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Cumbo C, Orsini P, Anelli L, Zagaria A, Iannò MF, De Cecco L, Minervini CF, Coccaro N, Tota G, Parciante E, Conserva MR, Redavid I, Tarantini F, Minervini A, Carluccio P, De Grassi A, Pierri CL, Specchia G, Musto P, Albano F. Case report: biallelic DNMT3A mutations in acute myeloid leukemia. Front Oncol 2023; 13:1205220. [PMID: 37448520 PMCID: PMC10336536 DOI: 10.3389/fonc.2023.1205220] [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: 04/13/2023] [Accepted: 06/09/2023] [Indexed: 07/15/2023] Open
Abstract
DNMT3A gene mutations, detected in 20-25% of de novo acute myeloid leukemia (AML) patients, are typically heterozygous. Biallelic variants are uncommon, affecting ~3% of cases and identifying a worse prognosis. Indeed, two concomitant DNMT3A mutations were recently associated with shorter event-free survival and overall survival in AML. We present an AML case bearing an unusual DNMT3A molecular status, strongly affecting its function and strangely impacting the global genomic methylation profile. A 56-year-old Caucasian male with a diagnosis of AML not otherwise specified (NOS) presented a complex DNMT3A molecular profile consisting of four different somatic variants mapping on different alleles (in trans). 3D modelling analysis predicted the effect of the DNMT3A mutational status, showing that all the investigated mutations decreased or abolished DNMT3A activity. Although unexpected, DNMT3A's severe loss of function resulted in a global genomic hypermethylation in genes generally involved in cell differentiation. The mechanisms through which DNMT3A contributes to AML remain elusive. We present a unique AML case bearing multiple biallelic DNMT3A variants abolishing its activity and resulting in an unexpected global hypermethylation. The unusual DNMT3A behavior described requires a reflection on its role in AML development and persistence, highlighting the heterogeneity of its deregulation.
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Affiliation(s)
- Cosimo Cumbo
- Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), Hematology and Stem Cell Transplantation Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Paola Orsini
- Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), Hematology and Stem Cell Transplantation Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Luisa Anelli
- Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), Hematology and Stem Cell Transplantation Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Antonella Zagaria
- Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), Hematology and Stem Cell Transplantation Unit, University of Bari "Aldo Moro", Bari, Italy
| | | | - Loris De Cecco
- Molecular Mechanisms Unit, Department of Research Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Crescenzio Francesco Minervini
- Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), Hematology and Stem Cell Transplantation Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Nicoletta Coccaro
- Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), Hematology and Stem Cell Transplantation Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Giuseppina Tota
- Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), Hematology and Stem Cell Transplantation Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Elisa Parciante
- Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), Hematology and Stem Cell Transplantation Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Maria Rosa Conserva
- Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), Hematology and Stem Cell Transplantation Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Immacolata Redavid
- Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), Hematology and Stem Cell Transplantation Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Francesco Tarantini
- Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), Hematology and Stem Cell Transplantation Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Angela Minervini
- Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), Hematology and Stem Cell Transplantation Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Paola Carluccio
- Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), Hematology and Stem Cell Transplantation Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Anna De Grassi
- Laboratory of Biochemistry, Molecular and Computational Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - Ciro Leonardo Pierri
- Laboratory of Biochemistry, Molecular and Computational Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | | | - Pellegrino Musto
- Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), Hematology and Stem Cell Transplantation Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Francesco Albano
- Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), Hematology and Stem Cell Transplantation Unit, University of Bari "Aldo Moro", Bari, Italy
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Galimberti S, Balducci S, Guerrini F, Del Re M, Cacciola R. Digital Droplet PCR in Hematologic Malignancies: A New Useful Molecular Tool. Diagnostics (Basel) 2022; 12:1305. [PMID: 35741115 PMCID: PMC9221914 DOI: 10.3390/diagnostics12061305] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/21/2022] [Accepted: 05/22/2022] [Indexed: 01/27/2023] Open
Abstract
Digital droplet PCR (ddPCR) is a recent version of quantitative PCR (QT-PCR), useful for measuring gene expression, doing clonality assays and detecting hot spot mutations. In respect of QT-PCR, ddPCR is more sensitive, does not need any reference curve and can quantify one quarter of samples already defined as "positive but not quantifiable". In the IgH and TCR clonality assessment, ddPCR recapitulates the allele-specific oligonucleotide PCR (ASO-PCR), being not adapt for detecting clonal evolution, that, on the contrary, does not represent a pitfall for the next generation sequencing (NGS) technique. Differently from NGS, ddPCR is not able to sequence the whole gene, but it is useful, cheaper, and less time-consuming when hot spot mutations are the targets, such as occurs with IDH1, IDH2, NPM1 in acute leukemias or T315I mutation in Philadelphia-positive leukemias or JAK2 in chronic myeloproliferative neoplasms. Further versions of ddPCR, that combine different primers/probes fluorescences and concentrations, allow measuring up to four targets in the same PCR reaction, sparing material, time, and money. ddPCR is also useful for quantitating BCR-ABL1 fusion gene, WT1 expression, donor chimerism, and minimal residual disease, so helping physicians to realize that "patient-tailored therapy" that is the aim of the modern hematology.
