1
|
Li F, Liu J, Maldonado-Gómez MX, Frese SA, Gänzle MG, Walter J. Highly accurate and sensitive absolute quantification of bacterial strains in human fecal samples. MICROBIOME 2024; 12:168. [PMID: 39244633 PMCID: PMC11380787 DOI: 10.1186/s40168-024-01881-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 07/26/2024] [Indexed: 09/09/2024]
Abstract
BACKGROUND Next-generation sequencing (NGS) approaches have revolutionized gut microbiome research and can provide strain-level resolution, but these techniques have limitations in that they are only semi-quantitative, suffer from high detection limits, and generate data that is compositional. The present study aimed to systematically compare quantitative PCR (qPCR) and droplet digital PCR (ddPCR) for the absolute quantification of Limosilactobacillus reuteri strains in human fecal samples and to develop an optimized protocol for the absolute quantification of bacterial strains in fecal samples. RESULTS Using strain-specific PCR primers for L. reuteri 17938, ddPCR showed slightly better reproducibility, but qPCR was almost as reproducible and showed comparable sensitivity (limit of detection [LOD] around 104 cells/g feces) and linearity (R2 > 0.98) when kit-based DNA isolation methods were used. qPCR further had a wider dynamic range and is cheaper and faster. Based on these findings, we conclude that qPCR has advantages over ddPCR for the absolute quantification of bacterial strains in fecal samples. We provide an optimized and easy-to-follow step-by-step protocol for the design of strain-specific qPCR assays, starting from primer design from genome sequences to the calibration of the PCR system. Validation of this protocol to design PCR assays for two L. reuteri strains, PB-W1 and DSM 20016 T, resulted in a highly accurate qPCR with a detection limit in spiked fecal samples of around 103 cells/g feces. Applying our strain-specific qPCR assays to fecal samples collected from human subjects who received live L. reuteri PB-W1 or DSM 20016 T during a human trial demonstrated a highly accurate quantification and sensitive detection of these two strains, with a much lower LOD and a broader dynamic range compared to NGS approaches (16S rRNA gene sequencing and whole metagenome sequencing). CONCLUSIONS Based on our analyses, we consider qPCR with kit-based DNA extraction approaches the best approach to accurately quantify gut bacteria at the strain level in fecal samples. The provided step-by-step protocol will allow scientists to design highly sensitive strain-specific PCR systems for the accurate quantification of bacterial strains of not only L. reuteri but also other bacterial taxa in a broad range of applications and sample types. Video Abstract.
Collapse
Affiliation(s)
- Fuyong Li
- Department of Animal Science and Technology, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2E1, Canada.
| | - Junhong Liu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | | | - Steven A Frese
- Department of Nutrition, University of Nevada, Reno, NV, 89557, USA
| | - Michael G Gänzle
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Jens Walter
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2E1, Canada.
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E1, Canada.
- School of Microbiology, Department of Medicine, and APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland.
| |
Collapse
|
2
|
Chea M, Rigolot L, Canali A, Vergez F. Minimal Residual Disease in Acute Myeloid Leukemia: Old and New Concepts. Int J Mol Sci 2024; 25:2150. [PMID: 38396825 PMCID: PMC10889505 DOI: 10.3390/ijms25042150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/01/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Minimal residual disease (MRD) is of major importance in onco-hematology, particularly in acute myeloid leukemia (AML). MRD measures the amount of leukemia cells remaining in a patient after treatment, and is an essential tool for disease monitoring, relapse prognosis, and guiding treatment decisions. Patients with a negative MRD tend to have superior disease-free and overall survival rates. Considerable effort has been made to standardize MRD practices. A variety of techniques, including flow cytometry and molecular methods, are used to assess MRD, each with distinct strengths and weaknesses. MRD is recognized not only as a predictive biomarker, but also as a prognostic tool and marker of treatment efficacy. Expected advances in MRD assessment encompass molecular techniques such as NGS and digital PCR, as well as optimization strategies such as unsupervised flow cytometry analysis and leukemic stem cell monitoring. At present, there is no perfect method for measuring MRD, and significant advances are expected in the future to fully integrate MRD assessment into the management of AML patients.
Collapse
Affiliation(s)
- Mathias Chea
- Laboratoire d’Hématologie Biologique, Institut Universitaire du Cancer de Toulouse Oncopole, Centre Hospitalier Universitaire de Toulouse, 31059 Toulouse, France; (M.C.); (L.R.); (A.C.)
| | - Lucie Rigolot
- Laboratoire d’Hématologie Biologique, Institut Universitaire du Cancer de Toulouse Oncopole, Centre Hospitalier Universitaire de Toulouse, 31059 Toulouse, France; (M.C.); (L.R.); (A.C.)
- School of Medicine, Université Toulouse III Paul Sabatier, 31062 Toulouse, France
| | - Alban Canali
- Laboratoire d’Hématologie Biologique, Institut Universitaire du Cancer de Toulouse Oncopole, Centre Hospitalier Universitaire de Toulouse, 31059 Toulouse, France; (M.C.); (L.R.); (A.C.)
