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Pessoa FMCDP, Machado CB, Barreto IV, Sampaio GF, Oliveira DDS, Ribeiro RM, Lopes GS, de Moraes MEA, de Moraes Filho MO, de Souza LEB, Khayat AS, Moreira-Nunes CA. Association between Immunophenotypic Parameters and Molecular Alterations in Acute Myeloid Leukemia. Biomedicines 2023; 11:biomedicines11041098. [PMID: 37189716 DOI: 10.3390/biomedicines11041098] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/17/2023] [Accepted: 03/23/2023] [Indexed: 04/08/2023] Open
Abstract
Acute myeloid leukemia (AML) is a hematologic malignancy that occurs due to alterations such as genetic mutations, chromosomal translocations, or changes in molecular levels. These alterations can accumulate in stem cells and hematopoietic progenitors, leading to the development of AML, which has a prevalence of 80% of acute leukemias in the adult population. Recurrent cytogenetic abnormalities, in addition to mediating leukemogenesis onset, participate in its evolution and can be used as established diagnostic and prognostic markers. Most of these mutations confer resistance to the traditionally used treatments and, therefore, the aberrant protein products are also considered therapeutic targets. The surface antigens of a cell are characterized through immunophenotyping, which has the ability to identify and differentiate the degrees of maturation and the lineage of the target cell, whether benign or malignant. With this, we seek to establish a relationship according to the molecular aberrations and immunophenotypic alterations that cells with AML present.
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Affiliation(s)
- Flávia Melo Cunha de Pinho Pessoa
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil
| | - Caio Bezerra Machado
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil
| | - Igor Valentim Barreto
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil
| | - Giulia Freire Sampaio
- Unichristus University Center, Faculty of Biomedicine, Fortaleza 60430-275, CE, Brazil
| | | | | | - Germison Silva Lopes
- Department of Hematology, César Cals General Hospital, Fortaleza 60015-152, CE, Brazil
| | - Maria Elisabete Amaral de Moraes
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil
| | - Manoel Odorico de Moraes Filho
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil
| | - Lucas Eduardo Botelho de Souza
- Center for Cell-Based Therapy, Regional Blood Center of Ribeirão Preto, University of São Paulo, São Paulo 14040-900, SP, Brazil
| | - André Salim Khayat
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil
| | - Caroline Aquino Moreira-Nunes
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil
- Unichristus University Center, Faculty of Biomedicine, Fortaleza 60430-275, CE, Brazil
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil
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Pan-cancer landscape of the RUNX protein family reveals their potential as carcinogenic biomarkers and the mechanisms underlying their action. J Transl Int Med 2022; 10:156-174. [PMID: 35959452 PMCID: PMC9328034 DOI: 10.2478/jtim-2022-0013] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Background
The RUNX family of transcription factors plays an important regulatory role in tumor development. Although the importance of RUNX in certain cancer types is well known, the pan-cancer landscape remains unclear.
Materials and Methods
Data from The Cancer Genome Atlas (TCGA) provides a pan-cancer overview of the RUNX genes. Hence, herein, we performed a pan-cancer analysis of abnormal RUNX expression and deciphered the potential regulatory mechanism. Specifically, we used TCGA multi-omics data combined with multiple online tools to analyze transcripts, genetic alterations, DNA methylation, clinical prognoses, miRNA networks, and potential target genes.
Results
RUNX genes are consistently overexpressed in esophageal, gastric, pancreatic, and pan-renal cancers. The total protein expression of RUNX1 in lung adenocarcinoma, kidney renal clear cell carcinoma (KIRC), and uterine corpus endometrial carcinoma (UCEC) is consistent with the mRNA expression results. Moreover, increased phosphorylation on the T14 and T18 residues of RUNX1 may represent potential pathogenic factors. The RUNX genes are significantly associated with survival in pan-renal cancer, brain lower-grade glioma, and uveal melanoma. Meanwhile, various mutations and posttranscriptional changes, including the RUNX1 D96 mutation in invasive breast carcinoma, the co-occurrence of RUNX gene mutations in UCEC, and methylation changes in the RUNX2 promoter in KIRC, may be associated with cancer development. Finally, analysis of epigenetic regulator co-expression, miRNA networks, and target genes revealed the carcinogenicity, abnormal expression, and direct regulation of RUNX genes.
