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Digital PCR: A Reliable Tool for Analyzing and Monitoring Hematologic Malignancies.

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.

SUBMITTER: Coccaro N

PROVIDER: S-EPMC7247671 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

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Digital PCR: A Reliable Tool for Analyzing and Monitoring Hematologic Malignancies.

Coccaro Nicoletta N Tota Giuseppina G Anelli Luisa L Zagaria Antonella A Specchia Giorgina G Albano Francesco F

International journal of molecular sciences 20200429 9

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 seri ...[more]

PMID: 32365599

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Project description:Patient-reported outcomes (PROs) are an emerging paradigm in clinical research and healthcare, aiming to capture the patient's self-assessed health status in order to gauge efficacy of treatment from their perspective. As these patient-generated health data provide insights into the effects of healthcare processes in real-life settings beyond the clinical setting, they can also be viewed as a resolution beyond what can be gleaned directly by the clinician. To this end, patients are identified as a key stakeholder of the healthcare decision making process, instead of passively following their doctor's guidance. As this joint decision-making process requires constant and high-quality communication between the patient and his/her healthcare providers, novel methodologies and tools have been proposed to promote richer and preemptive communication to facilitate earlier recognition of potential complications. To this end, as PROs can be used to quantify the patient impact (especially important for chronic conditions such as cancer), they can play a prominent role in providing patient-centric care. In this paper, we introduce the MyPal platform that aims to support adults suffering from hematologic malignancies, focusing on the technical design and highlighting the respective challenges. MyPal is a Horizon 2020 European project aiming to support palliative care for cancer patients via the electronic PROs (ePROs) paradigm, building upon modern eHealth technologies. To this end, MyPal project evaluate the proposed eHealth intervention via clinical studies and assess its potential impact on the provided palliative care. More specifically, MyPal platform provides specialized applications supporting the regular answering of well-defined and standardized questionnaires, spontaneous symptoms reporting, educational material provision, notifications etc. The presented platform has been validated by end-users and is currently in the phase of pilot testing in a clinical study to evaluate its feasibility and its potential impact on the quality of life of palliative care patients with hematologic malignancies.

Project description:BACKGROUND:Alu repeats, belonging to the Short Interspersed Repetitive Elements (SINEs) class, contain about 25% of CpG sites in the human genome. Alu sequences lie in gene-rich regions, so their methylation is an important transcriptional regulation mechanism. Aberrant Alu methylation has been associated with tumor aggressiveness, and also previously discussed in hematological malignancies, by applying different approaches. Moreover, today different techniques designed to measure global DNA methylation are focused on the methylation level of specific repeat elements. In this work we propose a new method of investigating Alu differential methylation, based on droplet digital PCR (ddPCR) technology. METHODS:Forty-six patients with hematological neoplasms were included in the study: 30 patients affected by chronic lymphocytic leukemia, 7 patients with myelodysplastic syndromes at intermediate/high risk, according with the International Prognostic Scoring System, and 9 patients with myelomonocytic leukemia. Ten healthy donors were included as controls. Acute promyelocytic leukemia-derived NB4 cell line, either untreated or treated with decitabine (DEC) hypomethylating agent, was also analyzed. DNA samples were investigated for Alu methylation level by digestion of genomic DNA with isoschizomers with differential sensitivity to DNA methylation, followed by ddPCR. RESULTS:Using ddPCR, a significant decrease of the global Alu methylation level in DNA extracted from NB4 cells treated with DEC, as compared to untreated cells, was observed. Moreover, comparing the global Alu methylation levels at diagnosis and after azacytidine (AZA) treatment in MDS patients, a statistically significant decrease of Alu sequences methylation after therapy as compared to diagnosis was evident. We also observed a significant decrease of the Alu methylation level in CLL patients compared to HD, and, finally, for CMML patients, a decrease of Alu sequences methylation was observed in patients harboring the SRSF2 hotspot gene mutation c.284C>D. CONCLUSIONS:In our work, we propose a method to investigate Alu differential methylation based on ddPCR technology. This assay introduces ddPCR as a more sensitive and immediate technique for Alu methylation analysis. To date, this is the first application of ddPCR to study DNA repetitive elements. This approach may be useful to profile patients affected by hematologic malignancies for diagnostic/prognostic purpose.

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Dataset Information

Digital PCR: A Reliable Tool for Analyzing and Monitoring Hematologic Malignancies.

Publications

Digital PCR: A Reliable Tool for Analyzing and Monitoring Hematologic Malignancies.

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