- School of Medicine, Université Toulouse III Paul Sabatier, 31062 Toulouse, France
| | - Francois Vergez
- Laboratoire d’Hématologie Biologique, Institut Universitaire du Cancer de Toulouse Oncopole, Centre Hospitalier Universitaire de Toulouse, 31059 Toulouse, France; (M.C.); (L.R.); (A.C.)
- School of Medicine, Université Toulouse III Paul Sabatier, 31062 Toulouse, France
| |
Collapse
|
3
|
Zhou K, Gong D, He C, Xiao M, Zhang M, Huang W. Targeted therapy using larotrectinib and venetoclax for the relapsed/refractory T-cell acute lymphoblastic leukemia harboring a cryptic ETV6-NTRK3 fusion. Mol Carcinog 2023. [PMID: 37036164 DOI: 10.1002/mc.23534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/17/2023] [Indexed: 04/11/2023]
Abstract
Outcomes for patients with relapsed and refractory (R/R) T-cell acute lymphoblastic leukemia (T-ALL) after allogeneic hematopoietic stem cell transplantation (allo-HSCT) are dismal, with few available treatments. Recently, identification of cancer patients harboring neurotrophic tropomyosin receptor kinase (NTRK) gene fusions is constantly increasing, especially with the advent of NTRK inhibitors. However, the role of ETV6-NTRK3 in T-ALL has not been investigated. This case represented the first detailed report of T-ALL patient harboring a cryptic ETV6-NTRK3 fusion with an unfavorable prognosis, not only because of leukemia resistant to the standard multiagent chemotherapy but also early relapse after allo-HSCT. Acquired EP300 mutation was found at relapse, which could explain the cause of recurrence and affect the follow-up treatment. Combined targeted therapy like larotrectinib allied with pan-targeted BCL-2 inhibitor venetoclax, may be a potential maintenance treatment in R/R ETV6-NTRK3 positive leukemia after allo-HSCT. The leukemic clonal evolution might be revealed through transcriptome sequencing and overcome by drugs with universal targets. Our case demonstrated that both comprehensive profiling techniques (such as transcriptome sequencing, multiparameter flow cytometry, and digital droplet polymerase chain reaction) and a multimodality treatment strategy were critical for anticipating an early relapse and personalized therapy of R/R T-cell leukemia.
Collapse
Affiliation(s)
- Kuangguo Zhou
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Duanhao Gong
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Cheng He
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Min Xiao
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Meilan Zhang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Huang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|
4
|
Teixeira A, Carreira L, Abalde-Cela S, Sampaio-Marques B, Areias AC, Ludovico P, Diéguez L. Current and Emerging Techniques for Diagnosis and MRD Detection in AML: A Comprehensive Narrative Review. Cancers (Basel) 2023; 15:cancers15051362. [PMID: 36900154 PMCID: PMC10000116 DOI: 10.3390/cancers15051362] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/06/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
Acute myeloid leukemia (AML) comprises a group of hematologic neoplasms characterized by abnormal differentiation and proliferation of myeloid progenitor cells. AML is associated with poor outcome due to the lack of efficient therapies and early diagnostic tools. The current gold standard diagnostic tools are based on bone marrow biopsy. These biopsies, apart from being very invasive, painful, and costly, have low sensitivity. Despite the progress uncovering the molecular pathogenesis of AML, the development of novel detection strategies is still poorly explored. This is particularly important for patients that check the criteria for complete remission after treatment, since they can relapse through the persistence of some leukemic stem cells. This condition, recently named as measurable residual disease (MRD), has severe consequences for disease progression. Hence, an early and accurate diagnosis of MRD would allow an appropriate therapy to be tailored, improving a patient's prognosis. Many novel techniques with high potential in disease prevention and early detection are being explored. Among them, microfluidics has flourished in recent years due to its ability at processing complex samples as well as its demonstrated capacity to isolate rare cells from biological fluids. In parallel, surface-enhanced Raman scattering (SERS) spectroscopy has shown outstanding sensitivity and capability for multiplex quantitative detection of disease biomarkers. Together, these technologies can allow early and cost-effective disease detection as well as contribute to monitoring the efficiency of treatments. In this review, we aim to provide a comprehensive overview of AML disease, the conventional techniques currently used for its diagnosis, classification (recently updated in September 2022), and treatment selection, and we also aim to present how novel technologies can be applied to improve the detection and monitoring of MRD.
