise both in the number and proportion of cancer-related publications on that gene. The dynamics of publications on bystander genes was markedly different. Although there is a slow but continuous time-dependent rise in the proportion of papers mentioning cancer, this phenomenon just reflects the increasing publication bias that favors cancer research. Despite this bias, the proportion of cancer papers on bystander genes remains low. Here, we show that the distinctive publication dynamics of cancer genes and bystander genes may be used for the identification of cancer genes.
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Kumari S, Ali MS, Singh J, Arora M, Verma D, Pandey AK, Benjamin M, Bakhshi S, Palanichamy JK, Sharma A, Singh I, Tanwar P, Singh AR, Pushpam D, Qamar I, Chopra A. Prognostic utility of key copy number alterations in T cell acute lymphoblastic leukemia. Hematol Oncol 2022; 40:577-587. [DOI: 10.1002/hon.3030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/26/2022] [Accepted: 05/21/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Sarita Kumari
- Laboratory Oncology Unit Dr. BRA‐IRCH All India Institute of Medical Sciences New Delhi110029 India
- School of Biotechnology Gautam Buddha University Uttar Pradesh201312 India
| | - Md Shadab Ali
- Department of Pulmonary Medicine and Sleep Disorders All India Institute of Medical Sciences New Delhi New Delhi110029 India
| | - Jay Singh
- Laboratory Oncology Unit Dr. BRA‐IRCH All India Institute of Medical Sciences New Delhi110029 India
| | - Mohit Arora
- Department of Biochemistry All India Institute of Medical Sciences New Delhi110029 India
| | - Deepak Verma
- Laboratory Oncology Unit Dr. BRA‐IRCH All India Institute of Medical Sciences New Delhi110029 India
| | - Avanish Kumar Pandey
- Laboratory Oncology Unit Dr. BRA‐IRCH All India Institute of Medical Sciences New Delhi110029 India
| | - Mercilena Benjamin
- Laboratory Oncology Unit Dr. BRA‐IRCH All India Institute of Medical Sciences New Delhi110029 India
| | - Sameer Bakhshi
- Laboratory Oncology Unit Dr. BRA‐IRCH All India Institute of Medical Sciences New Delhi110029 India
| | | | - Atul Sharma
- Department of Medical Oncology Dr. BRA‐IRCH All India Institute of Medical Sciences New Delhi110029 India
| | - Inder Singh
- Department of Neurology All India Institute of Medical Sciences New Delhi New Delhi110029 India
| | - Pranay Tanwar
- Laboratory Oncology Unit Dr. BRA‐IRCH All India Institute of Medical Sciences New Delhi110029 India
| | - Amar Ranjan Singh
- Laboratory Oncology Unit Dr. BRA‐IRCH All India Institute of Medical Sciences New Delhi110029 India
| | - Deepam Pushpam
- Department of Medical Oncology Dr. BRA‐IRCH All India Institute of Medical Sciences New Delhi110029 India
| | - Imteyaz Qamar
- School of Biotechnology Gautam Buddha University Uttar Pradesh201312 India
| | - Anita Chopra
- Laboratory Oncology Unit Dr. BRA‐IRCH All India Institute of Medical Sciences New Delhi110029 India
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Genescà E, González-Gil C. Latest Contributions of Genomics to T-Cell Acute Lymphoblastic Leukemia (T-ALL). Cancers (Basel) 2022; 14:2474. [PMID: 35626077 PMCID: PMC9140158 DOI: 10.3390/cancers14102474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 12/04/2022] Open
Abstract
As for many neoplasms, initial genetic data about T-cell acute lymphoblastic leukemia (T-ALL) came from the application of cytogenetics. This information helped identify some recurrent chromosomal alterations in T-ALL at the time of diagnosis, although it was difficult to determine their prognostic impact because of their low incidence in the specific T-ALL cohort analyzed. Genetic knowledge accumulated rapidly following the application of genomic techniques, drawing attention to the importance of using high-resolution genetic techniques to detect cryptic aberrations present in T-ALL, which are not usually detected by cytogenetics. We now have a clearer appreciation of the genetic landscape of the different T-ALL subtypes at diagnosis, explaining the particular oncogenetic processes taking place in each T-ALL, and we have begun to understand relapse-specific mechanisms. This review aims to summarize the latest advances in our knowledge of the genome in T-ALL. We highlight areas where the research in this subtype of ALL is progressing with the aim of identifying key questions that need to be answered in the medium-long term if this knowledge is to be applied in clinics.