Conclusions
We successfully analyzed the pan-cancer abnormal expression and prognostic value of RUNX genes, thereby providing potential biomarkers for various cancers. Further, mutations revealed via genetic alteration analysis may serve as a basis for personalized patient therapies.
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Kiani-Zadeh M, Rezvany MR, Namjoo S, Barati M, Mohammadi MH, Ghasemi B, Tabatabaei T, Ghavamzadeh A, Zaker F, Teimoori-Toolabi L. Studying the potential of upregulated PTGS2 and VEGF-C besides hyper-methylation of PTGS2 promoter as biomarkers of Acute myeloid leukemia. Mol Biol Rep 2022; 49:7849-7862. [PMID: 35733068 DOI: 10.1007/s11033-022-07615-7] [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: 06/12/2021] [Revised: 04/27/2022] [Accepted: 05/18/2022] [Indexed: 11/29/2022]
Abstract
Hereby, we aimed to investigate the expression of prostaglandin-endoperoxide synthase 2 (PTGS2) and Vascular Endothelial Factor-C (VEGF-C) besides the methylation of PTGS2 in AML patients. VEGF-C and PTGS2 expression analysis were evaluated in newly diagnosed AML patients and healthy controls by quantitative Reverse Transcriptase PCR method. Also, PTGS2 methylation status was evaluated by Methylation-Sensitive High-Resolution Melting Curve Analysis (MS-HRM). While 34% of patients were female, the mean age of the patients was 43.41 ± 17.60 years suffering mostly from M4 (48.21%) type of AML. Although methylation level between patients and controls was not significantly different, none of the normal controls showed methylation in the PTGS2 promoter. PTGS2 and VEGF-C levels were elevated in AML cases and correlated with WBC, Platelet, and Hemoglobin levels. The survival of patients with overexpressed VEGF-C and PTGS2 was poorer than others. It can be concluded that PTGS2 and especially VEGF-C expression but not PTGS2 methylation can be considered as diagnostic biomarkers for AML.
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Affiliation(s)
- Masoumeh Kiani-Zadeh
- Department of Hematology and Blood Transfusion, School of Allied Medical Sciences, University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Rezvany
- Department of Hematology and Blood Transfusion, School of Allied Medical Sciences, University of Medical Sciences, Tehran, Iran.,Pediatric Growth and Development Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences, Tehran, Iran.,Department of Oncology-Pathology, Immune and Gene Therapy Lab, Cancer Center Karolinska (CCK), Karolinska University Hospital Solna and Karolinska Institute, 17176, Stockholm, Sweden
| | - Soodeh Namjoo
- Department of Hematology and Blood Transfusion, School of Allied Medical Sciences, University of Medical Sciences, Tehran, Iran.,Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mahmood Barati
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Hossein Mohammadi
- Department of HSCT research center, Laboratory Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bahare Ghasemi
- Department of Hematology and Blood Transfusion, School of Allied Medical Sciences, University of Medical Sciences, Tehran, Iran
| | - Tahere Tabatabaei
- Department of Hematology and Blood Transfusion, School of Allied Medical Sciences, University of Medical Sciences, Tehran, Iran
| | - Ardeshir Ghavamzadeh
- Department of Hematology, Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Science, Tehran, Iran
| | - Farhad Zaker
- Department of Hematology and Blood Transfusion, School of Allied Medical Sciences, University of Medical Sciences, Tehran, Iran. .,Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran. .,Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, 69th Pasteur Street Kargar Avenue, 1316943551, Tehran, Iran.