Collapse
Affiliation(s)
- Alexandra Teixeira
- International Iberian Nanotechnology Laboratory (INL), Avda Mestre José Veiga, 4715-310 Braga, Portugal
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057 Braga, Portugal
- ICVS/3B’s–PT Government Associate Laboratory, 4710-057 Braga, Portugal
| | - Luís Carreira
- International Iberian Nanotechnology Laboratory (INL), Avda Mestre José Veiga, 4715-310 Braga, Portugal
| | - Sara Abalde-Cela
- International Iberian Nanotechnology Laboratory (INL), Avda Mestre José Veiga, 4715-310 Braga, Portugal
| | - Belém Sampaio-Marques
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057 Braga, Portugal
- ICVS/3B’s–PT Government Associate Laboratory, 4710-057 Braga, Portugal
| | - Anabela C. Areias
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057 Braga, Portugal
- ICVS/3B’s–PT Government Associate Laboratory, 4710-057 Braga, Portugal
| | - Paula Ludovico
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057 Braga, Portugal
- ICVS/3B’s–PT Government Associate Laboratory, 4710-057 Braga, Portugal
- Correspondence: (P.L.); (L.D.)
| | - Lorena Diéguez
- International Iberian Nanotechnology Laboratory (INL), Avda Mestre José Veiga, 4715-310 Braga, Portugal
- Correspondence: (P.L.); (L.D.)
| |
Collapse
|
5
|
Schwinghammer C, Koopmann J, Chitadze G, Karawajew L, Brüggemann M, Eckert C. Droplet Digital PCR: A New View on Minimal Residual Disease Quantification in Acute Lymphoblastic Leukemia. J Mol Diagn 2022; 24:856-866. [PMID: 35691569 DOI: 10.1016/j.jmoldx.2022.04.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 03/05/2022] [Accepted: 04/06/2022] [Indexed: 11/27/2022] Open
Abstract
Real-time quantitative PCR (qPCR) using immunoglobulin/T-cell receptor gene rearrangements has been used as the gold standard for minimal residual disease (MRD) monitoring in acute lymphoblastic leukemia (ALL) for >20 years. Recently, new PCR-based technologies have emerged, such as droplet digital PCR (ddPCR), which could offer several methodologic advances for MRD monitoring. In the current work, qPCR and ddPCR were compared in an unbiased blinded prospective study (n = 88 measurements) and in a retrospective study with selected critical low positive samples (n = 65 measurements). The former included flow cytometry (Flow; n = 31 measurements) as a third MRD detection method. Published guidelines (qPCR) and the latest, revised evaluation criteria (ie, ddPCR, Flow) have been applied for data analysis. The prospective study shows that ddPCR outperforms qPCR with a significantly better quantitative limit of detection and sensitivity. The number of critical MRD estimates below quantitative limit was reduced by sixfold and by threefold in the retrospective and prospective cohorts, respectively. Furthermore, the concordance of quantitative values between ddPCR and Flow was higher than between ddPCR and qPCR, probably because ddPCR and Flow are absolute quantification methods independent of the diagnostic sample, unlike qPCR. In summary, our data highlight the advantages of ddPCR as a more precise and sensitive technology that could be used to refine response monitoring in ALL.
Collapse
Affiliation(s)
- Claudia Schwinghammer
- Department of Paediatric Oncology/Haematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Johannes Koopmann
- Department of Haematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Guranda Chitadze
- Department of Haematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Leonid Karawajew
- Department of Paediatric Oncology/Haematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Monika Brüggemann
- Department of Haematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Cornelia Eckert
- Department of Paediatric Oncology/Haematology, Charité-Universitätsmedizin Berlin, Berlin, Germany; German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany.
| |
Collapse
|
6
|
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: 14] [Impact Index Per Article: 7.0] [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.
Collapse
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
| |
Collapse
|
7
|
Datorre JG, de Carvalho AC, dos Reis MB, dos Reis M, Matsushita M, Santos F, Guimarães DP, Reis RM. Accuracy and Clinical Relevance of Intra-Tumoral Fusobacterium nucleatum Detection in Formalin-Fixed Paraffin-Embedded (FFPE) Tissue by Droplet Digital PCR (ddPCR) in Colorectal Cancer. Diagnostics (Basel) 2022; 12:114. [PMID: 35054281 PMCID: PMC8775036 DOI: 10.3390/diagnostics12010114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 11/02/2021] [Accepted: 11/02/2021] [Indexed: 12/24/2022] Open
Abstract
The use of droplet digital PCR (ddPCR) to identify and quantify low-abundance targets is a significant advantage for accurately detecting potentially oncogenic bacteria. Fusobacterium nucleatum (Fn) is implicated in colorectal cancer (CRC) tumorigenesis and is becoming an important prognostic biomarker. We evaluated the detection accuracy and clinical relevance of Fn DNA by ddPCR in a molecularly characterized, formalin-fixed, paraffin-embedded (FFPE) CRC cohort previously analyzed by qPCR for Fn levels. Following a ddPCR assay optimization and an analytical evaluation, Fn DNA were measured in 139 CRC FFPE cases. The measures of accuracy for Fn status compared to the prior results generated by qPCR and the association with clinicopathological and molecular patients' features were also evaluated. The ddPCR-based Fn assay was sensitive and specific to positive controls. Fn DNA were detected in 20.1% of cases and further classified as Fn-high and Fn-low/negative, according to the median amount of Fn DNA that were detected in all cases and associated with the patient's worst prognosis. There was a low agreement between the Fn status determined by ddPCR and qPCR (Cohen's Kappa = 0.210). Our findings show that ddPCR can detect and quantify Fn in FFPE tumor tissues and highlights its clinical relevance in Fn detection in a routine CRC setting.