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Affiliation(s)
- Eulàlia Genescà
- Institut d’Investigació Contra la Leucemia Josep Carreras (IJC), Campus ICO-Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain;
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Han C, Khodadadi-Jamayran A, Lorch AH, Jin Q, Serafin V, Zhu P, Politanska Y, Sun L, Gutierrez-Diaz BT, Pryzhkova MV, Abdala-Valencia H, Bartom ET, Buldini B, Basso G, Velu SE, Sarma K, Mattamana BB, Cho BK, Obeng RC, Goo YA, Jordan PW, Tsirigos A, Zhou Y, Ntziachristos P. SF3B1 homeostasis is critical for survival and therapeutic response in T cell leukemia. SCIENCE ADVANCES 2022; 8:eabj8357. [PMID: 35061527 PMCID: PMC8782448 DOI: 10.1126/sciadv.abj8357] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 11/29/2021] [Indexed: 05/05/2023]
Abstract
The production of noncanonical mRNA transcripts is associated with cell transformation. Driven by our previous findings on the sensitivity of T cell acute lymphoblastic leukemia (T-ALL) cells to SF3B1 inhibitors, we identified that SF3B1 inhibition blocks T-ALL growth in vivo with no notable associated toxicity. We also revealed protein stabilization of the U2 complex component SF3B1 via deubiquitination. Our studies showed that SF3B1 inhibition perturbs exon skipping, leading to nonsense-mediated decay and diminished levels of DNA damage response-related transcripts, such as the serine/threonine kinase CHEK2, and impaired DNA damage response. We also identified that SF3B1 inhibition leads to a general decrease in R-loop formation. We further demonstrate that clinically used SF3B1 inhibitors synergize with CHEK2 inhibitors and chemotherapeutic drugs to block leukemia growth. Our study provides the proof of principle for posttranslational regulation of splicing components and associated roles and therapeutic implications for the U2 complex in T cell leukemia.
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Affiliation(s)
- Cuijuan Han
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Alireza Khodadadi-Jamayran
- Applied Bioinformatics Laboratories, Office of Science and Research, New York University School of Medicine, New York, NY, USA
| | - Adam H. Lorch
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Qi Jin
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Valentina Serafin
- Division of Pediatric Hematology, Oncology and Stem Cell Transplant, Maternal and Child Health Department, Padua University, Padova, Italy
| | - Ping Zhu
- H3 Biomedicine Inc., Cambridge, MA, USA
| | - Yuliya Politanska
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Limin Sun
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Blanca T. Gutierrez-Diaz
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Marina V. Pryzhkova
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Hiam Abdala-Valencia
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Elizabeth Thomas Bartom
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Barbara Buldini
- Division of Pediatric Hematology, Oncology and Stem Cell Transplant, Maternal and Child Health Department, Padua University, Padova, Italy
| | - Giuseppe Basso
- Division of Pediatric Hematology, Oncology and Stem Cell Transplant, Maternal and Child Health Department, Padua University, Padova, Italy
| | - Sadanandan E. Velu
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Kavitha Sarma
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Basil B. Mattamana
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Byoung-Kyu Cho
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Rebecca C. Obeng
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
| | - Young Ah Goo
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Philip W. Jordan
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Aristotelis Tsirigos
- Applied Bioinformatics Laboratories, Office of Science and Research, New York University School of Medicine, New York, NY, USA
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
- Institute for Computational Medicine, NYU School of Medicine, New York, NY, USA
| | - Yalu Zhou
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Panagiotis Ntziachristos
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