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Affiliation(s)
- Sara Galimberti
- Department of Clinical and Experimental Medicine, Section of Hematology, University of Pisa, 56126 Pisa, Italy; (S.G.); (S.B.); (F.G.); (M.D.R.)
| | - Serena Balducci
- Department of Clinical and Experimental Medicine, Section of Hematology, University of Pisa, 56126 Pisa, Italy; (S.G.); (S.B.); (F.G.); (M.D.R.)
| | - Francesca Guerrini
- Department of Clinical and Experimental Medicine, Section of Hematology, University of Pisa, 56126 Pisa, Italy; (S.G.); (S.B.); (F.G.); (M.D.R.)
| | - Marzia Del Re
- Department of Clinical and Experimental Medicine, Section of Hematology, University of Pisa, 56126 Pisa, Italy; (S.G.); (S.B.); (F.G.); (M.D.R.)
| | - Rossella Cacciola
- Department of Clinical and Experimental Medicine, Section of Hemostasis, University of Catania, 95123 Catania, Italy
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Ho Lee M, Hee Hwang J, Min Seong K, Jin Ahn J, Jun Kim S, Yong Hwang S, Lim SK. Application of droplet digital PCR method for DNA methylation-based age prediction from saliva. Leg Med (Tokyo) 2021; 54:101992. [PMID: 34814096 DOI: 10.1016/j.legalmed.2021.101992] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/12/2021] [Accepted: 11/11/2021] [Indexed: 10/19/2022]
Abstract
The recent studies reported that DNA methylation markers show changes with age, and expected that the DNA methylation markers can be effectively used for estimation of age in forensic genetics. In this study, we applied droplet digital PCR (ddPCR) method to investigate the DNA methylation pattern in the CpG sites, and we constructed an age prediction model based on the ddPCR method. The ddPCR is capable of highly sensitive quantitation of nucleic acid and detection of sequence variations in gene by separating the sample into large number of partitions and clonally amplifying nucleic acids in each partition. We extracted DNA from saliva samples collected from several age groups. The DNA was bisulfite converted and subjected to ddPCR using specifically designed primers and probes. The methylation ratio of each sample was calculated and correlation between the methylation ratio and the chronological age was analyzed. In the results, methylated DNA ratio at the 4 CpG sites (cg14361627, cg14361627, cg08928145 and cg07547549) showed strong correlation with chronological age. Percent-methylation values at 4 CpG markers and chronological ages of the 76 individuals were analyzed by multiple regression analysis, and we constructed an age prediction model. We observed a strong correlation (Spearman's rho = 0.922) between predicted and chronological ages of 76 individuals with a MAD from chronological age of 3.3 years. Collectively, the result in this study showed the potential applicability of ddPCR to predict age from saliva.
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Affiliation(s)
- Min Ho Lee
- Forensic DNA Division, National Forensic Service, Wonju, Gangwon-do, South Korea
| | - Jung Hee Hwang
- DNA Analysis Division, National Forensic Service Daejeon Institute, Daejeon, South Korea
| | - Ki Min Seong
- Forensic DNA Division, National Forensic Service, Wonju, Gangwon-do, South Korea
| | | | | | - Seung Yong Hwang
- Department of Bio-Nanotechnology, Hanyang University, Ansan, Gyeonggi-do, South Korea
| | - Si-Keun Lim
- Department of Forensic Sciences, Graduate School of Sungkyunkwan University, Suwon, Gyeongi-do, South Korea.