Collapse
Affiliation(s)
- José Guilherme Datorre
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784400, Brazil; (J.G.D.); (A.C.d.C.); (M.B.d.R.); (D.P.G.)
| | - Ana Carolina de Carvalho
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784400, Brazil; (J.G.D.); (A.C.d.C.); (M.B.d.R.); (D.P.G.)
| | - Mariana Bisarro dos Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784400, Brazil; (J.G.D.); (A.C.d.C.); (M.B.d.R.); (D.P.G.)
| | - Monise dos Reis
- Department of Pathology, Barretos Cancer Hospital, Barretos 14784400, Brazil; (M.d.R.); (M.M.)
| | - Marcus Matsushita
- Department of Pathology, Barretos Cancer Hospital, Barretos 14784400, Brazil; (M.d.R.); (M.M.)
| | - Florinda Santos
- Department of Medical Oncology, Barretos Cancer Hospital, Barretos 14784400, Brazil;
| | - Denise Peixoto Guimarães
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784400, Brazil; (J.G.D.); (A.C.d.C.); (M.B.d.R.); (D.P.G.)
- Department of Prevention, Barretos Cancer Hospital, Barretos 14784400, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784400, Brazil; (J.G.D.); (A.C.d.C.); (M.B.d.R.); (D.P.G.)
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4704553 Braga, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, 4704553 Braga, Portugal
| |
Collapse
|
8
|
Lou Y, Chen C, Long X, Gu J, Xiao M, Wang D, Zhou X, Li T, Hong Z, Li C, Zhou J, Chen L. Detection and Quantification of Chimeric Antigen Receptor Transgene Copy Number by Droplet Digital PCR versus Real-Time PCR. J Mol Diagn 2021; 22:699-707. [PMID: 32409121 DOI: 10.1016/j.jmoldx.2020.02.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/01/2020] [Accepted: 02/10/2020] [Indexed: 12/30/2022] Open
Abstract
Chimeric antigen receptor (CAR) T-cell immunotherapy is a new strategy for the treatment of refractory B-cell malignancies; therefore, the rapid and accurate quantification of CAR transgene copy number is essential. Real-time PCR was used for quantifying the copy number of chimeric antigen receptor transgene. Droplet digital PCR (ddPCR) is an absolute quantification method that does not require a standard curve. In this study, key performance parameters of the ddPCR and real-time PCR methods were assessed, including linearity, detection range, the lower limit of detection, repeatability, reproducibility, and accuracy, using a series of gradient diluted standards and clinical peripheral blood samples from CAR T-cell patients. The two platforms showed a good correlation for the standards (Pearson R2 = 0.9966; P < 0.0001) and clinical samples (Pearson R2 = 0.8952; P < 0.0001), and both showed good linearity (R2 = 0.9996 for ddPCR; R2 = 0.9984 for real-time PCR) over the detection range. Compared with real-time PCR, ddPCR showed lower intra-assay and interassay CVs for the series of diluted standards, which indicated ddPCR has better repeatability and reproducibility. The limit of detection of ddPCR was lower compared with that of real-time PCR. The combined results suggest that ddPCR is a more promising tool for the detection and quantification of the chimeric antigen receptor transgene copy number.
Collapse
Affiliation(s)
- Yaoyao Lou
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Caixia Chen
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Xiaolu Long
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Jia Gu
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Min Xiao
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Di Wang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Xiaoxi Zhou
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Tongjuan Li
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Zhenya Hong
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Chunrui Li
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Jianfeng Zhou
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Liting Chen
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China.