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Park J, Kim HS, Lee JM, Jung J, Kang D, Choi H, Lee GD, Son J, Park S, Cho BS, Kim HJ, Kim S, Lee JW, Chung NG, Cho B, Zhang H, Khazanov NA, Choi J, Jung JW, Kim Y, Kim M. Analytical and Potential Clinical Performance of Oncomine Myeloid Research Assay for Myeloid Neoplasms. Mol Diagn Ther 2021; 24:579-592. [PMID: 32676933 DOI: 10.1007/s40291-020-00484-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Next-generation sequencing (NGS) panels have recently been introduced to efficiently detect genetic variations in hematologic malignancies. OBJECTIVES Our aim was to evaluate the performance of the commercialized Oncomine™ myeloid research assay (OMA) for myeloid neoplasms. METHODS Certified reference materials and clinical research samples were used, including 60 genomic DNA and 56 RNA samples. NGS was performed using OMA, which enables the interrogation of 40 target genes, 29 gene fusions, and five expression target genes with five expression control genes by the Ion S5 XL Sequencer. The analyzed data were compared with clinical data using karyotyping, reverse transcription polymerase chain reaction (PCR), fluorescence in situ hybridization, Sanger sequencing, customized NGS panel, and fragment analysis. RESULTS All targets of reference materials were detected except three (two ASXL1 and one CEBPA) mutations, which we had not expected OMA to detect. In clinical search samples, OMA satisfactorily identified DNA variants, including 90 single nucleotide variants (SNVs), 48 small insertions and deletions (indels), and eight FLT3 internal tandem duplications (ITDs) (Kappa agreement 0.938). The variant allele frequencies of SNVs and indels measured by OMA correlated well with clinical data, whereas those of FLT3-ITDs were significantly lower than with fragment analysis (P = 0.008). Together, OMA showed strong ability to identify RNA gene fusions (Kappa agreement 0.961), except one RUNX1-MECOM. The MECOM gene was highly expressed in all five samples with MECOM-associated rearrangements, including inv(3), t(3;3), and t(3;21). CONCLUSION OMA revealed excellent analytical and potential clinical performance and could be a good replacement for conventional molecular tests.
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Affiliation(s)
- Joonhong Park
- Department of Laboratory Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 06591, Republic of Korea
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hoon Seok Kim
- Department of Laboratory Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 06591, Republic of Korea
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jong-Mi Lee
- Department of Laboratory Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 06591, Republic of Korea
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jin Jung
- Department of Laboratory Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 06591, Republic of Korea
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Dain Kang
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hayoung Choi
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Gun Dong Lee
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jungok Son
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Silvia Park
- Division of Acute Leukemia, Department of Hematology, Catholic Hematology Hospital, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Byung-Sik Cho
- Division of Acute Leukemia, Department of Hematology, Catholic Hematology Hospital, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hee-Je Kim
- Division of Acute Leukemia, Department of Hematology, Catholic Hematology Hospital, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Seongkoo Kim
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jae Wook Lee
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Nack-Gyun Chung
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Bin Cho
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hua Zhang
- Thermo Fisher Scientific, Waltham, MA, USA
| | | | - Jongpill Choi
- Thermo Fisher Scientific Solutions, Seoul, Republic of Korea
| | - Jae-Won Jung
- Thermo Fisher Scientific Solutions, Seoul, Republic of Korea
| | - Yonggoo Kim
- Department of Laboratory Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 06591, Republic of Korea.
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
| | - Myungshin Kim
- Department of Laboratory Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 06591, Republic of Korea.