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Olmedillas-López S, Olivera-Salazar R, García-Arranz M, García-Olmo D. Current and Emerging Applications of Droplet Digital PCR in Oncology: An Updated Review. Mol Diagn Ther 2021; 26:61-87. [PMID: 34773243 DOI: 10.1007/s40291-021-00562-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2021] [Indexed: 12/14/2022]
Abstract
In the era of personalized medicine and targeted therapies for the management of patients with cancer, ultrasensitive detection methods for tumor genotyping, such as next-generation sequencing or droplet digital polymerase chain reaction (ddPCR), play a significant role. In the search for less invasive strategies for diagnosis, prognosis and disease monitoring, the number of publications regarding liquid biopsy approaches using ddPCR has increased substantially in recent years. There is a long list of malignancies in which ddPCR provides a reliable and accurate tool for detection of nucleic acid-based markers derived from cell-free DNA, cell-free RNA, circulating tumor cells, extracellular vesicles or exosomes when isolated from whole blood, plasma and serum, helping to anticipate tumor relapse or unveil intratumor heterogeneity and clonal evolution in response to treatment. This updated review describes recent developments in ddPCR platforms and provides a general overview about the major applications of liquid biopsy in blood, including its utility for molecular response and minimal residual disease monitoring in hematological malignancies or the therapeutic management of patients with colorectal or lung cancer, particularly for the selection and monitoring of treatment with tyrosine kinase inhibitors. Although plasma is the main source of genetic material for tumor genomic profiling, liquid biopsy by ddPCR is being investigated in a wide variety of biologic fluids, such as cerebrospinal fluid, urine, stool, ocular fluids, sputum, saliva, bronchoalveolar lavage, pleural effusion, mucin, peritoneal fluid, fine needle aspirate, bile or pancreatic juice. The present review focuses on these "alternative" sources of genetic material and their analysis by ddPCR in different kinds of cancers.
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Affiliation(s)
- Susana Olmedillas-López
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Avda. Reyes Católicos, 2, 28040, Madrid, Spain.
| | - Rocío Olivera-Salazar
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Avda. Reyes Católicos, 2, 28040, Madrid, Spain
| | - Mariano García-Arranz
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Avda. Reyes Católicos, 2, 28040, Madrid, Spain.,Department of Surgery, School of Medicine, Universidad Autónoma de Madrid (UAM), 28029, Madrid, Spain
| | - Damián García-Olmo
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Avda. Reyes Católicos, 2, 28040, Madrid, Spain.,Department of Surgery, School of Medicine, Universidad Autónoma de Madrid (UAM), 28029, Madrid, Spain.,Department of Surgery, Fundación Jiménez Díaz University Hospital (FJD), 28040, Madrid, Spain
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Coccaro N, Tota G, Anelli L, Zagaria A, Specchia G, Albano F. Digital PCR: A Reliable Tool for Analyzing and Monitoring Hematologic Malignancies. Int J Mol Sci 2020; 21:ijms21093141. [PMID: 32365599 PMCID: PMC7247671 DOI: 10.3390/ijms21093141] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 02/06/2023] Open
Abstract
The digital polymerase chain reaction (dPCR) is considered to be the third-generation polymerase chain reaction (PCR), as it yields direct, absolute and precise measures of target sequences. dPCR has proven particularly useful for the accurate detection and quantification of low-abundance nucleic acids, highlighting its advantages in cancer diagnosis and in predicting recurrence and monitoring minimal residual disease, mostly coupled with next generation sequencing. In the last few years, a series of studies have employed dPCR for the analysis of hematologic malignancies. In this review, we will summarize these findings, attempting to focus on the potential future perspectives of the application of this promising technology.
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Affiliation(s)
| | | | | | | | | | - Francesco Albano
- Correspondence: ; Tel.: +39-(0)80-5478031; Fax: +39-(0)80-5508369
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