| |
Collapse
|
9
|
Bai Y, Chen C, Guo X, Ding T, Yang X, Yu J, Yang J, Ruan J, Zheng X, Chen Z. miR-638 in circulating leukaemia cells as a non-invasive biomarker in diagnosis, treatment response and MRD surveillance of acute promyelocytic leukaemia. Cancer Biomark 2021; 29:125-137. [PMID: 32568176 DOI: 10.3233/cbm-190899] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND MicroRNA (miRNA) expression has been implicated in leukaemia. In recent years, miRNAs have been under investigation for their potential as non-invasive biomarkers in acute promyelocytic leukaemia (APL). We investigated whether miR-638 in circulating leukaemia cells is a non-invasive biomarker in diagnosis, assessment of the treatment response and minimal residual disease (MRD) surveillance of APL. METHODS Sixty cases of acute myeloid leukaemia (AML), including 30 cases of APL and 30 cases of non-APL AML, were selected. Thirty healthy controls were also selected. Bone marrow (BM) and peripheral blood (PB) samples were collected from APL patients at diagnosis and post-induction. Microarray analysis and quantitative real-time PCR (qRT-PCR) were performed for miRNA profiling and miR-638 expression analysis, respectively. For statistical analysis, Mann-Whitney U test, Wilcoxon Signed Rank test, receiver operating characteristic (ROC) curve analysis and Spearman's rho correlation test were used. RESULTS Both microarray and qRT-PCR data showed that miR-638 was significantly upregulated in BM after APL patients received induction therapy. Moreover, miR-638, which is specifically downregulated in APL cell lines, was upregulated after all-trans retinoic acid (ATRA)-induced myeloid differentiation. Receiver operating characteristic (ROC) curve analyses revealed that miR-638 could serve as a valuable biomarker for differentiating APL from controls or non-APL AML. Furthermore, miR-638 expression was sharply increased after induction therapy and complete remission (CR). An inverse correlation was observed between miR-638 and PML-RARα transcripts levels in BM samples, while a positive correlation was revealed between PB miR-638 and BM miR-638 levels in APL patients after induction therapy. CONCLUSIONS Our study suggested that miR-638 may serve as a potential APL biomarker for diagnosis and assessment of the response to targeted therapy, and PB miR-638 could be used for non-invasive MRD surveillance in APL.
Collapse
Affiliation(s)
- Yuanyuan Bai
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.,Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Cheng Chen
- Department of Hematology, Wenzhou Key Laboratory of Hematology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.,Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiaoling Guo
- Center of Scientific Research, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Ting Ding
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.,The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xinyun Yang
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.,The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jian Yu
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Junjun Yang
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jichen Ruan
- Department of Pediatric Hematology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiaoqun Zheng
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zhanguo Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| |
Collapse
|
10
|
Skórka K, Chojnacki M, Masternak M, Karczmarczyk A, Subocz E, Wawrzyniak E, Giannopoulos K. The Predominant Prognostic Significance of NOTCH1 Mutation Defined by Emulsion PCR in Chronic Lymphocytic Leukemia. Cancer Manag Res 2021; 13:3663-3674. [PMID: 33986614 PMCID: PMC8110254 DOI: 10.2147/cmar.s302245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/22/2021] [Indexed: 11/24/2022] Open
Abstract
Purpose NOTCH1mut represents a new prognostic marker in chronic lymphocytic leukaemia (CLL). The low sensitivity of the current methods may increase the risk of false-negative results, particularly in patients with low NOTCH1mut allelic burden. This study compared two methods of the NOTCH1mut assessment including droplet digital PCR (ddPCR) and amplification-refractory mutation system PCR (ARMS-PCR) untreated CLL patients. Patients and Methods This study included 319 untreated CLL patients. Two PCR-based methods; ddPCR and ARMS-PCR were performed to assess the mutational status of NOTCH1. The Mann–Whitney, Fisher’s exact test, Kruskal–Wallis, Kaplan–Meier, Log rank tests and multivariate Cox proportional hazard regression model were used to analyze collected data. Results We proved that ddPCR increased the detectability of the NOTCH1mut compared to ARMS-PCR in CLL (18.55% vs 6%). We showed a shorter time to first treatment (TTFT) in the NOTCH1mut group of patients compared to the NOTCH1wt defined by ddPCR (1.5 vs 33 months, p=0.01). The TTFT survival curves analysis in subgroups divided according to the mutational status of IGHV and NOTCH1 assessed by ddPCR discriminated group with the best prognosis: IGHVmutNOTCH1wt. Multivariate analysis revealed that the mutational status of IGHV represented an independent prognostic factor for TTFT, while NOTCH1mut determined by ddPCR constituted as a dependent prognostic factor for TTFT. Conclusion The selection of the precise method of NOTCH1mut detection as ddPCR might significantly improve prognostic stratification of CLL patient. Assessment of IGHV might be relevant to more accurate discrimination of prognostic groups of CLL patients, especially in harboring NOTCH1mut irrespective of the quantity of allelic burden.