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
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[The characteristics and prognostic impact of NOTCH1/FBXW7 mutation and CDKN2A/B deletion in adult T-cell acute lymphoblastic leukemia patients]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2021; 42:432-435. [PMID: 34218589 PMCID: PMC8293003 DOI: 10.3760/cma.j.issn.0253-2727.2021.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Mroczek A, Zawitkowska J, Kowalczyk J, Lejman M. Comprehensive Overview of Gene Rearrangements in Childhood T-Cell Acute Lymphoblastic Leukaemia. Int J Mol Sci 2021; 22:E808. [PMID: 33467425 PMCID: PMC7829804 DOI: 10.3390/ijms22020808] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 12/11/2022] Open
Abstract
Acute lymphoblastic leukaemia (ALL) is a relevant form of childhood neoplasm, as it accounts for over 80% of all leukaemia cases. T-cell ALL constitutes a genetically heterogeneous cancer derived from T-lymphoid progenitors. The diagnosis of T-ALL is based on morphologic, immunophenotypic, cytogenetic, and molecular features, thus the results are used for patient stratification. Due to the expression of surface and intracellular antigens, several subtypes of T-ALL can be distinguished. Although the aetiology of T-ALL remains unclear, a wide spectrum of rearrangements and mutations affecting crucial signalling pathways has been described so far. Due to intensive chemotherapy regimens and supportive care, overall cure rates of more than 80% in paediatric T-ALL patients have been accomplished. However, improved knowledge of the mechanisms of relapse, drug resistance, and determination of risk factors are crucial for patients in the high-risk group. Even though some residual disease studies have allowed the optimization of therapy, the identification of novel diagnostic and prognostic markers is required to individualize therapy. The following review summarizes our current knowledge about genetic abnormalities in paediatric patients with T-ALL. As molecular biology techniques provide insights into the biology of cancer, our study focuses on new potential therapeutic targets and predictive factors which may improve the outcome of young patients with T-ALL.
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Affiliation(s)
- Anna Mroczek
- Department of Paediatric Haematology, Oncology and Transplantology, Medical University of Lublin, 20-093 Lublin, Poland; (A.M.); (J.Z.); (J.K.)
| | - Joanna Zawitkowska
- Department of Paediatric Haematology, Oncology and Transplantology, Medical University of Lublin, 20-093 Lublin, Poland; (A.M.); (J.Z.); (J.K.)
| | - Jerzy Kowalczyk
- Department of Paediatric Haematology, Oncology and Transplantology, Medical University of Lublin, 20-093 Lublin, Poland; (A.M.); (J.Z.); (J.K.)
| | - Monika Lejman
- Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland
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11
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González-Gil C, Ribera J, Ribera JM, Genescà E. The Yin and Yang-Like Clinical Implications of the CDKN2A/ARF/CDKN2B Gene Cluster in Acute Lymphoblastic Leukemia. Genes (Basel) 2021; 12:genes12010079. [PMID: 33435487 PMCID: PMC7827355 DOI: 10.3390/genes12010079] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 12/13/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is a malignant clonal expansion of lymphoid hematopoietic precursors that exhibit developmental arrest at varying stages of differentiation. Similar to what occurs in solid cancers, transformation of normal hematopoietic precursors is governed by a multistep oncogenic process that drives initiation, clonal expansion and metastasis. In this process, alterations in genes encoding proteins that govern processes such as cell proliferation, differentiation, and growth provide us with some of the clearest mechanistic insights into how and why cancer arises. In such a scenario, deletions in the 9p21.3 cluster involving CDKN2A/ARF/CDKN2B genes arise as one of the oncogenic hallmarks of ALL. Deletions in this region are the most frequent structural alteration in T-cell acute lymphoblastic leukemia (T-ALL) and account for roughly 30% of copy number alterations found in B-cell-precursor acute lymphoblastic leukemia (BCP-ALL). Here, we review the literature concerning the involvement of the CDKN2A/B genes as a prognosis marker of good or bad response in the two ALL subtypes (BCP-ALL and T-ALL). We compare frequencies observed in studies performed on several ALL cohorts (adult and child), which mainly consider genetic data produced by genomic techniques. We also summarize what we have learned from mouse models designed to evaluate the functional involvement of the gene cluster in ALL development and in relapse/resistance to treatment. Finally, we examine the range of possibilities for targeting the abnormal function of the protein-coding genes of this cluster and their potential to act as anti-leukemic agents in patients.
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Affiliation(s)
- Celia González-Gil
- Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), 08916 Badalona, Spain; (C.G.-G.); (J.R.); (J.M.R.)
| | - Jordi Ribera
- Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), 08916 Badalona, Spain; (C.G.-G.); (J.R.); (J.M.R.)
| | - Josep Maria Ribera
- Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), 08916 Badalona, Spain; (C.G.-G.); (J.R.); (J.M.R.)
- Clinical Hematology Department, ICO-Hospital Germans Trias i Pujol, 08916 Badalona, Spain
| | - Eulàlia Genescà
- Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), 08916 Badalona, Spain; (C.G.-G.); (J.R.); (J.M.R.)