| | - Ladan Teimoori-Toolabi
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
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Lin TC. RUNX1 and cancer. Biochim Biophys Acta Rev Cancer 2022; 1877:188715. [DOI: 10.1016/j.bbcan.2022.188715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 03/02/2022] [Accepted: 03/02/2022] [Indexed: 10/18/2022]
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Park S, Lee C, Ku BM, Kim M, Park WY, Kim NKD, Ahn MJ. Paired analysis of tumor mutation burden calculated by targeted deep sequencing panel and whole exome sequencing in non-small cell lung cancer. BMB Rep 2021. [PMID: 34154699 PMCID: PMC8328823 DOI: 10.5483/bmbrep.2021.54.7.045] [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] [Indexed: 01/10/2023] Open
Abstract
Owing to rapid advancements in NGS (next generation sequen-cing), genomic alteration is now considered an essential pre-dictive biomarkers that impact the treatment decision in many cases of cancer. Among the various predictive biomarkers, tumor mutation burden (TMB) was identified by NGS and was con-sidered to be useful in predicting a clinical response in cancer cases treated by immunotherapy. In this study, we directly com-pared the lab-developed-test (LDT) results by target sequencing panel, K-MASTER panel v3.0 and whole-exome sequencing (WES) to evaluate the concordance of TMB. As an initial step, the reference materials (n = 3) with known TMB status were used as an exploratory test. To validate and evaluate TMB, we used one hundred samples that were acquired from surgically resected tissues of non-small cell lung cancer (NSCLC) patients. The TMB of each sample was tested by using both LDT and WES methods, which extracted the DNA from samples at the same time. In addition, we evaluated the impact of capture re-gion, which might lead to different values of TMB; the evalu-ation of capture region was based on the size of NGS and target sequencing panels. In this pilot study, TMB was evalu-ated by LDT and WES by using duplicated reference samples; the results of TMB showed high concordance rate (R2 = 0.887). This was also reflected in clinical samples (n = 100), which showed R2 of 0.71. The difference between the coding sequence ratio (3.49%) and the ratio of mutations (4.8%) indicated that the LDT panel identified a relatively higher number of mutations. It was feasible to calculate TMB with LDT panel, which can be useful in clinical practice. Furthermore, a customized approach must be developed for calculating TMB, which differs according to cancer types and specific clinical settings.
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Affiliation(s)
- Sehhoon Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Chung Lee
- Geninus Inc., Seoul 05836, 3Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea
| | - Bo Mi Ku
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Minjae Kim
- Geninus Inc., Seoul 05836, 3Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea
| | - Woong-Yang Park
- Geninus Inc., Seoul 05836, 3Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea
| | - Nayoung K. D. Kim
- Geninus Inc., Seoul 05836, 3Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea
| | - Myung-Ju Ahn
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
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Gene Transcription as a Therapeutic Target in Leukemia. Int J Mol Sci 2021; 22:ijms22147340. [PMID: 34298959 PMCID: PMC8304797 DOI: 10.3390/ijms22147340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/02/2021] [Accepted: 07/05/2021] [Indexed: 12/11/2022] Open
Abstract
Blood malignancies often arise from undifferentiated hematopoietic stem cells or partially differentiated stem-like cells. A tight balance of multipotency and differentiation, cell division, and quiescence underlying normal hematopoiesis requires a special program governed by the transcriptional machinery. Acquisition of drug resistance by tumor cells also involves reprogramming of their transcriptional landscape. Limiting tumor cell plasticity by disabling reprogramming of the gene transcription is a promising strategy for improvement of treatment outcomes. Herein, we review the molecular mechanisms of action of transcription-targeted drugs in hematological malignancies (largely in leukemia) with particular respect to the results of clinical trials.
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Liu S, Zhang Y, Huang C, Lin S. miR‐215‐5p is an anticancer gene in multiple myeloma by targeting RUNX1 and deactivating the PI3K/AKT/mTOR pathway. J Cell Biochem 2019; 121:1475-1490. [PMID: 31498483 DOI: 10.1002/jcb.29383] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 08/13/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Shuyan Liu
- Department of Hematology, Zhejiang Provincial Hospital of Traditional Chinese Medical The First Affiliated Hospital of Zhejiang Chinese Medical University Hangzhou Zhejiang China
| | - Yun Zhang
- Department of Hematology, Zhejiang Provincial Hospital of Traditional Chinese Medical The First Affiliated Hospital of Zhejiang Chinese Medical University Hangzhou Zhejiang China
| | - Chang Huang
- Department of Hematology Zhejiang Hospital Hangzhou Zhejiang China
| | - Shengyun Lin
- Department of Hematology, Zhejiang Provincial Hospital of Traditional Chinese Medical The First Affiliated Hospital of Zhejiang Chinese Medical University Hangzhou Zhejiang China
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