Collapse
Affiliation(s)
- Katarzyna Skórka
- Department of Experimental Hematooncology, Medical University of Lublin, Lublin, Poland
| | - Michał Chojnacki
- Department of Experimental Hematooncology, Medical University of Lublin, Lublin, Poland
| | - Marta Masternak
- Department of Experimental Hematooncology, Medical University of Lublin, Lublin, Poland
| | | | - Edyta Subocz
- Department of Internal Medicine and Hematology, Military Institute of Medicine, Warsaw, Poland
| | - Ewa Wawrzyniak
- Department of Hematology, Medical University of Lodz, Lodz, Poland
| | - Krzysztof Giannopoulos
- Department of Experimental Hematooncology, Medical University of Lublin, Lublin, Poland.,Department of Hematology, St. John's Cancer Centre, Lublin, Poland
| |
Collapse
|
11
|
Martinez RJ, Kang Q, Nennig D, Bailey NG, Brown NA, Betz BL, Tewari M, Thyagarajan B, Bachanova V, Mroz P. One-Step Multiplexed Droplet Digital Polymerase Chain Reaction for Quantification of p190 BCR-ABL1 Fusion Transcript in B-Lymphoblastic Leukemia. Arch Pathol Lab Med 2021; 146:92-100. [PMID: 33769465 DOI: 10.5858/arpa.2020-0454-oa] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2021] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Quantification and detection of the t(9;22) (BCR-ABL1) translocation in chronic myelogenous leukemia and B-lymphoblastic leukemia are important for directing treatment protocols and monitoring disease relapse. However, quantification using traditional reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) is dependent on a calibration curve and is prone to laboratory-to-laboratory variation. Droplet digital polymerase chain reaction (ddPCR) is a novel method that allows for highly sensitive absolute quantification of transcript copy number. As such, ddPCR is a good candidate for disease monitoring, an assay requiring reproducible measurements with high specificity and sensitivity. OBJECTIVE.— To compare results of ddPCR and RT-qPCR BCR-ABL1 fusion transcript measurements of patient samples and determine if either method is superior. DESIGN.— We optimized and standardized a 1-step multiplexed ddPCR assay to detect BCR-ABL1 p190 and ABL1 e10 transcripts. The ddPCR optimization included varying cycle number and primer concentration with standardization of droplet generation and droplet number and analyses to improve data sensitivity. Following optimization, ddPCR measurements were performed on clinical samples and compared with traditional RT-qPCR results. RESULTS.— Droplet digital polymerase chain reaction was able to detect the BCR-ABL1 p190 transcript to 0.001% (1:10-5) with a calculated limit of detection and limit of quantitation of 4.1 and 5.3 transcripts, respectively. When tested on patient samples, ddPCR was able to identify 20% more positives than a laboratory-developed 2-step RT-qPCR assay. CONCLUSIONS.— Droplet digital polymerase chain reaction demonstrated increased detection of BCR-ABL1 compared with RT-qPCR. Improved detection of BCR-ABL1 p190 and the potential for improved standardization across multiple laboratories makes ddPCR a suitable method for the disease monitoring in patients with acute B-lymphoblastic leukemia.
Collapse
Affiliation(s)
- Ryan J Martinez
- From the Department of Laboratory Medicine and Pathology (Martinez, Nennig, Thyagarajan, Mroz)
| | - Qing Kang
- the Division of Hematology and Oncology, Department of Internal Medicine (Kang, Tewari)
| | - Davis Nennig
- From the Department of Laboratory Medicine and Pathology (Martinez, Nennig, Thyagarajan, Mroz)
| | - Nathanael G Bailey
- the Division of Hematopathology, Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania (Bailey)
| | | | | | - Muneesh Tewari
- the Division of Hematology and Oncology, Department of Internal Medicine (Kang, Tewari).,the Center for Computational Medicine and Bioinformatics (Tewari).,the Department of Biomedical Engineering (Tewari), University of Michigan, Ann Arbor
| | - Bharat Thyagarajan
- From the Department of Laboratory Medicine and Pathology (Martinez, Nennig, Thyagarajan, Mroz)
| | - Veronika Bachanova
- the Division of Hematology-Oncology and Transplantation (Bachanova), University of Minnesota, Minneapolis
| | - Pawel Mroz
- From the Department of Laboratory Medicine and Pathology (Martinez, Nennig, Thyagarajan, Mroz)
| |
Collapse
|
12
|
Jiang XW, Chen SZ, Zhu XY, Xu XX, Liu Y. Development and validation of a droplet digital PCR assay for the evaluation of PML-RARα fusion transcripts in acute promyelocytic leukemia. Mol Cell Probes 2020; 53:101617. [PMID: 32585184 DOI: 10.1016/j.mcp.2020.101617] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/25/2020] [Accepted: 06/03/2020] [Indexed: 11/11/2022]
Abstract
Acute promyelocytic leukemia (APL) is an aggressive disease that requires prompt treatment. Promyelocytic leukemia protein-retinoic acid receptor α (PML-RARα) fusion genes resulting from reciprocal translocation are considered a molecular basis for diagnosing APL. Moreover, PML-RARα fusion gene testing is an essential tool for monitoring the response to therapy via minimal residual disease and providing a diagnosis before rapid disease progression in APL. The present study developed a novel droplet digital PCR (ddPCR) assay to rapidly detect two PML-RARα variants (bcr1 and bcr3) and compared its limit of detection (LOD) with quantitative PCR (qPCR). It was demonstrated that the LOD of ddPCR for PML-RARα reached 0.001%, and the evaluation of high copy number samples of PML-RARα by ddPCR correlated well with qPCR. Furthermore, clinical sample testing with ddPCR found that 34 and 24% samples were bcr-1-positive and bcr3-positive, respectively. However, according to qPCR, 30% of the samples were bcr1-positive and 20% were bcr3-positive. In addition, the concordance rate between ddPCR and qPCR reaction was 86%. While monitoring minimal residual disease, the PML-RARα mutation rate of three patients who recovered well decreased to 0.34%. However, one patient who was bcr3-positive and relapsed had a mutation rate of 13% while in remission, indicating that the bcr3 isoform may be an adverse prognostic factor affecting recovery. Therefore, the present results suggested that this novel ddPCR assay may be useful for monitoring and evaluating the treatment effects and prognosis of APL.