- Correspondence: ; Tel.: +34-93-557-28-08
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12
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Cordo' V, van der Zwet JC, Canté-Barrett K, Pieters R, Meijerink JP. T-cell Acute Lymphoblastic Leukemia: A Roadmap to Targeted Therapies. Blood Cancer Discov 2021; 2:19-31. [PMID: 34661151 PMCID: PMC8447273 DOI: 10.1158/2643-3230.bcd-20-0093] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 10/08/2020] [Accepted: 10/28/2020] [Indexed: 11/16/2022] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic malignancy characterized by aberrant proliferation of immature thymocytes. Despite an overall survival of 80% in the pediatric setting, 20% of patients with T-ALL ultimately die from relapsed or refractory disease. Therefore, there is an urgent need for novel therapies. Molecular genetic analyses and sequencing studies have led to the identification of recurrent T-ALL genetic drivers. This review summarizes the main genetic drivers and targetable lesions of T-ALL and gives a comprehensive overview of the novel treatments for patients with T-ALL that are currently under clinical investigation or that are emerging from preclinical research. SIGNIFICANCE T-ALL is driven by oncogenic transcription factors that act along with secondary acquired mutations. These lesions, together with active signaling pathways, may be targeted by therapeutic agents. Bridging research and clinical practice can accelerate the testing of novel treatments in clinical trials, offering an opportunity for patients with poor outcome.
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13
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Lejman M, Włodarczyk M, Styka B, Pastorczak A, Zawitkowska J, Taha J, Sędek Ł, Skonieczka K, Braun M, Haus O, Szczepański T, Młynarski W, Kowalczyk JR. Advantages and Limitations of SNP Array in the Molecular Characterization of Pediatric T-Cell Acute Lymphoblastic Leukemia. Front Oncol 2020; 10:1184. [PMID: 32766158 PMCID: PMC7379740 DOI: 10.3389/fonc.2020.01184] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 06/11/2020] [Indexed: 01/03/2023] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is a highly heterogeneous disease, and numerous genetic aberrations in the leukemic genome are responsible for the biological and clinical differences among particular ALL subtypes. However, there is limited knowledge regarding the association of whole-genome copy number abnormalities (CNAs) in childhood T-ALL with the course of leukemia and its outcome. The aim of this study was to identify the pattern of whole-genome CNAs in 86 newly diagnosed childhood T-ALL cases using a high-density single-nucleotide polymorphism array. We analyzed the presence of whole-genome CNAs with respect to immunophenotype, clinical features, and treatment outcomes. A total of 769 CNAs, including trisomies, duplications, deletions, and segmental loss of heterozygosity, were detected in 86 analyzed samples. Gain or loss of chromosomal regions exceeding 10 Mb occurred in 46 cases (53%), including six cases (7%) with complex chromosomal alterations. We observed that microdeletions in selected genes (e.g., FIP1L1 and PDGFRB) were related to the clinical features. Interestingly, 13% of samples have a duplication of the two loci (MYB and AIH1—6q23.3), which never occurred alone. Single-nucleotide polymorphism array significantly improved the molecular characterization of pediatric T-ALL. Further studies with larger cohorts of patients may contribute to the selection of prognostic CNAs in this group of patients.