Collapse
Affiliation(s)
- Xi-Wen Jiang
- DAAN Gene Co., Ltd. of Sun Yat-sen University, 19 Xiangshan Road, Science Park, High & New Technology Development District, Guangzhou, 510080, China; The Medicine and Biological Engineering Technology Research Center of the Ministry of Health, Guangzhou, 510080, China.
| | - Si-Ze Chen
- Central Laboratory, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080, China; The Precise Therapy Engineering Technology Research Cente of Guangdong Province for Esophageal Cancer, Guangzhou, 510080, China
| | - Xiao-Ya Zhu
- DAAN Gene Co., Ltd. of Sun Yat-sen University, 19 Xiangshan Road, Science Park, High & New Technology Development District, Guangzhou, 510080, China; The Medicine and Biological Engineering Technology Research Center of the Ministry of Health, Guangzhou, 510080, China
| | - Xiao-Xie Xu
- DAAN Gene Co., Ltd. of Sun Yat-sen University, 19 Xiangshan Road, Science Park, High & New Technology Development District, Guangzhou, 510080, China; The Medicine and Biological Engineering Technology Research Center of the Ministry of Health, Guangzhou, 510080, China
| | - Yue Liu
- DAAN Gene Co., Ltd. of Sun Yat-sen University, 19 Xiangshan Road, Science Park, High & New Technology Development District, Guangzhou, 510080, China; The Medicine and Biological Engineering Technology Research Center of the Ministry of Health, Guangzhou, 510080, China
| |
Collapse
|
13
|
Rosales-Chilama M, Diaz-Moreno N, Prieto MD, Giraldo-Parra L, Martínez-Valencia ÁJ, Gomez MA. Comparative Assessment of DNA Targets and Amplification Methods for Leishmania (Viannia) Detection in Human Samples. Am J Trop Med Hyg 2020; 102:1323-1327. [PMID: 32228793 PMCID: PMC7253133 DOI: 10.4269/ajtmh.19-0691] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Multiple polymerase chain reaction (PCR)-based approaches have been developed for Leishmania detection in clinical and laboratory samples, and this diversity limits inter-study comparisons, meta-analyses, and generalization of findings. Towards harmonization of a molecular tool for detection of Leishmania (Viannia) for research purposes, we evaluated the concordance of 18SrDNA quantitative polymerase chain reaction (qPCR) and minicircle kinetoplastid DNA (mkDNA) PCR followed by Southern blot (PCR-SB) in in vitro infection systems and in lesion and mucosal swab samples from Colombian patients with cutaneous leishmaniasis caused by L. (Viannia). The lower limit of parasite detection of 18SrDNA qPCR and mkDNA PCR-SB was 10−1 promastigotes and one intracellular amastigote per reaction. From cutaneous lesions (n = 63), an almost perfect concordance was found between the methods (κ = 0.92, 95% CI: 0.82–1.00). Despite equal limits of detection, mkDNA PCR-SB was more efficient for parasite detection in mucosal samples than 18SrDNA qPCR or 18SrDNA digital droplet PCR. The high concordance, sensitivity, scaling potential, and feasibility of implementation of the 18SrDNA qPCR, support its selection as the L. (Viannia) in research laboratories, as a first step towards harmonization of research protocols in the region.
Collapse
Affiliation(s)
- Mariana Rosales-Chilama
- Universidad Icesi, Cali, Colombia.,Centro Internacional de Entrenamiento e Investigaciones Médicas-CIDEIM, Cali, Colombia
| | - Nicole Diaz-Moreno
- Universidad Icesi, Cali, Colombia.,Centro Internacional de Entrenamiento e Investigaciones Médicas-CIDEIM, Cali, Colombia
| | - Miguel Darío Prieto
- Centro Internacional de Entrenamiento e Investigaciones Médicas-CIDEIM, Cali, Colombia
| | - Lina Giraldo-Parra
- Centro Internacional de Entrenamiento e Investigaciones Médicas-CIDEIM, Cali, Colombia
| | | | - María Adelaida Gomez
- Universidad Icesi, Cali, Colombia.,Centro Internacional de Entrenamiento e Investigaciones Médicas-CIDEIM, Cali, Colombia
| |
Collapse
|
14
|
Liang M, Wang L, Xiao M, Xiong J, Wang J, Wang Z, Huang W, Zhou J. Clinical significance of increased PML-RARa transcripts after induction therapy for acute promyelocytic leukaemia. Ann Med 2020; 52:233-238. [PMID: 32323584 PMCID: PMC7877940 DOI: 10.1080/07853890.2020.1753886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/02/2020] [Accepted: 04/06/2020] [Indexed: 10/24/2022] Open
Abstract
Objective: To analyze the clinical and biological significance of the acute promyelocytic leukemia (APL) whose PML-RARa transcripts increased after induction therapy.Methods: We analyzed 9 cases of APL whose PML-RARa transcripts increased after induction treatment and compare them with APL whose PML-RARa transcripts decreased.Results: The only factor affecting increased PML-RARa transcripts was the induction protocol. The cases of increased PML-RARa transcripts received induction treatment mainly based on ATRA and ATO. The evaluation of bone marrow aspirate cytology showed that the cell percentage from myelocyte to segmented neutrophil of the patients with increased PML-RARa transcripts was significantly higher than that of the patients with decreased PML-RARa transcripts. In the follow-up, MRD in 9 cases was consistently negative.Conclusions: Our studies showed the increased PML-RARa transcripts after induction treatment had different clinical significance from the decreased PML-RARa transcripts.
Collapse
Affiliation(s)
- Mi Liang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei, China
| | - Lei Wang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei, China
| | - Min Xiao
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei, China
| | - Jie Xiong
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei, China
| | - Jin Wang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei, China
| | - Zhiqiong Wang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei, China
| | - Wei Huang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei, China
| | - Jianfeng Zhou
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei, China
| |
Collapse
|
15
|
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.
Collapse
Affiliation(s)
| | | | | | | | | | - Francesco Albano
- Correspondence: ; Tel.: +39-(0)80-5478031; Fax: +39-(0)80-5508369
| |
Collapse
|
16
|
Advances in the study of exosomal lncRNAs in tumors and the selection of research methods. Biomed Pharmacother 2019; 123:109716. [PMID: 31896067 DOI: 10.1016/j.biopha.2019.109716] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 11/19/2019] [Accepted: 11/29/2019] [Indexed: 02/07/2023] Open
Abstract
Exosomes are endosome-derived extracellular vesicles that are released upon the fusion of multivesicular bodies with the plasma membrane. These vesicles contain proteins, lipids, and nucleic acids and are found in various human body fluids. Exosomes can transfer bioactive molecules to nearby or distant recipient cells, thereby affecting their function. Recently, exosomes have gained importance as a medium of communication between tumor cells. An increasing number of studies have found that non-coding RNAs in tumor cell-derived exosomes can regulate tumor microenvironments, inhibit immune cell function, promote the growth and invasion of tumor cells, and impart resistance to chemicals in tumor cells. In this review, we focus on the effects of exosomal long non-coding RNAs (lncRNAs) on tumors. As exosomes and their parent cells have similar biological characteristics and coated lncRNAs can exist stably in vivo without being degraded by RNases, exosomal lncRNAs have emerged as novel non-invasive tumor biomarkers for use in the early diagnosis and evaluation of prognosis of tumors. Advancements in the field have led to the development of a variety of techniques in exosomal non-coding RNA research. Currently, most methods include the separation and purification of exosomes, followed by RNA extraction, reverse transcription, and subsequent analyses; thus, these processes are very tedious and vulnerable to contamination and could lead to inaccurate and inconsistent results. Thus, there has been an increase in the development of detection methods for exosomal RNAs. Here, we discuss the existing research methods, their advantages and disadvantages, and a few new techniques.
Collapse
|
17
|
Digital PCR in Myeloid Malignancies: Ready to Replace Quantitative PCR? Int J Mol Sci 2019; 20:ijms20092249. [PMID: 31067725 PMCID: PMC6540058 DOI: 10.3390/ijms20092249] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/01/2019] [Accepted: 05/03/2019] [Indexed: 01/13/2023] Open
Abstract
New techniques are on the horizon for the detection of small leukemic clones in both, acute leukemias and myeloproliferative disorders. A promising approach is based on digital polymerase chain reaction (PCR). Digital PCR (dPCR) is a breakthrough technology designed to provide absolute nucleic acid quantification. It is particularly useful to detect a low amount of target and therefore it represents an alternative method for detecting measurable residual disease (MRD). The main advantages are the high precision, the very reliable quantification, the absolute quantification without the need for a standard curve, and the excellent reproducibility. Nowadays the main disadvantages of this strategy are the costs that are still higher than standard qPCR, the lack of standardized methods, and the limited number of laboratories that are equipped with instruments for dPCR. Several studies describing the possibility and advantages of using digital PCR for the detection of specific leukemic transcripts or mutations have already been published. In this review we summarize the available data on the use of dPCR in acute myeloid leukemia and myeloproliferative disorders.
Collapse
|