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Affiliation(s)
- Monika Lejman
- Laboratory of Genetic Diagnostics, Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, Lublin, Poland
| | - Monika Włodarczyk
- Laboratory of Genetic Diagnostics, University Children's Hospital, Lublin, Poland
| | - Borys Styka
- Laboratory of Genetic Diagnostics, University Children's Hospital, Lublin, Poland
| | - Agata Pastorczak
- Department of Pediatric, Oncology, Hematology and Diabetology, Medical University of Łódz, Łódź, Poland
| | - Joanna Zawitkowska
- Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, Lublin, Poland
| | - Joanna Taha
- Department of Pediatric, Oncology, Hematology and Diabetology, Medical University of Łódz, Łódź, Poland
| | - Łukasz Sędek
- Department of Microbiology and Oncology, Medical University of Silesia in Katowice, Katowice, Poland
| | - Katarzyna Skonieczka
- Department of Clinical Genetics, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Marcin Braun
- Department of Pathology, Chair of Oncology, Medical University of Łódz, Łódź, Poland
| | - Olga Haus
- Department of Clinical Genetics, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Tomasz Szczepański
- Department of Microbiology and Oncology, Medical University of Silesia in Katowice, Katowice, Poland
| | - Wojciech Młynarski
- Department of Pediatric, Oncology, Hematology and Diabetology, Medical University of Łódz, Łódź, Poland
| | - Jerzy R Kowalczyk
- Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, Lublin, Poland
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14
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Abstract
Acute lymphoblastic leukaemia develops in both children and adults, with a peak incidence between 1 year and 4 years. Most acute lymphoblastic leukaemia arises in healthy individuals, and predisposing factors such as inherited genetic susceptibility or environmental exposure have been identified in only a few patients. It is characterised by chromosomal abnormalities and genetic alterations involved in differentiation and proliferation of lymphoid precursor cells. Along with response to treatment, these abnormalities are important prognostic factors. Disease-risk stratification and the development of intensified chemotherapy protocols substantially improves the outcome of patients with acute lymphoblastic leukaemia, particularly in children (1-14 years), but also in adolescents and young adults (15-39 years). However, the outcome of older adults (≥40 years) and patients with relapsed or refractory acute lymphoblastic leukaemia remains poor. New immunotherapeutic strategies, such as monoclonal antibodies and chimeric antigen receptor (CAR) T cells, are being developed and over the next few years could change the options for acute lymphoblastic leukaemia treatment.
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Affiliation(s)
- Florent Malard
- Department of Clinical Hematology and Cellular Therapy, Saint-Antoine Hospital, AP-HP, Sorbonne University, Paris, France; Sorbonne University, INSERM, Saint-Antoine Research Centre, Paris, France
| | - Mohamad Mohty
- Department of Clinical Hematology and Cellular Therapy, Saint-Antoine Hospital, AP-HP, Sorbonne University, Paris, France; Sorbonne University, INSERM, Saint-Antoine Research Centre, Paris, France.
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15
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Park DJ, Kwon A, Cho BS, Kim HJ, Hwang KA, Kim M, Kim Y. Characteristics of DNMT3A mutations in acute myeloid leukemia. Blood Res 2020; 55:17-26. [PMID: 32269971 PMCID: PMC7106122 DOI: 10.5045/br.2020.55.1.17] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 01/23/2020] [Accepted: 02/03/2020] [Indexed: 12/19/2022] Open
Abstract
Background DNMT3A mutations occur in approximately 20% of AML cases and are associated with changes in DNA methylation. CDKN2B plays an important role in the regulation of hematopoietic progenitor cells and DNMT3A mutation is associated with CDKN2B promoter methylation. We analyzed the characteristics of DNMT3A mutations including their clinical significance in AML and their influence on promoter methylation and CDKN2B expression. Methods A total of 142 adults, recently diagnosed with de novo AML, were enrolled in the study. Mutations in DNMT3A, CEBPA, and NPM1 were analyzed by bidirectional Sanger sequencing. We evaluated CDKN2B promoter methylation and expression using pyrosequencing and RT-qPCR. Results We identified DNMT3A mutations in 19.7% (N=28) of enrolled patients with AML, which increased to 29.5% when analysis was restricted to cytogenetically normal-AML. Mutations were located on exons from 8–23, and the majority, including R882, were found to be present on exon 23. We also identified a novel frameshift mutation, c.1590delC, in AML with biallelic mutation of CEBPA. There was no significant difference in CDKN2B promoter methylation according to the presence or type of DNMT3A mutations. CDKN2B expression inversely correlated with CDKN2B promoter methylation and was significantly higher in AML with R882H mutation in DNMT3A. We demonstrated that DNMT3A mutation was associated with poor AML outcomes, especially in cytogenetically normal-AML. The DNMT3A mutation remained as the independent unfavorable prognostic factor after multivariate analysis. Conclusion We characterized DNMT3A mutations in AML and revealed the association between the DNMT3A mutation and CDKN2B expression and clinical outcome.
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Affiliation(s)
- Dong Jin Park
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Ahlm Kwon
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Byung-Sik Cho
- Cancer Research Institute, Division of Hematology, Department of Internal Medicine, Catholic Blood and Marrow Transplantation Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Hee-Je Kim
- Cancer Research Institute, Division of Hematology, Department of Internal Medicine, Catholic Blood and Marrow Transplantation Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Kyung-Ah Hwang
- Department of Research and Development, Genetree Research, Seoul, Korea
| | - Myungshin Kim
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yonggoo Kim
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
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16
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Transcriptional Regulation of Genes by Ikaros Tumor Suppressor in Acute Lymphoblastic Leukemia. Int J Mol Sci 2020; 21:ijms21041377. [PMID: 32085659 PMCID: PMC7073093 DOI: 10.3390/ijms21041377] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 12/27/2022] Open
Abstract
Regulation of oncogenic gene expression by transcription factors that function as tumor suppressors is one of the major mechanisms that regulate leukemogenesis. Understanding this complex process is essential for explaining the pathogenesis of leukemia as well as developing targeted therapies. Here, we provide an overview of the role of Ikaros tumor suppressor and its role in regulation of gene transcription in acute leukemia. Ikaros (IKZF1) is a DNA-binding protein that functions as a master regulator of hematopoiesis and the immune system, as well as a tumor suppressor in acute lymphoblastic leukemia (ALL). Genetic alteration or functional inactivation of Ikaros results in the development of high-risk leukemia. Ikaros binds to the specific consensus binding motif at upstream regulatory elements of its target genes, recruits chromatin-remodeling complexes and activates or represses transcription via chromatin remodeling. Over the last twenty years, a large number of Ikaros target genes have been identified, and the role of Ikaros in the regulation of their expression provided insight into the mechanisms of Ikaros tumor suppressor function in leukemia. Here we summarize the role of Ikaros in the regulation of the expression of the genes whose function is critical for cellular proliferation, development, and progression of acute lymphoblastic leukemia.
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17
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Aberuyi N, Rahgozar S, Ghodousi ES, Ghaedi K. Drug Resistance Biomarkers and Their Clinical Applications in Childhood Acute Lymphoblastic Leukemia. Front Oncol 2020; 9:1496. [PMID: 32010613 PMCID: PMC6978753 DOI: 10.3389/fonc.2019.01496] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 12/12/2019] [Indexed: 12/12/2022] Open
Abstract
Biomarkers are biological molecules found in body fluids or tissues, which can be considered as indications of a normal or abnormal process, or of a condition or disease. There are various types of biomarkers based on their application and molecular alterations. Treatment-sensitivity or drug resistance biomarkers include prognostic and predictive molecules with utmost importance in selecting appropriate treatment protocols and improving survival rates. Acute lymphoblastic leukemia (ALL) is the most prevalent hematological malignancy diagnosed in children with nearly 80% cure rate. Despite the favorable survival rates of childhood ALL (chALL), resistance to chemotherapeutic agents and, as a consequence, a dismal prognosis develops in a significant number of patients. Therefore, there are urgent needs to have robust, sensitive, and disease-specific molecular prognostic and predictive biomarkers, which could allow better risk classification and then better clinical results. In this article, we review the currently known drug resistance biomarkers, including somatic or germ line nucleic acids, epigenetic alterations, protein expressions and metabolic variations. Moreover, biomarkers with potential clinical applications are discussed.
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Affiliation(s)
- Narges Aberuyi
- Division of Cellular and Molecular Biology, Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Sciences and Technologies, University of Isfahan, Isfahan, Iran
| | - Soheila Rahgozar
- Division of Cellular and Molecular Biology, Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Sciences and Technologies, University of Isfahan, Isfahan, Iran
| | - Elaheh Sadat Ghodousi
- Division of Cellular and Molecular Biology, Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Sciences and Technologies, University of Isfahan, Isfahan, Iran
| | - Kamran Ghaedi
- Division of Cellular and Molecular Biology, Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Sciences and Technologies, University of Isfahan, Isfahan, Iran
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18
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The effect of co-occurring lesions on leukaemogenesis and drug response in T-ALL and ETP-ALL. Br J Cancer 2019; 122:455-464. [PMID: 31792348 PMCID: PMC7028932 DOI: 10.1038/s41416-019-0647-7] [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: 06/25/2019] [Revised: 10/14/2019] [Accepted: 10/30/2019] [Indexed: 01/27/2023] Open
Abstract
Despite advances in the management of acute lymphoblastic leukaemia (ALL), current regimens fail to significantly transform outcomes for patients with high-risk subtypes. Advances in genomic analyses have identified novel lesions including mutations in genes that encode chromatin modifiers and those that influence cytokine and kinase signalling, rendering many of these alterations potentially targetable by tyrosine kinase and epigenetic inhibitors currently in clinical use. Although specific genomic lesions, gene expression patterns, and immunophenotypic profiles have been associated with specific clinical outcomes in some cancers, the application of precision medicine approaches based on these data has been slow. This approach is complicated by the reality that patients often harbour multiple mutations, and in many cases, the precise functional significance and interaction of these mutations in driving leukaemia and drug responsiveness/resistance remains unknown. Given that signalling pathways driving leukaemic pathogenesis could plausibly result from the co-existence of specific lesions and the resultant perturbation of protein interactions, the use of combined therapeutics that target multiple aberrant pathways, according to an individual’s mutational profile, might improve outcomes and lower a patient’s risk of relapse. Here we outline the genomic alterations that occur in T cell ALL (T-ALL) and early T cell precursor (ETP)-ALL and review studies highlighting the possible effects of co-occurring lesions on leukaemogenesis and drug response.
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19
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Ege B, Yumrutas O, Ege M, Pehlivan M, Bozgeyik I. Pharmacological properties and therapeutic potential of saffron (Crocus sativus L.) in osteosarcoma. J Pharm Pharmacol 2019; 72:56-67. [DOI: 10.1111/jphp.13179] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/14/2019] [Indexed: 12/15/2022]
Abstract
Abstract
Objectives
In this comprehensive study, we aimed to investigate pharmacological properties and therapeutic significance of saffron in osteosarcoma cancer cells.
Methods
Plant materials were obtained from Safranbolu district of Karabuk, Turkey. For the determination of anticancer properties, thiazolyl blue tetrazolium bromide (MTT) cell viability, colony formation, wound closure, DNA ladder assays and gene expression analysis by real-time PCR were performed. Also, cellular inflammation, total antioxidant and oxidants status were determined.
Key findings
Dichloromethane and hexane extracts of saffron were significantly inhibited cell proliferation and interfered with colony forming and migration capabilities of U2-OS osteosarcoma cancer cells. Also, both extracts induced the activation of tumour suppressor CDKN2B gene and altered cellular morphology resembling the induction of apoptosis. However, DNA fragmentation was not observed after extract treatments. Saffron was also found to have no significant effect on cellular inflammation. Unexpectedly, both dichloromethane and hexane extracts of saffron had no marked effect on cellular total antioxidant and oxidant status. Lastly, vanillic acid, resveratrol, caffeic acid and 4-hydroxybenzoic acid were found to be highly rich in our extracts.
Conclusions
Findings of this study demonstrated significant antiproliferative and antitumorigenic properties of saffron in osteosarcoma.
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Affiliation(s)
- Bilal Ege
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Adiyaman University, Adiyaman, Turkey
| | - Onder Yumrutas
- Department of Medical Biology, Faculty of Medicine, Adiyaman University, Adiyaman, Turkey
| | - Miray Ege
- Department of Pharmacognosy, Faculty of Pharmacy, Adiyaman University, Adiyaman, Turkey
| | - Mustafa Pehlivan
- Department of Medical and Aromatic Plants, Nurdagi Vocational Higher School, Gaziantep University, Gaziantep, Turkey
| | - Ibrahim Bozgeyik
- Department of Medical Biology, Faculty of Medicine, Adiyaman University, Adiyaman, Turkey
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20
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Zia S, Shahid R. Mutagenic players in ALL progression and their associated signaling pathways. Cancer Genet 2019; 233-234:7-20. [DOI: 10.1016/j.cancergen.2019.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 02/10/2019] [Accepted: 02/25/2019] [Indexed: 12/19/2022]
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